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Protein

Chromodomain Y-like protein

Gene

CDYL

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Acts as a RE1-silencing transcription factor (REST) corepressor that facilitates histone-lysine N-methyltransferase EHMT2 recruitment and H3K9 dimethylation at REST target genes for repression. Required for chromatin targeting and maximal enzymatic activity of polycomb repressive complex 2 (PRC2); acts as a positive regulator of PRC2 activity by bridging the pre-existing histone H3K27me3 and newly recruited PRC2 on neighboring nucleosomes. Has histone acetyltransferase activity, with a preference for histone H4.3 Publications

Catalytic activityi

Acetyl-CoA + [histone] = CoA + acetyl-[histone].

GO - Molecular functioni

  • histone acetyltransferase activity Source: UniProtKB-EC
  • methylated histone binding Source: UniProtKB
  • transcription corepressor activity Source: UniProtKB

GO - Biological processi

  • regulation of transcription, DNA-templated Source: UniProtKB-KW
  • spermatogenesis Source: ProtInc
  • transcription, DNA-templated Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Acyltransferase, Repressor, Transferase

Keywords - Biological processi

Transcription, Transcription regulation

Enzyme and pathway databases

BioCyciZFISH:HS07876-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Chromodomain Y-like protein (EC:2.3.1.48)
Short name:
CDY-like
Gene namesi
Name:CDYL
Synonyms:CDYL1
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 6

Organism-specific databases

HGNCiHGNC:1811. CDYL.

Subcellular locationi

GO - Cellular componenti

  • nucleoplasm Source: HPA
  • nucleus Source: MGI
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Organism-specific databases

DisGeNETi9425.
OpenTargetsiENSG00000153046.
PharmGKBiPA26356.

Polymorphism and mutation databases

BioMutaiCDYL.
DMDMi150421527.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000802211 – 598Chromodomain Y-like proteinAdd BLAST598

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei88PhosphoserineCombined sources1
Modified residuei135N6,N6,N6-trimethyllysine; by EHMT2; alternate1 Publication1
Modified residuei135N6,N6-dimethyllysine; by EHMT2; alternate1 Publication1
Modified residuei135N6-methyllysine; by EHMT2; alternate1 Publication1
Modified residuei170PhosphoserineCombined sources1
Modified residuei201PhosphoserineCombined sources1
Modified residuei216PhosphoserineCombined sources1

Keywords - PTMi

Methylation, Phosphoprotein

Proteomic databases

EPDiQ9Y232.
PaxDbiQ9Y232.
PeptideAtlasiQ9Y232.
PRIDEiQ9Y232.

PTM databases

iPTMnetiQ9Y232.
PhosphoSitePlusiQ9Y232.

Expressioni

Tissue specificityi

Ubiquitous. Expressed at moderate levels in all tissues examined. Isoform 2 is the most abundantly expressed isoform.1 Publication

Gene expression databases

BgeeiENSG00000153046.
CleanExiHS_CDYL.
ExpressionAtlasiQ9Y232. baseline and differential.
GenevisibleiQ9Y232. HS.

Organism-specific databases

HPAiCAB012249.
HPA035577.
HPA035578.

Interactioni

Subunit structurei

Forms multimers and multimerization is required for stable binding to chromatin. Interacts with HDAC1 and HDAC2 via its C-terminal acetyl-CoA-binding domain (By similarity). Interacts with histone H3K9me3, histone H3K27me2 and histone H3K27me3. Interacts with EZH2, EED, SUZ12, REST, EHMT1 and EHMT2. Part of a complex containing at least CDYL, REST, WIZ, SETB1, EHMT1 and EHMT2. Part of a complex containing at least CDYL, MIER1, MIER2, HDAC1 and HDAC2.By similarity3 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
HIST1H3DP684315EBI-1387386,EBI-79722

GO - Molecular functioni

  • methylated histone binding Source: UniProtKB

Protein-protein interaction databases

BioGridi114818. 41 interactors.
IntActiQ9Y232. 19 interactors.
MINTiMINT-2829840.
STRINGi9606.ENSP00000380718.

