The Human Transcription Factors

Conclusion

Assessment	Binding Mode	Motif Status	Notes	Comments
Likely to be sequence specific TF	1 Monomer or homomultimer	No motif	Has a putative AT-hook

Description

Description:	PHD finger protein 21A [Source:HGNC Symbol;Acc:HGNC:24156]
Entrez Summary	TBA
Ensembl ID:	ENSG00000135365
External Link:
Interpro	IPR001965; IPR011011; IPR017956; IPR019786; IPR019787; ;
Protein Domain:
Protein: ENSP00000323152	DBD: Other	Other: C1_1, PHD, PHD_2
Protein: ENSP00000398824	DBD: Other	Other: C1_1, PHD, PHD_2, zf-HC5HC2H
Protein: ENSP00000431621	DBD: Other	Other: DUF1043, DUF1664, HOOK, S6OS1

Previous Annotations

Source	Annotation
TF-CAT classification	Indeterminate - There is no evidence for or against this genes role as a TF___ PMIDS:0
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.	x
CisBP considers it as a TF?	No
TFclass considers it as a TF?	No
Has GO:0003700 "transcription factor activity, sequence-specific DNA binding"	No
GO-Info
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	1a1, Direct HQ evidence
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": 489, "endStyle": "straight", "aliStart": 444, "text": "PHD", "colour": "#9999ff", "aliEnd": 488, "start": 444, "href": "http://pfam.xfam.org/family/PF00628.27", "type": "pfama", "display": "true", "metadata": {"end": 489, "description": "PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains [2].  Several PHD fingers have been identified as binding modules of methylated histone H3 [3].", "database": "PfamA", "aliStart": 444, "scoreName": "E-value", "accession": "PF00628.27", "start": 444, "score": 1.3999999999999999e-12, "identifier": "PHD-finger", "type": "DBD", "aliEnd": 488}}, {"startStyle": "straight", "end": 471, "endStyle": "jagged", "aliStart": 434, "text": "C1_1", "colour": "#9999ff", "aliEnd": 469, "start": 434, "href": "http://pfam.xfam.org/family/PF00130.20", "type": "pfama", "display": "true", "metadata": {"end": 471, "description": "This domain is also known as the Protein kinase C conserved region 1 (C1) domain.", "database": "PfamA", "aliStart": 434, "scoreName": "E-value", "accession": "PF00130.20", "start": 434, "score": 0.0021, "identifier": "Phorbol esters/diacylglycerol binding domain (C1 domain)", "type": "DBD", "aliEnd": 469}}, {"startStyle": "straight", "end": 487, "endStyle": "straight", "aliStart": 453, "text": "PHD_2", "colour": "#9999ff", "aliEnd": 486, "start": 451, "href": "http://pfam.xfam.org/family/PF13831.4", "type": "pfama", "display": "true", "metadata": {"end": 487, "description": "PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains [2].  Several PHD fingers have been identified as binding modules of methylated histone H3 [3].", "database": "PfamA", "aliStart": 453, "scoreName": "E-value", "accession": "PF13831.4", "start": 451, "score": 0.0027, "identifier": "PHD-finger", "type": "DBD", "aliEnd": 486}}], "length": 635}

