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== Protein ==
== Protein ==


SH3D21 contains three [[SH3 domain]]s.<ref name=CD>{{cite web|title=Conserved Domain Analysis of SH3D21|url=https://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi|work=NCBI Conserved Domain Search|accessdate=2 May 2013}}</ref><ref name="pmid15335710">{{cite journal | vauthors = Pawson T, Schlessingert J | title = SH2 and SH3 domains | journal = Current Biology | volume = 3 | issue = 7 | pages = 434–42 | date = July 1993 | pmid = 15335710 | doi = 10.1016/0960-9822(93)90350-W }}</ref><ref name="pmid11256992">{{cite journal | vauthors = Mayer BJ | title = SH3 domains: complexity in moderation | journal = Journal of Cell Science | volume = 114 | issue = Pt 7 | pages = 1253–63 | date = April 2001 | pmid = 11256992 | doi =  }}</ref> These domains are located near the N-terminus of the protein. In humans, these SH3 domains have a common [[amino acid]] sequence Asp-Glu-Leu. This [[sequence motif]] is also conserved in other species. SH3D21 has been found to interact with [[Adenylate kinase|Adenylate Kinase 2]], [[Artemin]], and [[Importin|Importin 13]].<ref name=genecards>{{cite web|title=SH3D21|url=http://www.genecards.org/cgi-bin/carddisp.pl?gene=SH3D21&search=SH3D21|work=Genecards|accessdate=3 May 2013}}</ref> The human protein has two [[Protein isoform|isoforms]] and no [[Homology (biology)|paralogs]].<ref name=ncbigene>{{cite web|title=SH3D21|url=https://www.ncbi.nlm.nih.gov/gene?Db=gene&Cmd=DetailsSearch&Term=79729|work=Gene|publisher=NCBI|accessdate=8 May 2013}}</ref> The second isoform is 645 amino acids long and is identical to the first isoform, except it is missing the first 111 amino acids.<ref name=secondisoform />  Due to this, the second isoform is missing the first, and half of the second, N-terminal [[SH3 domain]].<ref name=secondisoform>{{cite web|title=SH3 domain-containing protein 21 isoform 2|url=https://www.ncbi.nlm.nih.gov/protein/NP_078952.4|work=NCBI|accessdate=9 May 2013}}</ref> Secondary structure analysis of SH3D21 indicates a long alpha helical structure near the C-terminus.<ref name=phyre>{{cite web|title=Phyre 2 Secondary Structure Analysis|url=http://www.sbg.bio.ic.ac.uk/phyre2/html/page.cgi?id=index|accessdate=14 May 2013}}</ref><ref>{{cite web|title=PELE Analysis|url=http://seqtool.sdsc.edu/CGI/BW.cgi#!|accessdate=14 May 2013}}</ref>  The purpose of this structure is unknown. SH3D21 is predicted to have many [[phosphorylation]] sites and multiple [[SUMO protein|sumolyation]] sites throughout the entirety of the protein.<ref>{{cite web|title=SUMOplot Analysis|url=http://www.abgent.com/sumoplot|accessdate=14 May 2013}}</ref><ref>{{cite web|title=NetPhos 2.0 Analysis|url=http://www.cbs.dtu.dk/services/NetPhos/|accessdate=14 May 2013}}</ref>  
