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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.

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