CDY1 chromodomain Y-linked 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: CDY1provided by HGNC
Official Full Name: chromodomain Y-linked 1provided by HGNC
Primary source: HGNC:HGNC:1809
See related: Ensembl:ENSG00000172288 MIM:400016; AllianceGenome:HGNC:1809
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: CDY; CDY1A
Summary: This gene encodes a protein containing a chromodomain and a histone acetyltransferase catalytic domain. Chromodomain proteins are components of heterochromatin-like complexes and can act as gene repressors. This protein is localized to the nucleus of late spermatids where histone hyperacetylation takes place. Histone hyperacetylation is thought to facilitate the transition in which protamines replace histones as the major DNA-packaging protein. The human chromosome Y has two identical copies of this gene within a palindromic region; this record represents the more telomeric copy. Chromosome Y also contains a pair of closely related genes in another more telomeric palindrome as well as several related pseudogenes. Two protein isoforms are encoded by transcript variants of this gene. Additional transcript variants have been described, but their full-length nature has not been determined. [provided by RefSeq, Jul 2008]
Expression: Restricted expression toward testis (RPKM 2.1) See more
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Genomic context

Location:: Yq11.23

Exon count:: 3

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	Y	NC_000024.10 (25622115..25625511)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	Y	NC_060948.1 (26434508..26437904)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	Y	NC_000024.9 (27768264..27771049)

Chromosome Y - NC_000024.10 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: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Y-chromosome haplogroups and Azoospermia Factor (AZF) analysis in Tunisian infertile male.
Title: Y-chromosome haplogroups and Azoospermia Factor (AZF) analysis in Tunisian infertile male.
Findings showed that deletion of CDY1b copy gene is a significant risk factor for male infertility independent of sperm concentration, whereas deletion of CDY1a gene seems to have no effect on fertility in the Tunisian population.
Title: Deletion of CDY1b copy of Y chromosome CDY1 gene is a risk factor of male infertility in Tunisian men.
Assessing the expression of both CDY1 and BOULE by qualitative RT-PCR is a sensitive and feasible test for predicting the presence of sperm cells in testicular tissue biopsies.
Title: CDY1 and BOULE transcripts assessed in the same biopsy as predictive markers for successful testicular sperm retrieval.
Partial AZFc deletions including CDY1-DAZ gene is associated with impaired spermatogenesis.
Title: Partial AZFc deletions and duplications: clinical correlates in the Italian population.
Observational study of gene-disease association. (HuGE Navigator)
Title: Features of constitutive gr/gr deletion in a Japanese population.
different functional roles for CDY isoforms during spermatogenesis
Title: Members of the CDY family have different expression patterns: CDY1 transcripts have the best correlation with complete spermatogenesis.

Submit: New GeneRIF Correction

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Spermatogenic failure, Y-linked, 2 MedGen: C1839071 OMIM: 415000 GeneReviews: Y Chromosome Infertility	not available

Copy number response

Description
Copy number response Haploinsufficency No evidence available (Last evaluated 2012-08-22) ClinGen Genome Curation Page Triplosensitivity No evidence available (Last evaluated 2012-08-22) ClinGen Genome Curation Page

