Conclusion
Assessment
Binding Mode
Motif Status
Notes
Comments
Known motif
1 Monomer or homomultimer
High-throughput in vitro
Contains 3 AT-hook domain, a CXXC domain, and a possible C2H2 domain.
Description
Description:
lysine methyltransferase 2A [Source:HGNC Symbol;Acc:HGNC:7132]
Entrez Summary
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This gene encodes a transcriptional coactivator that plays an
essential role in regulating gene expression during early development and
hematopoiesis. The encoded protein contains multiple conserved functional
domains. One of these domains, the SET domain, is responsible for its histone
H3 lysine 4 (H3K4) methyltransferase activity which mediates chromatin
modifications associated with epigenetic transcriptional activation. This
protein is processed by the enzyme Taspase 1 into two fragments, MLL-C and
MLL-N. These fragments reassociate and further assemble into different
multiprotein complexes that regulate the transcription of specific target
genes, including many of the HOX genes. Multiple chromosomal translocations
involving this gene are the cause of certain acute lymphoid leukemias and
acute myeloid leukemias. Alternate splicing results in multiple transcript
variants.[provided by RefSeq, Oct 2010]
Ensembl ID:
ENSG00000118058
External Link:
CisBP
Interpro
IPR001214 ; IPR001487 ; IPR001965 ; IPR002857 ; IPR003616 ; IPR003888 ; IPR003889 ; IPR011011 ; IPR016569 ; IPR019787 ;
Protein Domain:
ENSP00000374157
Protein Domain:
ENSP00000376612
Protein Domain:
ENSP00000436786
Protein Domain:
ENSP00000436564
Protein Domain:
ENSP00000432391
Protein Domain:
ENSP00000434618
Protein Domain:
ENSP00000436700
Protein Domain:
ENSP00000432652
Domain:
Protein: ENSP00000374157DBD: CxxCOther: Bromodomain, FYRC, FYRN, PHD, PHD_2, SET, zf-HC5HCProtein: ENSP00000376612DBD: CxxCOther: PHD, PHD_2, PHD_4, zf-PHD-likeProtein: ENSP00000436786DBD: CxxCOther: Bromodomain, FYRC, FYRN, PHD, PHD_2, SET, zf-HC5HCProtein: ENSP00000436564DBD: CxxCOther: Protein: ENSP00000432391DBD: CxxCOther: Protein: ENSP00000434618DBD: CxxCOther: Protein: ENSP00000436700DBD: CxxCOther: Protein: ENSP00000432652DBD: CxxCOther:
Previous Annotations
Source
Annotation
TF-CAT classification
TF Gene_DNA-Binding sequence-specific_DNA Binding Transactivation_ PMIDS:12453418
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.
c
CisBP considers it as a TF?
Yes
TFclass considers it as a TF?
Yes
Has GO:0003700 "transcription factor activity, sequence-specific DNA binding"
Yes
GO-Info
GO:0003700 sequence-specific DNA binding transcription factor activity NAS - PMID:10821850
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
Structure
Experimental History
{"regions": [{"startStyle": "curved", "end": 1194, "endStyle": "curved", "aliStart": 1148, "text": "zfCXXC", "colour": "#009900", "aliEnd": 1194, "start": 1147, "href": "http://pfam.xfam.org/family/PF02008.18", "type": "pfama", "display": "true", "metadata": {"end": 1194, "description": "This domain contains eight conserved cysteine residues that bind to two zinc ions. The CXXC domain is found in a variety of chromatin-associated proteins. This domain binds to nonmethyl-CpG dinucleotides. The domain is characterised by two repeats [3], and shows a peculiar internal duplication in which the second unit is inserted into the first one [4]. Each of these units is characterised by four conserved cysteines, displaying a CXXCXXCX(n)C motif that chelate a Zn+2 ion. The DNA binding interface has been identified by NMR [3]. In eukaryotes, the CXXC domain is found in stramenopiles, plants and metazoans. Plants possess a mono-CXXC domain that is present in distinct