DNA damage response element gene transcriptions: Difference between revisions

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==Consensus sequences==
==Consensus sequences==
===DNA damage response elements===
DNA damage response element (DRE) has the consensus sequence TTTCAAT.<ref name=Smith>{{ cite journal
|author=Joshua J. Smith, Eric S. Cole, Daniel P. Romero
|title=Transcriptional control of RAD51 expression in the ciliate ''Tetrahymena thermophila''
|journal=Nucleic Acids Research
|date=15 July 2004
|volume=32
|issue=14
|pages=4313-4321
|url=https://academic.oup.com/nar/article/32/14/4313/1279821
|arxiv=
|bibcode=
|doi=10.1093/nar/gkh771
|pmid=15304567
|accessdate=4 September 2020 }}</ref>
===Upstream repressor sites===


"A consensus sequence, 5'-TAGCCGCCGRRRR-3' (where R = an unspecified purine nucleoside [A/G],was generated from these data."<ref name=Sumrada>{{ cite journal
"A consensus sequence, 5'-TAGCCGCCGRRRR-3' (where R = an unspecified purine nucleoside [A/G],was generated from these data."<ref name=Sumrada>{{ cite journal
Line 36: Line 55:


"The extent of homology for the entire 13 bp ranged from 56 to 100%. However, for the symmetrical core sequence CCGCC 75 to 100% homology was observed with only conservative substitutions occurring in the nonhomologous positions."<ref name=Sumrada/>
"The extent of homology for the entire 13 bp ranged from 56 to 100%. However, for the symmetrical core sequence CCGCC 75 to 100% homology was observed with only conservative substitutions occurring in the nonhomologous positions."<ref name=Sumrada/>
DNA damage response element (DRE) has the consensus sequence TTTCAAT.<ref name=Smith>{{ cite journal
|author=Joshua J. Smith, Eric S. Cole, Daniel P. Romero
|title=Transcriptional control of RAD51 expression in the ciliate ''Tetrahymena thermophila''
|journal=Nucleic Acids Research
|date=15 July 2004
|volume=32
|issue=14
|pages=4313-4321
|url=https://academic.oup.com/nar/article/32/14/4313/1279821
|arxiv=
|bibcode=
|doi=10.1093/nar/gkh771
|pmid=15304567
|accessdate=4 September 2020 }}</ref>


"The majority of early meiotic genes are characterised by the presence of a URS1 (upstream repressor site 1) motif (GGCGGC) in their upstream untranslated regions (Chu et al., 1998). The URS1 site is commonly found in the upstream sequences of many yeast genes, and is also widespread in the upstream regulatory regions of other eukaryotes (Sumrada and Cooper, 1987)."<ref name=Tam>{{ cite book
"The majority of early meiotic genes are characterised by the presence of a URS1 (upstream repressor site 1) motif (GGCGGC) in their upstream untranslated regions (Chu et al., 1998). The URS1 site is commonly found in the upstream sequences of many yeast genes, and is also widespread in the upstream regulatory regions of other eukaryotes (Sumrada and Cooper, 1987)."<ref name=Tam>{{ cite book
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# A DNA damage response element does not participate in the transcription of A1BG.
# A DNA damage response element does not participate in the transcription of A1BG.


==DRE (Sumrada) samplings==
==DRE (Smith) samplings==
 
Copying the consensus of the DDRE: TTTCAAT and putting the sequence in "⌘F" finds no locations for this sequence in any A1BG direction as can be found by the computer programs.
 
For the Basic programs testing consensus sequence TTTCAAT (starting with SuccessablesDDRE.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), the programs are, are looking for, and found:
# negative strand, negative direction, looking for TTTCAAT, 0.
# negative strand, positive direction, looking for TTTCAAT, 0.
# positive strand, negative direction, looking for TTTCAAT, 0.
# positive strand, positive direction, looking for TTTCAAT, 0.
# complement, negative strand, negative direction, looking for AAAGTTA, 0.
# complement, negative strand, positive direction, looking for AAAGTTA, 0.
# complement, positive strand, negative direction, looking for AAAGTTA, 0.
# complement, positive strand, positive direction, looking for AAAGTTA, 0.
# inverse complement, negative strand, negative direction, looking for ATTGAAA, 0.
# inverse complement, negative strand, positive direction, looking for ATTGAAA, 0.
# inverse complement, positive strand, negative direction, looking for ATTGAAA, 0.
# inverse complement, positive strand, positive direction, looking for ATTGAAA, 0.
# inverse negative strand, negative direction, looking for TAACTTT, 0.
# inverse negative strand, positive direction, looking for TAACTTT, 0.
# inverse positive strand, negative direction, looking for TAACTTT, 0.
# inverse positive strand, positive direction, looking for TAACTTT, 0.
 
==URS (Sumrada) samplings==


Copying the consensus URS: TAGCCGCCG and putting the sequence in "⌘F" finds no locations between ZNF497 and A1BG or between ZSCAN22 and A1BG as can be found by the computer programs.
Copying the consensus URS: TAGCCGCCG and putting the sequence in "⌘F" finds no locations between ZNF497 and A1BG or between ZSCAN22 and A1BG as can be found by the computer programs.
Line 91: Line 117:
# inverse positive strand, positive direction, looking for nCCGCCnnn, 11, CCCGCCCTT at 4442, CCCGCCCTC at 4432, TCCGCCAAC at 3490, TCCGCCCAG at 2488, CCCGCCGTC at 1904, CCCGCCGGA at 1796, ACCGCCTCG at 1205, ACCGCCCCG at 1028, CCCGCCCTG at 409, GCCGCCTGC at 359, CCCGCCGCC at 356.
# inverse positive strand, positive direction, looking for nCCGCCnnn, 11, CCCGCCCTT at 4442, CCCGCCCTC at 4432, TCCGCCAAC at 3490, TCCGCCCAG at 2488, CCCGCCGTC at 1904, CCCGCCGGA at 1796, ACCGCCTCG at 1205, ACCGCCCCG at 1028, CCCGCCCTG at 409, GCCGCCTGC at 359, CCCGCCGCC at 356.


==DRE (Sumrada, core) samplings==
==URS1 (Sumrada, core) samplings==


Copying the consensus URS: CCGCC and putting the sequence in "⌘F" finds no locations between ZNF497 and A1BG or between ZSCAN22 and A1BG as can be found by the computer programs.
Copying the consensus URS: CCGCC and putting the sequence in "⌘F" finds no locations between ZNF497 and A1BG or between ZSCAN22 and A1BG as can be found by the computer programs.
Line 103: Line 129:
The ci is the complement of the direct.
The ci is the complement of the direct.


===DRE (Sumrada, core) (4560-2846) UTRs===
===URS1 (Sumrada, core) (4560-2846) UTRs===


# Negative strand, negative direction: CCGCC at 3999, CCGCC at 3090.
# Negative strand, negative direction: CCGCC at 3999, CCGCC at 3090.


===DRE (Sumrada, core) positive direction (4445-4265) core promoters===
===URS1 (Sumrada, core) positive direction (4445-4265) core promoters===


# Negative strand, positive direction: CCGCC at 4291.
# Negative strand, positive direction: CCGCC at 4291.
# Positive strand, positive direction: CCGCC at 4439, CCGCC at 4429.
# Positive strand, positive direction: CCGCC at 4439, CCGCC at 4429.


===DRE (Sumrada, core) negative direction (2811-2596) proximal promoters===
===URS (Sumrada, core) negative direction (2811-2596) proximal promoters===


# Negative strand, negative direction: CCGCC at 2727, CCGCC at 2724.
# Negative strand, negative direction: CCGCC at 2727, CCGCC at 2724.


===DRE (Sumrada, core) positive direction (4265-4050) proximal promoters===
===URS1 (Sumrada, core) positive direction (4265-4050) proximal promoters===


# Negative strand, positive direction: CCGCC at 4238.
# Negative strand, positive direction: CCGCC at 4238.


===DRE (Sumrada, core) negative direction (2596-1) distal promoters===
===URS1 (Sumrada, core) negative direction (2596-1) distal promoters===


# Negative strand, negative direction: CCGCC at 2392, CCGCC at 2231, CCGCC at 1809, CCGCC at 1752, CCGCC at 1250, CCGCC at 956, CCGCC at 856, CCGCC at 700, CCGCC at 427.
# Negative strand, negative direction: CCGCC at 2392, CCGCC at 2231, CCGCC at 1809, CCGCC at 1752, CCGCC at 1250, CCGCC at 956, CCGCC at 856, CCGCC at 700, CCGCC at 427.
# Positive strand, negative direction: CCGCC at 1503.
# Positive strand, negative direction: CCGCC at 1503.


