Hmces 5-hydroxymethylcytosine binding, ES cell specific [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Hmcesprovided by RGD
Official Full Name: 5-hydroxymethylcytosine binding, ES cell specificprovided by RGD
Primary source: RGD:1559800
See related: EnsemblRapid:ENSRNOG00000079966 AllianceGenome:RGD:1559800
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Predicted to enable DNA-(abasic site) binding activity; protein-DNA covalent cross-linking activity; and single-stranded DNA binding activity. Predicted to be involved in DNA repair; positive regulation of isotype switching; and somatic hypermutation of immunoglobulin genes. Predicted to be located in Golgi membrane. Predicted to be part of COPI vesicle coat. Predicted to be active in replication fork. Orthologous to human HMCES (5-hydroxymethylcytosine binding, ES cell specific). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Brain (RPKM 79.7), Testes (RPKM 76.7) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 4q34

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	4	NC_086022.1 (121950129..121972937)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	4	NC_051339.1 (120392812..120415616)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	4	NC_005103.4 (119841088..119864115)

Chromosome 4 - NC_086022.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables DNA-(abasic site) binding	ISO Inferred from Sequence Orthology more info
NOT enables DNA-(apurinic or apyrimidinic site) endonuclease activity	ISO Inferred from Sequence Orthology more info
NOT enables DNA-(apurinic or apyrimidinic site) endonuclease activity	ISS Inferred from Sequence or Structural Similarity more info
enables peptidase activity	IEA Inferred from Electronic Annotation more info
enables protein-DNA covalent cross-linking activity	ISO Inferred from Sequence Orthology more info
enables protein-DNA covalent cross-linking activity	ISS Inferred from Sequence or Structural Similarity more info
enables single-stranded DNA binding	ISO Inferred from Sequence Orthology more info
enables single-stranded DNA binding	ISS Inferred from Sequence or Structural Similarity more info
enables structural molecule activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in DNA damage response	ISO Inferred from Sequence Orthology more info
involved_in DNA damage response	ISS Inferred from Sequence or Structural Similarity more info
involved_in double-strand break repair via alternative nonhomologous end joining	ISO Inferred from Sequence Orthology more info
involved_in interstrand cross-link repair	ISO Inferred from Sequence Orthology more info
involved_in interstrand cross-link repair	ISS Inferred from Sequence or Structural Similarity more info
involved_in intracellular protein transport	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of isotype switching	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of isotype switching	ISS Inferred from Sequence or Structural Similarity more info
involved_in protein-DNA covalent cross-linking repair	ISO Inferred from Sequence Orthology more info
involved_in protein-DNA covalent cross-linking repair	ISS Inferred from Sequence or Structural Similarity more info
involved_in proteolysis	IEA Inferred from Electronic Annotation more info
involved_in somatic hypermutation of immunoglobulin genes	ISO Inferred from Sequence Orthology more info
involved_in somatic hypermutation of immunoglobulin genes	ISS Inferred from Sequence or Structural Similarity more info
involved_in vesicle-mediated transport	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
part_of COPI vesicle coat	IEA Inferred from Electronic Annotation more info
located_in Golgi membrane	IEA Inferred from Electronic Annotation more info
located_in endomembrane system	IEA Inferred from Electronic Annotation more info
part_of membrane coat	IEA Inferred from Electronic Annotation more info
is_active_in replication fork	ISO Inferred from Sequence Orthology more info
is_active_in replication fork	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: abasic site processing protein HMCES

Names: 5-hydroxymethylcytosine (hmC) binding, ES cell-specific; 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_001025047.2 → NP_001020218.1 abasic site processing protein HMCES

See identical proteins and their annotated locations for NP_001020218.1

Status: PROVISIONAL

Source sequence(s)

JAXUCZ010000004

UniProtKB/Swiss-Prot

Q5XIJ1

UniProtKB/TrEMBL

A6IB31

Related

ENSRNOP00000054105.3, ENSRNOT00000057286.5

Conserved Domains (1) summary

pfam02586
Location:1 → 258

SRAP; SOS response associated peptidase (SRAP)

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086022.1 Reference GRCr8

Range

121950129..121972937

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006236851.5 → XP_006236913.1 abasic site processing protein HMCES isoform X1

See identical proteins and their annotated locations for XP_006236913.1

UniProtKB/Swiss-Prot

Q5XIJ1

UniProtKB/TrEMBL

A6IB31

Conserved Domains (1) summary

pfam02586
Location:1 → 258

SRAP; SOS response associated peptidase (SRAP)
XM_039108165.2 → XP_038964093.1 abasic site processing protein HMCES isoform X2

Conserved Domains (1) summary

pfam02586
Location:1 → 213

SRAP; SOS response associated peptidase (SRAP)
XM_063286537.1 → XP_063142607.1 abasic site processing protein HMCES isoform X2