chromatin proteins [4]. Structural comparisons show that the mono-CXXC is homologous to the structural-zinc binding domain of medium chain dehydrogenases [4].", "database": "PfamA", "aliStart": 1148, "scoreName": "E-value", "accession": "PF02008.18", "start": 1147, "score": 3.7e-13, "identifier": "CXXC zinc finger domain", "type": "DBD", "aliEnd": 1194}}, {"startStyle": "straight", "end": 3748, "endStyle": "straight", "aliStart": 3669, "text": "FYRC", "colour": "#9999ff", "aliEnd": 3748, "start": 3666, "href": "http://pfam.xfam.org/family/PF05965.12", "type": "pfama", "display": "true", "metadata": {"end": 3748, "description": "This region is normally found in the trithorax/ALL1 family proteins. It is similar to SMART:SM00542.", "database": "PfamA", "aliStart": 3669, "scoreName": "E-value", "accession": "PF05965.12", "start": 3666, "score": 8.300000000000001e-22, "identifier": "F/Y rich C-terminus", "type": "DBD", "aliEnd": 3748}}, {"startStyle": "straight", "end": 3945, "endStyle": "straight", "aliStart": 3840, "text": "SET", "colour": "#9999ff", "aliEnd": 3944, "start": 3840, "href": "http://pfam.xfam.org/family/PF00856.26", "type": "pfama", "display": "true", "metadata": {"end": 3945, "description": "SET domains are protein lysine methyltransferase enzymes. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases) [2]. A subset of SET domains have been called PR domains. These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction [3]. The SET domain consists of two regions known as SET-N and SET-C. SET-C forms an unusual and conserved knot-like structure of probably functional importance. Additionally to SET-N and SET-C, an insert region (SET-I) and flanking regions of high structural variability form part of the overall structure [5].", "database": "PfamA", "aliStart": 3840, "scoreName": "E-value", "accession": "PF00856.26", "start": 3840, "score": 1.5999999999999999e-21, "identifier": "SET domain", "type": "DBD", "aliEnd": 3944}}, {"startStyle": "straight", "end": 1482, "endStyle": "straight", "aliStart": 1434, "text": "PHD", "colour": "#9999ff", "aliEnd": 1482, "start": 1433, "href": "http://pfam.xfam.org/family/PF00628.27", "type": "pfama", "display": "true", "metadata": {"end": 1482, "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": 1434, "scoreName": "E-value", "accession": "PF00628.27", "start": 1433, "score": 1.7000000000000002e-17, "identifier": "PHD-finger", "type": "DBD", "aliEnd": 1482}}, {"startStyle": "straight", "end": 1533, "endStyle": "straight", "aliStart": 1481, "text": "PHD", "colour": "#9999ff", "aliEnd": 1533, "start": 1481, "href": "http://pfam.xfam.org/family/PF00628.27", "type": "pfama", "display": "true", "metadata": {"end": 1533, "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": 1481, "scoreName": "E-value", "accession": "PF00628.27", "start": 1481, "score": 1.7000000000000002e-17, "identifier": "PHD-finger", "type": "DBD", "aliEnd": 1533}}, {"startStyle": "straight", "end": 1627, "endStyle": "straight", "aliStart": 1569, "text": "PHD", "colour": "#9999ff", "aliEnd": 1626, "start": 1568, "href": "http://pfam.xfam.org/family/PF00628.27", "type": "pfama", "display": "true", "metadata": {"end": 1627, "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": 1569, "scoreName": "E-value", "accession": "PF00628.27", "start": 1568, "score": 1.7000000000000002e-17, "identifier": "PHD-finger", "type": "DBD", "aliEnd": 1626}}, {"startStyle": "straight", "end": 2071, "endStyle": "straight", "aliStart": 2024, "text": "FYRN", "colour": "#9999ff", "aliEnd": 2071, "start": 2024, "href": "http://pfam.xfam.org/family/PF05964.12", "type": "pfama", "display": "true", "metadata": {"end": 