Telomeric repeat DNA-binding factor gene transcriptions

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

Homo sapiens genes containing these are found using Homo sapiens "TRF (TTAGGG repeat binding factor)".[1]

Human genes

Consensus sequences

The apparent consensus sequence for the telomeric repeat DNA-binding factor (TRF) appears to be 5'-TTAGGG-3'.

TRF samplings

Copying the consensus telomeric repeat DNA-binding factor (TRF): TTAGGG and putting the sequence in "⌘F" locates ten of this sequence between ZSCAN22 and A1BG in the negative direction and two nucleotides between ZNF497 and A1BG as can be found by the computer programs.

In the nucleotides between ZSCAN22 and A1BG there is are ten TTAGGG beginning about 300 nucleotides from ZSCAN22 or ending at about 3900 nts. There are two among the nucleotides between ZNF497 and A1BG as A1BG is approached from ZNF497.

For the Basic programs testing consensus sequence TTAGGG (starting with SuccessablesTRF.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 TTAGGG, 10, TTAGGG at 3976, TTAGGG at 3067, TTAGGG at 2678, TTAGGG at 1917, TTAGGG at 1782, TTAGGG at 1264, TTAGGG at 1137, TTAGGG at 807, TTAGGG at 673, TTAGGG at 400.
  2. positive strand, negative direction, looking for TTAGGG, 0.
  3. positive strand, positive direction, looking for TTAGGG, 0.
  4. negative strand, positive direction, looking for TTAGGG, 2, TTAGGG at 2766, TTAGGG at 2669.
  5. complement, negative strand, negative direction, looking for AATCCC, 0.
  6. complement, positive strand, negative direction, looking for AATCCC, 10, AATCCC at 3976, AATCCC at 3067, AATCCC at 2678, AATCCC at 1917, AATCCC at 1782, AATCCC at 1264, AATCCC at 1137, AATCCC at 807, AATCCC at 673, AATCCC at 400.
  7. complement, positive strand, positive direction, looking for AATCCC, 2, AATCCC at 2766, AATCCC at 2669.
  8. complement, negative strand, positive direction, looking for AATCCC, 0.
  9. inverse complement, negative strand, negative direction, looking for CCCTAA, 0.
  10. inverse complement, positive strand, negative direction, looking for CCCTAA, 0.
  11. inverse complement, positive strand, positive direction, looking for CCCTAA, 1, CCCTAA at 2545.
  12. inverse complement, negative strand, positive direction, looking for CCCTAA, 0.
  13. inverse negative strand, negative direction, looking for GGGATT, 0.
  14. inverse positive strand, negative direction, looking for GGGATT, 0.
  15. inverse positive strand, positive direction, looking for GGGATT, 0.
  16. inverse negative strand, positive direction, looking for GGGATT, 1, GGGATT at 2545.

TRF (4560-2846) UTRs

  1. Negative strand, negative direction: TTAGGG at 3976, TTAGGG at 3067.

TRF negative direction (2811-2596) proximal promoters

  1. Negative strand, negative direction: TTAGGG at 2678.

TRF negative direction (2596-1) distal promoters

  1. Negative strand, negative direction: TTAGGG at 1917, TTAGGG at 1782, TTAGGG at 1264, TTAGGG at 1137, TTAGGG at 807, TTAGGG at 673, TTAGGG at 400.

TRF positive direction (4050-1) distal promoters

  1. Negative strand, positive direction: TTAGGG at 2766, TTAGGG at 2669.
  2. Positive strand, positive direction: CCCTAA at 2545.

TRF random dataset samplings

  1. TRFr0: 6, TTAGGG at 4466, TTAGGG at 4393, TTAGGG at 3947, TTAGGG at 2792, TTAGGG at 1025, TTAGGG at 759.
  2. TRFr1: 3, TTAGGG at 4537, TTAGGG at 3614, TTAGGG at 196.
  3. TRFr2: 0.
  4. TRFr3: 5, TTAGGG at 4501, TTAGGG at 4124, TTAGGG at 2648, TTAGGG at 1069, TTAGGG at 625.
  5. TRFr4: 3, TTAGGG at 2207, TTAGGG at 406, TTAGGG at 124.
  6. TRFr5: 2, TTAGGG at 4260, TTAGGG at 4058.
  7. TRFr6: 1, TTAGGG at 1829.
  8. TRFr7: 1, TTAGGG at 4527.
  9. TRFr8: 0.
  10. TRFr9: 3, TTAGGG at 4512, TTAGGG at 1104, TTAGGG at 658.
  11. TRFr0ci: 1, CCCTAA at 471.
  12. TRFr1ci: 0.
  13. TRFr2ci: 1, CCCTAA at 928.
  14. TRFr3ci: 1, CCCTAA at 2629.
  15. TRFr4ci: 0.
  16. TRFr5ci: 3, CCCTAA at 4015, CCCTAA at 3763, CCCTAA at 1163.
  17. TRFr6ci: 1, CCCTAA at 2454.
  18. TRFr7ci: 3, CCCTAA at 1735, CCCTAA at 904, CCCTAA at 186.
  19. TRFr8ci: 0.
  20. TRFr9ci: 1, CCCTAA at 1507.

