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

    Gene ID: 56941, updated on 2-Nov-2024

    Summary

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    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
    mouse all
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    Genomic context

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    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

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues 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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    Related articles in PubMed

    1. Cross-region reduction in 5-hydroxymethylcytosine in Alzheimer's disease brain. Condliffe D, et al. Neurobiol Aging, 2014 Aug. PMID 24679604, Free PMC Article
    2. A non-proteolytic release mechanism for HMCES-DNA-protein crosslinks. Donsbach M, et al. EMBO J, 2023 Sep 18. PMID 37519246, Free PMC Article
    3. Self-reversal facilitates the resolution of HMCES DNA-protein crosslinks in cells. Rua-Fernandez J, et al. Cell Rep, 2023 Nov 28. PMID 37950866, Free PMC Article
    4. Characterization of global 5-hydroxymethylcytosine in pediatric posterior fossa ependymoma. Wu T, et al. Clin Epigenetics, 2020 Jan 28. PMID 31992357, Free PMC Article
    5. HMCES safeguards replication from oxidative stress and ensures error-free repair. Srivastava M, et al. EMBO Rep, 2020 Jun 4. PMID 32307824, Free PMC Article

    See all (48) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. 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.
    2. 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.
    3. Characterization of global 5-hydroxymethylcytosine in pediatric posterior fossa ependymoma.
      Title: Characterization of global 5-hydroxymethylcytosine in pediatric posterior fossa ependymoma.
    4. 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.
    5. HMCES safeguards replication from oxidative stress and ensures error-free repair.
      Title: HMCES safeguards replication from oxidative stress and ensures error-free repair.
    6. Structural biology of DNA abasic site protection by SRAP proteins.
      Title: Structural biology of DNA abasic site protection by SRAP proteins.
    7. 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.
    8. 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.
    9. 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.
    10. 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)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC111075

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA-(abasic site) binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    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 protein-DNA covalent cross-linking activity IDA
    Inferred from Direct Assay
    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 interstrand cross-link repair IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of isotype switching ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in protein-DNA covalent cross-linking repair IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in proteolysis IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in somatic hypermutation of immunoglobulin genes IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_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)

    1. 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
      A6NJR9, Q96FZ2, Q96G34, Q9NRP3
      UniProtKB/TrEMBL
      B4DMK2
      Related
      ENSP00000374385.3, ENST00000389735.7
      Conserved Domains (1) summary
      pfam02586
      Location:1 → 259
      SRAP; SOS response associated peptidase (SRAP)

    2. 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
      B4DMK2, E7EMP6
      Related
      ENSP00000392966.2, ENST00000417226.6
      Conserved Domains (1) summary
      cl03646
      Location:31 → 230
      SRAP; SOS response associated peptidase (SRAP)

    3. 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
      A6NJR9, Q96FZ2, Q96G34, Q9NRP3
      UniProtKB/TrEMBL
      B4DMK2
      Related
      ENSP00000426215.1, ENST00000502878.6
      Conserved Domains (1) summary
      pfam02586
      Location:1 → 259
      SRAP; SOS response associated peptidase (SRAP)

    4. 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
      A6NJR9, Q96FZ2, Q96G34, Q9NRP3
      UniProtKB/TrEMBL
      B4DMK2
      Conserved Domains (1) summary
      pfam02586
      Location:1 → 259
      SRAP; SOS response associated peptidase (SRAP)

    5. NM_001370345.1 → NP_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:1 → 211
      SRAP; SOS response associated peptidase (SRAP)

    6. 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
      A6NJR9, Q96FZ2, Q96G34, Q9NRP3
      UniProtKB/TrEMBL
      B4DMK2
      Related
      ENSP00000372955.3, ENST00000383463.9
      Conserved Domains (1) summary
      pfam02586
      Location:1 → 259
      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)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96FZ2.1 GenPept UniProtKB/Swiss-Prot:Q96FZ2

    Gene LinkOut

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