===DRE (Sumrada, core) positive direction (4050-1) distal promoters===
===URS1 (Sumrada, core) positive direction (4050-1) distal promoters===


# Negative strand, positive direction: CCGCC at 1757, CCGCC at 904.
# Negative strand, positive direction: CCGCC at 1757, CCGCC at 904.
# Positive strand, positive direction: CCGCC at 3487, CCGCC at 2485, CCGCC at 1901, CCGCC at 1793, CCGCC at 1202, CCGCC at 1025, CCGCC at 406, CCGCC at 356, CCGCC at 353.
# Positive strand, positive direction: CCGCC at 3487, CCGCC at 2485, CCGCC at 1901, CCGCC at 1793, CCGCC at 1202, CCGCC at 1025, CCGCC at 406, CCGCC at 356, CCGCC at 353.


==DRE (Sumrada, core) random dataset samplings==
==URS1 (Sumrada, core) random dataset samplings==
 
# DREr0: 8, CCGCC at 4330, CCGCC at 3890, CCGCC at 3407, CCGCC at 2405, CCGCC at 2380, CCGCC at 1384, CCGCC at 806, CCGCC at 368.
# DREr1: 3, CCGCC at 3758, CCGCC at 2403, CCGCC at 1645.
# DREr2: 7, CCGCC at 4509, CCGCC at 3586, CCGCC at 3583, CCGCC at 2598, CCGCC at 1966, CCGCC at 1939, CCGCC at 639.
# DREr3: 11, CCGCC at 4138, CCGCC at 3450, CCGCC at 3376, CCGCC at 3079, CCGCC at 2792, CCGCC at 2246, CCGCC at 1866, CCGCC at 1452, CCGCC at 484, CCGCC at 439, CCGCC at 117.
# DREr4: 10, CCGCC at 4280, CCGCC at 3492, CCGCC at 1199, CCGCC at 1092, CCGCC at 1089, CCGCC at 1022, CCGCC at 876, CCGCC at 502, CCGCC at 80, CCGCC at 14.
# DREr5: 9, CCGCC at 4353, CCGCC at 4099, CCGCC at 3847, CCGCC at 2815, CCGCC at 1159, CCGCC at 987, CCGCC at 792, CCGCC at 349, CCGCC at 7.
# DREr6: 3, CCGCC at 4337, CCGCC at 3319, CCGCC at 1643.
# DREr7: 6, CCGCC at 4436, CCGCC at 3979, CCGCC at 2755, CCGCC at 2742, CCGCC at 2667, CCGCC at 1770.
# DREr8: 7, CCGCC at 2689, CCGCC at 2573, CCGCC at 2518, CCGCC at 2473, CCGCC at 2012, CCGCC at 1263, CCGCC at 746.
# DREr9: 8, CCGCC at 4446, CCGCC at 3551, CCGCC at 2809, CCGCC at 2761, CCGCC at 2666, CCGCC at 2449, CCGCC at 1558, CCGCC at 1415.
# DREr0ci: 5, GGCGG at 3546, GGCGG at 3292, GGCGG at 2996, GGCGG at 2032, GGCGG at 969.
# DREr1ci: 2, GGCGG at 3213, GGCGG at 1152.
# DREr2ci: 6, GGCGG at 4347, GGCGG at 3975, GGCGG at 2818, GGCGG at 2036, GGCGG at 964, GGCGG at 462.
# DREr3ci: 7, GGCGG at 3925, GGCGG at 3146, GGCGG at 2911, GGCGG at 1969, GGCGG at 1441, GGCGG at 854, GGCGG at 518.
# DREr4ci: 7, GGCGG at 4496, GGCGG at 4108, GGCGG at 3549, GGCGG at 3466, GGCGG at 1874, GGCGG at 1484, GGCGG at 711.
# DREr5ci: 11, GGCGG at 3745, GGCGG at 3181, GGCGG at 2931, GGCGG at 2532, GGCGG at 2034, GGCGG at 965, GGCGG at 734, GGCGG at 677, GGCGG at 580, GGCGG at 414, GGCGG at 177.
# DREr6ci: 5, GGCGG at 4433, GGCGG at 4350, GGCGG at 4288, GGCGG at 2576, GGCGG at 1801.
# DREr7ci: 6, GGCGG at 3879, GGCGG at 1777, GGCGG at 1220, GGCGG at 1064, GGCGG at 1044, GGCGG at 786.
# DREr8ci: 9, GGCGG at 4282, GGCGG at 4279, GGCGG at 4121, GGCGG at 4090, GGCGG at 3634, GGCGG at 3359, GGCGG at 3242, GGCGG at 2336, GGCGG at 241.
# DREr9ci: 8, GGCGG at 3998, GGCGG at 3895, GGCGG at 3630, GGCGG at 3627, GGCGG at 2854, GGCGG at 2134, GGCGG at 1726, GGCGG at 1142.


===DREr arbitrary (evens) (4560-2846) UTRs===
# URSr0: 8, CCGCC at 4330, CCGCC at 3890, CCGCC at 3407, CCGCC at 2405, CCGCC at 2380, CCGCC at 1384, CCGCC at 806, CCGCC at 368.
# URSr1: 3, CCGCC at 3758, CCGCC at 2403, CCGCC at 1645.
# URSr2: 7, CCGCC at 4509, CCGCC at 3586, CCGCC at 3583, CCGCC at 2598, CCGCC at 1966, CCGCC at 1939, CCGCC at 639.
# URSr3: 11, CCGCC at 4138, CCGCC at 3450, CCGCC at 3376, CCGCC at 3079, CCGCC at 2792, CCGCC at 2246, CCGCC at 1866, CCGCC at 1452, CCGCC at 484, CCGCC at 439, CCGCC at 117.
# URSr4: 10, CCGCC at 4280, CCGCC at 3492, CCGCC at 1199, CCGCC at 1092, CCGCC at 1089, CCGCC at 1022, CCGCC at 876, CCGCC at 502, CCGCC at 80, CCGCC at 14.
# URSr5: 9, CCGCC at 4353, CCGCC at 4099, CCGCC at 3847, CCGCC at 2815, CCGCC at 1159, CCGCC at 987, CCGCC at 792, CCGCC at 349, CCGCC at 7.
# URSr6: 3, CCGCC at 4337, CCGCC at 3319, CCGCC at 1643.
# URSr7: 6, CCGCC at 4436, CCGCC at 3979, CCGCC at 2755, CCGCC at 2742, CCGCC at 2667, CCGCC at 1770.
# URSr8: 7, CCGCC at 2689, CCGCC at 2573, CCGCC at 2518, CCGCC at 2473, CCGCC at 2012, CCGCC at 1263, CCGCC at 746.
# URSr9: 8, CCGCC at 4446, CCGCC at 3551, CCGCC at 2809, CCGCC at 2761, CCGCC at 2666, CCGCC at 2449, CCGCC at 1558, CCGCC at 1415.
# URSr0ci: 5, GGCGG at 3546, GGCGG at 3292, GGCGG at 2996, GGCGG at 2032, GGCGG at 969.
# URSr1ci: 2, GGCGG at 3213, GGCGG at 1152.
# URSr2ci: 6, GGCGG at 4347, GGCGG at 3975, GGCGG at 2818, GGCGG at 2036, GGCGG at 964, GGCGG at 462.
# URSr3ci: 7, GGCGG at 3925, GGCGG at 3146, GGCGG at 2911, GGCGG at 1969, GGCGG at 1441, GGCGG at 854, GGCGG at 518.
# URSr4ci: 7, GGCGG at 4496, GGCGG at 4108, GGCGG at 3549, GGCGG at 3466, GGCGG at 1874, GGCGG at 1484, GGCGG at 711.
# URSr5ci: 11, GGCGG at 3745, GGCGG at 3181, GGCGG at 2931, GGCGG at 2532, GGCGG at 2034, GGCGG at 965, GGCGG at 734, GGCGG at 677, GGCGG at 580, GGCGG at 414, GGCGG at 177.
# URSr6ci: 5, GGCGG at 4433, GGCGG at 4350, GGCGG at 4288, GGCGG at 2576, GGCGG at 1801.
# URSr7ci: 6, GGCGG at 3879, GGCGG at 1777, GGCGG at 1220, GGCGG at 1064, GGCGG at 1044, GGCGG at 786.
# URSr8ci: 9, GGCGG at 4282, GGCGG at 4279, GGCGG at 4121, GGCGG at 4090, GGCGG at 3634, GGCGG at 3359, GGCGG at 3242, GGCGG at 2336, GGCGG at 241.
# URSr9ci: 8, GGCGG at 3998, GGCGG at 3895, GGCGG at 3630, GGCGG at 3627, GGCGG at 2854, GGCGG at 2134, GGCGG at 1726, GGCGG at 1142.