Structurei

Secondary structure

1598
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi66 – 71Combined sources6
Beta strandi77 – 81Combined sources5
Helixi88 – 90Combined sources3
Beta strandi92 – 95Combined sources4
Turni96 – 98Combined sources3
Helixi103 – 113Combined sources11
Beta strandi342 – 349Combined sources8
Beta strandi352 – 357Combined sources6
Beta strandi360 – 363Combined sources4
Helixi369 – 384Combined sources16
Beta strandi390 – 397Combined sources8
Helixi405 – 414Combined sources10
Helixi416 – 436Combined sources21
Beta strandi441 – 445Combined sources5
Helixi452 – 455Combined sources4
Helixi457 – 459Combined sources3
Beta strandi460 – 466Combined sources7
Beta strandi470 – 472Combined sources3
Turni475 – 479Combined sources5
Helixi486 – 494Combined sources9
Helixi496 – 505Combined sources10
Helixi511 – 516Combined sources6
Beta strandi521 – 524Combined sources4
Helixi526 – 528Combined sources3
Helixi529 – 541Combined sources13
Helixi545 – 556Combined sources12
Turni557 – 559Combined sources3
Helixi560 – 579Combined sources20
Turni581 – 584Combined sources4
Helixi585 – 596Combined sources12

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2DNTNMR-A63-119[»]
2GTRX-ray1.90A/B/C338-598[»]
ProteinModelPortaliQ9Y232.
SMRiQ9Y232.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9Y232.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini61 – 121ChromoPROSITE-ProRule annotationAdd BLAST61

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni61 – 309Interaction with EZH21 PublicationAdd BLAST249

Sequence similaritiesi

Contains 1 chromo domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiKOG0016. Eukaryota.
KOG1911. Eukaryota.
COG1024. LUCA.
GeneTreeiENSGT00760000119100.
HOVERGENiHBG006723.
InParanoidiQ9Y232.
KOiK00653.
OMAiHDFNRRH.
OrthoDBiEOG091G0T5I.
PhylomeDBiQ9Y232.
TreeFamiTF313375.

Family and domain databases

Gene3Di3.90.226.10. 1 hit.
InterProiIPR000953. Chromo/shadow_dom.
IPR023780. Chromo_domain.
IPR016197. Chromodomain-like.
IPR023779. Chromodomain_CS.
IPR029045. ClpP/crotonase-like_dom.
IPR001753. Crotonase_core_superfam.
[Graphical view]
PfamiPF00385. Chromo. 1 hit.
PF00378. ECH_1. 1 hit.
[Graphical view]
SMARTiSM00298. CHROMO. 1 hit.
[Graphical view]
SUPFAMiSSF52096. SSF52096. 1 hit.
SSF54160. SSF54160. 1 hit.
PROSITEiPS00598. CHROMO_1. 1 hit.
PS50013. CHROMO_2. 1 hit.
[Graphical view]

Sequences (4)i

Sequence statusi: Complete.

This entry describes 4 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q9Y232-1) [UniParc]FASTAAdd to basket
Also known as: a

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MTFQASHRSA WGKSRKKNWQ YEGPTQKLFL KRNNVSAPDG PSDPSISVSS
60 70 80 90 100
EQSGAQQPPA LQVERIVDKR KNKKGKTEYL VRWKGYDSED DTWEPEQHLV
110 120 130 140 150
NCEEYIHDFN RRHTEKQKES TLTRTNRTSP NNARKQISRS TNSNFSKTSP
160 170 180 190 200
KALVIGKDHE SKNSQLFAAS QKFRKNTAPS LSSRKNMDLA KSGIKILVPK
210 220 230 240 250
SPVKSRTAVD GFQSESPEKL DPVEQGQEDT VAPEVAAEKP VGALLGPGAE
260 270 280 290 300
RARMGSRPRI HPLVPQVPGP VTAAMATGLA VNGKGTSPFM DALTANGTTN
310 320 330 340 350
IQTSVTGVTA SKRKFIDDRR DQPFDKRLRF SVRQTESAYR YRDIVVRKQD
360 370 380 390 400
GFTHILLSTK SSENNSLNPE VMREVQSALS TAAADDSKLV LLSAVGSVFC
410 420 430 440 450
CGLDFIYFIR RLTDDRKRES TKMAEAIRNF VNTFIQFKKP IIVAVNGPAI
460 470 480 490 500
GLGASILPLC DVVWANEKAW FQTPYTTFGQ SPDGCSTVMF PKIMGGASAN
510 520 530 540 550
EMLLSGRKLT AQEACGKGLV SQVFWPGTFT QEVMVRIKEL ASCNPVVLEE
560 570 580 590
SKALVRCNMK MELEQANERE CEVLKKIWGS AQGMDSMLKY LQRKIDEF
Length:598
Mass (Da):66,482
Last modified:June 26, 2007 - v2
Checksum:iA34E7221130626EC
GO
Isoform 2 (identifier: Q9Y232-2) [UniParc]FASTAAdd to basket
Also known as: b