2071, "description": "This region is normally found in the trithorax/ALL1 family proteins. It is similar to SMART:SM00541.", "database": "PfamA", "aliStart": 2024, "scoreName": "E-value", "accession": "PF05964.12", "start": 2024, "score": 3.6000000000000003e-16, "identifier": "F/Y-rich N-terminus", "type": "DBD", "aliEnd": 2071}}, {"startStyle": "straight", "end": 1978, "endStyle": "straight", "aliStart": 1900, "text": "zf-HC5HC2H", "colour": "#9999ff", "aliEnd": 1978, "start": 1900, "href": "http://pfam.xfam.org/family/PF13771.4", "type": "pfama", "display": "true", "metadata": {"end": 1978, "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": 1900, "scoreName": "E-value", "accession": "PF13771.4", "start": 1900, "score": 3.8e-10, "identifier": "PHD-like zinc-binding domain", "type": "DBD", "aliEnd": 1978}}, {"startStyle": "straight", "end": 1977, "endStyle": "jagged", "aliStart": 1886, "text": "zf-HC5HC2H_2", "colour": "#9999ff", "aliEnd": 1966, "start": 1871, "href": "http://pfam.xfam.org/family/PF13832.4", "type": "pfama", "display": "true", "metadata": {"end": 1977, "description": NaN, "database": "PfamA", "aliStart": 1886, "scoreName": "E-value", "accession": "PF13832.4", "start": 1871, "score": 1.3e-08, "identifier": "PHD-zinc-finger like domain", "type": "DBD", "aliEnd": 1966}}, {"startStyle": "jagged", "end": 1751, "endStyle": "jagged", "aliStart": 1694, "text": "Bromodomain", "colour": "#9999ff", "aliEnd": 1739, "start": 1689, "href": "http://pfam.xfam.org/family/PF00439.23", "type": "pfama", "display": "true", "metadata": {"end": 1751, "description": "Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine [3].", "database": "PfamA", "aliStart": 1694, "scoreName": "E-value", "accession": "PF00439.23", "start": 1689, "score": 0.004, "identifier": "Bromodomain", "type": "DBD", "aliEnd": 1739}}, {"startStyle": "jagged", "end": 1480, "endStyle": "straight", "aliStart": 1445, "text": "PHD_2", "colour": "#9999ff", "aliEnd": 1480, "start": 1444, "href": "http://pfam.xfam.org/family/PF13831.4", "type": "pfama", "display": "true", "metadata": {"end": 1480, "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": 1445, "scoreName": "E-value", "accession": "PF13831.4", "start": 1444, "score": 0.0068, "identifier": "PHD-finger", "type": "DBD", "aliEnd": 1480}}, {"startStyle": "straight", "end": 1531, "endStyle": "straight", "aliStart": 1494, "text": "PHD_2", "colour": "#9999ff", "aliEnd": 1530, "start": 1492, "href": "http://pfam.xfam.org/family/PF13831.4", "type": "pfama", "display": "true", "metadata": {"end": 1531, "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": 1494, "scoreName": "E-value", "accession": "PF13831.4", "start": 1492, "score": 0.0068, "identifier": "PHD-finger", "type": "DBD", "aliEnd": 1530}}], "length": 3970}
{"regions": [{"startStyle": "jagged", "end": 194, "endStyle": "straight", "aliStart": 156, "text": "PHD", "colour": "#9999ff", "aliEnd": 194, "start": 150, "href": "http://pfam.xfam.org/family/PF00628.27", "type": "pfama", "display": "true", "metadata": {"end": 194, "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": 156, "scoreName": "E-value", "accession": "PF00628.27", "start": 150, "score": 9.199999999999999e-24, "identifier": "PHD-finger", "type": "DBD", "aliEnd": 194}}, {"startStyle": "straight", "end": 245, "endStyle": "straight", "aliStart": 193, "text": "PHD", "colour": "#9999ff", "aliEnd": 245, "start": 193, "href": "http://pfam.xfam.org/family/PF00628.27", "type": "pfama", "display": "true", "metadata": {"end": 245, "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": 193, "scoreName": "E-value", "accession": "PF00628.27", "start": 