Nfx1 nuclear transcription factor, X-box binding 1 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Nfx1provided by RGD
Official Full Name: nuclear transcription factor, X-box binding 1provided by RGD
Primary source: RGD:1310277
See related: EnsemblRapid:ENSRNOG00000009015 AllianceGenome:RGD:1310277
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 repressor activity, RNA polymerase II-specific; RNA polymerase II transcription regulatory region sequence-specific DNA binding activity; and ubiquitin protein ligase activity. Predicted to be involved in negative regulation of transcription by RNA polymerase II and protein autoubiquitination. Predicted to act upstream of or within negative regulation of MHC class II biosynthetic process. Predicted to be located in cytosol; nuclear lumen; and plasma membrane. Predicted to be active in nucleus. Orthologous to human NFX1 (nuclear transcription factor, X-box binding 1). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Adrenal (RPKM 182.0), Liver (RPKM 126.8) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 5q22

Exon count:: 25

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	5	NC_086023.1 (60900140..60958889)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	5	NC_051340.1 (56104945..56162912)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	5	NC_005104.4 (57290916..57348720)

Chromosome 5 - NC_086023.1 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 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

D5Rat224 (e-PCR), detects polymorphism
- UniSTS:227922

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info
enables DNA-binding transcription repressor activity, RNA polymerase II-specific	ISO Inferred from Sequence Orthology more info
enables RNA polymerase II transcription 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 ubiquitin protein ligase activity	ISO Inferred from Sequence Orthology more info
enables zinc ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within negative regulation of MHC class II biosynthetic process	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in protein autoubiquitination	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in cytosol	IEA Inferred from Electronic Annotation more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
located_in nucleolus	IEA Inferred from Electronic Annotation 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
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	IEA Inferred from Electronic Annotation more info
located_in plasma membrane	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: transcriptional repressor NF-X1

NP_001019955.2

EC 6.3.2.-

XP_008761845.1

EC 6.3.2.-

XP_063143670.1

EC 6.3.2.-

XP_063143671.1

EC 6.3.2.-

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_001024784.2 → NP_001019955.2 transcriptional repressor NF-X1

See identical proteins and their annotated locations for NP_001019955.2

Status: VALIDATED

Source sequence(s)

JAXUCZ010000005

UniProtKB/TrEMBL

A0A8I6AMR9, A6IIT2, D4AE50

Related

ENSRNOP00000057423.2, ENSRNOT00000060692.6

Conserved Domains (2) summary

cd02643
Location:981 → 1054

R3H_NF-X1; R3H domain of the X1 box binding protein (NF-X1) and related proteins. Human NF-X1 is a transcription factor that regulates the expression of class II major histocompatibility complex (MHC) genes. The Drosophila homolog shuttle craft (STC) has been shown ...

cd06008
Location:616 → 668

NF-X1-zinc-finger; Presumably a zinc binding domain, which has been shown to bind to DNA in the human nuclear transcriptional repressor NF-X1. The zinc finger can be characterized by the pattern C-X(1-6)-H-X-C-X3-C(H/C)-X(3-4)-(H/C)-X(1-10)-C. The NF-X1 zinc finger ...

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_086023.1 Reference GRCr8

Range

60900140..60958889

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_008763623.4 → XP_008761845.1 transcriptional repressor NF-X1 isoform X3

See identical proteins and their annotated locations for XP_008761845.1

UniProtKB/TrEMBL

A0A8I6ALJ0, Q4V7B3

Related

ENSRNOP00000096312.2, ENSRNOT00000105959.2

Conserved Domains (1) summary

cd06008
Location:616 → 668

NF-X1-zinc-finger; Presumably a zinc binding domain, which has been shown to bind to DNA in the human nuclear transcriptional repressor NF-X1. The zinc finger can be characterized by the pattern C-X(1-6)-H-X-C-X3-C(H/C)-X(3-4)-(H/C)-X(1-10)-C. The NF-X1 zinc finger ...
XM_063287600.1 → XP_063143670.1 transcriptional repressor NF-X1 isoform X1

Related

ENSRNOP00000108253.1, ENSRNOT00000160551.1
XM_063287601.1 → XP_063143671.1 transcriptional repressor NF-X1 isoform X2