SH3D21 contains three [[SH3 domain]]s.<ref name=CD>{{cite web|title=Conserved Domain Analysis of SH3D21|url=https://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi|work=NCBI Conserved Domain Search|accessdate=2 May 2013}}</ref><ref name="pmid15335710">{{cite journal | vauthors = Pawson T, Schlessingert J | title = SH2 and SH3 domains | journal = Current Biology | volume = 3 | issue = 7 | pages = 434–42 | date = July 1993 | pmid = 15335710 | doi = 10.1016/0960-9822(93)90350-W }}</ref><ref name="pmid11256992">{{cite journal | vauthors = Mayer BJ | title = SH3 domains: complexity in moderation | journal = Journal of Cell Science | volume = 114 | issue = Pt 7 | pages = 1253–63 | date = April 2001 | pmid = 11256992 | doi =  }}</ref> These domains are located near the N-terminus of the protein. In humans, these SH3 domains have a common [[amino acid]] sequence Asp-Glu-Leu. This [[sequence motif]] is also conserved in other species. SH3D21 has been found to interact with [[Adenylate kinase|Adenylate Kinase 2]], [[Artemin]], and [[Importin|Importin 13]].<ref name=genecards>{{cite web|title=SH3D21|url=https://www.genecards.org/cgi-bin/carddisp.pl?gene=SH3D21&search=SH3D21|work=Genecards|accessdate=3 May 2013}}</ref> The human protein has two [[Protein isoform|isoforms]] and no [[Homology (biology)|paralogs]].<ref name=ncbigene>{{cite web|title=SH3D21|url=https://www.ncbi.nlm.nih.gov/gene?Db=gene&Cmd=DetailsSearch&Term=79729|work=Gene|publisher=NCBI|accessdate=8 May 2013}}</ref> The second isoform is 645 amino acids long and is identical to the first isoform, except it is missing the first 111 amino acids.<ref name=secondisoform />  Due to this, the second isoform is missing the first, and half of the second, N-terminal [[SH3 domain]].<ref name=secondisoform>{{cite web|title=SH3 domain-containing protein 21 isoform 2|url=https://www.ncbi.nlm.nih.gov/protein/NP_078952.4|work=NCBI|accessdate=9 May 2013}}</ref> Secondary structure analysis of SH3D21 indicates a long alpha helical structure near the C-terminus.<ref name=phyre>{{cite web|title=Phyre 2 Secondary Structure Analysis|url=http://www.sbg.bio.ic.ac.uk/phyre2/html/page.cgi?id=index|accessdate=14 May 2013}}</ref><ref>{{cite web|title=PELE Analysis|url=http://seqtool.sdsc.edu/CGI/BW.cgi#!|accessdate=14 May 2013}}{{dead link|date=April 2018 |bot=InternetArchiveBot |fix-attempted=yes }}</ref>  The purpose of this structure is unknown. SH3D21 is predicted to have many [[phosphorylation]] sites and multiple [[SUMO protein|sumolyation]] sites throughout the entirety of the protein.<ref>{{cite web|title=SUMOplot Analysis|url=http://www.abgent.com/sumoplot|accessdate=14 May 2013}}</ref><ref>{{cite web|title=NetPhos 2.0 Analysis|url=http://www.cbs.dtu.dk/services/NetPhos/|accessdate=14 May 2013}}</ref>  
[[File:Human SH3D21 SH3 Domain analysis.PNG|thumb|none|left|upright 2.0|This image is a multiple sequence alignment of the three SH3 domains found in the human SH3D21 protein. Note the conserved Asp-Glu-Leu motif. This image was generated using publicly available sequence data and open source software.]]
[[File:Human SH3D21 SH3 Domain analysis.PNG|thumb|none|left|upright 2.0|This image is a multiple sequence alignment of the three SH3 domains found in the human SH3D21 protein. Note the conserved Asp-Glu-Leu motif. This image was generated using publicly available sequence data and open source software.]]