193, "score": 9.199999999999999e-24, "identifier": "PHD-finger", "type": "DBD", "aliEnd": 245}}, {"startStyle": "straight", "end": 339, "endStyle": "straight", "aliStart": 281, "text": "PHD", "colour": "#9999ff", "aliEnd": 338, "start": 280, "href": "http://pfam.xfam.org/family/PF00628.27", "type": "pfama", "display": "true", "metadata": {"end": 339, "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": 281, "scoreName": "E-value", "accession": "PF00628.27", "start": 280, "score": 9.199999999999999e-24, "identifier": "PHD-finger", "type": "DBD", "aliEnd": 338}}, {"startStyle": "jagged", "end": 192, "endStyle": "straight", "aliStart": 157, "text": "PHD_2", "colour": "#9999ff", "aliEnd": 192, "start": 156, "href": "http://pfam.xfam.org/family/PF13831.4", "type": "pfama", "display": "true", "metadata": {"end": 192, "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": 157, "scoreName": "E-value", "accession": "PF13831.4", "start": 156, "score": 0.0017, "identifier": "PHD-finger", "type": "DBD", "aliEnd": 192}}, {"startStyle": "straight", "end": 243, "endStyle": "straight", "aliStart": 206, "text": "PHD_2", "colour": "#9999ff", "aliEnd": 242, "start": 204, "href": "http://pfam.xfam.org/family/PF13831.4", "type": "pfama", "display": "true", "metadata": {"end": 243, "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": 206, "scoreName": "E-value", "accession": "PF13831.4", "start": 204, "score": 0.0017, "identifier": "PHD-finger", "type": "DBD", "aliEnd": 242}}, {"startStyle": "straight", "end": 337, "endStyle": "jagged", "aliStart": 295, "text": "PHD_2", "colour": "#9999ff", "aliEnd": 311, "start": 294, "href": "http://pfam.xfam.org/family/PF13831.4", "type": "pfama", "display": "true", "metadata": {"end": 337, "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": 295, "scoreName": "E-value", "accession": "PF13831.4", "start": 294, "score": 0.0017, "identifier": "PHD-finger", "type": "DBD", "aliEnd": 311}}, {"startStyle": "straight", "end": 191, "endStyle": "jagged", "aliStart": 156, "text": "zf-PHD-like", "colour": "#9999ff", "aliEnd": 174, "start": 148, "href": "http://pfam.xfam.org/family/PF15446.4", "type": "pfama", "display": "true", "metadata": {"end": 191, "description": "This family appears to be a combination domain of several consecutive zinc-binding regions.", "database": "PfamA", "aliStart": 156, "scoreName": "E-value", "accession": "PF15446.4", "start": 148, "score": 0.0027, "identifier": "PHD/FYVE-zinc-finger like domain", "type": "DBD", "aliEnd": 174}}, {"startStyle": "straight", "end": 283, "endStyle": "jagged", "aliStart": 194, "text": "zf-PHD-like", "colour": "#9999ff", "aliEnd": 273, "start": 194, "href": "http://pfam.xfam.org/family/PF15446.4", "type": "pfama", "display": "true", "metadata": {"end": 283, "description": "This family appears to be a combination domain of several consecutive zinc-binding regions.", "database": "PfamA", "aliStart": 194, "scoreName": "E-value", "accession": "PF15446.4", "start": 194, "score": 0.0027, "identifier": "PHD/FYVE-zinc-finger like domain", "type": "DBD", "aliEnd": 273}}, {"startStyle": "jagged", "end": 192, "endStyle": "straight", "aliStart": 156, "text": "PHD_4", "colour": "#9999ff", "aliEnd": 191, "start": 136, "href": "http://pfam.xfam.org/family/PF16866.3", "type": "pfama", "display": "true", "metadata": {"end": 192, "description": NaN, "database": "PfamA", "aliStart": 156, "scoreName": "E-value", "accession": "PF16866.3", "start": 136, "score": 0.0095, "identifier": "PHD-finger", "type": "DBD", "aliEnd": 191}}, {"startStyle": "straight", "end": 248, "endStyle": "straight", "aliStart": 190, "text": "PHD_4", "colour": "#9999ff", "aliEnd": 243, "start": 189, "href": "http://pfam.xfam.org/family/PF16866.3", "type": "pfama", "display": "true", "metadata": {"end": 248, "description": NaN, "database": "PfamA", "aliStart": 190, "scoreName": "E-value", "accession": "PF16866.3", "start": 189, "score": 0.0095, "identifier": "PHD-finger", "type": "DBD", "aliEnd": 243}}], "length": 366}
