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    Shprh SNF2 histone linker PHD RING helicase [ Rattus norvegicus (Norway rat) ]

    Gene ID: 308282, updated on 11-Apr-2024

    Summary

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    Official Symbol
    Shprhprovided by RGD
    Official Full Name
    SNF2 histone linker PHD RING helicaseprovided by RGD
    Primary source
    RGD:1310342
    See related
    Ensembl:ENSRNOG00000014450 AllianceGenome:RGD:1310342
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Predicted to enable ubiquitin protein ligase activity and ubiquitin protein ligase binding activity. Predicted to be involved in cellular response to DNA damage stimulus and protein polyubiquitination. Predicted to be part of nucleosome. Orthologous to human SHPRH (SNF2 histone linker PHD RING helicase). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Brain (RPKM 102.7), Thymus (RPKM 102.2) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    Location:
    1p13
    Exon count:
    31
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 1 NC_086019.1 (7349073..7422804)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 1 NC_051336.1 (5528827..5602537)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 1 NC_005100.4 (5240139..5313064)

    Chromosome 1 - NC_086019.1Genomic Context describing neighboring genes Neighboring gene glutamate metabotropic receptor 1 Neighboring gene dynactin 3-like 1 Neighboring gene uncharacterized LOC102547024 Neighboring gene F-box protein 30

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. Human SHPRH suppresses genomic instability through proliferating cell nuclear antigen polyubiquitination. Motegi A, et al. J Cell Biol, 2006 Dec 4. PMID 17130289, Free PMC Article
    2. Human SHPRH is a ubiquitin ligase for Mms2-Ubc13-dependent polyubiquitylation of proliferating cell nuclear antigen. Unk I, et al. Proc Natl Acad Sci U S A, 2006 Nov 28. PMID 17108083, Free PMC Article
    3. Polyubiquitination of proliferating cell nuclear antigen by HLTF and SHPRH prevents genomic instability from stalled replication forks. Motegi A, et al. Proc Natl Acad Sci U S A, 2008 Aug 26. PMID 18719106, Free PMC Article
    4. DNA damage-specific deubiquitination regulates Rad18 functions to suppress mutagenesis. Zeman MK, et al. J Cell Biol, 2014 Jul 21. PMID 25023518, Free PMC Article
    5. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables ATP binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ATP-dependent chromatin remodeler activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables hydrolase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ubiquitin protein ligase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables ubiquitin protein ligase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables ubiquitin protein ligase binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables ubiquitin-protein transferase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in DNA damage response IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within DNA damage response ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in nucleosome assembly IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in protein polyubiquitination IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in protein polyubiquitination ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    part_of nucleosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    E3 ubiquitin-protein ligase SHPRH
    Names
    SNF2 histone linker PHD RING helicase, E3 ubiquitin protein ligase
    NP_001100940.1
    XP_006227701.1
    XP_063144705.1

    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_001107470.1 → NP_001100940.1  E3 ubiquitin-protein ligase SHPRH

      See identical proteins and their annotated locations for NP_001100940.1

      Status: PROVISIONAL

      Source sequence(s)
      CH473994
      UniProtKB/TrEMBL
      A0A0G2K1Q2, A6JP42, D4A9B2
      Related
      ENSRNOP00000019893.5, ENSRNOT00000019893.7
      Conserved Domains (6) summary
      COG0553
      Location:1341 → 1696
      HepA; Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination and repair]
      cd00162
      Location:1450 → 1500
      RING; RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in ...
      cd15547
      Location:658 → 704
      PHD_SHPRH; PHD finger found in E3 ubiquitin-protein ligase SHPRH
      pfam00176
      Location:714 → 985
      SNF2_N; SNF2 family N-terminal domain
      pfam00271
      Location:1531 → 1640
      Helicase_C; Helicase conserved C-terminal domain
      pfam00538
      Location:433 → 504
      Linker_histone; linker histone H1 and H5 family

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086019.1 Reference GRCr8

      Range
      7349073..7422804
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006227639.4 → XP_006227701.1  E3 ubiquitin-protein ligase SHPRH isoform X2

      UniProtKB/TrEMBL
      A0A0G2K1Q2
      Related
      ENSRNOP00000084462.1
      Conserved Domains (7) summary
      COG0553
      Location:1322 → 1677
      HepA; Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination and repair]
      cd00162
      Location:1431 → 1481
      RING; RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in ...
      cd15547
      Location:659 → 705
      PHD_SHPRH; PHD finger found in E3 ubiquitin-protein ligase SHPRH
      pfam00176
      Location:715 → 986
      SNF2_N; SNF2 family N-terminal domain
      pfam00271
      Location:1512 → 1621
      Helicase_C; Helicase conserved C-terminal domain
      pfam00538
      Location:434 → 505
      Linker_histone; linker histone H1 and H5 family
      pfam13424
      Location:1019 → 1103
      TPR_12; Tetratricopeptide repeat

    2. XM_063288635.1 → XP_063144705.1  E3 ubiquitin-protein ligase SHPRH isoform X1

    Nucleotide Protein Strain
    Heading Accession and Version

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