The sequence of this isoform differs from the canonical sequence as follows:
     1-54: Missing.
     55-62: AQQPPALQ → MASEELYE

Show »
Length:544
Mass (Da):60,609
Checksum:iD30E1CE197B67FC7
GO
Isoform 3 (identifier: Q9Y232-3) [UniParc]FASTAAdd to basket
Also known as: c

The sequence of this isoform differs from the canonical sequence as follows:
     1-289: Missing.

Show »
Length:309
Mass (Da):34,561
Checksum:i6033C3171A80CB47
GO
Isoform 4 (identifier: Q9Y232-4) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-186: Missing.

Show »
Length:412
Mass (Da):45,135
Checksum:i6AFC72E69A0462A3
GO

Sequence cautioni

The sequence CAB43304 differs from that shown.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti205S → N in BAF84290 (PubMed:14702039).Curated1
Sequence conflicti291D → N in BAG59526 (PubMed:14702039).Curated1
Sequence conflicti443V → L in BAF84290 (PubMed:14702039).Curated1
Sequence conflicti558N → S in BAG59526 (PubMed:14702039).Curated1
Sequence conflicti584M → T in AAI19683 (PubMed:15489334).Curated1
Sequence conflicti591L → M in AAI19683 (PubMed:15489334).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_0329362T → A.1 PublicationCorresponds to variant rs3812179dbSNPEnsembl.1
Natural variantiVAR_0329379S → P.1 PublicationCorresponds to variant rs3812178dbSNPEnsembl.1
Natural variantiVAR_03293848V → A.1 PublicationCorresponds to variant rs13196069dbSNPEnsembl.1
Natural variantiVAR_03293960A → G.1 PublicationCorresponds to variant rs28360500dbSNPEnsembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0263821 – 289Missing in isoform 3. 1 PublicationAdd BLAST289
Alternative sequenceiVSP_0410251 – 186Missing in isoform 4. 1 PublicationAdd BLAST186
Alternative sequenceiVSP_0263831 – 54Missing in isoform 2. 2 PublicationsAdd BLAST54
Alternative sequenceiVSP_02638455 – 62AQQPPALQ → MASEELYE in isoform 2. 2 Publications8

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF081258 mRNA. Translation: AAD22734.1.
AF081259 mRNA. Translation: AAD22735.1.
AK291601 mRNA. Translation: BAF84290.1.
AK296985 mRNA. Translation: BAG59526.1.
AL356747, AL022725, AL359643 Genomic DNA. Translation: CAC36888.2.
AL359643, AL022725, AL356747 Genomic DNA. Translation: CAH73737.1.
AL022725, AL356747, AL359643 Genomic DNA. Translation: CAI20892.1.
BC061516 mRNA. Translation: AAH61516.1.
BC108725 mRNA. Translation: AAI08726.1.
BC119682 mRNA. Translation: AAI19683.1.
AL050164 mRNA. Translation: CAB43304.1. Sequence problems.
CCDSiCCDS4491.2. [Q9Y232-2]
CCDS47364.1. [Q9Y232-4]
PIRiT08789.
RefSeqiNP_001137442.1. NM_001143970.1. [Q9Y232-4]
NP_001137443.1. NM_001143971.1. [Q9Y232-4]
NP_004815.3. NM_004824.3. [Q9Y232-2]
UniGeneiHs.269092.