{"regions": [{"startStyle": "curved", "end": 1194, "endStyle": "curved", "aliStart": 1148, "text": "zfCXXC", "colour": "#009900", "aliEnd": 1194, "start": 1147, "href": "http://pfam.xfam.org/family/PF02008.18", "type": "pfama", "display": "true", "metadata": {"end": 1194, "description": "This domain contains eight conserved cysteine residues that bind to two zinc ions. The CXXC domain is found in a variety of chromatin-associated proteins. This domain binds to nonmethyl-CpG dinucleotides. The domain is characterised by two repeats [3], and shows a peculiar internal duplication in which the second unit is inserted into the first one [4]. Each of these units is characterised by four conserved cysteines, displaying a CXXCXXCX(n)C motif that chelate a Zn+2 ion. The DNA binding interface has been identified by NMR [3]. In eukaryotes, the CXXC domain is found in stramenopiles, plants and metazoans. Plants possess a mono-CXXC domain that is present in distinct chromatin proteins [4]. Structural comparisons show that the mono-CXXC is homologous to the structural-zinc binding domain of medium chain dehydrogenases [4].", "database": "PfamA", "aliStart": 1148, "scoreName": "E-value", "accession": "PF02008.18", "start": 1147, "score": 3.7e-13, "identifier": "CXXC zinc finger domain", "type": "DBD", "aliEnd": 1194}}, {"startStyle": "straight", "end": 3751, "endStyle": "straight", "aliStart": 3672, "text": "FYRC", "colour": "#9999ff", "aliEnd": 3751, "start": 3669, "href": "http://pfam.xfam.org/family/PF05965.12", "type": "pfama", "display": "true", "metadata": {"end": 3751, "description": "This region is normally found in the trithorax/ALL1 family proteins. It is similar to SMART:SM00542.", "database": "PfamA", "aliStart": 3672, "scoreName": "E-value", "accession": "PF05965.12", "start": 3669, "score": 8.300000000000001e-22, "identifier": "F/Y rich C-terminus", "type": "DBD", "aliEnd": 3751}}, {"startStyle": "straight", "end": 3948, "endStyle": "straight", "aliStart": 3843, "text": "SET", "colour": "#9999ff", "aliEnd": 3947, "start": 3843, "href": "http://pfam.xfam.org/family/PF00856.26", "type": "pfama", "display": "true", "metadata": {"end": 3948, "description": "SET domains are protein lysine methyltransferase enzymes. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases) [2]. A subset of SET domains have been called PR domains. These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction [3]. The SET domain consists of two regions known as SET-N and SET-C. SET-C forms an unusual and conserved knot-like structure of probably functional importance. Additionally to SET-N and SET-C, an insert region (SET-I) and flanking regions of high structural variability form part of the overall structure [5].", "database": "PfamA", "aliStart": 3843, "scoreName": "E-value", "accession": "PF00856.26", "start": 3843, "score": 1.5999999999999999e-21, "identifier": "SET domain", "type": "DBD", "aliEnd": 3947}}, {"startStyle": "straight", "end": 2074, "endStyle": "straight", "aliStart": 2027, "text": "FYRN", "colour": "#9999ff", "aliEnd": 2074, "start": 2027, "href": "http://pfam.xfam.org/family/PF05964.12", "type": "pfama", "display": "true", "metadata": {"end": 2074, "description": "This region is normally found in the trithorax/ALL1 family proteins. It is similar