The Human Transcription Factors

Conclusion

Assessment	Binding Mode	Motif Status	Notes	Comments
Likely to be sequence specific TF	1 Monomer or homomultimer	No motif		Binds specifically to the PSE (PMID: 9732265)

Description

Description:	small nuclear RNA activating complex polypeptide 5 [Source:HGNC Symbol;Acc:HGNC:15484]
Entrez Summary	TBA
Ensembl ID:	ENSG00000174446
External Link:
Interpro	IPR029138;
Protein Domain:
Protein: ENSP00000308439	DBD: Other	Other: GDE_N, SNAPc19
Protein: ENSP00000319597	DBD: Other	Other: DUF4724, SNAPc19
Protein: ENSP00000378954	DBD: Other	Other: DUF4724, SNAPc19
Protein: ENSP00000457892	DBD: Other	Other: DUF4724, SNAPc19

Previous Annotations

Source	Annotation
TF-CAT classification	No PMIDS:
Vaquerizas 2009 TF classification "a" Has direct evidence of TF function; "b" Has evidence for an orthologous TF; "c" contains likely DBDs, but has no functional evidence; "x" is an unlikely TF such as predicted gene, genes with likely non-specific DBDs or that have function outside transcription; "other" category contains proteins without clear DBDs they curated from external sources.	No
CisBP considers it as a TF?	No
TFclass considers it as a TF?	No
Has GO:0003700 "transcription factor activity, sequence-specific DNA binding"	Yes
GO-Info	GO:0003700 sequence-specific DNA binding transcription factor activity IEA - GO_REF:0000002
Initial Assessment 1a1 Protein has a high confidence PWM (HT-SELEX, PBM or B1H model) or there is a crystal structure that supports sequence specific DNA binding; 1a2 There is high confidence data for a close ortholog (as defined in CisBP); 2a1 There is lower confidence direct evidence, such as a Jaspar, Hocomoco or Transfac model; 2a2 There is lower confidence evidence for an close ortholog; 3a There is decent circumstantial evidence for its role as a TF or not; 4a Two or more datasets predict it as a TF; 5a One of the source datasets predicts is as a TF	5a, one of the source datasets predicts is as a TF
TF has conditional DNA-binding requirements

DNA-Binding

Published Motif Data

Source	Annotation	Motif	Evidence

Structure

Structure	PDB	Not_Covered

Experimental History

Method	Constructs
Tried in PBM? (Whether the protein was tried in PBM or not)
Tried in HT-SELEX (Whether the protein was tried in HT-SELEX or not, and if so, then what kind of clones were tested)
Other Information? (Tried with another method and failed?)