Genome annotation databases

EnsembliENST00000328908; ENSP00000330512; ENSG00000153046. [Q9Y232-1]
ENST00000343762; ENSP00000340908; ENSG00000153046. [Q9Y232-4]
ENST00000397588; ENSP00000380718; ENSG00000153046. [Q9Y232-2]
ENST00000449732; ENSP00000394076; ENSG00000153046. [Q9Y232-4]
GeneIDi9425.
KEGGihsa:9425.
UCSCiuc003mwi.4. human. [Q9Y232-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF081258 mRNA. Translation: AAD22734.1.
AF081259 mRNA. Translation: AAD22735.1.
AK291601 mRNA. Translation: BAF84290.1.
AK296985 mRNA. Translation: BAG59526.1.
AL356747, AL022725, AL359643 Genomic DNA. Translation: CAC36888.2.
AL359643, AL022725, AL356747 Genomic DNA. Translation: CAH73737.1.
AL022725, AL356747, AL359643 Genomic DNA. Translation: CAI20892.1.
BC061516 mRNA. Translation: AAH61516.1.
BC108725 mRNA. Translation: AAI08726.1.
BC119682 mRNA. Translation: AAI19683.1.
AL050164 mRNA. Translation: CAB43304.1. Sequence problems.
CCDSiCCDS4491.2. [Q9Y232-2]
CCDS47364.1. [Q9Y232-4]
PIRiT08789.
RefSeqiNP_001137442.1. NM_001143970.1. [Q9Y232-4]
NP_001137443.1. NM_001143971.1. [Q9Y232-4]
NP_004815.3. NM_004824.3. [Q9Y232-2]
UniGeneiHs.269092.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2DNTNMR-A63-119[»]
2GTRX-ray1.90A/B/C338-598[»]
ProteinModelPortaliQ9Y232.
SMRiQ9Y232.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi114818. 41 interactors.
IntActiQ9Y232. 19 interactors.
MINTiMINT-2829840.
STRINGi9606.ENSP00000380718.

PTM databases

iPTMnetiQ9Y232.
PhosphoSitePlusiQ9Y232.

Polymorphism and mutation databases

BioMutaiCDYL.
DMDMi150421527.

Proteomic databases

EPDiQ9Y232.
PaxDbiQ9Y232.
PeptideAtlasiQ9Y232.
PRIDEiQ9Y232.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000328908; ENSP00000330512; ENSG00000153046. [Q9Y232-1]
ENST00000343762; ENSP00000340908; ENSG00000153046. [Q9Y232-4]
ENST00000397588; ENSP00000380718; ENSG00000153046. [Q9Y232-2]
ENST00000449732; ENSP00000394076; ENSG00000153046. [Q9Y232-4]
GeneIDi9425.
KEGGihsa:9425.
UCSCiuc003mwi.4. human. [Q9Y232-1]

Organism-specific databases

CTDi9425.
DisGeNETi9425.
GeneCardsiCDYL.
HGNCiHGNC:1811. CDYL.
HPAiCAB012249.
HPA035577.
HPA035578.
MIMi603778. gene.
neXtProtiNX_Q9Y232.
OpenTargetsiENSG00000153046.
PharmGKBiPA26356.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG0016. Eukaryota.
KOG1911. Eukaryota.
COG1024. LUCA.
GeneTreeiENSGT00760000119100.
HOVERGENiHBG006723.
InParanoidiQ9Y232.
KOiK00653.
OMAiHDFNRRH.
OrthoDBiEOG091G0T5I.
PhylomeDBiQ9Y232.
TreeFamiTF313375.

Enzyme and pathway databases

BioCyciZFISH:HS07876-MONOMER.

Miscellaneous databases

ChiTaRSiCDYL. human.
EvolutionaryTraceiQ9Y232.
GenomeRNAii9425.
PROiQ9Y232.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000153046.
CleanExiHS_CDYL.
ExpressionAtlasiQ9Y232. baseline and differential.
GenevisibleiQ9Y232. HS.

Family and domain databases

Gene3Di3.90.226.10. 1 hit.
InterProiIPR000953. Chromo/shadow_dom.
IPR023780. Chromo_domain.
IPR016197. Chromodomain-like.
IPR023779. Chromodomain_CS.
IPR029045. ClpP/crotonase-like_dom.
IPR001753. Crotonase_core_superfam.
[Graphical view]
PfamiPF00385. Chromo. 1 hit.
PF00378. ECH_1. 1 hit.
[Graphical view]
SMARTiSM00298. CHROMO. 1 hit.
[Graphical view]
SUPFAMiSSF52096. SSF52096. 1 hit.
SSF54160. SSF54160. 1 hit.
PROSITEiPS00598. CHROMO_1. 1 hit.
PS50013. CHROMO_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiCDYL1_HUMAN
AccessioniPrimary (citable) accession number: Q9Y232
Secondary accession number(s): A8K6D6
, B4DLG4, Q0VDG7, Q32NC5, Q5VX99, Q6P7T5, Q9BWZ2, Q9Y424
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 19, 2003
Last sequence update: June 26, 2007
Last modified: November 2, 2016
This is version 145 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Miscellaneous

Interaction with HDAC1 or HDAC2 prevents Coenzyme A binding.By similarity

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 6
    Human chromosome 6: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.