Hmces 5-hydroxymethylcytosine (hmC) binding, ES cell specific [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Hmcesprovided by MGI
Official Full Name: 5-hydroxymethylcytosine (hmC) binding, ES cell specificprovided by MGI
Primary source: MGI:MGI:1914053
See related: Ensembl:ENSMUSG00000030060 AllianceGenome:MGI:1914053
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: Srap1; 8430410A17Rik
Summary: Enables single-stranded DNA binding activity. Involved in double-strand break repair via alternative nonhomologous end joining and positive regulation of isotype switching. Predicted to be located in replication fork. Is expressed in several structures, including adipose tissue; genitourinary system; gut; hemolymphoid system gland; and liver. Orthologous to human HMCES (5-hydroxymethylcytosine binding, ES cell specific). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Ubiquitous expression in limb E14.5 (RPKM 8.7), CNS E18 (RPKM 8.2) and 28 other tissues See more
Orthologs: human all
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Genomic context

Location:: 6; 6 D1

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
109	current	GRCm39 (GCF_000001635.27)	6	NC_000072.7 (87890889..87913603)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	6	NC_000072.6 (87913907..87936619)

Chromosome 6 - NC_000072.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

HMCES protects immunoglobulin genes specifically from deletions during somatic hypermutation.
Title: HMCES protects immunoglobulin genes specifically from deletions during somatic hypermutation.
Further evidence for a specialized role for HMCES in DNA repair.
Title: HMCES Functions in the Alternative End-Joining Pathway of the DNA DSB Repair during Class Switch Recombination in B Cells.
Inactivation of murine Srap1 results in accumulation of 5hmC in genomic DNA. Srap1 deficient mice display embryonic sublethality and altered DNA methylation.
Title: Erasure of Tet-Oxidized 5-Methylcytosine by a SRAP Nuclease.
Correlation analyses showed that 5hmC enrichment in gene body is positively associated with gene expression level in mouse kidney. Moreover, ischemia reperfusion (IR) injury-associated genes (both up- and down-regulated genes during renal IR injury) in mouse kidney exhibit significantly higher 5hmC enrichment in their gene body regions when compared to those un-changed genes.
Title: Genomic distribution of 5-Hydroxymethylcytosine in mouse kidney and its relationship with gene expression.
The findings of this study described in this study emphasise the importance of 5hmC in brain development and ageing and will help to better understand the complexity and plasticity of the brain.
Title: 5-Hydroxymethylcytosine, the "Sixth Base", during brain development and ageing.

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Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (6) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH125682 (e-PCR)
- UniSTS:142652

D6Ertd71e (e-PCR), detects polymorphism
- UniSTS:167498

RH136550 (e-PCR)
- UniSTS:210532

D18356 (e-PCR)
- UniSTS:124773

AW546958 (e-PCR)
- UniSTS:207991

RH127177 (e-PCR)
- UniSTS:207992

Homology

Orthologs from Annotation Pipeline: 504 organisms have orthologs with human gene Hmces
Orthologs

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables hydrolase activity	IEA Inferred from Electronic Annotation more info
enables peptidase activity	IEA Inferred from Electronic Annotation more info
enables single-stranded DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables single-stranded DNA binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in DNA damage response	ISO Inferred from Sequence Orthology more info
involved_in double-strand break repair via alternative nonhomologous end joining	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of isotype switching	IDA Inferred from Direct Assay more info	PubMed
involved_in protein-DNA covalent cross-linking	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within proteolysis	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in chromosome	IEA Inferred from Electronic Annotation more info
located_in replication fork	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: abasic site processing protein HMCES

Names: ES cell-specific 5hmC-binding protein; SRAP domain-containing protein 1; UPF0361 protein C3orf37 homolog; embryonic stem cell-specific 5-hydroxymethylcytosine-binding protein; peptidase HMCES; putative endonuclease HMCES; putative peptidase SRAPD1

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_001418193.1 → NP_001405122.1 abasic site processing protein HMCES isoform a

Status: VALIDATED

Source sequence(s)

AC153872
NM_001418194.1 → NP_001405123.1 abasic site processing protein HMCES isoform b

Status: VALIDATED

Source sequence(s)

AC153872
NM_001418195.1 → NP_001405124.1 abasic site processing protein HMCES isoform b

Status: VALIDATED

Source sequence(s)

AC153872
NM_001418196.1 → NP_001405125.1 abasic site processing protein HMCES isoform b

Status: VALIDATED

Source sequence(s)

AC153872
NM_001418197.1 → NP_001405126.1 abasic site processing protein HMCES isoform b

Status: VALIDATED

Source sequence(s)

AC153872
NM_001418198.1 → NP_001405127.1 abasic site processing protein HMCES isoform c

Status: VALIDATED

Source sequence(s)

AC153872
NM_001418199.1 → NP_001405128.1 abasic site processing protein HMCES isoform c

Status: VALIDATED

Source sequence(s)

AC153872
NM_173737.3 → NP_776098.1 abasic site processing protein HMCES isoform a

See identical proteins and their annotated locations for NP_776098.1

Status: VALIDATED

Source sequence(s)

AC153872

Consensus CDS

CCDS39551.1

UniProtKB/Swiss-Prot

Q8R1M0

Related

ENSMUSP00000032141.8, ENSMUST00000032141.14

Conserved Domains (1) summary

pfam02586
Location:1 → 258

SRAP; SOS response associated peptidase (SRAP)