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

Gene ID: 56941, updated on 1-Jun-2020

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
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
Expression
Ubiquitous expression in lymph node (RPKM 40.1), testis (RPKM 20.9) and 24 other tissues See more
Orthologs

Genomic context

See HMCES in Genome Data Viewer
Location:
3q21.3
Exon count:
8
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 3 NC_000003.12 (129278832..129306186)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (128997680..129025029)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene CRISPRi-FlowFISH-validated H1-10 regulatory element Neighboring gene COPI coat complex subunit gamma 1 Neighboring gene microRNA 6826 Neighboring gene CRISPRi-FlowFISH-validated H1-10 regulatory element Neighboring gene H1-10 antisense RNA 1 Neighboring gene H1.10 linker histone Neighboring gene nucleoporin 210 pseudogene 3

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC111075

Gene Ontology Provided by GOA

Function Evidence Code Pubs
NOT DNA-(apurinic or apyrimidinic site) endonuclease activity IDA
Inferred from Direct Assay
more info
PubMed 
endonuclease activity IEA
Inferred from Electronic Annotation
more info
 
peptidase activity IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
single-stranded DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
cellular response to DNA damage stimulus IDA
Inferred from Direct Assay
more info
PubMed 
double-strand break repair via alternative nonhomologous end joining IEA
Inferred from Electronic Annotation
more info
 
nucleic acid phosphodiester bond hydrolysis IEA
Inferred from Electronic Annotation
more info
 
positive regulation of isotype switching ISS
Inferred from Sequence or Structural Similarity
more info
 
protein-DNA covalent cross-linking IDA
Inferred from Direct Assay
more info
PubMed 
proteolysis IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
replication fork IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

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)

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)

  1. NM_001006109.1NP_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
    Related
    ENSP00000374385.3, ENST00000389735.7
    Conserved Domains (1) summary
    pfam02586
    Location:1259
    SRAP; SOS response associated peptidase (SRAP)
  2. NM_001363881.1NP_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
    Related
    ENSP00000392966.2, ENST00000417226.6
    Conserved Domains (1) summary
    pfam02586
    Location:4217
    SRAP; SOS response associated peptidase (SRAP)
  3. NM_001370343.1NP_001357272.1  abasic site processing protein HMCES isoform a

    Status: VALIDATED

    Source sequence(s)
    AC137695, AK025883, BC009993, CN335364
    Related
    ENSP00000426215.1, ENST00000502878.6
    Conserved Domains (1) summary
    pfam02586
    Location:1259
    SRAP; SOS response associated peptidase (SRAP)
  4. NM_001370344.1NP_001357273.1  abasic site processing protein HMCES isoform a

    Status: VALIDATED

    Source sequence(s)
    AC137695, BC009993, BE790516
    Conserved Domains (1) summary
    pfam02586
    Location:1259
    SRAP; SOS response associated peptidase (SRAP)
  5. NM_001370345.1NP_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:1211
    SRAP; SOS response associated peptidase (SRAP)
  6. NM_020187.3NP_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
    Related
    ENSP00000372955.3, ENST00000383463.9
    Conserved Domains (1) summary
    pfam02586
    Location:1259
    SRAP; SOS response associated peptidase (SRAP)

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p13 Primary Assembly

    Range
    129278832..129306186
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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