to SMART:SM00541.", "database": "PfamA", "aliStart": 2027, "scoreName": "E-value", "accession": "PF05964.12", "start": 2027, "score": 3.6000000000000003e-16, "identifier": "F/Y-rich N-terminus", "type": "DBD", "aliEnd": 2074}}, {"startStyle": "straight", "end": 1482, "endStyle": "straight", "aliStart": 1434, "text": "PHD", "colour": "#9999ff", "aliEnd": 1482, "start": 1433, "href": "http://pfam.xfam.org/family/PF00628.27", "type": "pfama", "display": "true", "metadata": {"end": 1482, "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": 1434, "scoreName": "E-value", "accession": "PF00628.27", "start": 1433, "score": 5.599999999999999e-16, "identifier": "PHD-finger", "type": "DBD", "aliEnd": 1482}}, {"startStyle": "straight", "end": 1533, "endStyle": "straight", "aliStart": 1481, "text": "PHD", "colour": "#9999ff", "aliEnd": 1533, "start": 1481, "href": "http://pfam.xfam.org/family/PF00628.27", "type": "pfama", "display": "true", "metadata": {"end": 1533, "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": 1481, "scoreName": "E-value", "accession": "PF00628.27", "start": 1481, "score": 5.599999999999999e-16, "identifier": "PHD-finger", "type": "DBD", "aliEnd": 1533}}, {"startStyle": "straight", "end": 1630, "endStyle": "straight", "aliStart": 1569, "text": "PHD", "colour": "#9999ff", "aliEnd": 1629, "start": 1568, "href": "http://pfam.xfam.org/family/PF00628.27", "type": "pfama", "display": "true", "metadata": {"end": 1630, "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": 1569, "scoreName": "E-value", "accession": "PF00628.27", "start": 1568, "score": 5.599999999999999e-16, "identifier": "PHD-finger", "type": "DBD", "aliEnd": 1629}}, {"startStyle": "straight", "end": 1981, "endStyle": "straight", "aliStart": 1903, "text": "zf-HC5HC2H", "colour": "#9999ff", "aliEnd": 1981, "start": 1903, "href": "http://pfam.xfam.org/family/PF13771.4", "type": "pfama", "display": "true", "metadata": {"end": 1981, "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": 1903, "scoreName": "E-value", "accession": "PF13771.4", "start": 1903, "score": 3.8e-10, "identifier": "PHD-like zinc-binding domain", "type": "DBD", "aliEnd": 1981}}, {"startStyle": "straight", "end": 1980, "endStyle": "jagged", "aliStart": 1889, "text": "zf-HC5HC2H_2", "colour": "#9999ff", "aliEnd": 1969, "start": 1874, "href": "http://pfam.xfam.org/family/PF13832.4", "type": "pfama", "display": "true", "metadata": {"end": 1980, "description": NaN, "database": "PfamA", "aliStart": 1889, "scoreName": "E-value", "accession": "PF13832.4", "start": 1874, "score": 1.3e-08, "identifier": "PHD-zinc-finger like domain", "type": "DBD", "aliEnd": 1969}}, {"startStyle": "jagged", "end": 1480, "endStyle": "straight", "aliStart": 1445, "text": "PHD_2", "colour": "#9999ff", "aliEnd": 1480, "start": 1444, "href": "http://pfam.xfam.org/family/PF13831.4", "type": "pfama", "display": "true", "metadata": {"end": 1480, "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": 1445, "scoreName": "E-value", "accession": "PF13831.4", "start": 1444, "score": 0.00011999999999999999, "identifier": "PHD-finger", "type": "DBD", "aliEnd": 1480}}, {"startStyle": "straight", "end": 1531, "endStyle": "straight", "aliStart": 1494, "text": "PHD_2", "colour": "#9999ff", "aliEnd": 1530, "start": 1492, "href": "http://pfam.xfam.org/family/PF13831.4", "type": "pfama", "display": "true", "metadata": {"end": 1531, "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": 1494, "scoreName": "E-value", "accession": "PF13831.4", "start": 1492, "score": 0.00011999999999999999, "identifier": "PHD-finger", "type": "DBD", "aliEnd": 1530}}, {"startStyle": "straight", "end": 