HMCES 5-hydroxymethylcytosine binding, ES cell specific [Homo sapiens (human)] - Gene

Summary

Official Symbol: HMCESprovided by HGNC
Official Full Name: 5-hydroxymethylcytosine binding, ES cell specificprovided by HGNC
Primary source: HGNC:HGNC:24446
See related: Ensembl:ENSG00000183624 MIM:618288; AllianceGenome:HGNC:24446
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: DC12; SRAPD1; C3orf37
Summary: Enables single-stranded DNA binding activity. Involved in cellular response to DNA damage stimulus and protein-DNA covalent cross-linking. Located in replication fork. [provided by Alliance of Genome Resources, Apr 2022]
Expression: Ubiquitous expression in lymph node (RPKM 40.1), testis (RPKM 20.9) and 24 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 3q21.3

Exon count:: 8

Annotation release	Status	Assembly	Chr	Location
RS_2023_03	current	GRCh38.p14 (GCF_000001405.40)	3	NC_000003.12 (129278832..129306186)
RS_2023_03	current	T2T-CHM13v2.0 (GCF_009914755.1)	3	NC_060927.1 (132023631..132050984)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	3	NC_000003.11 (128997675..129025029)

Chromosome 3 - NC_000003.12 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
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?

5-Hydroxymethylation highlights the heterogeneity in keratinization and cell junctions in head and neck cancers.
Title: 5-Hydroxymethylation highlights the heterogeneity in keratinization and cell junctions in head and neck cancers.
Loss of the abasic site sensor HMCES is synthetic lethal with the activity of the APOBEC3A cytosine deaminase in cancer cells.
Title: Loss of the abasic site sensor HMCES is synthetic lethal with the activity of the APOBEC3A cytosine deaminase in cancer cells.
Characterization of global 5-hydroxymethylcytosine in pediatric posterior fossa ependymoma.
Title: Characterization of global 5-hydroxymethylcytosine in pediatric posterior fossa ependymoma.
HMCES Maintains Replication Fork Progression and Prevents Double-Strand Breaks in Response to APOBEC Deamination and Abasic Site Formation.
Title: HMCES Maintains Replication Fork Progression and Prevents Double-Strand Breaks in Response to APOBEC Deamination and Abasic Site Formation.
HMCES safeguards replication from oxidative stress and ensures error-free repair.
Title: HMCES safeguards replication from oxidative stress and ensures error-free repair.
Structural biology of DNA abasic site protection by SRAP proteins.
Title: Structural biology of DNA abasic site protection by SRAP proteins.
This study reports crystal structures of the human HMCES SOS response-associated peptidase (SRAP) domain in complex with DNA-damage substrates, including HMCES cross-linked with an abasic site within a 3' overhang DNA.
Title: Structural basis of HMCES interactions with abasic DNA and multivalent substrate recognition.
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.
5-hmC might be involved in the pathogenesis of Nonalcoholic Fatty Liver Disease by regulating liver mitochondrial biogenesis and PPARGC1A expression.
Title: Epigenetic Modifications in the Biology of Nonalcoholic Fatty Liver Disease: The Role of DNA Hydroxymethylation and TET Proteins.
The expression of 5-hmC was an independent prognostic factor for overall survival of EOC [epithelial ovarian canc] patients.
Title: Prognostic values of 5-hmC, 5-mC and TET2 in epithelial ovarian cancer.

Submit: New GeneRIF Correction See all GeneRIFs (12)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

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

HSC2JD062 (e-PCR)
- UniSTS:20514

DBEST27818 (e-PCR)
- UniSTS:46135

D3S3816 (e-PCR)
- UniSTS:53885

A002R07 (e-PCR)
- UniSTS:2696

RH98834 (e-PCR)
- UniSTS:85450

SHGC-4168 (e-PCR)
- UniSTS:50172

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
NOT enables DNA-(apurinic or apyrimidinic site) endonuclease activity	IDA Inferred from Direct Assay more info	PubMed
enables peptidase activity	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables single-stranded DNA binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in DNA damage response	IDA Inferred from Direct Assay more info	PubMed
involved_in double-strand break repair via alternative nonhomologous end joining	IEA Inferred from Electronic Annotation 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	IDA Inferred from Direct Assay more info	PubMed
involved_in proteolysis	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in replication fork	IDA Inferred from Direct Assay more info	PubMed

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; SOS response associated peptidase domain containing 1; SRAP domain-containing protein 1; UPF0361 protein C3orf37; 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_001006109.1 → NP_001006109.1 abasic site processing protein HMCES isoform a

See identical proteins and their annotated locations for NP_001006109.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longest transcript. Variants 1 and 2 both encode the same isoform (a).

Source sequence(s)

BC050686, BU728549

Consensus CDS

CCDS33852.1

UniProtKB/Swiss-Prot

Q96FZ2, Q9NRP3

Related

ENSP00000374385.3, ENST00000389735.7

Conserved Domains (1) summary

pfam02586
Location:1 → 259

SRAP; SOS response associated peptidase (SRAP)
NM_001363881.1 → NP_001350810.1 abasic site processing protein HMCES isoform b

Status: VALIDATED

Description

Transcript Variant: This variant (3) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (b) has the same N- and C-termini but is shorter compared to isoform a.

Source sequence(s)

AC137695

Consensus CDS

CCDS87134.1

UniProtKB/TrEMBL

E7EMP6

Related

ENSP00000392966.2, ENST00000417226.6

Conserved Domains (1) summary

cl03646
Location:31 → 230

SRAP; SOS response associated peptidase (SRAP)
NM_001370343.1 → NP_001357272.1 abasic site processing protein HMCES isoform a

Status: VALIDATED

Source sequence(s)

AC137695, AK025883, BC009993, CN335364

Consensus CDS

CCDS33852.1

UniProtKB/Swiss-Prot

Q9NRP3

Related

ENSP00000426215.1, ENST00000502878.6

Conserved Domains (1) summary

pfam02586
Location:1 → 259

SRAP; SOS response associated peptidase (SRAP)
NM_001370344.1 → NP_001357273.1 abasic site processing protein HMCES isoform a

Status: VALIDATED

Source sequence(s)

AC137695, BC009993, BE790516

Consensus CDS

CCDS33852.1

UniProtKB/Swiss-Prot

Q9NRP3

Conserved Domains (1) summary

pfam02586
Location:1 → 259

SRAP; SOS response associated peptidase (SRAP)
NM_001370345.1 → NP_001357274.1 abasic site processing protein HMCES isoform c

Status: VALIDATED

Source sequence(s)

AC137695

Related

ENSP00000423132.1, ENST00000509042.5

Conserved Domains (1) summary

pfam02586
Location:1 → 211

SRAP; SOS response associated peptidase (SRAP)
NM_020187.3 → NP_064572.2 abasic site processing protein HMCES isoform a

See identical proteins and their annotated locations for NP_064572.2

Status: VALIDATED

Description

Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 both encode the same isoform (a).

Source sequence(s)

AC137695, AF201934, BC010125

Consensus CDS

CCDS33852.1

UniProtKB/Swiss-Prot

Q96FZ2, Q9NRP3

Related

ENSP00000372955.3, ENST00000383463.9

Conserved Domains (1) summary

pfam02586
Location:1 → 259

SRAP; SOS response associated peptidase (SRAP)