# DREr0: CCGCC at 4330, CCGCC at 3890, CCGCC at 3407.
===URSr arbitrary (evens) (4560-2846) UTRs===
# DREr2: CCGCC at 4509, CCGCC at 3586, CCGCC at 3583.
# DREr4: CCGCC at 4280, CCGCC at 3492.
# DREr6: CCGCC at 4337, CCGCC at 3319.
# DREr8: CCGCC at 2689, CCGCC at 2573, CCGCC at 2518, CCGCC at 2473, CCGCC at 2012, CCGCC at 1263, CCGCC at 746.


===DREr alternate (odds) (4560-2846) UTRs===
# URSr0: CCGCC at 4330, CCGCC at 3890, CCGCC at 3407.
# URSr2: CCGCC at 4509, CCGCC at 3586, CCGCC at 3583.
# URSr4: CCGCC at 4280, CCGCC at 3492.
# URSr6: CCGCC at 4337, CCGCC at 3319.
# URSr8: CCGCC at 2689, CCGCC at 2573, CCGCC at 2518, CCGCC at 2473, CCGCC at 2012, CCGCC at 1263, CCGCC at 746.
# URSr0ci: GGCGG at 3546, GGCGG at 3292, GGCGG at 2996.
# URSr2ci: GGCGG at 4347, GGCGG at 3975.
# URSr4ci: GGCGG at 4496, GGCGG at 4108, GGCGG at 3549, GGCGG at 3466.
# URSr6ci: GGCGG at 4433, GGCGG at 4350, GGCGG at 4288.
# URSr8ci: GGCGG at 4282, GGCGG at 4279, GGCGG at 4121, GGCGG at 4090, GGCGG at 3634, GGCGG at 3359, GGCGG at 3242.


# DREr1: CCGCC at 3758.
===URSr alternate (odds) (4560-2846) UTRs===
# DREr3: CCGCC at 4138, CCGCC at 3450, CCGCC at 3376, CCGCC at 3079.
# DREr5: CCGCC at 4353, CCGCC at 4099, CCGCC at 3847.
# DREr7: CCGCC at 4436, CCGCC at 3979.
# DREr9: CCGCC at 4446, CCGCC at 3551.


===RDr arbitrary negative direction (evens) (2846-2811) core promoters===
# URSr1: CCGCC at 3758.
# URSr3: CCGCC at 4138, CCGCC at 3450, CCGCC at 3376, CCGCC at 3079.
# URSr5: CCGCC at 4353, CCGCC at 4099, CCGCC at 3847.
# URSr7: CCGCC at 4436, CCGCC at 3979.
# URSr9: CCGCC at 4446, CCGCC at 3551.
# URSr1ci: GGCGG at 3213.
# URSr3ci: GGCGG at 3925, GGCGG at 3146, GGCGG at 2911.
# URSr5ci: GGCGG at 3745, GGCGG at 3181, GGCGG at 2931.
# URSr7ci: GGCGG at 3879.
# URSr9ci: GGCGG at 3998, GGCGG at 3895, GGCGG at 3630, GGCGG at 3627, GGCGG at 2854.


===URSr arbitrary negative direction (evens) (2846-2811) core promoters===


===DREr alternate negative direction (odds) (2846-2811) core promoters===
# URSr2ci: GGCGG at 2818.


# DREr5: CCGCC at 2815.
===URSr alternate negative direction (odds) (2846-2811) core promoters===


===DREr arbitrary positive direction (odds) (4445-4265) core promoters===
# URSr5: CCGCC at 2815.


# DREr5: CCGCC at 4353.
===URSr arbitrary positive direction (odds) (4445-4265) core promoters===
# DREr7: CCGCC at 4436.
# DREr9: CCGCC at 3551, CCGCC at 2809, CCGCC at 2761, CCGCC at 2666, CCGCC at 2449, CCGCC at 1558, CCGCC at 1415.


===DREr alternate positive direction (evens) (4445-4265) core promoters===
# URSr5: CCGCC at 4353.
# URSr7: CCGCC at 4436.
# URSr9: CCGCC at 3551, CCGCC at 2809, CCGCC at 2761, CCGCC at 2666, CCGCC at 2449, CCGCC at 1558, CCGCC at 1415.


# DREr0: CCGCC at 4330.
===URSr alternate positive direction (evens) (4445-4265) core promoters===
# DREr4: CCGCC at 4280.
# DREr6: CCGCC at 4337.


===DREr arbitrary negative direction (evens) (2811-2596) proximal promoters===
# URSr0: CCGCC at 4330.
# URSr4: CCGCC at 4280.
# URSr6: CCGCC at 4337.
# URSr2ci: GGCGG at 4347.
# URSr6ci: GGCGG at 4433, GGCGG at 4350, GGCGG at 4288.
# URSr8ci: GGCGG at 4282, GGCGG at 4279.


# DREr2: CCGCC at 2598.
===URSr arbitrary negative direction (evens) (2811-2596) proximal promoters===
# DREr8: CCGCC at 2689.


===DREr alternate negative direction (odds) (2811-2596) proximal promoters===
# URSr2: CCGCC at 2598.
# URSr8: CCGCC at 2689.


# DREr3: CCGCC at 2792.
===URSr alternate negative direction (odds) (2811-2596) proximal promoters===
# DREr7: CCGCC at 2755, CCGCC at 2742, CCGCC at 2667.
# DREr9: CCGCC at 2809, CCGCC at 2761, CCGCC at 2666.


===DREr arbitrary positive direction (odds) (4265-4050) proximal promoters===
# URSr3: CCGCC at 2792.
# URSr7: CCGCC at 2755, CCGCC at 2742, CCGCC at 2667.
# URSr9: CCGCC at 2809, CCGCC at 2761, CCGCC at 2666.


# DREr3: CCGCC at 4138.
===URSr arbitrary positive direction (odds) (4265-4050) proximal promoters===
# DREr5: CCGCC at 4099.


===RDr alternate positive direction (evens) (4265-4050) proximal promoters===
# URSr3: CCGCC at 4138.
# URSr5: CCGCC at 4099.


===URSr alternate positive direction (evens) (4265-4050) proximal promoters===


===DREr arbitrary negative direction (evens) (2596-1) distal promoters===
# URSr4ci: GGCGG at 4108.
# URSr8ci: GGCGG at 4121, GGCGG at 4090.


# DREr0: CCGCC at 2405, CCGCC at 2380, CCGCC at 1384, CCGCC at 806, CCGCC at 368.
===URSr arbitrary negative direction (evens) (2596-1) distal promoters===
# DREr2: CCGCC at 1966, CCGCC at 1939, CCGCC at 639.
# DREr4: CCGCC at 1199, CCGCC at 1092, CCGCC at 1089, CCGCC at 1022, CCGCC at 876, CCGCC at 502, CCGCC at 80, CCGCC at 14.
# DREr6: CCGCC at 1643.
# DREr8: CCGCC at 2573, CCGCC at 2518, CCGCC at 2473, CCGCC at 2012, CCGCC at 1263, CCGCC at 746.


===DREr alternate negative direction (odds) (2596-1) distal promoters===
# URSr0: CCGCC at 2405, CCGCC at 2380, CCGCC at 1384, CCGCC at 806, CCGCC at 368.
# URSr2: CCGCC at 1966, CCGCC at 1939, CCGCC at 639.
# URSr4: CCGCC at 1199, CCGCC at 1092, CCGCC at 1089, CCGCC at 1022, CCGCC at 876, CCGCC at 502, CCGCC at 80, CCGCC at 14.
# URSr6: CCGCC at 1643.
# URSr8: CCGCC at 2573, CCGCC at 2518, CCGCC at 2473, CCGCC at 2012, CCGCC at 1263, CCGCC at 746.
# URSr0ci: GGCGG at 2032, GGCGG at 969.
# URSr2ci: GGCGG at 2818, GGCGG at 2036, GGCGG at 964, GGCGG at 462.
# URSr4ci: GGCGG at 1874, GGCGG at 1484, GGCGG at 711.
# URSr6ci: GGCGG at 2576, GGCGG at 1801.
# URSr8ci: GGCGG at 2336, GGCGG at 241.


# DREr1: CCGCC at 2403, CCGCC at 1645.
===URSr alternate negative direction (odds) (2596-1) distal promoters===
# DREr3: CCGCC at 2246, CCGCC at 1866, CCGCC at 1452, CCGCC at 484, CCGCC at 439, CCGCC at 117.
# DREr5: CCGCC at 1159, CCGCC at 987, CCGCC at 792, CCGCC at 349, CCGCC at 7.
# DREr7: CCGCC at 1770.
# DREr9: CCGCC at 2449, CCGCC at 1558, CCGCC at 1415.