TRFr arbitrary (evens) (4560-2846) UTRs

  1. TRFr0: TTAGGG at 4466, TTAGGG at 4393, TTAGGG at 3947.

TRFr alternate (odds) (4560-2846) UTRs

  1. TRFr1: TTAGGG at 4537, TTAGGG at 3614.
  2. TRFr3: TTAGGG at 4501, TTAGGG at 4124.
  3. TRFr5: TTAGGG at 4260, TTAGGG at 4058.
  4. TRFr7: TTAGGG at 4527.
  5. TRFr9: TTAGGG at 4512.
  6. TRFr5ci: CCCTAA at 4015, CCCTAA at 3763.

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

  1. TRFr0: TTAGGG at 4393.

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

  1. TRFr3ci: CCCTAA at 2629.

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

  1. TRFr3: TTAGGG at 4124.
  2. TRFr5: TTAGGG at 4260, TTAGGG at 4058.

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

  1. TRFr0: TTAGGG at 1025, TTAGGG at 759.
  2. TRFr4: TTAGGG at 2207, TTAGGG at 406, TTAGGG at 124.
  3. TRFr6: TTAGGG at 1829.
  4. TRFr0ci: CCCTAA at 471.
  5. TRFr2ci: CCCTAA at 928.
  6. TRFr6ci: CCCTAA at 2454.

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

  1. TRFr1: TTAGGG at 196.
  2. TRFr3: TTAGGG at 1069, TTAGGG at 625.
  3. TRFr9: TTAGGG at 1104, TTAGGG at 658.
  4. TRFr5ci: CCCTAA at 1163.
  5. TRFr7ci: CCCTAA at 1735, CCCTAA at 904, CCCTAA at 186.
  6. TRFr9ci: CCCTAA at 1507.

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

  1. TRFr1: TTAGGG at 3614, TTAGGG at 196.
  2. TRFr3: TTAGGG at 2648, TTAGGG at 1069, TTAGGG at 625.
  3. TRFr9: TTAGGG at 1104, TTAGGG at 658.
  4. TRFr3ci: CCCTAA at 2629.
  5. TRFr5ci: CCCTAA at 4015, CCCTAA at 3763, CCCTAA at 1163.
  6. TRFr7ci: CCCTAA at 1735, CCCTAA at 904, CCCTAA at 186.
  7. TRFr9ci: CCCTAA at 1507.

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

  1. TRFr0: TTAGGG at 3947, TTAGGG at 2792, TTAGGG at 1025, TTAGGG at 759.
  2. TRFr4: TTAGGG at 2207, TTAGGG at 406, TTAGGG at 124.
  3. TRFr6: TTAGGG at 1829.
  4. TRFr0ci: CCCTAA at 471.
  5. TRFr2ci: CCCTAA at 928.
  6. TRFr6ci: CCCTAA at 2454.

TRF analysis and results

Main article: Complex locus A1BG and ZNF497 § TRFs

Homo sapiens genes containing these are found using Homo sapiens "TRF (TTAGGG repeat binding factor)".[1]

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 3 10 0.3 0.65 ± 0.35
Randoms UTR alternate negative 10 10 1.0 0.65 ± 0.35
Reals Core negative 0 2 0 0
Randoms Core arbitrary negative 0 10 0 0
Randoms Core alternate negative 0 10 0 0
Reals Core positive 0 2 0 0
Randoms Core arbitrary positive 0 10 0 0.05
Randoms Core alternate positive 1 10 0.1 0.05
Reals Proximal negative 1 2 0.5 0.5 ± 0.5 (--1,+-0)
Randoms Proximal arbitrary negative 0 10 0 0.05
Randoms Proximal alternate negative 1 10 0.1 0.05
Reals Proximal positive 0 2 0 0
Randoms Proximal arbitrary positive 3 10 0.3 0.15
Randoms Proximal alternate positive 0 10 0 0.15
Reals Distal negative 7 2 3.5 3.5 ± 3.5 (--7,+-0)
Randoms Distal arbitrary negative 9 10 0.9 0.95
Randoms Distal alternate negative 10 10 1 0.95
Reals Distal positive 3 2 1.5 1.5 ± 0.5 (-+2,++1)
Randoms Distal arbitrary positive 15 10 1.5 1.3
Randoms Distal alternate positive 11 10 1.1 1.3

Comparison:

The occurrences of real TRF UTRs, proximals, negative distals are greater than the randoms, positive distals are outside the randoms. This suggests that the real TRFs are likely active or activable.

See also

References

  1. ↑ 1.0 1.1 Yoshiro Maru (2016). Basic Research, In: "Inflammation and Metastasis". Tokyo: Springer. pp. 193–231. doi:10.1007/978-4-431-56024-1_10. ISBN 978-4-431-56022-7. Retrieved 28 August 2020.

External links

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