1609, "endStyle": "jagged", "aliStart": 1583, "text": "PHD_2", "colour": "#9999ff", "aliEnd": 1599, "start": 1582, "href": "http://pfam.xfam.org/family/PF13831.4", "type": "pfama", "display": "true", "metadata": {"end": 1609, "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": 1583, "scoreName": "E-value", "accession": "PF13831.4", "start": 1582, "score": 0.00011999999999999999, "identifier": "PHD-finger", "type": "DBD", "aliEnd": 1599}}, {"startStyle": "jagged", "end": 1754, "endStyle": "jagged", "aliStart": 1697, "text": "Bromodomain", "colour": "#9999ff", "aliEnd": 1742, "start": 1692, "href": "http://pfam.xfam.org/family/PF00439.23", "type": "pfama", "display": "true", "metadata": {"end": 1754, "description": "Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine [3].", "database": "PfamA", "aliStart": 1697, "scoreName": "E-value", "accession": "PF00439.23", "start": 1692, "score": 0.0047, "identifier": "Bromodomain", "type": "DBD", "aliEnd": 1742}}], "length": 3973}
{"regions": [{"startStyle": "curved", "end": 1227, "endStyle": "curved", "aliStart": 1181, "text": "zfCXXC", "colour": "#009900", "aliEnd": 1227, "start": 1180, "href": "http://pfam.xfam.org/family/PF02008.18", "type": "pfama", "display": "true", "metadata": {"end": 1227, "description": "This domain contains eight conserved cysteine residues that bind to two zinc ions. The CXXC domain is found in a variety of chromatin-associated proteins. This domain binds to nonmethyl-CpG dinucleotides. The domain is characterised by two repeats [3], and shows a peculiar internal duplication in which the second unit is inserted into the first one [4]. Each of these units is characterised by four conserved cysteines, displaying a CXXCXXCX(n)C motif that chelate a Zn+2 ion. The DNA binding interface has been identified by NMR [3]. In eukaryotes, the CXXC domain is found in stramenopiles, plants and metazoans. Plants possess a mono-CXXC domain that is present in distinct chromatin proteins [4]. Structural comparisons show that the mono-CXXC is homologous to the structural-zinc binding domain of medium chain dehydrogenases [4].", "database": "PfamA", "aliStart": 1181, "scoreName": "E-value", "accession": "PF02008.18", "start": 1180, "score": 5.1e-14, "identifier": "CXXC zinc finger domain", "type": "DBD", "aliEnd": 1227}}], "length": 1439}
{"regions": [{"startStyle": "curved", "end": 268, "endStyle": "curved", "aliStart": 226, "text": "zfCXXC", "colour": "#009900", "aliEnd": 268, "start": 225, "href": "http://pfam.xfam.org/family/PF02008.18", "type": "pfama", "display": "true", "metadata": {"end": 268, "description": "This domain contains eight conserved cysteine residues that bind to two zinc ions. The CXXC domain is found in a variety of chromatin-associated proteins. This domain binds to nonmethyl-CpG dinucleotides. The domain is characterised by two repeats [3], and shows a peculiar internal duplication in which the second unit is inserted into the first one [4]. Each of these units is characterised by four conserved cysteines, displaying a CXXCXXCX(n)C motif that chelate a Zn+2 ion. The DNA binding interface has been identified by NMR [3]. In eukaryotes, the CXXC domain is found in stramenopiles, plants and metazoans. Plants possess a mono-CXXC domain that is present in distinct chromatin proteins [4]. Structural comparisons show that the mono-CXXC is homologous to the structural-zinc binding domain of medium chain dehydrogenases [4].", "database": "PfamA", "aliStart": 226, "scoreName": "E-value", "accession": "PF02008.18", "start": 225, "score": 7.6e-13, "identifier": "CXXC zinc finger domain", "type": "DBD", "aliEnd": 268}}], "length": 268}