CDYL chromodomain Y like [Homo sapiens (human)] - Gene

Summary

Official Symbol: CDYLprovided by HGNC
Official Full Name: chromodomain Y likeprovided by HGNC
Primary source: HGNC:HGNC:1811
See related: Ensembl:ENSG00000153046 MIM:603778; AllianceGenome:HGNC:1811
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: CDYL1
Summary: Chromodomain Y is a primate-specific Y-chromosomal gene family expressed exclusively in the testis and implicated in infertility. Although the Y-linked genes are testis-specific, this autosomal gene is ubiquitously expressed. The Y-linked genes arose by retrotransposition of an mRNA from this gene, followed by amplification of the retroposed gene. Proteins encoded by this gene superfamily possess a chromodomain, a motif implicated in chromatin binding and gene suppression, and a catalytic domain believed to be involved in histone acetylation. Multiple proteins are encoded by transcript variants of this gene. [provided by RefSeq, Jul 2008]
Expression: Ubiquitous expression in placenta (RPKM 8.5), endometrium (RPKM 8.1) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 6p25.1

Exon count:: 13

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	6	NC_000006.12 (4706138..4955544)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	6	NC_060930.1 (4575080..4824553)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	6	NC_000006.11 (4706372..4955778)

Chromosome 6 - NC_000006.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

The chromodomain protein CDYL confers forebrain identity to human cortical organoids by inhibiting neuronatin.
Title: The chromodomain protein CDYL confers forebrain identity to human cortical organoids by inhibiting neuronatin.
Interaction between Chromodomain Y-like Protein and Androgen Receptor Signaling in Sertoli Cells Accounts for Spermatogenesis.
Title: Interaction between Chromodomain Y-like Protein and Androgen Receptor Signaling in Sertoli Cells Accounts for Spermatogenesis.
Emerging functions and significance of circCDYL in human disorders.
Title: Emerging functions and significance of circCDYL in human disorders.
Hypoxia-induced circ-CDYL-EEF1A2 transcriptional complex drives lung metastasis of cancer stem cells from hepatocellular carcinoma.
Title: Hypoxia-induced circ-CDYL-EEF1A2 transcriptional complex drives lung metastasis of cancer stem cells from hepatocellular carcinoma.
circCDYL Acts as a Tumor Suppressor in Triple Negative Breast Cancer by Sponging miR-190a-3p and Upregulating TP53INP1.
Title: circCDYL Acts as a Tumor Suppressor in Triple Negative Breast Cancer by Sponging miR-190a-3p and Upregulating TP53INP1.
CDYL promotes the chemoresistance of small cell lung cancer by regulating H3K27 trimethylation at the CDKN1C promoter.
Title: CDYL promotes the chemoresistance of small cell lung cancer by regulating H3K27 trimethylation at the CDKN1C promoter.
circCDYL overexpression repressed cellular growth and migration via repressing miR-150-5p in colon cancer cells
Title: circCDYL/microRNA-105-5p participates in modulating growth and migration of colon cancer cells.
CDYL1 promotes the recruitment of enhancer of zeste homolog 2 (EZH2), stimulates local increase of the repressive methyl mark H3K27me3, and promotes transcription silencing at double-strand break sites.
Title: CDYL1 fosters double-strand break-induced transcription silencing and promotes homology-directed repair.
This study demonstrated that CDYL is the most likely candidate gene for responsiveness to ketogenic dietary therapies for drug-resistant epilepsy.
Title: Genome-wide association study: Exploring the genetic basis for responsiveness to ketogenic dietary therapies for drug-resistant epilepsy.
CDYL plays an important role in the maintenance of repressive histone marks during replication, providing a mechanism for understanding of the epigenetic inheritance and memory.
Title: Chromodomain protein CDYL is required for transmission/restoration of repressive histone marks.

Submit: New GeneRIF Correction See all GeneRIFs (17)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genome-wide association study of smoking behaviours in patients with COPD. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D6S2182 (e-PCR)
- UniSTS:12069

RH46857 (e-PCR)
- UniSTS:55372

SHGC-146031 (e-PCR)
- UniSTS:174950

RH16984 (e-PCR)
- UniSTS:85636

D6S2104 (e-PCR)
- UniSTS:21638

CDYL_8937 (e-PCR)
- UniSTS:467600

G20517 (e-PCR)
- UniSTS:17845

RH80105 (e-PCR)
- UniSTS:89783

AL035376 (e-PCR)
- UniSTS:95173

G17019 (e-PCR)
- UniSTS:41927

RH46718 (e-PCR)
- UniSTS:54985

SHGC-58608 (e-PCR)
- UniSTS:94424

G30950 (e-PCR)
- UniSTS:3296

WI-16846 (e-PCR)
- UniSTS:29174

SHGC-149249 (e-PCR)
- UniSTS:176886

RH36541 (e-PCR)
- UniSTS:19191

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables chromatin binding	ISS Inferred from Sequence or Structural Similarity more info
enables crotonyl-CoA hydratase activity	IDA Inferred from Direct Assay more info	PubMed
enables identical protein binding	IPI Inferred from Physical Interaction more info	PubMed
NOT enables methylated histone binding	IDA Inferred from Direct Assay more info	PubMed
enables methylated histone binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein-macromolecule adaptor activity	IPI Inferred from Physical Interaction more info	PubMed
enables transcription corepressor activity	IBA Inferred from Biological aspect of Ancestor more info
enables transcription corepressor activity	IMP Inferred from Mutant Phenotype more info	PubMed