===DREr arbitrary positive direction (odds) (4050-1) distal promoters===
# URSr1: CCGCC at 2403, CCGCC at 1645.
# URSr3: CCGCC at 2246, CCGCC at 1866, CCGCC at 1452, CCGCC at 484, CCGCC at 439, CCGCC at 117.
# URSr5: CCGCC at 1159, CCGCC at 987, CCGCC at 792, CCGCC at 349, CCGCC at 7.
# URSr7: CCGCC at 1770.
# URSr9: CCGCC at 2449, CCGCC at 1558, CCGCC at 1415.
# URSr1ci: GGCGG at 1152.
# URSr3ci: GGCGG at 1969, GGCGG at 1441, GGCGG at 854, GGCGG at 518.
# URSr5ci: GGCGG at 2532, GGCGG at 2034, GGCGG at 965, GGCGG at 734, GGCGG at 677, GGCGG at 580, GGCGG at 414, GGCGG at 177.
# URSr7ci: GGCGG at 1777, GGCGG at 1220, GGCGG at 1064, GGCGG at 1044, GGCGG at 786.
# URSr9ci: GGCGG at 2134, GGCGG at 1726, GGCGG at 1142.


# DREr1: CCGCC at 3758, CCGCC at 2403, CCGCC at 1645.
===URSr arbitrary positive direction (odds) (4050-1) distal promoters===
# DREr3: CCGCC at 3450, CCGCC at 3376, CCGCC at 3079, CCGCC at 2792, CCGCC at 2246, CCGCC at 1866, CCGCC at 1452, CCGCC at 484, CCGCC at 439, CCGCC at 117.
# DREr5: CCGCC at 3847, CCGCC at 2815, CCGCC at 1159, CCGCC at 987, CCGCC at 792, CCGCC at 349, CCGCC at 7.
# DREr7: CCGCC at 3979, CCGCC at 2755, CCGCC at 2742, CCGCC at 2667, CCGCC at 1770.
# DREr9: CCGCC at 3551, CCGCC at 2809, CCGCC at 2761, CCGCC at 2666, CCGCC at 2449, CCGCC at 1558, CCGCC at 1415.


===DREr alternate positive direction (evens) (4050-1) distal promoters===
# URSr1: CCGCC at 3758, CCGCC at 2403, CCGCC at 1645.
# URSr3: CCGCC at 3450, CCGCC at 3376, CCGCC at 3079, CCGCC at 2792, CCGCC at 2246, CCGCC at 1866, CCGCC at 1452, CCGCC at 484, CCGCC at 439, CCGCC at 117.
# URSr5: CCGCC at 3847, CCGCC at 2815, CCGCC at 1159, CCGCC at 987, CCGCC at 792, CCGCC at 349, CCGCC at 7.
# URSr7: CCGCC at 3979, CCGCC at 2755, CCGCC at 2742, CCGCC at 2667, CCGCC at 1770.
# URSr9: CCGCC at 3551, CCGCC at 2809, CCGCC at 2761, CCGCC at 2666, CCGCC at 2449, CCGCC at 1558, CCGCC at 1415.
# URSr1ci: GGCGG at 3213, GGCGG at 1152.
# URSr3ci: GGCGG at 3925, GGCGG at 3146, GGCGG at 2911, GGCGG at 1969, GGCGG at 1441, GGCGG at 854, GGCGG at 518.
# URSr5ci: GGCGG at 3745, GGCGG at 3181, GGCGG at 2931, GGCGG at 2532, GGCGG at 2034, GGCGG at 965, GGCGG at 734, GGCGG at 677, GGCGG at 580, GGCGG at 414, GGCGG at 177.
# URSr7ci: GGCGG at 3879, GGCGG at 1777, GGCGG at 1220, GGCGG at 1064, GGCGG at 1044, GGCGG at 786.
# URSr9ci: GGCGG at 3998, GGCGG at 3895, GGCGG at 3630, GGCGG at 3627, GGCGG at 2854, GGCGG at 2134, GGCGG at 1726, GGCGG at 1142.


# DREr0: CCGCC at 3890, CCGCC at 3407, CCGCC at 2405, CCGCC at 2380, CCGCC at 1384, CCGCC at 806, CCGCC at 368.
===URSr alternate positive direction (evens) (4050-1) distal promoters===
# DREr2: CCGCC at 3586, CCGCC at 3583, CCGCC at 2598, CCGCC at 1966, CCGCC at 1939, CCGCC at 639.
# DREr4: CCGCC at 3492, CCGCC at 1199, CCGCC at 1092, CCGCC at 1089, CCGCC at 1022, CCGCC at 876, CCGCC at 502, CCGCC at 80, CCGCC at 14.
# DREr6: CCGCC at 3319, CCGCC at 1643.
# DREr8: CCGCC at 2689, CCGCC at 2573, CCGCC at 2518, CCGCC at 2473, CCGCC at 2012, CCGCC at 1263, CCGCC at 746.


===DREr UTRs===
# URSr0: CCGCC at 3890, CCGCC at 3407, CCGCC at 2405, CCGCC at 2380, CCGCC at 1384, CCGCC at 806, CCGCC at 368.
{{main|UTR promoter gene transcriptions}}
# URSr2: CCGCC at 3586, CCGCC at 3583, CCGCC at 2598, CCGCC at 1966, CCGCC at 1939, CCGCC at 639.
# DREr0ci: GGCGG at 3546, GGCGG at 3292, GGCGG at 2996.
# URSr4: CCGCC at 3492, CCGCC at 1199, CCGCC at 1092, CCGCC at 1089, CCGCC at 1022, CCGCC at 876, CCGCC at 502, CCGCC at 80, CCGCC at 14.
# DREr2ci: GGCGG at 4347, GGCGG at 3975.
# URSr6: CCGCC at 3319, CCGCC at 1643.
# DREr4ci: GGCGG at 4496, GGCGG at 4108, GGCGG at 3549, GGCGG at 3466.
# URSr8: CCGCC at 2689, CCGCC at 2573, CCGCC at 2518, CCGCC at 2473, CCGCC at 2012, CCGCC at 1263, CCGCC at 746.
# DREr6ci: GGCGG at 4433, GGCGG at 4350, GGCGG at 4288.
# URSr0ci: GGCGG at 3546, GGCGG at 3292, GGCGG at 2996, GGCGG at 2032, GGCGG at 969.
# DREr8ci: GGCGG at 4282, GGCGG at 4279, GGCGG at 4121, GGCGG at 4090, GGCGG at 3634, GGCGG at 3359, GGCGG at 3242.
# URSr2ci: GGCGG at 3975, GGCGG at 2818, GGCGG at 2036, GGCGG at 964, GGCGG at 462.
# URSr4ci: GGCGG at 3549, GGCGG at 3466, GGCGG at 1874, GGCGG at 1484, GGCGG at 711.
# URSr6ci: GGCGG at 2576, GGCGG at 1801.
# URSr8ci: GGCGG at 3634, GGCGG at 3359, GGCGG at 3242, GGCGG at 2336, GGCGG at 241.


===DREr core promoters===
==URS (Sumrada, core) analysis and results==
{{main|Core promoter gene transcriptions}}
{{main|Complex locus A1BG and ZNF497#URS (Sumrada, core)}}
# DREr2ci: GGCGG at 2818.
For "the symmetrical core sequence CCGCC 75 to 100% homology was observed with only conservative substitutions occurring in the nonhomologous positions."<ref name=Sumrada/>


===DREr distal promoters===
{|class="wikitable"
{{main|Distal promoter gene transcriptions}}
|-
# DREr2: CCGCC at 1966, CCGCC at 1939, CCGCC at 639.
! Reals or randoms !! Promoters !! direction !! Numbers !! Strands !! Occurrences !! Averages (± 0.1)
# DREr4: CCGCC at 1199, CCGCC at 1092, CCGCC at 1089, CCGCC at 1022, CCGCC at 876, CCGCC at 502, CCGCC at 80, CCGCC at 14.
|-
# DREr6: CCGCC at 1643.
| Reals || UTR || negative || 2 || 2 || 1 || 1 ± 1 (--2,+-0)
# DREr8: CCGCC at 2573, CCGCC at 2518, CCGCC at 2473, CCGCC at 2012, CCGCC at 1263, CCGCC at 746.
|-
# DREr0ci: GGCGG at 2032, GGCGG at 969.
| Randoms || UTR || arbitrary negative || 36 || 10 || 3.6 || 3.05 ± 0.55
# DREr2ci: GGCGG at 2036, GGCGG at 964, GGCGG at 462.
|-
# DREr4ci: GGCGG at 1874, GGCGG at 1484, GGCGG at 711.
| Randoms || UTR || alternate negative || 25 || 10 || 2.5 || 3.05 ± 0.55
# DREr6ci: GGCGG at 2576, GGCGG at 1801.
|-
# DREr8ci: GGCGG at 2336, GGCGG at 241.
| Reals || Core || negative || 0 || 2 || 0 || 0
 