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

sY639 (e-PCR)
- UniSTS:243208

sY1262 (e-PCR)
- UniSTS:514654

G65845 (e-PCR)
- UniSTS:230511

sY1260 (e-PCR)
- UniSTS:478845

sY1263 (e-PCR)
- UniSTS:478846

G65870 (e-PCR)
- UniSTS:230536

CDY1_8893 (e-PCR)
- UniSTS:467599

G34975 (e-PCR)
- UniSTS:53237

RH103714 (e-PCR)
- UniSTS:98039

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables histone H2AK5 acetyltransferase activity	IEA Inferred from Electronic Annotation more info
enables histone H2AK9 acetyltransferase activity	IEA Inferred from Electronic Annotation more info
enables histone H2BK12 acetyltransferase activity	IEA Inferred from Electronic Annotation more info
enables histone H2BK5 acetyltransferase activity	IEA Inferred from Electronic Annotation more info
enables histone H3K122 acetyltransferase activity	IEA Inferred from Electronic Annotation more info
enables histone H3K14 acetyltransferase activity	IEA Inferred from Electronic Annotation more info
enables histone H3K18 acetyltransferase activity	IEA Inferred from Electronic Annotation more info
enables histone H3K23 acetyltransferase activity	IEA Inferred from Electronic Annotation more info
enables histone H3K27 acetyltransferase activity	IEA Inferred from Electronic Annotation more info
enables histone H3K36 acetyltransferase activity	IEA Inferred from Electronic Annotation more info
enables histone H3K4 acetyltransferase activity	IEA Inferred from Electronic Annotation more info
enables histone H3K56 acetyltransferase activity	IEA Inferred from Electronic Annotation more info
enables histone H3K9 acetyltransferase activity	IEA Inferred from Electronic Annotation more info
enables histone H4K12 acetyltransferase activity	IEA Inferred from Electronic Annotation more info
enables histone H4K16 acetyltransferase activity	IEA Inferred from Electronic Annotation more info
enables histone H4K5 acetyltransferase activity	IEA Inferred from Electronic Annotation more info
enables histone H4K8 acetyltransferase activity	IEA Inferred from Electronic Annotation more info
enables methylated histone binding	IDA Inferred from Direct Assay more info	PubMed
enables transcription corepressor activity	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
involved_in chromatin remodeling	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in spermatogenesis	TAS Traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
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: testis-specific chromodomain protein Y 1

Names: chromodomain protein, Y chromosome, 1; chromodomain protein, Y-linked, 1; testis-specific chromodomain protein on Y

NP_004671.1

EC 2.3.1.48

NP_733841.1

EC 2.3.1.48

XP_011529814.1

EC 2.3.1.48

XP_054184366.1

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.

Genomic

NG_011754.1 RefSeqGene

Range

5001..7786

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_004680.3 → NP_004671.1 testis-specific chromodomain protein Y 1 isoform b

See identical proteins and their annotated locations for NP_004671.1

Status: REVIEWED

Description

Transcript Variant: This variant (2), also called the minor variant, lacks a segment in the 3' end of the coding sequence, compared to variant 1. Variant 2 encodes isoform b which has a longer and distinct C-terminus, compared to isoform a.

Source sequence(s)

AC007562

Consensus CDS

CCDS14801.1

UniProtKB/TrEMBL

A8K8F3

Related

ENSP00000302968.4, ENST00000306609.5

Conserved Domains (2) summary

cd06558
Location:286 → 482

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. ...

smart00298
Location:5 → 58

CHROMO; Chromatin organization modifier domain
NM_170723.2 → NP_733841.1 testis-specific chromodomain protein Y 1 isoform a

See identical proteins and their annotated locations for NP_733841.1

Status: REVIEWED

Description

Transcript Variant: This variant (1), also called the major transcript, is unspliced. It encodes isoform a.

Source sequence(s)

AC007562

Consensus CDS

CCDS14802.1

UniProtKB/Swiss-Prot

A2RUK1, O14600, Q9Y6F8

UniProtKB/TrEMBL

A8K8L0

Related

ENSP00000354799.2, ENST00000361963.3

Conserved Domains (2) summary

cd06558
Location:286 → 482

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. ...

smart00298
Location:5 → 58

CHROMO; Chromatin organization modifier domain

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_000024.10 Reference GRCh38.p14 Primary Assembly

Range

25622115..25625511

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011531512.3 → XP_011529814.1 testis-specific chromodomain protein Y 1 isoform X1

See identical proteins and their annotated locations for XP_011529814.1

UniProtKB/TrEMBL

A8K8L0

Conserved Domains (2) summary

cd06558
Location:286 → 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. ...

smart00298
Location:5 → 58

CHROMO; Chromatin organization modifier domain