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

    Gene ID: 56941, updated on 27-Nov-2024

    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 DNA-(abasic site) binding activity; protein-DNA covalent cross-linking activity; and single-stranded DNA binding activity. Involved in interstrand cross-link repair; protein-DNA covalent cross-linking repair; and somatic hypermutation of immunoglobulin genes. Is active in replication fork. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in lymph node (RPKM 40.1), testis (RPKM 20.9) and 24 other tissues See more
    Orthologs
    NEW
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    Try the new Transcript table

    Genomic context

    See HMCES in Genome Data Viewer
    Location:
    3q21.3
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (129278832..129306186)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (132023631..132050984)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (128997675..129025029)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105374102 Neighboring gene NANOG hESC enhancer GRCh37_chr3:128950251-128950752 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20507 Neighboring gene CRISPRi-FlowFISH-validated H1-10 regulatory element 3 Neighboring gene COPI coat complex subunit gamma 1 Neighboring gene microRNA 6826 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14719 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14720 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20508 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:129024401-129024985 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20509 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14721 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14722 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14723 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

    Clone Names

    • MGC111075

    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)

    NEW Try the new Transcript table

    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
      A6NJR9, Q96FZ2, Q96G34, Q9NRP3
      UniProtKB/TrEMBL
      B4DMK2
      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
      UniProtKB/TrEMBL
      B4DMK2, E7EMP6
      Related
      ENSP00000392966.2, ENST00000417226.6
      Conserved Domains (1) summary
      cl03646
      Location:31230
      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
      Consensus CDS
      CCDS33852.1
      UniProtKB/Swiss-Prot
      A6NJR9, Q96FZ2, Q96G34, Q9NRP3
      UniProtKB/TrEMBL
      B4DMK2
      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
      Consensus CDS
      CCDS33852.1
      UniProtKB/Swiss-Prot
      A6NJR9, Q96FZ2, Q96G34, Q9NRP3
      UniProtKB/TrEMBL
      B4DMK2
      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
      UniProtKB/TrEMBL
      D6R9T3
      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
      A6NJR9, Q96FZ2, Q96G34, Q9NRP3
      UniProtKB/TrEMBL
      B4DMK2
      Related
      ENSP00000372955.3, ENST00000383463.9
      Conserved Domains (1) summary
      pfam02586
      Location:1259
      SRAP; SOS response associated peptidase (SRAP)

    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

    1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

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

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      132023631..132050984
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)