|-
 
| Randoms || Core || arbitrary negative || 1 || 10 || 0.1 || 0.1
# DREr1: 3CCGCC at 3758, CCGCC at 2403, CCGCC at 1645.
|-
# DREr3: CCGCC at 3450, CCGCC at 3376, CCGCC at 3079, CCGCC at 2792, CCGCC at 2246, CCGCC at 1866, CCGCC at 1452, CCGCC at 484, CCGCC at 439, CCGCC at 117.
| Randoms || Core || alternate negative || 1 || 10 || 0.1 || 0.1
# DREr5: CCGCC at 3847, CCGCC at 2815, CCGCC at 1159, CCGCC at 987, CCGCC at 792, CCGCC at 349, CCGCC at 7.
|-
# DREr7: CCGCC at 3979, CCGCC at 2755, CCGCC at 2742, CCGCC at 2667, CCGCC at 1770.
| Reals || Core || positive || 3 || 2 || 1.5 || 1.5 ± 0.5 (-+1,++2)  
# DREr9: CCGCC at 3551, CCGCC at 2809, CCGCC at 2761, CCGCC at 2666, CCGCC at 2449, CCGCC at 1558, CCGCC at 1415.
|-
# DREr1ci: GGCGG at 3213, GGCGG at 1152.
| Randoms || Core || arbitrary positive || 9 || 10 || 0.9 || 0.9
# DREr3ci: GGCGG at 3925, GGCGG at 3146, GGCGG at 2911, GGCGG at 1969, GGCGG at 1441, GGCGG at 854, GGCGG at 518.
|-
# DREr5ci: GGCGG at 3745, GGCGG at 3181, GGCGG at 2931, GGCGG at 2532, GGCGG at 2034, GGCGG at 965, GGCGG at 734, GGCGG at 677, GGCGG at 580, GGCGG at 414, GGCGG at 177.
| Randoms || Core || alternate positive || 9 || 10 || 0.9 || 0.9
# DREr7ci: GGCGG at 3879, GGCGG at 1777, GGCGG at 1220, GGCGG at 1064, GGCGG at 1044, GGCGG at 786.
|-
# DREr9ci: GGCGG at 3998, GGCGG at 3895, GGCGG at 3630, GGCGG at 3627, GGCGG at 2854, GGCGG at 2134, GGCGG at 1726, GGCGG at 1142.
| Reals || Proximal || negative || 1 || 2 || 0.5 || 0.5 ± (-+1,++2)
 
|-
==DRE (Sumrada, core) analysis and results==
| Randoms || Proximal || arbitrary negative || 2 || 10 || 0.2 || 0.45 ± 0.25
{{main|Complex locus A1BG and ZNF497#DRE (Sumrada, core)}}
|-
The real UTR has two consensus sequences for an occurrence of 1.0.
| Randoms || Proximal || alternate negative || 7 || 10 || 0.7 || 0.45 ± 0.25
 
|-
The core promoters are only in the positive direction (three) for an occurrence of 0.75.
| Reals || Proximal || positive || 1 || 2 || 0.5 || 0.5 ± 0.5 (-+1,++0)
 
|-
The proximal promoters have two in the negative direction and one in the positive direction for occurrences of 1.0 and 0.5, respectively.
| Randoms || Proximal || arbitrary positive || 2 || 10 || 0.2 || 0.25 ± 0.05
 
|-
The distal promoters have ten in the negative direction for an occurrence of 5.0. In the positive direction the reals have eleven for an occurrence of 5.5.
| Randoms || Proximal || alternate positive || 3 || 10 || 0.3 || 0.25 ± 0.05
 
|-
The random datasets had twenty-nine UTR consensus sequences for an occurrence of 2.9.
| Reals || Distal || negative || 10 || 2 || 5.0 || 5.0 ± 4.0 (--9,+-1)
 
|-
Randoms had four core promoters for an occurrence of 0.2.
| Randoms || Distal || arbitrary negative || 36 || 10 || 3.6 || 3.7 ± 0.1
 
|-
Randoms had four proximal promoters for an occurrence of 0.2.
| Randoms || Distal || alternate negative || 38 || 10 || 3.8 || 3.7 ± 0.1
 
|-
Randoms had thirty-five arbitrary negative direction distal promoters for an occurrence of 3.5.
| Reals || Distal || positive || 11 || 2 || 5.5 || 5.5 ± 3.5 (-+2,++9)  
 
|-
In the arbitrary positive direction the randoms had sixty-six distastes promoters for an occurrence of 6.6.
| Randoms || Distal || arbitrary positive || 66 || 10 || 6.6 || 5.95 ± 0.65
 
|-
By comparison, the randoms outnumber the reals for UTRs (2.9 vs. 1.0, respectively), but the reals outnumber the randoms regarding core promoters (0.75 vs. 0.2), proximal promoters (1.5 vs. 0.2), and just for the distal promoters (total of 10.5 vs. 10.1, respectively). The disparity rather than overlap suggests that the reals are likely active or activable.
| Randoms || Distal || alternate positive || 53 || 10 || 5.3 || 5.95 ± 0.65
 
|}
==DRE (Smith) samplings==


Copying the consensus of the DDRE: 5'-TTTCAAT-3' and putting the sequence in "⌘F" finds no locations for this sequence in any A1BG direction as can be found by the computer programs.
Comparison:


For the Basic programs testing consensus sequence 5'-TTTCAAT-3' (starting with SuccessablesDDRE.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), the programs are, are looking for, and found:
The occurrences of real URS (Sumrada, core) UTRs are less than the randoms, cores and proximals are greater than the randoms, and the distals are outside the randoms. This suggests that the real URS (Sumrada, core)s are likely active or activable.
# negative strand, negative direction, looking for 5'-TTTCAAT-3', 0.
# negative strand, positive direction, looking for 5'-TTTCAAT-3', 0.
# positive strand, negative direction, looking for 5'-TTTCAAT-3', 0.
# positive strand, positive direction, looking for 5'-TTTCAAT-3', 0.
# complement, negative strand, negative direction, looking for 5'-AAAGTTA-3', 0.
# complement, negative strand, positive direction, looking for 5'-AAAGTTA-3', 0.
# complement, positive strand, negative direction, looking for 5'-AAAGTTA-3', 0.
# complement, positive strand, positive direction, looking for 5'-AAAGTTA-3', 0.
# inverse complement, negative strand, negative direction, looking for 5'-ATTGAAA-3', 0.
# inverse complement, negative strand, positive direction, looking for 5'-ATTGAAA-3', 0.
# inverse complement, positive strand, negative direction, looking for 5'-ATTGAAA-3', 0.
# inverse complement, positive strand, positive direction, looking for 5'-ATTGAAA-3', 0.
# inverse negative strand, negative direction, looking for 5'-TAACTTT-3', 0.
# inverse negative strand, positive direction, looking for 5'-TAACTTT-3', 0.
# inverse positive strand, negative direction, looking for 5'-TAACTTT-3', 0.
# inverse positive strand, positive direction, looking for 5'-TAACTTT-3', 0.


==Acknowledgements==
==Acknowledgements==
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[[Category:Resources last modified in December 2020]]

Latest revision as of 19:07, 25 July 2023

Associate Editor(s)-in-Chief: Henry A. Hoff

"The corepressor complex is recruited to the RNR genes by the sequence-specific DNA-binding protein Crt1, which recognizes the DNA damage response elements (DREs) in the upstream repression sequence (URS) (19, 35)."[1]

Human genes

Consensus sequences

DNA damage response elements

DNA damage response element (DRE) has the consensus sequence TTTCAAT.[2]

Upstream repressor sites

"A consensus sequence, 5'-TAGCCGCCGRRRR-3' (where R = an unspecified purine nucleoside [A/G],was generated from these data."[3]

"The extent of homology for the entire 13 bp ranged from 56 to 100%. However, for the symmetrical core sequence CCGCC 75 to 100% homology was observed with only conservative substitutions occurring in the nonhomologous positions."[3]

"The majority of early meiotic genes are characterised by the presence of a URS1 (upstream repressor site 1) motif (GGCGGC) in their upstream untranslated regions (Chu et al., 1998). The URS1 site is commonly found in the upstream sequences of many yeast genes, and is also widespread in the upstream regulatory regions of other eukaryotes (Sumrada and Cooper, 1987)."[4]

Hypotheses

Main article: Hypotheses
  1. A1BG has no DNA damage response elements in either promoter.
  2. A1BG is not transcribed by a DNA damage response element.
  3. A DNA damage response element does not participate in the transcription of A1BG.

DRE (Smith) samplings

Copying the consensus of the DDRE: TTTCAAT and putting the sequence in "⌘F" finds no locations for this sequence in any A1BG direction as can be found by the computer programs.

