CDY1B chromodomain Y-linked 1B [Homo sapiens (human)] - Gene

Summary

Official Symbol: CDY1Bprovided by HGNC
Official Full Name: chromodomain Y-linked 1Bprovided by HGNC
Primary source: HGNC:HGNC:23920
See related: Ensembl:ENSG00000172352 AllianceGenome:HGNC:23920
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
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 centromeric 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 (24044620..24048019, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	Y	NC_060948.1 (24814541..24817940)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	Y	NC_000024.9 (26191376..26194166, complement)

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?

study reported a new type of AZFc deletion (gr/gr-DAZ2-DAZ4-CDY1b) and hypothesis that this new deletion is the result of 2 successive events favored by the unstable structure of AZFc region; also demonstrated that this deletion constitutes a relative high-risk factor for male infertility in Tunisian population
Title: gr/gr-DAZ2-DAZ4-CDY1b deletion is a high-risk factor for male infertility in Tunisian population.

Submit: New GeneRIF Correction

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

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

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, centromeric; chromodomain protein, Y-linked, 1B; testis-specific chromodomain protein on Y, centromeric

NP_001003894.1

EC 2.3.1.48

NP_001003895.1

EC 2.3.1.48

XP_011529786.1

EC 2.3.1.48

XP_054184245.1

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_001003894.2 → NP_001003894.1 testis-specific chromodomain protein Y 1 isoform a

See identical proteins and their annotated locations for NP_001003894.1

Status: REVIEWED

Description

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

Source sequence(s)

AC068601

Consensus CDS

CCDS35487.1

UniProtKB/Swiss-Prot

A2RUK1, O14600, Q9Y6F8

UniProtKB/TrEMBL

A8K8L0

Related

ENSP00000371844.1, ENST00000382407.1

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_001003895.1 → NP_001003895.1 testis-specific chromodomain protein Y 1 isoform b

See identical proteins and their annotated locations for NP_001003895.1

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)

AC068601

Consensus CDS

CCDS35486.1

UniProtKB/TrEMBL

A8K8F3

Related

ENSP00000303178.4, ENST00000306882.4

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

24044620..24048019 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011531484.3 → XP_011529786.1 testis-specific chromodomain protein Y 1 isoform X1

See identical proteins and their annotated locations for XP_011529786.1

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