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    Hmces 5-hydroxymethylcytosine (hmC) binding, ES cell specific [ Mus musculus (house mouse) ]

    Gene ID: 232210, updated on 27-Nov-2024

    Summary

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    Official Symbol
    Hmcesprovided by MGI
    Official Full Name
    5-hydroxymethylcytosine (hmC) binding, ES cell specificprovided by MGI
    Primary source
    MGI:MGI:1914053
    See related
    Ensembl:ENSMUSG00000030060 AllianceGenome:MGI:1914053
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    Srap1; 8430410A17Rik
    Summary
    Enables single-stranded DNA binding activity. Involved in double-strand break repair via alternative nonhomologous end joining; positive regulation of isotype switching; and somatic hypermutation of immunoglobulin genes. Predicted to be active in replication fork. Is expressed in several structures, including adipose tissue; genitourinary system; gut; hemolymphoid system gland; and liver. Orthologous to human HMCES (5-hydroxymethylcytosine binding, ES cell specific). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in limb E14.5 (RPKM 8.7), CNS E18 (RPKM 8.2) and 28 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Hmces in Genome Data Viewer
    Location:
    6 D1; 6 39.13 cM
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 6 NC_000072.7 (87890889..87913603)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 6 NC_000072.6 (87913907..87936619)

    Chromosome 6 - NC_000072.7Genomic Context describing neighboring genes Neighboring gene cellular nucleic acid binding protein Neighboring gene STARR-seq mESC enhancer starr_16568 Neighboring gene STARR-positive B cell enhancer ABC_E2793 Neighboring gene coatomer protein complex, subunit gamma 1 Neighboring gene STARR-positive B cell enhancer ABC_E1704 Neighboring gene eukaryotic translation elongation factor 1 alpha 1 pseudogene Neighboring gene ribosomal protein S19, pseudogene 9 Neighboring gene H1.10 linker histone

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

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    Related articles in PubMed

    1. HMCES safeguards genome integrity and long-term self-renewal of hematopoietic stem cells during stress responses. Pan Y, et al. Leukemia, 2022 Apr. PMID 35039639
    2. Genomic distribution of 5-Hydroxymethylcytosine in mouse kidney and its relationship with gene expression. Wang H, et al. Ren Fail, 2016 Jul. PMID 27097670
    3. HMCES Functions in the Alternative End-Joining Pathway of the DNA DSB Repair during Class Switch Recombination in B Cells. Shukla V, et al. Mol Cell, 2020 Jan 16. PMID 31806351, Free PMC Article
    4. 5-Hydroxymethylcytosine, the "Sixth Base", during brain development and ageing. Kraus TF, et al. J Neural Transm (Vienna), 2015 Jul. PMID 25471351
    5. HMCES protects immunoglobulin genes specifically from deletions during somatic hypermutation. Wu L, et al. Genes Dev, 2022 Apr 1. PMID 35450882, Free PMC Article

    See all (24) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. HMCES protects immunoglobulin genes specifically from deletions during somatic hypermutation.
      Title: HMCES protects immunoglobulin genes specifically from deletions during somatic hypermutation.
    2. Further evidence for a specialized role for HMCES in DNA repair.
      Title: HMCES Functions in the Alternative End-Joining Pathway of the DNA DSB Repair during Class Switch Recombination in B Cells.
    3. Inactivation of murine Srap1 results in accumulation of 5hmC in genomic DNA. Srap1 deficient mice display embryonic sublethality and altered DNA methylation.
      Title: Erasure of Tet-Oxidized 5-Methylcytosine by a SRAP Nuclease.
    4. Correlation analyses showed that 5hmC enrichment in gene body is positively associated with gene expression level in mouse kidney. Moreover, ischemia reperfusion (IR) injury-associated genes (both up- and down-regulated genes during renal IR injury) in mouse kidney exhibit significantly higher 5hmC enrichment in their gene body regions when compared to those un-changed genes.
      Title: Genomic distribution of 5-Hydroxymethylcytosine in mouse kidney and its relationship with gene expression.
    5. 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.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables DNA-(abasic site) binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables DNA-(abasic site) binding 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 IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein-DNA covalent cross-linking activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables single-stranded DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables single-stranded DNA binding ISO
    Inferred from Sequence Orthology
    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 IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    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 positive regulation of isotype switching IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    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 IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in somatic hypermutation of immunoglobulin genes ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    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
    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)

    1. NM_001418193.1 → NP_001405122.1  abasic site processing protein HMCES isoform a

      Status: VALIDATED

      Source sequence(s)
      AC153872
      UniProtKB/Swiss-Prot
      Q8R1M0
      Related
      ENSMUSP00000109236.2, ENSMUST00000113606.2

    2. NM_001418194.1 → NP_001405123.1  abasic site processing protein HMCES isoform b

      Status: VALIDATED

      Source sequence(s)
      AC153872

    3. NM_001418195.1 → NP_001405124.1  abasic site processing protein HMCES isoform b

      Status: VALIDATED

      Source sequence(s)
      AC153872

    4. NM_001418196.1 → NP_001405125.1  abasic site processing protein HMCES isoform b

      Status: VALIDATED

      Source sequence(s)
      AC153872

    5. NM_001418197.1 → NP_001405126.1  abasic site processing protein HMCES isoform b

      Status: VALIDATED

      Source sequence(s)
      AC153872

    6. NM_001418198.1 → NP_001405127.1  abasic site processing protein HMCES isoform c

      Status: VALIDATED

      Source sequence(s)
      AC153872

    7. NM_001418199.1 → NP_001405128.1  abasic site processing protein HMCES isoform c

      Status: VALIDATED

      Source sequence(s)
      AC153872

    8. NM_173737.3 → NP_776098.1  abasic site processing protein HMCES isoform a

      See identical proteins and their annotated locations for NP_776098.1

      Status: VALIDATED

      Source sequence(s)
      AC153872
      Consensus CDS
      CCDS39551.1
      UniProtKB/Swiss-Prot
      Q8R1M0
      Related
      ENSMUSP00000032141.8, ENSMUST00000032141.14
      Conserved Domains (1) summary
      pfam02586
      Location:1 → 258
      SRAP; SOS response associated peptidase (SRAP)

    RNA

    1. NR_184690.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC153872

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000072.7 Reference GRCm39 C57BL/6J

      Range
      87890889..87913603
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    RNA

    1. XR_001785121.2 RNA Sequence

    2. XR_377441.3 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8R1M0.1 GenPept UniProtKB/Swiss-Prot:Q8R1M0

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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