== Function ==
== Function ==


The function of this gene is still unclear. However, research has linked SH3D21 expression changes to male infertility and [[Ataxia Telangiectasia]].<ref>{{cite journal | vauthors = Mallott J, Kwan A, Church J, Gonzalez-Espinosa D, Lorey F, Tang LF, Sunderam U, Rana S, Srinivasan R, Brenner SE, Puck J | title = Newborn screening for SCID identifies patients with ataxia telangiectasia | journal = Journal of Clinical Immunology | volume = 33 | issue = 3 | pages = 540–9 | date = April 2013 | pmid = 23264026 | pmc = 3591536 | doi = 10.1007/s10875-012-9846-1 | url = https://link.springer.com/article/10.1007/s10875-012-9846-1 }}</ref><ref>{{cite journal | vauthors = Stouffs K, Vandermaelen D, Massart A, Menten B, Vergult S, Tournaye H, Lissens W | title = Array comparative genomic hybridization in male infertility | journal = Human Reproduction | volume = 27 | issue = 3 | pages = 921–9 | date = March 2012 | pmid = 22238114 | doi = 10.1093/humrep/der440 }}</ref>
The function of this gene is still unclear. However, research has linked SH3D21 expression changes to male infertility and [[Ataxia Telangiectasia]].<ref>{{cite journal | vauthors = Mallott J, Kwan A, Church J, Gonzalez-Espinosa D, Lorey F, Tang LF, Sunderam U, Rana S, Srinivasan R, Brenner SE, Puck J | title = Newborn screening for SCID identifies patients with ataxia telangiectasia | journal = Journal of Clinical Immunology | volume = 33 | issue = 3 | pages = 540–9 | date = April 2013 | pmid = 23264026 | pmc = 3591536 | doi = 10.1007/s10875-012-9846-1 }}</ref><ref>{{cite journal | vauthors = Stouffs K, Vandermaelen D, Massart A, Menten B, Vergult S, Tournaye H, Lissens W | title = Array comparative genomic hybridization in male infertility | journal = Human Reproduction | volume = 27 | issue = 3 | pages = 921–9 | date = March 2012 | pmid = 22238114 | doi = 10.1093/humrep/der440 }}</ref>
Further studies have implicated the chromosomal region of 1p34.3 in Intracranial Aneurysm and as a negative prognosis sign in [[colorectal cancer]].<ref>{{cite journal | vauthors = Nahed BV, Seker A, Guclu B, Ozturk AK, Finberg K, Hawkins AA, DiLuna ML, State M, Lifton RP, Gunel M | title = Mapping a Mendelian form of intracranial aneurysm to 1p34.3-p36.13 | journal = American Journal of Human Genetics | volume = 76 | issue = 1 | pages = 172–9 | date = January 2005 | pmid = 15540160 | pmc = 1196421 | doi = 10.1086/426953 }}</ref><ref>{{cite journal|last=Kashkin|first=K.N|author2=A.G. Perevoschoikov | name-list-format = vanc |title=Deletion of the Alu-VpA/MycL1(1p34.3) locus is a negative prognostic sign in human colorectal cancer|journal=Molecular Biology|date=May–June 2000|volume=34|issue=3|pages=337–344|url=https://link.springer.com/article/10.1007%2FBF02759663|doi=10.1007/bf02759663}}</ref> These studies do not, however, directly mention SH3D21.
Further studies have implicated the chromosomal region of 1p34.3 in Intracranial Aneurysm and as a negative prognosis sign in [[colorectal cancer]].<ref>{{cite journal | vauthors = Nahed BV, Seker A, Guclu B, Ozturk AK, Finberg K, Hawkins AA, DiLuna ML, State M, Lifton RP, Gunel M | title = Mapping a Mendelian form of intracranial aneurysm to 1p34.3-p36.13 | journal = American Journal of Human Genetics | volume = 76 | issue = 1 | pages = 172–9 | date = January 2005 | pmid = 15540160 | pmc = 1196421 | doi = 10.1086/426953 }}</ref><ref>{{cite journal|last=Kashkin|first=K.N|author2=A.G. Perevoschoikov | name-list-format = vanc |title=Deletion of the Alu-VpA/MycL1(1p34.3) locus is a negative prognostic sign in human colorectal cancer|journal=Molecular Biology|date=May–June 2000|volume=34|issue=3|pages=337–344|doi=10.1007/bf02759663}}</ref> These studies do not, however, directly mention SH3D21.


