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

Summary

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

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_086021.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages 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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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General gene information

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Markers

AV141009 (e-PCR), detects polymorphism
- UniSTS:462681

RH139226 (e-PCR)
- UniSTS:221312

RH130882 (e-PCR)
- UniSTS:214166

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 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 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
located_in cytoplasm	ISO Inferred from Sequence Orthology 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

EC 3.6.4.10

XP_038961818.1

EC 3.6.4.10

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)

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

NC_086021.1 Reference GRCr8

Range

130148061..130162458

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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