Process	Evidence Code	Pubs
involved_in negative regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of peptidyl-lysine crotonylation	IDA Inferred from Direct Assay more info	PubMed
involved_in random inactivation of X chromosome	ISS Inferred from Sequence or Structural Similarity more info
involved_in spermatid development	ISS Inferred from Sequence or Structural Similarity more info
involved_in spermatogenesis	TAS Traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
located_in chromosome	ISS Inferred from Sequence or Structural Similarity more info
located_in cytoplasm	ISS Inferred from Sequence or Structural Similarity more info
located_in nuclear speck	IDA Inferred from Direct Assay more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: chromodomain Y-like protein

Names: CDY-like, autosomal; chromodomain protein, Y-like; crotonyl-CoA hydratase; testis-specific chromodomain Y-like protein

NP_001137442.1

EC 2.3.1.48

NP_001137443.1

EC 2.3.1.48

NP_001355054.1

EC 2.3.1.48

NP_001355055.1

EC 2.3.1.48

NP_001355056.1

EC 2.3.1.48

NP_004815.3

EC 2.3.1.48

XP_047275519.1

EC 2.3.1.48

XP_047275520.1

EC 2.3.1.48

XP_054212800.1

EC 2.3.1.48

XP_054212801.1

EC 2.3.1.48

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001143970.2 → NP_001137442.1 chromodomain Y-like protein isoform d

See identical proteins and their annotated locations for NP_001137442.1

Status: REVIEWED

Description

Transcript Variant: This variant (4) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (d) has a shorter N-terminus compared to isoform a. Variants 4 and 5 both encode isoform d.

Source sequence(s)

AK296985, BC043397, BE874176

Consensus CDS

CCDS47364.1

UniProtKB/Swiss-Prot

Q9Y232

Related

ENSP00000394076.2, ENST00000449732.6

Conserved Domains (1) summary

cd06558
Location:158 → 354

crotonase-like; Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase. ...
NM_001143971.2 → NP_001137443.1 chromodomain Y-like protein isoform d

See identical proteins and their annotated locations for NP_001137443.1

Status: REVIEWED

Description

Transcript Variant: This variant (5) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (d) has a shorter N-terminus compared to isoform a. Variants 4 and 5 both encode isoform d.

Source sequence(s)

AF081258, BC043397, BE874176

Consensus CDS

CCDS47364.1

UniProtKB/Swiss-Prot

Q9Y232

Related

ENSP00000340908.5, ENST00000343762.5

Conserved Domains (1) summary

cd06558
Location:158 → 354

crotonase-like; Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase. ...
NM_001368125.1 → NP_001355054.1 chromodomain Y-like protein isoform e

Status: REVIEWED

Description

Transcript Variant: This variant (7) is predicted to encode the longest isoform (e). However, the presence of an upstream ORF may interfere with translation of the longest ORF. Translation of the upstream ORF would render the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AL022725, AL356747, AL359643

Consensus CDS

CCDS93853.1

UniProtKB/Swiss-Prot

A8K6D6, B4DLG4, Q0VDG7, Q32NC5, Q5VX99, Q6P7T5, Q9BWZ2, Q9Y232, Q9Y424

Related

ENSP00000330512.5, ENST00000328908.9
NM_001368126.1 → NP_001355055.1 chromodomain Y-like protein isoform f

Status: REVIEWED

Source sequence(s)

AL022725, AL359643

Conserved Domains (2) summary

cd06558
Location:268 → 464

crotonase-like; Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase. ...

cd18634
Location:6 → 57

CD_CDY; chromodomain of the Chromodomain Y-like protein family
NM_001368127.1 → NP_001355056.1 chromodomain Y-like protein isoform g

Status: REVIEWED

Source sequence(s)

AL022725, AL359643

Conserved Domains (1) summary

cd06558
Location:55 → 251

crotonase-like; Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase. ...
NM_004824.4 → NP_004815.3 chromodomain Y-like protein isoform a

See identical proteins and their annotated locations for NP_004815.3

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longest transcript.

Source sequence(s)

AL022725, BC043397, BC108725, BE874176

Consensus CDS

CCDS4491.2

UniProtKB/Swiss-Prot

Q9Y232

Related

ENSP00000380718.3, ENST00000397588.8

Conserved Domains (2) summary

cd06558
Location:290 → 486

crotonase-like; Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase. ...

cd18634
Location:6 → 57

CD_CDY; chromodomain of the Chromodomain Y-like protein family

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000006.12 Reference GRCh38.p14 Primary Assembly

Range

4706138..4955544

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047419563.1 → XP_047275519.1 chromodomain Y-like protein isoform X1
XM_047419564.1 → XP_047275520.1 chromodomain Y-like protein isoform X1

Alternate T2T-CHM13v2.0

Genomic

NC_060930.1 Alternate T2T-CHM13v2.0

Range

4575080..4824553

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054356825.1 → XP_054212800.1 chromodomain Y-like protein isoform X1
XM_054356826.1 → XP_054212801.1 chromodomain Y-like protein isoform X1

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_170752.1: Suppressed sequence

Description

NM_170752.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.