For the Basic programs testing consensus sequence TTTCAAT (starting with SuccessablesDDRE.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), the programs are, are looking for, and found:

  1. negative strand, negative direction, looking for TTTCAAT, 0.
  2. negative strand, positive direction, looking for TTTCAAT, 0.
  3. positive strand, negative direction, looking for TTTCAAT, 0.
  4. positive strand, positive direction, looking for TTTCAAT, 0.
  5. complement, negative strand, negative direction, looking for AAAGTTA, 0.
  6. complement, negative strand, positive direction, looking for AAAGTTA, 0.
  7. complement, positive strand, negative direction, looking for AAAGTTA, 0.
  8. complement, positive strand, positive direction, looking for AAAGTTA, 0.
  9. inverse complement, negative strand, negative direction, looking for ATTGAAA, 0.
  10. inverse complement, negative strand, positive direction, looking for ATTGAAA, 0.
  11. inverse complement, positive strand, negative direction, looking for ATTGAAA, 0.
  12. inverse complement, positive strand, positive direction, looking for ATTGAAA, 0.
  13. inverse negative strand, negative direction, looking for TAACTTT, 0.
  14. inverse negative strand, positive direction, looking for TAACTTT, 0.
  15. inverse positive strand, negative direction, looking for TAACTTT, 0.
  16. inverse positive strand, positive direction, looking for TAACTTT, 0.

URS (Sumrada) samplings

Copying the consensus URS: TAGCCGCCG and putting the sequence in "⌘F" finds no locations between ZNF497 and A1BG or between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence nnnCCGCCn (starting with SuccessablesDRES.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), the programs are, are looking for, and found:

  1. negative strand, negative direction, looking for nnnCCGCCn, 13, ACTCCGCCC at 4000, ACTCCGCCC at 3091, CCGCCGCCT at 2728, GACCCGCCG at 2725, CGTCCGCCT at 2393, ACTCCGCCA at 2232, CACCCGCCT at 1810, CCTCCGCCG at 1753, CCACCGCCC at 1251, GTACCGCCG at 957, CCTCCGCCT at 857, CGTCCGCCT at 701, TGTCCGCCT at 428.
  2. negative strand, positive direction, looking for nnnCCGCCn, 4, CCACCGCCC at 4292, CCCCCGCCT at 4239, GGGCCGCCG at 1758, CTGCCGCCT at 905.
  3. positive strand, negative direction, looking for nnnCCGCCn, 1, GCTCCGCCT at 1504.
  4. positive strand, positive direction, looking for nnnCCGCCn, 11, CCCCCGCCC at 4440, ACCCCGCCC at 4430, GATCCGCCA at 3488, GATCCGCCC at 2486, CTCCCGCCG at 1902, TCCCCGCCG at 1794, GGACCGCCT at 1203, ACACCGCCC at 1026, CACCCGCCC at 407, CCGCCGCCT at 357, CCCCCGCCG at 354.
  5. complement, negative strand, negative direction, looking for nnnGGCGGn, 1, CGAGGCGGA at 1504.
  6. complement, negative strand, positive direction, looking for nnnGGCGGn, 11, GGGGGCGGG at 4440, TGGGGCGGG at 4430, CTAGGCGGT at 3488, CTAGGCGGG at 2486, GAGGGCGGC at 1902, AGGGGCGGC at 1794, CCTGGCGGA at 1203, TGTGGCGGG at 1026, GTGGGCGGG at 407, GGCGGCGGA at 357, GGGGGCGGC at 354.
  7. complement, positive strand, negative direction, looking for nnnGGCGGn, 13, TGAGGCGGG at 4000, TGAGGCGGG at 3091, GGCGGCGGA at 2728, CTGGGCGGC at 2725, GCAGGCGGA at 2393, TGAGGCGGT at 2232, GTGGGCGGA at 1810, GGAGGCGGC at 1753, GGTGGCGGG at 1251, CATGGCGGC at 957, GGAGGCGGA at 857, GCAGGCGGA at 701, ACAGGCGGA at 428.
  8. complement, positive strand, positive direction, looking for nnnGGCGGn, 4, GGTGGCGGG at 4292, GGGGGCGGA at 4239, CCCGGCGGC at 1758, GACGGCGGA at 905.
  9. inverse complement, negative strand, negative direction, looking for nGGCGGnnn, 1, AGGCGGAGG at 1506.
  10. inverse complement, negative strand, positive direction, looking for nGGCGGnnn, 11, GGGCGGGAA at 4442, GGGCGGGAG at 4432, AGGCGGTTG at 3490, AGGCGGGTC at 2488, GGGCGGCAG at 1904, GGGCGGCCT at 1796, TGGCGGAGC at 1205, TGGCGGGGC at 1028, GGGCGGGAC at 409, CGGCGGACG at 359, GGGCGGCGG at 356.
  11. inverse complement, positive strand, negative direction, looking for nGGCGGnnn, 13, AGGCGGGAG at 4002, AGGCGGGTG at 3093, CGGCGGAAG at 2730, GGGCGGCGG at 2727, AGGCGGAGG at 2395, AGGCGGTTG at 2234, GGGCGGATC at 1812, AGGCGGCTG at 1755, TGGCGGGTG at 1253, TGGCGGCAC at 959, AGGCGGAGG at 859, AGGCGGATC at 703, AGGCGGATC at 430.
  12. inverse complement, positive strand, positive direction, looking for nGGCGGnnn, 4, TGGCGGGAG at 4294, GGGCGGAAG at 4241, CGGCGGCCA at 1760, CGGCGGACG at 907.
  13. inverse negative strand, negative direction, looking for nCCGCCnnn, 13, TCCGCCCTC at 4002, TCCGCCCAC at 3093, GCCGCCTTC at 2730, CCCGCCGCC at 2727, TCCGCCTCC at 2395, TCCGCCAAC at 2234, CCCGCCTAG at 1812, TCCGCCGAC at 1755, ACCGCCCAC at 1253, ACCGCCGTG at 959, TCCGCCTCC at 859, TCCGCCTAG at 703, TCCGCCTAG at 430.
  14. inverse negative strand, positive direction, looking for nCCGCCnnn, 4, ACCGCCCTC at 4294, CCCGCCTTC at 4241, GCCGCCGGT at 1760, GCCGCCTGC at 907.
  15. inverse positive strand, negative direction, looking for nCCGCCnnn, 1, TCCGCCTCC at 1506.
  16. inverse positive strand, positive direction, looking for nCCGCCnnn, 11, CCCGCCCTT at 4442, CCCGCCCTC at 4432, TCCGCCAAC at 3490, TCCGCCCAG at 2488, CCCGCCGTC at 1904, CCCGCCGGA at 1796, ACCGCCTCG at 1205, ACCGCCCCG at 1028, CCCGCCCTG at 409, GCCGCCTGC at 359, CCCGCCGCC at 356.

URS1 (Sumrada, core) samplings

Copying the consensus URS: CCGCC and putting the sequence in "⌘F" finds no locations between ZNF497 and A1BG or between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence CCGCC (starting with SuccessablesCORES.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), the programs are, are looking for, and found:

  1. negative strand, negative direction, looking for CCGCC, 13, CCGCC at 3999, CCGCC at 3090, CCGCC at 2727, CCGCC at 2724, CCGCC at 2392, CCGCC at 2231, CCGCC at 1809, CCGCC at 1752, CCGCC at 1250, CCGCC at 956, CCGCC at 856, CCGCC at 700, CCGCC at 427.
  2. positive strand, negative direction, looking for CCGCC, 1, CCGCC at 1503.
  3. negative strand, positive direction, looking for CCGCC, 4, CCGCC at 4291, CCGCC at 4238, CCGCC at 1757, CCGCC at 904.
  4. positive strand, positive direction, looking for CCGCC, 11, CCGCC at 4439, CCGCC at 4429, CCGCC at 3487, CCGCC at 2485, CCGCC at 1901, CCGCC at 1793, CCGCC at 1202, CCGCC at 1025, CCGCC at 406, CCGCC at 356, CCGCC at 353.

The ci is the complement of the direct.

URS1 (Sumrada, core) (4560-2846) UTRs

  1. Negative strand, negative direction: CCGCC at 3999, CCGCC at 3090.

URS1 (Sumrada, core) positive direction (4445-4265) core promoters

  1. Negative strand, positive direction: CCGCC at 4291.
  2. Positive strand, positive direction: CCGCC at 4439, CCGCC at 4429.

URS (Sumrada, core) negative direction (2811-2596) proximal promoters

  1. Negative strand, negative direction: CCGCC at 2727, CCGCC at 2724.

URS1 (Sumrada, core) positive direction (4265-4050) proximal promoters

  1. Negative strand, positive direction: CCGCC at 4238.

URS1 (Sumrada, core) negative direction (2596-1) distal promoters

  1. Negative strand, negative direction: CCGCC at 2392, CCGCC at 2231, CCGCC at 1809, CCGCC at 1752, CCGCC at 1250, CCGCC at 956, CCGCC at 856, CCGCC at 700, CCGCC at 427.
  2. Positive strand, negative direction: CCGCC at 1503.

