Taf1b TATA-box binding protein associated factor, RNA polymerase I subunit B [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Taf1bprovided by RGD
Official Full Name: TATA-box binding protein associated factor, RNA polymerase I subunit Bprovided by RGD
Primary source: RGD:1596058
See related: Ensembl:ENSRNOG00000061415 AllianceGenome:RGD:1596058
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: TAFI63
Summary: Predicted to enable RNA polymerase I core promoter sequence-specific DNA binding activity. Predicted to be involved in RNA polymerase I preinitiation complex assembly and nucleolar large rRNA transcription by RNA polymerase I. Predicted to be located in nucleolus and nucleoplasm. Predicted to be part of RNA polymerase I core factor complex and RNA polymerase transcription factor SL1 complex. Orthologous to human TAF1B (TATA-box binding protein associated factor, RNA polymerase I subunit B). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Thymus (RPKM 64.7), Spleen (RPKM 41.9) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 6q16

Exon count:: 18

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	6	NC_086024.1 (46845571..46923209)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	6	NC_051341.1 (41116980..41194593)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	6	NC_005105.4 (43644931..43722124)

Chromosome 6 - NC_086024.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables RNA polymerase I core promoter sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables RNA polymerase I core promoter sequence-specific DNA binding	IEA Inferred from Electronic Annotation more info
enables RNA polymerase I core promoter sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables RNA polymerase I core promoter sequence-specific DNA binding	ISS Inferred from Sequence or Structural Similarity more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in RNA polymerase I preinitiation complex assembly	IEA Inferred from Electronic Annotation more info
involved_in RNA polymerase I preinitiation complex assembly	ISO Inferred from Sequence Orthology more info
involved_in RNA polymerase I preinitiation complex assembly	ISS Inferred from Sequence or Structural Similarity more info
involved_in biological_process	ND No biological Data available more info
involved_in nucleolar large rRNA transcription by RNA polymerase I	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
part_of RNA polymerase I core factor complex	IBA Inferred from Biological aspect of Ancestor more info
part_of RNA polymerase I core factor complex	IEA Inferred from Electronic Annotation more info
part_of RNA polymerase I core factor complex	ISO Inferred from Sequence Orthology more info
part_of RNA polymerase transcription factor SL1 complex	IBA Inferred from Biological aspect of Ancestor more info
part_of RNA polymerase transcription factor SL1 complex	IEA Inferred from Electronic Annotation more info
part_of RNA polymerase transcription factor SL1 complex	ISO Inferred from Sequence Orthology more info
located_in nucleolus	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: TATA box-binding protein-associated factor RNA polymerase I subunit B

Names: RNA polymerase I-specific TBP-associated factor 63 kDa; TATA box binding protein (Tbp)-associated factor, RNA polymerase I, B; TATA box-binding protein-associated factor 1B; TBP-associated factor 1B; transcription initiation factor SL1/TIF-IB subunit B

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_001191107.1 → NP_001178036.1 TATA box-binding protein-associated factor RNA polymerase I subunit B

See identical proteins and their annotated locations for NP_001178036.1

Status: PROVISIONAL

Source sequence(s)

JAXUCZ010000006

UniProtKB/Swiss-Prot

D3ZYB7

Related

ENSRNOP00000069237.1, ENSRNOT00000086798.2

Conserved Domains (1) summary

pfam11781
Location:12 → 37

zf-RRN7; Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7

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_086024.1 Reference GRCr8

Range

46845571..46923209

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039112970.2 → XP_038968898.1 TATA box-binding protein-associated factor RNA polymerase I subunit B isoform X5

Conserved Domains (1) summary

pfam11781
Location:34 → 59

zf-RRN7; Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7
XM_063262521.1 → XP_063118591.1 TATA box-binding protein-associated factor RNA polymerase I subunit B isoform X6
XM_063262520.1 → XP_063118590.1 TATA box-binding protein-associated factor RNA polymerase I subunit B isoform X1
XM_039112967.2 → XP_038968895.1 TATA box-binding protein-associated factor RNA polymerase I subunit B isoform X3

Conserved Domains (1) summary

pfam11781
Location:12 → 37

zf-RRN7; Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7
XM_006239995.5 → XP_006240057.1 TATA box-binding protein-associated factor RNA polymerase I subunit B isoform X2

UniProtKB/TrEMBL

A0A8I6AA63

Related

ENSRNOP00000090154.1

Conserved Domains (1) summary

pfam11781
Location:28 → 61

RRN7; RNA polymerase I-specific transcription initiation factor Rrn7
XM_039112968.2 → XP_038968896.1 TATA box-binding protein-associated factor RNA polymerase I subunit B isoform X4