{"regions": [{"startStyle": "straight", "end": 535, "endStyle": "straight", "aliStart": 490, "text": "PHD", "colour": "#9999ff", "aliEnd": 534, "start": 490, "href": "http://pfam.xfam.org/family/PF00628.27", "type": "pfama", "display": "true", "metadata": {"end": 535, "description": "PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains [2].  Several PHD fingers have been identified as binding modules of methylated histone H3 [3].", "database": "PfamA", "aliStart": 490, "scoreName": "E-value", "accession": "PF00628.27", "start": 490, "score": 1.6e-12, "identifier": "PHD-finger", "type": "DBD", "aliEnd": 534}}, {"startStyle": "straight", "end": 533, "endStyle": "straight", "aliStart": 499, "text": "PHD_2", "colour": "#9999ff", "aliEnd": 532, "start": 497, "href": "http://pfam.xfam.org/family/PF13831.4", "type": "pfama", "display": "true", "metadata": {"end": 533, "description": "PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains [2].  Several PHD fingers have been identified as binding modules of methylated histone H3 [3].", "database": "PfamA", "aliStart": 499, "scoreName": "E-value", "accession": "PF13831.4", "start": 497, "score": 0.0031, "identifier": "PHD-finger", "type": "DBD", "aliEnd": 532}}, {"startStyle": "jagged", "end": 519, "endStyle": "jagged", "aliStart": 487, "text": "zf-HC5HC2H", "colour": "#9999ff", "aliEnd": 515, "start": 474, "href": "http://pfam.xfam.org/family/PF13771.4", "type": "pfama", "display": "true", "metadata": {"end": 519, "description": "The members of this family are annotated as containing PHD domain, but the zinc-binding region here is not typical of PHD domains.  The conformation here is a well-conserved cysteine-histidine rich region spanning 90 residues, where the Cys and His are arranged as HxxC(31)CxxC(6)CxxCxxxxCxxxxHxxC (21)CxxH.", "database": "PfamA", "aliStart": 487, "scoreName": "E-value", "accession": "PF13771.4", "start": 474, "score": 0.0039, "identifier": "PHD-like zinc-binding domain", "type": "DBD", "aliEnd": 515}}, {"startStyle": "jagged", "end": 517, "endStyle": "jagged", "aliStart": 487, "text": "C1_1", "colour": "#9999ff", "aliEnd": 515, "start": 484, "href": "http://pfam.xfam.org/family/PF00130.20", "type": "pfama", "display": "true", "metadata": {"end": 517, "description": "This domain is also known as the Protein kinase C conserved region 1 (C1) domain.", "database": "PfamA", "aliStart": 487, "scoreName": "E-value", "accession": "PF00130.20", "start": 484, "score": 0.0047, "identifier": "Phorbol esters/diacylglycerol binding domain (C1 domain)", "type": "DBD", "aliEnd": 515}}], "length": 681}

{"regions": [{"startStyle": "straight", "end": 134, "endStyle": "jagged", "aliStart": 26, "text": "DUF1043", "colour": "#9999ff", "aliEnd": 97, "start": 23, "href": "http://pfam.xfam.org/family/PF06295.10", "type": "pfama", "display": "true", "metadata": {"end": 134, "description": "This family consists of several hypothetical bacterial proteins of unknown function.", "database": "PfamA", "aliStart": 26, "scoreName": "E-value", "accession": "PF06295.10", "start": 23, "score": 0.00063, "identifier": "Protein of unknown function (DUF1043)", "type": "DBD", "aliEnd": 97}}, {"startStyle": "jagged", "end": 105, "endStyle": "jagged", "aliStart": 41, "text": "DUF1664", "colour": "#9999ff", "aliEnd": 101, "start": 32, "href": "http://pfam.xfam.org/family/PF07889.10", "type": "pfama", "display": "true", "metadata": {"end": 105, "description": "The members of this family are hypothetical plant proteins of unknown function. The region  featured in this family is approximately 100  amino acids long.", "database": "PfamA", "aliStart": 41, "scoreName": "E-value", "accession": "PF07889.10", "start": 32, "score": 0.0012, "identifier": "Protein of unknown function (DUF1664)", "type": "DBD", "aliEnd": 101}}, {"startStyle": "jagged", "end": 114, "endStyle": "jagged", "aliStart": 38, "text": "HOOK", "colour": "#9999ff", "aliEnd": 94, "start": 27, "href": "http://pfam.xfam.org/family/PF05622.10", "type": "pfama", "display": "true", "metadata": {"end": 114, "description": "This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organisms. The different members of the human gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three human HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas the central coiled-coil motif mediates homodimerisation and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes [1], whereas both HOOK1 and HOOK2 are localised to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head [2].", "database": "PfamA", "aliStart": 38, "scoreName": "E-value", "accession": "PF05622.10", "start": 27, "score": 0.0023, "identifier": "HOOK protein", "type": "DBD", "aliEnd": 94}}, {"startStyle": "jagged", "end": 107, "endStyle": "jagged", "aliStart": 43, "text": "S6OS1", "colour": "#9999ff", "aliEnd": 97, "start": 23, "href": "http://pfam.xfam.org/family/PF15676.3", "type": "pfama", "display": "true", "metadata": {"end": 107, "description": "This family of proteins is found in eukaryotes. Proteins in this family are typically between 114 and 587 amino acids in length. The function is not known.", "database": "PfamA", "aliStart": 43, "scoreName": "E-value", "accession": "PF15676.3", "start": 23, "score": 0.0054, "identifier": "Six6 opposite strand transcript 1 family", "type": "DBD", "aliEnd": 97}}], "length": 150}

TF Info Page for PHF21A (AT hook)