URS1 (Sumrada, core) positive direction (4050-1) distal promoters

  1. Negative strand, positive direction: CCGCC at 1757, CCGCC at 904.
  2. Positive strand, positive direction: CCGCC at 3487, CCGCC at 2485, CCGCC at 1901, CCGCC at 1793, CCGCC at 1202, CCGCC at 1025, CCGCC at 406, CCGCC at 356, CCGCC at 353.

URS1 (Sumrada, core) random dataset samplings

  1. URSr0: 8, CCGCC at 4330, CCGCC at 3890, CCGCC at 3407, CCGCC at 2405, CCGCC at 2380, CCGCC at 1384, CCGCC at 806, CCGCC at 368.
  2. URSr1: 3, CCGCC at 3758, CCGCC at 2403, CCGCC at 1645.
  3. URSr2: 7, CCGCC at 4509, CCGCC at 3586, CCGCC at 3583, CCGCC at 2598, CCGCC at 1966, CCGCC at 1939, CCGCC at 639.
  4. URSr3: 11, CCGCC at 4138, CCGCC at 3450, CCGCC at 3376, CCGCC at 3079, CCGCC at 2792, CCGCC at 2246, CCGCC at 1866, CCGCC at 1452, CCGCC at 484, CCGCC at 439, CCGCC at 117.
  5. URSr4: 10, CCGCC at 4280, CCGCC at 3492, CCGCC at 1199, CCGCC at 1092, CCGCC at 1089, CCGCC at 1022, CCGCC at 876, CCGCC at 502, CCGCC at 80, CCGCC at 14.
  6. URSr5: 9, CCGCC at 4353, CCGCC at 4099, CCGCC at 3847, CCGCC at 2815, CCGCC at 1159, CCGCC at 987, CCGCC at 792, CCGCC at 349, CCGCC at 7.
  7. URSr6: 3, CCGCC at 4337, CCGCC at 3319, CCGCC at 1643.
  8. URSr7: 6, CCGCC at 4436, CCGCC at 3979, CCGCC at 2755, CCGCC at 2742, CCGCC at 2667, CCGCC at 1770.
  9. URSr8: 7, CCGCC at 2689, CCGCC at 2573, CCGCC at 2518, CCGCC at 2473, CCGCC at 2012, CCGCC at 1263, CCGCC at 746.
  10. URSr9: 8, CCGCC at 4446, CCGCC at 3551, CCGCC at 2809, CCGCC at 2761, CCGCC at 2666, CCGCC at 2449, CCGCC at 1558, CCGCC at 1415.
  11. URSr0ci: 5, GGCGG at 3546, GGCGG at 3292, GGCGG at 2996, GGCGG at 2032, GGCGG at 969.
  12. URSr1ci: 2, GGCGG at 3213, GGCGG at 1152.
  13. URSr2ci: 6, GGCGG at 4347, GGCGG at 3975, GGCGG at 2818, GGCGG at 2036, GGCGG at 964, GGCGG at 462.
  14. URSr3ci: 7, GGCGG at 3925, GGCGG at 3146, GGCGG at 2911, GGCGG at 1969, GGCGG at 1441, GGCGG at 854, GGCGG at 518.
  15. URSr4ci: 7, GGCGG at 4496, GGCGG at 4108, GGCGG at 3549, GGCGG at 3466, GGCGG at 1874, GGCGG at 1484, GGCGG at 711.
  16. URSr5ci: 11, GGCGG at 3745, GGCGG at 3181, GGCGG at 2931, GGCGG at 2532, GGCGG at 2034, GGCGG at 965, GGCGG at 734, GGCGG at 677, GGCGG at 580, GGCGG at 414, GGCGG at 177.
  17. URSr6ci: 5, GGCGG at 4433, GGCGG at 4350, GGCGG at 4288, GGCGG at 2576, GGCGG at 1801.
  18. URSr7ci: 6, GGCGG at 3879, GGCGG at 1777, GGCGG at 1220, GGCGG at 1064, GGCGG at 1044, GGCGG at 786.
  19. URSr8ci: 9, GGCGG at 4282, GGCGG at 4279, GGCGG at 4121, GGCGG at 4090, GGCGG at 3634, GGCGG at 3359, GGCGG at 3242, GGCGG at 2336, GGCGG at 241.
  20. URSr9ci: 8, GGCGG at 3998, GGCGG at 3895, GGCGG at 3630, GGCGG at 3627, GGCGG at 2854, GGCGG at 2134, GGCGG at 1726, GGCGG at 1142.

URSr arbitrary (evens) (4560-2846) UTRs

  1. URSr0: CCGCC at 4330, CCGCC at 3890, CCGCC at 3407.
  2. URSr2: CCGCC at 4509, CCGCC at 3586, CCGCC at 3583.
  3. URSr4: CCGCC at 4280, CCGCC at 3492.
  4. URSr6: CCGCC at 4337, CCGCC at 3319.
  5. URSr8: CCGCC at 2689, CCGCC at 2573, CCGCC at 2518, CCGCC at 2473, CCGCC at 2012, CCGCC at 1263, CCGCC at 746.
  6. URSr0ci: GGCGG at 3546, GGCGG at 3292, GGCGG at 2996.
  7. URSr2ci: GGCGG at 4347, GGCGG at 3975.
  8. URSr4ci: GGCGG at 4496, GGCGG at 4108, GGCGG at 3549, GGCGG at 3466.
  9. URSr6ci: GGCGG at 4433, GGCGG at 4350, GGCGG at 4288.
  10. URSr8ci: GGCGG at 4282, GGCGG at 4279, GGCGG at 4121, GGCGG at 4090, GGCGG at 3634, GGCGG at 3359, GGCGG at 3242.

URSr alternate (odds) (4560-2846) UTRs

  1. URSr1: CCGCC at 3758.
  2. URSr3: CCGCC at 4138, CCGCC at 3450, CCGCC at 3376, CCGCC at 3079.
  3. URSr5: CCGCC at 4353, CCGCC at 4099, CCGCC at 3847.
  4. URSr7: CCGCC at 4436, CCGCC at 3979.
  5. URSr9: CCGCC at 4446, CCGCC at 3551.
  6. URSr1ci: GGCGG at 3213.
  7. URSr3ci: GGCGG at 3925, GGCGG at 3146, GGCGG at 2911.
  8. URSr5ci: GGCGG at 3745, GGCGG at 3181, GGCGG at 2931.
  9. URSr7ci: GGCGG at 3879.
  10. URSr9ci: GGCGG at 3998, GGCGG at 3895, GGCGG at 3630, GGCGG at 3627, GGCGG at 2854.

URSr arbitrary negative direction (evens) (2846-2811) core promoters

  1. URSr2ci: GGCGG at 2818.

URSr alternate negative direction (odds) (2846-2811) core promoters

  1. URSr5: CCGCC at 2815.

URSr arbitrary positive direction (odds) (4445-4265) core promoters

  1. URSr5: CCGCC at 4353.
  2. URSr7: CCGCC at 4436.
  3. URSr9: CCGCC at 3551, CCGCC at 2809, CCGCC at 2761, CCGCC at 2666, CCGCC at 2449, CCGCC at 1558, CCGCC at 1415.

URSr alternate positive direction (evens) (4445-4265) core promoters

  1. URSr0: CCGCC at 4330.
  2. URSr4: CCGCC at 4280.
  3. URSr6: CCGCC at 4337.
  4. URSr2ci: GGCGG at 4347.
  5. URSr6ci: GGCGG at 4433, GGCGG at 4350, GGCGG at 4288.
  6. URSr8ci: GGCGG at 4282, GGCGG at 4279.

URSr arbitrary negative direction (evens) (2811-2596) proximal promoters

  1. URSr2: CCGCC at 2598.
  2. URSr8: CCGCC at 2689.

URSr alternate negative direction (odds) (2811-2596) proximal promoters

  1. URSr3: CCGCC at 2792.
  2. URSr7: CCGCC at 2755, CCGCC at 2742, CCGCC at 2667.
  3. URSr9: CCGCC at 2809, CCGCC at 2761, CCGCC at 2666.

URSr arbitrary positive direction (odds) (4265-4050) proximal promoters

  1. URSr3: CCGCC at 4138.
  2. URSr5: CCGCC at 4099.

URSr alternate positive direction (evens) (4265-4050) proximal promoters

  1. URSr4ci: GGCGG at 4108.
  2. URSr8ci: GGCGG at 4121, GGCGG at 4090.

URSr arbitrary negative direction (evens) (2596-1) distal promoters

  1. URSr0: CCGCC at 2405, CCGCC at 2380, CCGCC at 1384, CCGCC at 806, CCGCC at 368.
  2. URSr2: CCGCC at 1966, CCGCC at 1939, CCGCC at 639.
  3. URSr4: CCGCC at 1199, CCGCC at 1092, CCGCC at 1089, CCGCC at 1022, CCGCC at 876, CCGCC at 502, CCGCC at 80, CCGCC at 14.
  4. URSr6: CCGCC at 1643.
  5. URSr8: CCGCC at 2573, CCGCC at 2518, CCGCC at 2473, CCGCC at 2012, CCGCC at 1263, CCGCC at 746.
  6. URSr0ci: GGCGG at 2032, GGCGG at 969.
  7. URSr2ci: GGCGG at 2818, GGCGG at 2036, GGCGG at 964, GGCGG at 462.
  8. URSr4ci: GGCGG at 1874, GGCGG at 1484, GGCGG at 711.
  9. URSr6ci: GGCGG at 2576, GGCGG at 1801.
  10. URSr8ci: GGCGG at 2336, GGCGG at 241.

