Rfx5 regulatory factor X5 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Rfx5provided by RGD
Official Full Name: regulatory factor X5provided by RGD
Primary source: RGD:1311677
See related: Ensembl:ENSRNOG00000021012 AllianceGenome:RGD:1311677
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Predicted to enable DNA-binding transcription activator activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in positive regulation of transcription by RNA polymerase II. Predicted to act upstream of or within negative regulation of transcription by RNA polymerase II. Predicted to be part of RNA polymerase II transcription regulator complex. Human ortholog(s) of this gene implicated in MHC class II deficiency and severe combined immunodeficiency. Orthologous to human RFX5 (regulatory factor X5). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Thymus (RPKM 96.2), Spleen (RPKM 79.3) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 2q34

Exon count:: 11

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	2	NC_086020.1 (185210206..185217735)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	2	NC_051337.1 (182521191..182528720)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	2	NC_005101.4 (196119054..196128109)

Chromosome 2 - NC_086020.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

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
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?

RFX5 binds to the collagen transcription start site and represses collagen gene expression.
Title: Interferon gamma repression of collagen (COL1A2) transcription is mediated by the RFX5 complex.

Submit: New GeneRIF Correction

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables DNA-binding transcription activator activity, RNA polymerase II-specific	ISO Inferred from Sequence Orthology more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables sequence-specific double-stranded DNA binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in biological_process	ND No biological Data available more info
acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
part_of RNA polymerase II transcription regulator complex	ISO Inferred from Sequence Orthology more info
located_in intracellular membrane-bounded organelle	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
located_in nucleus	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: DNA-binding protein RFX5

Names: regulator factor X 5; regulatory factor X, 5 (influences HLA class II expression)

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_001107694.1 → NP_001101164.1 DNA-binding protein RFX5

See identical proteins and their annotated locations for NP_001101164.1

Status: VALIDATED

Source sequence(s)

CH474015

UniProtKB/TrEMBL

A6K2T4, D3ZHD7

Related

ENSRNOP00000060480.1, ENSRNOT00000068528.2

Conserved Domains (3) summary

pfam18326
Location:27 → 85

RFX5_N; RFX5 N-terminal domain

pfam02257
Location:94 → 165

RFX_DNA_binding; RFX DNA-binding domain

pfam14621
Location:466 → 679

RFX5_DNA_bdg; RFX5 DNA-binding domain
NM_001419499.1 → NP_001406428.1 DNA-binding protein RFX5

Status: VALIDATED

Source sequence(s)

JAXUCZ010000002

UniProtKB/TrEMBL

A6K2T4, D3ZHD7