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

Gene ID: 232210, updated on 2-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 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

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