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    Afg2b AFG2 AAA ATPase homolog B [ Rattus norvegicus (Norway rat) ]

    Gene ID: 691729, updated on 27-Nov-2024

    Summary

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    Official Symbol
    Afg2bprovided by RGD
    Official Full Name
    AFG2 AAA ATPase homolog Bprovided by RGD
    Primary source
    RGD:1595990
    See related
    EnsemblRapid:ENSRNOG00000000169 AllianceGenome:RGD:1595990
    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
    Also known as
    Spata5l1
    Summary
    Predicted to enable ATP hydrolysis activity and preribosome binding activity. Predicted to be involved in ribosomal large subunit biogenesis. Predicted to be located in cytoplasm and spindle. Human ortholog(s) of this gene implicated in autosomal recessive nonsyndromic deafness. Orthologous to human AFG2B (AFG2 AAA ATPase homolog B). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Heart (RPKM 31.5), Thymus (RPKM 28.8) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Afg2b in Genome Data Viewer
    Location:
    3q35
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 3 NC_086021.1 (130148061..130162458)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 3 NC_051338.1 (109694739..109708356)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 3 NC_005102.4 (114747410..114760409)

    Chromosome 3 - NC_086021.1Genomic Context describing neighboring genes Neighboring gene transformer 2 beta, pseudogene 3 Neighboring gene glycine amidinotransferase Neighboring gene similar to human chromosome 15 open reading frame 48 Neighboring gene microRNA 147 Neighboring gene solute carrier family 30 member 4

    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. 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 hydrolysis activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables ATP hydrolysis activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables polyubiquitin modification-dependent protein binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables preribosome binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables preribosome binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Process Evidence Code Pubs
    involved_in autophagosome maturation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in mitotic spindle disassembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in proteasome-mediated ubiquitin-dependent protein catabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in retrograde protein transport, ER to cytosol IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in ribosomal large subunit biogenesis ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in ribosomal large subunit biogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    part_of VCP-NPL4-UFD1 AAA ATPase complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in cytosol IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in spindle ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    ATPase family gene 2 protein homolog B
    Names
    ribosome biogenesis protein SPATA5L1
    spermatogenesis associated 5-like 1
    spermatogenesis-associated protein 5-like protein 1
    NP_001103117.1
    XP_038961818.1

    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_001109647.1 → NP_001103117.1  ATPase family gene 2 protein homolog B

      See identical proteins and their annotated locations for NP_001103117.1

      Status: PROVISIONAL

      Source sequence(s)
      JAXUCZ010000003
      UniProtKB/Swiss-Prot
      D4A2B7
      UniProtKB/TrEMBL
      A0A8I5ZQZ5
      Conserved Domains (2) summary
      TIGR01243
      Location:14 → 738
      CDC48; AAA family ATPase, CDC48 subfamily
      pfam00004
      Location:230 → 362
      AAA; ATPase family associated with various cellular activities (AAA)

    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_086021.1 Reference GRCr8

      Range
      130148061..130162458
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039105890.2 → XP_038961818.1  ATPase family gene 2 protein homolog B isoform X1

      UniProtKB/TrEMBL
      A0A8I5ZQZ5
      Related
      ENSRNOP00000040861.4, ENSRNOT00000043414.5
      Conserved Domains (1) summary
      TIGR01243
      Location:14 → 693
      CDC48; AAA family ATPase, CDC48 subfamily

    RNA

    1. XR_010064697.1 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    D4A2B7.1 GenPept UniProtKB/Swiss-Prot:D4A2B7

    Gene LinkOut

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

    Chemical Information
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