URSr alternate negative direction (odds) (2596-1) distal promoters

  1. URSr1: CCGCC at 2403, CCGCC at 1645.
  2. URSr3: CCGCC at 2246, CCGCC at 1866, CCGCC at 1452, CCGCC at 484, CCGCC at 439, CCGCC at 117.
  3. URSr5: CCGCC at 1159, CCGCC at 987, CCGCC at 792, CCGCC at 349, CCGCC at 7.
  4. URSr7: CCGCC at 1770.
  5. URSr9: CCGCC at 2449, CCGCC at 1558, CCGCC at 1415.
  6. URSr1ci: GGCGG at 1152.
  7. URSr3ci: GGCGG at 1969, GGCGG at 1441, GGCGG at 854, GGCGG at 518.
  8. URSr5ci: GGCGG at 2532, GGCGG at 2034, GGCGG at 965, GGCGG at 734, GGCGG at 677, GGCGG at 580, GGCGG at 414, GGCGG at 177.
  9. URSr7ci: GGCGG at 1777, GGCGG at 1220, GGCGG at 1064, GGCGG at 1044, GGCGG at 786.
  10. URSr9ci: GGCGG at 2134, GGCGG at 1726, GGCGG at 1142.

URSr arbitrary positive direction (odds) (4050-1) distal promoters

  1. URSr1: CCGCC at 3758, CCGCC at 2403, CCGCC at 1645.
  2. URSr3: CCGCC at 3450, CCGCC at 3376, CCGCC at 3079, CCGCC at 2792, CCGCC at 2246, CCGCC at 1866, CCGCC at 1452, CCGCC at 484, CCGCC at 439, CCGCC at 117.
  3. URSr5: CCGCC at 3847, CCGCC at 2815, CCGCC at 1159, CCGCC at 987, CCGCC at 792, CCGCC at 349, CCGCC at 7.
  4. URSr7: CCGCC at 3979, CCGCC at 2755, CCGCC at 2742, CCGCC at 2667, CCGCC at 1770.
  5. URSr9: CCGCC at 3551, CCGCC at 2809, CCGCC at 2761, CCGCC at 2666, CCGCC at 2449, CCGCC at 1558, CCGCC at 1415.
  6. URSr1ci: GGCGG at 3213, GGCGG at 1152.
  7. URSr3ci: GGCGG at 3925, GGCGG at 3146, GGCGG at 2911, GGCGG at 1969, GGCGG at 1441, GGCGG at 854, GGCGG at 518.
  8. URSr5ci: GGCGG at 3745, GGCGG at 3181, GGCGG at 2931, GGCGG at 2532, GGCGG at 2034, GGCGG at 965, GGCGG at 734, GGCGG at 677, GGCGG at 580, GGCGG at 414, GGCGG at 177.
  9. URSr7ci: GGCGG at 3879, GGCGG at 1777, GGCGG at 1220, GGCGG at 1064, GGCGG at 1044, GGCGG at 786.
  10. URSr9ci: GGCGG at 3998, GGCGG at 3895, GGCGG at 3630, GGCGG at 3627, GGCGG at 2854, GGCGG at 2134, GGCGG at 1726, GGCGG at 1142.

URSr alternate positive direction (evens) (4050-1) distal promoters

  1. URSr0: CCGCC at 3890, CCGCC at 3407, CCGCC at 2405, CCGCC at 2380, CCGCC at 1384, CCGCC at 806, CCGCC at 368.
  2. URSr2: CCGCC at 3586, CCGCC at 3583, CCGCC at 2598, CCGCC at 1966, CCGCC at 1939, CCGCC at 639.
  3. URSr4: CCGCC at 3492, CCGCC at 1199, CCGCC at 1092, CCGCC at 1089, CCGCC at 1022, CCGCC at 876, CCGCC at 502, CCGCC at 80, CCGCC at 14.
  4. URSr6: CCGCC at 3319, CCGCC at 1643.
  5. URSr8: CCGCC at 2689, CCGCC at 2573, CCGCC at 2518, CCGCC at 2473, CCGCC at 2012, CCGCC at 1263, CCGCC at 746.
  6. URSr0ci: GGCGG at 3546, GGCGG at 3292, GGCGG at 2996, GGCGG at 2032, GGCGG at 969.
  7. URSr2ci: GGCGG at 3975, GGCGG at 2818, GGCGG at 2036, GGCGG at 964, GGCGG at 462.
  8. URSr4ci: GGCGG at 3549, GGCGG at 3466, GGCGG at 1874, GGCGG at 1484, GGCGG at 711.
  9. URSr6ci: GGCGG at 2576, GGCGG at 1801.
  10. URSr8ci: GGCGG at 3634, GGCGG at 3359, GGCGG at 3242, GGCGG at 2336, GGCGG at 241.

URS (Sumrada, core) analysis and results

Main article: Complex locus A1BG and ZNF497 § URS (Sumrada, core)

For "the symmetrical core sequence CCGCC 75 to 100% homology was observed with only conservative substitutions occurring in the nonhomologous positions."[3]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 2 2 1 1 ± 1 (--2,+-0)
Randoms UTR arbitrary negative 36 10 3.6 3.05 ± 0.55
Randoms UTR alternate negative 25 10 2.5 3.05 ± 0.55
Reals Core negative 0 2 0 0
Randoms Core arbitrary negative 1 10 0.1 0.1
Randoms Core alternate negative 1 10 0.1 0.1
Reals Core positive 3 2 1.5 1.5 ± 0.5 (-+1,++2)
Randoms Core arbitrary positive 9 10 0.9 0.9
Randoms Core alternate positive 9 10 0.9 0.9
Reals Proximal negative 1 2 0.5 0.5 ± (-+1,++2)
Randoms Proximal arbitrary negative 2 10 0.2 0.45 ± 0.25
Randoms Proximal alternate negative 7 10 0.7 0.45 ± 0.25
Reals Proximal positive 1 2 0.5 0.5 ± 0.5 (-+1,++0)
Randoms Proximal arbitrary positive 2 10 0.2 0.25 ± 0.05
Randoms Proximal alternate positive 3 10 0.3 0.25 ± 0.05
Reals Distal negative 10 2 5.0 5.0 ± 4.0 (--9,+-1)
Randoms Distal arbitrary negative 36 10 3.6 3.7 ± 0.1
Randoms Distal alternate negative 38 10 3.8 3.7 ± 0.1
Reals Distal positive 11 2 5.5 5.5 ± 3.5 (-+2,++9)
Randoms Distal arbitrary positive 66 10 6.6 5.95 ± 0.65
Randoms Distal alternate positive 53 10 5.3 5.95 ± 0.65

Comparison:

The occurrences of real URS (Sumrada, core) UTRs are less than the randoms, cores and proximals are greater than the randoms, and the distals are outside the randoms. This suggests that the real URS (Sumrada, core)s are likely active or activable.

Acknowledgements

The content on this page was first contributed by: Henry A. Hoff.

See also

References

  1. ↑ Zhengjian Zhang and Joseph C. Reese (17 September 2004). "Redundant Mechanisms Are Used by Ssn6-Tup1 in Repressing Chromosomal Gene Transcription in Saccharomyces cerevisiae". The Journal of Biological Chemistry. 279 (38): 39240–39250. doi:10.1074/jbc.M407159200. PMID 15254041. Retrieved 4 September 2020.
  2. ↑ Joshua J. Smith, Eric S. Cole, Daniel P. Romero (15 July 2004). "Transcriptional control of RAD51 expression in the ciliate Tetrahymena thermophila". Nucleic Acids Research. 32 (14): 4313–4321. doi:10.1093/nar/gkh771. PMID 15304567. Retrieved 4 September 2020.
  3. ↑ 3.0 3.1 3.2 Roberta A. Sumrada and Terrance G. Cooper (June 1987). "Ubiquitous upstream repression sequences control activation of the inducible arginase gene in yeast" (PDF). Proceedings of the National Academy of Sciences USA. 84: 3997–4001. doi:10.1073/pnas.84.12.3997. PMID 3295874. Retrieved 6 September 2020.
  4. ↑ Janis Tam (February 2020). Dissecting the regulation of entry into gametogenesis in budding yeast (PDF). London, UK: University College London. p. 309. Retrieved 27 February 2022.

External links


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