== Homology ==
== Homology ==


[[File:SH3D21 Phylogenetic Tree.PNG|thumb|right|Phylogenetic tree generated using open source, free software and publicly available sequence data.]]
[[File:SH3D21 Phylogenetic Tree.PNG|thumb|right|Phylogenetic tree generated using open source, free software and publicly available sequence data.]]
SH3D21 is well-conserved in mammals. [[BLAST]] analysis found distant [[Homology (biology)|orthologs]] in [[Osteichthyes]] with a max identity of 28%.<ref name=Blast>{{cite web|title=BLAST|url=http://blast.ncbi.nlm.nih.gov/Blast.cgi|work=NCBI|accessdate=3 May 2013}}</ref> Sequence identity was calculated using available sequence data and ALIGN software.<ref>{{cite web|title=Sequence Alignment|url=http://seqtool.sdsc.edu/|work=ALIGN|accessdate=8 May 2013}}</ref>
SH3D21 is well-conserved in mammals. [[BLAST]] analysis found distant [[Homology (biology)|orthologs]] in [[Osteichthyes]] with a max identity of 28%.<ref name=Blast>{{cite web|title=BLAST|url=http://blast.ncbi.nlm.nih.gov/Blast.cgi|work=NCBI|accessdate=3 May 2013}}</ref> Sequence identity was calculated using available sequence data and ALIGN software.<ref>{{cite web|title=Sequence Alignment|url=http://seqtool.sdsc.edu/|archive-url=https://web.archive.org/web/20030811031200/http://seqtool.sdsc.edu/|dead-url=yes|archive-date=11 August 2003|work=ALIGN|accessdate=8 May 2013}}</ref>


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Latest revision as of 04:52, 12 December 2018

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Identifiers
Aliases
External IDsGeneCards: [1]
Orthologs
SpeciesHumanMouse
Entrez

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Ensembl

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UniProt

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RefSeq (mRNA)

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RefSeq (protein)

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Location (UCSC)n/an/a
PubMed searchn/an/a
Wikidata
View/Edit Human

SH3D21 is a nuclear protein that is encoded by the SH3D21 gene. In humans, this gene is located on chromosome 1 p34.3.[1] The human mRNA transcript is 2527 base pairs and the final protein product is 756 amino acids.[2] While the exact function of this protein remains unknown, due to the presence of three SH3 domains, it has been implicated in protein-protein interactions.[3]

Gene

SH3D21 is expressed in low levels in most tissue.[4] Microarray analysis has shown SH3D21 expression to be decreased in TP63 knockout mice.[5] SH3D21 has been shown to be expressed highly in the superior cervical ganglion, the dorsal root ganglia and the trigeminal ganglion.[4][6] Transcription of SH3D21 is known to be upregulated in the presence of testosterone.[7]

Protein

SH3D21 contains three SH3 domains.[3][8][9] These domains are located near the N-terminus of the protein. In humans, these SH3 domains have a common amino acid sequence Asp-Glu-Leu. This sequence motif is also conserved in other species. SH3D21 has been found to interact with Adenylate Kinase 2, Artemin, and Importin 13.[1] The human protein has two isoforms and no paralogs.[2] The second isoform is 645 amino acids long and is identical to the first isoform, except it is missing the first 111 amino acids.[10] Due to this, the second isoform is missing the first, and half of the second, N-terminal SH3 domain.[10] Secondary structure analysis of SH3D21 indicates a long alpha helical structure near the C-terminus.[11][12] The purpose of this structure is unknown. SH3D21 is predicted to have many phosphorylation sites and multiple sumolyation sites throughout the entirety of the protein.[13][14]

File:Human SH3D21 SH3 Domain analysis.PNG
This image is a multiple sequence alignment of the three SH3 domains found in the human SH3D21 protein. Note the conserved Asp-Glu-Leu motif. This image was generated using publicly available sequence data and open source software.

Function

The function of this gene is still unclear. However, research has linked SH3D21 expression changes to male infertility and Ataxia Telangiectasia.[15][16] Further studies have implicated the chromosomal region of 1p34.3 in Intracranial Aneurysm and as a negative prognosis sign in colorectal cancer.[17][18] These studies do not, however, directly mention SH3D21.

Homology

File:SH3D21 Phylogenetic Tree.PNG
Phylogenetic tree generated using open source, free software and publicly available sequence data.