External Contribution

Name
Email
Comment
Reference

{"regions": [{"startStyle": "straight", "end": 32, "endStyle": "jagged", "aliStart": 7, "text": "SNAPc19", "colour": "#9999ff", "aliEnd": 30, "start": 7, "href": "http://pfam.xfam.org/family/PF15497.4", "type": "pfama", "display": "true", "metadata": {"end": 32, "description": "SNAPc19 is a family of proteins found in eukaryotes. It is one of the five core components of the snRNA-activating protein complex or SNAPc that helps direct the nucleation of RNA polymerases II and III. The core RNA polymerase II snRNA promoters consist of a single essential element, the proximal sequence element (PSE), whereas the core RNA polymerase III snRNA promoters consist of both a PSE and a TATA box. The SNAPc binds to the PSE of both of these. SNAPc recognises the PSE sequence common to all human snRNA genes, irrespective of polymerase specificity. SNAPc is also known as the PSE transcription factor (PTF) or PSE-binding protein (PBP). The human SNAP19 and SNAP45 subunits are dispensable for transcription in vitro and are not as widely conserved as the other three, SNAP190, SNAP43 and SNAP50, suggesting that these vertebrate-specific SNAPc subunits may have adapted specialised regulatory roles for snRNA gene transcription [3].", "database": "PfamA", "aliStart": 7, "scoreName": "E-value", "accession": "PF15497.4", "start": 7, "score": 1.1000000000000001e-10, "identifier": "snRNA-activating protein complex subunit 19, SNAPc subunit 19", "type": "DBD", "aliEnd": 30}}, {"startStyle": "jagged", "end": 67, "endStyle": "straight", "aliStart": 31, "text": "SNAPc19", "colour": "#9999ff", "aliEnd": 65, "start": 30, "href": "http://pfam.xfam.org/family/PF15497.4", "type": "pfama", "display": "true", "metadata": {"end": 67, "description": "SNAPc19 is a family of proteins found in eukaryotes. It is one of the five core components of the snRNA-activating protein complex or SNAPc that helps direct the nucleation of RNA polymerases II and III. The core RNA polymerase II snRNA promoters consist of a single essential element, the proximal sequence element (PSE), whereas the core RNA polymerase III snRNA promoters consist of both a PSE and a TATA box. The SNAPc binds to the PSE of both of these. SNAPc recognises the PSE sequence common to all human snRNA genes, irrespective of polymerase specificity. SNAPc is also known as the PSE transcription factor (PTF) or PSE-binding protein (PBP). The human SNAP19 and SNAP45 subunits are dispensable for transcription in vitro and are not as widely conserved as the other three, SNAP190, SNAP43 and SNAP50, suggesting that these vertebrate-specific SNAPc subunits may have adapted specialised regulatory roles for snRNA gene transcription [3].", "database": "PfamA", "aliStart": 31, "scoreName": "E-value", "accession": "PF15497.4", "start": 30, "score": 1.1000000000000001e-10, "identifier": "snRNA-activating protein complex subunit 19, SNAPc subunit 19", "type": "DBD", "aliEnd": 65}}, {"startStyle": "jagged", "end": 66, "endStyle": "jagged", "aliStart": 18, "text": "GDE_N", "colour": "#9999ff", "aliEnd": 57, "start": 16, "href": "http://pfam.xfam.org/family/PF12439.6", "type": "pfama", "display": "true", "metadata": {"end": 66, "description": "This domain family is found in bacteria and archaea, and is typically between 218 and 229 amino acids in length. The family is found in association with Pfam:PF06202. Glycogen debranching enzyme catalyses the debranching of amylopectin in glycogen. This is done by transferring three glucose subunits of glycogen from one parallel chain to another. This has the effect of enabling the glucose residues to become more accessible for glycolysis.", "database": "PfamA", "aliStart": 18, "scoreName": "E-value", "accession": "PF12439.6", "start": 16, "score": 0.0096, "identifier": "Glycogen debranching enzyme N terminal", "type": "DBD", "aliEnd": 57}}], "length": 69}

{"regions": [{"startStyle": "straight", "end": 97, "endStyle": "straight", "aliStart": 7, "text": "SNAPc19", "colour": "#9999ff", "aliEnd": 95, "start": 7, "href": "http://pfam.xfam.org/family/PF15497.4", "type": "pfama", "display": "true", "metadata": {"end": 97, "description": "SNAPc19 is a family of proteins found in eukaryotes. It is one of the five core components of the snRNA-activating protein complex or SNAPc that helps direct the nucleation of RNA polymerases II and III. The core RNA polymerase II snRNA promoters consist of a single essential element, the proximal sequence element (PSE), whereas the core RNA polymerase III snRNA promoters consist of both a PSE and a TATA box. The SNAPc binds to the PSE of both of these. SNAPc recognises the PSE sequence common to all human snRNA genes, irrespective of polymerase specificity. SNAPc is also known as the PSE transcription factor (PTF) or PSE-binding protein (PBP). The human SNAP19 and SNAP45 subunits are dispensable for transcription in vitro and are not as widely conserved as the other three, SNAP190, SNAP43 and SNAP50, suggesting that these vertebrate-specific SNAPc subunits may have adapted specialised regulatory roles for snRNA gene transcription [3].", "database": "PfamA", "aliStart": 7, "scoreName": "E-value", "accession": "PF15497.4", "start": 7, "score": 3.2e-24, "identifier": "snRNA-activating protein complex subunit 19, SNAPc subunit 19", "type": "DBD", "aliEnd": 95}}, {"startStyle": "straight", "end": 98, "endStyle": "straight", "aliStart": 14, "text": "DUF4724", "colour": "#9999ff", "aliEnd": 95, "start": 11, "href": "http://pfam.xfam.org/family/PF15852.3", "type": "pfama", "display": "true", "metadata": {"end": 98, "description": "This family of proteins is found in mammals. There is a conserved KVKPL sequence motif.", "database": "PfamA", "aliStart": 14, "scoreName": "E-value", "accession": "PF15852.3", "start": 11, "score": 0.0044, "identifier": "Domain of unknown function (DUF4724)", "type": "DBD", "aliEnd": 95}}], "length": 99}

TF Info Page for SNAPC5 (Unknown)