SH3D21 is well-conserved in mammals. BLAST analysis found distant orthologs in Osteichthyes with a max identity of 28%.[19] Sequence identity was calculated using available sequence data and ALIGN software.[20]

Species Species common name NCBI Accession Number (Protein) Length (aa) Sequence Identity
Homo sapiens Human NP_001156002 756aa 100%
Gorilla gorilla Gorilla XP_004025512 761 aa 97.1%
Pongo abelii Orangutan XP_002811093 755aa 94.9%
Macaca mulatta Macaques XP_001110607 755aa 91.4%
Papia anubir Olive Baboon XP_003891645/ 761aa 91.2%
Saimiri boliviensis Black Capped Squirrel Monkey XP_003308029 650aa 82.0%
Bos taurus Cattle NP_001156006 676aa 58.70%
Cavia porcellus Guinea pig XP_003471528 658aa 52.60%
Oreochromis niloticus Nile Talapia XP_003450596 505aa 28.1%

References

  1. ↑ 1.0 1.1 "SH3D21". Genecards. Retrieved 3 May 2013.
  2. ↑ 2.0 2.1 "SH3D21". Gene. NCBI. Retrieved 8 May 2013.
  3. ↑ 3.0 3.1 "Conserved Domain Analysis of SH3D21". NCBI Conserved Domain Search. Retrieved 2 May 2013.
  4. ↑ 4.0 4.1 "BioGPS Expression Profile". Retrieved 2 May 2013.
  5. ↑ "Transcription factor p63 null mutation effect on skin (MG-U74B)". Retrieved 1 March 2013.
  6. ↑ "GEO Expression Profile". GEO Database. Retrieved 2 May 2013.
  7. ↑ "Chemical Interaction Report". Retrieved 1 March 2013.
  8. ↑ Pawson T, Schlessingert J (July 1993). "SH2 and SH3 domains". Current Biology. 3 (7): 434–42. doi:10.1016/0960-9822(93)90350-W. PMID 15335710.
  9. ↑ Mayer BJ (April 2001). "SH3 domains: complexity in moderation". Journal of Cell Science. 114 (Pt 7): 1253–63. PMID 11256992.
  10. ↑ 10.0 10.1 "SH3 domain-containing protein 21 isoform 2". NCBI. Retrieved 9 May 2013.
  11. ↑ "Phyre 2 Secondary Structure Analysis". Retrieved 14 May 2013.
  12. ↑ "PELE Analysis". Retrieved 14 May 2013.[permanent dead link]
  13. ↑ "SUMOplot Analysis". Retrieved 14 May 2013.
  14. ↑ "NetPhos 2.0 Analysis". Retrieved 14 May 2013.
  15. ↑ Mallott J, Kwan A, Church J, Gonzalez-Espinosa D, Lorey F, Tang LF, Sunderam U, Rana S, Srinivasan R, Brenner SE, Puck J (April 2013). "Newborn screening for SCID identifies patients with ataxia telangiectasia". Journal of Clinical Immunology. 33 (3): 540–9. doi:10.1007/s10875-012-9846-1. PMC 3591536. PMID 23264026.
  16. ↑ Stouffs K, Vandermaelen D, Massart A, Menten B, Vergult S, Tournaye H, Lissens W (March 2012). "Array comparative genomic hybridization in male infertility". Human Reproduction. 27 (3): 921–9. doi:10.1093/humrep/der440. PMID 22238114.
  17. ↑ Nahed BV, Seker A, Guclu B, Ozturk AK, Finberg K, Hawkins AA, DiLuna ML, State M, Lifton RP, Gunel M (January 2005). "Mapping a Mendelian form of intracranial aneurysm to 1p34.3-p36.13". American Journal of Human Genetics. 76 (1): 172–9. doi:10.1086/426953. PMC 1196421. PMID 15540160.
  18. ↑ Kashkin K, A.G. Perevoschoikov (May–June 2000). "Deletion of the Alu-VpA/MycL1(1p34.3) locus is a negative prognostic sign in human colorectal cancer". Molecular Biology. 34 (3): 337–344. doi:10.1007/bf02759663.
  19. ↑ "BLAST". NCBI. Retrieved 3 May 2013.
  20. ↑ "Sequence Alignment". ALIGN. Archived from the original on 11 August 2003. Retrieved 8 May 2013.
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