Nfix nuclear factor I X [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Nfixprovided by RGD
Official Full Name: nuclear factor I Xprovided by RGD
Primary source: RGD:69080
See related: Ensembl:ENSRNOG00000002983 AllianceGenome:RGD:69080
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
Also known as: Nf1x
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 negative regulation of transcription by RNA polymerase II. Predicted to act upstream of or within central nervous system development and positive regulation of transcription by RNA polymerase II. Predicted to be located in nucleoplasm. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in Marshall-Smith syndrome and Sotos syndrome 2. Orthologous to human NFIX (nuclear factor I X). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Muscle (RPKM 131.0), Heart (RPKM 81.4) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 19q11

Exon count:: 15

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	19	NC_086037.1 (40259873..40356966)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	19	NC_051354.1 (23355388..23450360)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	19	NC_005118.4 (25818640..25914777, complement)

Chromosome 19 - NC_086037.1 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?

CircSLC8A1 and circNFIX can be used as auxiliary diagnostic markers for sudden cardiac death caused by acute ischemic heart disease.
Title: CircSLC8A1 and circNFIX can be used as auxiliary diagnostic markers for sudden cardiac death caused by acute ischemic heart disease.
activates the expression of Matn2, and activate myoblast differentiation
Title: Extracellular deposition of matrilin-2 controls the timing of the myogenic program during muscle regeneration.
cooperative interaction between NF1 family members and HNF1alpha plays an important role in hepatic L-PK transcription
Title: Nuclear factor 1 family members interact with hepatocyte nuclear factor 1alpha to synergistically activate L-type pyruvate kinase gene transcription.
gene structure and expression analysis of nuclear factor 1 family in rat
Title: Organization of gene structure and expression of nuclear factor 1 family in rat.

Submit: New GeneRIF Correction

General gene information

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Markers

NFIX (e-PCR)
- UniSTS:504112

UniSTS:474756 (e-PCR)
- UniSTS:474756

Nfix (e-PCR), detects polymorphism
- UniSTS:474756

Nfix (e-PCR), detects polymorphism
- UniSTS:507089

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 cis-regulatory region sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables chromatin 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 DNA replication	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within Rho protein signal transduction	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within astrocyte differentiation	ISO Inferred from Sequence Orthology more info
involved_in astrocyte differentiation	ISO Inferred from Sequence Orthology more info
involved_in atrioventricular canal morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in bone mineralization	ISO Inferred from Sequence Orthology more info
involved_in brain development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within brain morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in camera-type eye development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cell maturation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cell morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in cell morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in cell proliferation in forebrain	ISO Inferred from Sequence Orthology more info
involved_in cellular response to BMP stimulus	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cerebellar Purkinje cell layer development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cerebellar cortex morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cerebellar granule cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in cerebellar granule cell differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cerebellum development	ISO Inferred from Sequence Orthology more info
involved_in cerebral cortex development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within collateral sprouting	ISO Inferred from Sequence Orthology more info
involved_in ear development	ISO Inferred from Sequence Orthology more info
involved_in endochondral ossification	ISO Inferred from Sequence Orthology more info
involved_in epithelium development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within exit from mitosis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within forebrain development	ISO Inferred from Sequence Orthology more info
involved_in forebrain radial glial cell differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within gene expression	ISO Inferred from Sequence Orthology more info
involved_in gene expression	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within generation of neurons	ISO Inferred from Sequence Orthology more info
involved_in glial cell development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within glial cell fate specification	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within glial cell proliferation	ISO Inferred from Sequence Orthology more info
involved_in gliogenesis	ISO Inferred from Sequence Orthology more info
involved_in hippocampus development	ISO Inferred from Sequence Orthology more info
involved_in homeostasis of number of cells within a tissue	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within inflammatory response	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within lateral ventricle development	ISO Inferred from Sequence Orthology more info
involved_in lateral ventricle development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within learning	ISO Inferred from Sequence Orthology more info
involved_in learning	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within macrophage differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within memory	ISO Inferred from Sequence Orthology more info
involved_in memory	ISO Inferred from Sequence Orthology more info
involved_in multicellular organism growth	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of neuron apoptotic process	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within neural precursor cell proliferation	ISO Inferred from Sequence Orthology more info
involved_in neuroblast differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within neuroblast migration	ISO Inferred from Sequence Orthology more info
involved_in neuroblast migration	ISO Inferred from Sequence Orthology more info
involved_in neuroblast proliferation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within neurogenesis	ISO Inferred from Sequence Orthology more info
involved_in neurogenesis	ISO Inferred from Sequence Orthology more info
involved_in neuron differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within neuron fate specification	ISO Inferred from Sequence Orthology more info
involved_in olfactory bulb development	ISO Inferred from Sequence Orthology more info
involved_in oligodendrocyte differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within osteoclast differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within osteoclast proliferation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within phagocytosis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive 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
acts_upstream_of_or_within regeneration	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
acts_upstream_of_or_within response to wounding	ISO Inferred from Sequence Orthology more info
involved_in response to wounding	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within retina development in camera-type eye	ISO Inferred from Sequence Orthology more info
involved_in skeletal muscle satellite cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in skeletal muscle tissue development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within skeletal muscle tissue regeneration	ISO Inferred from Sequence Orthology more info
involved_in skeletal muscle tissue regeneration	ISO Inferred from Sequence Orthology more info
involved_in skeletal system development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within social behavior	ISO Inferred from Sequence Orthology more info
involved_in spinal cord development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within stem cell population maintenance	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within tissue homeostasis	ISO Inferred from Sequence Orthology more info
involved_in transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
is_active_in nucleus	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: nuclear factor 1 X-type

Names: NF1-X1 protein; nuclear factor 1 X; nuclear factor I/X (CCAAT-binding transcription factor)

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_030866.1 → NP_110493.1 nuclear factor 1 X-type

See identical proteins and their annotated locations for NP_110493.1

Status: VALIDATED

Source sequence(s)

AB012234, AB012235

UniProtKB/TrEMBL

A6IY74, F2Z3R4

Related

ENSRNOP00000034591.4, ENSRNOT00000039354.5

Conserved Domains (3) summary

pfam10524
Location:9 → 46

NfI_DNAbd_pre-N; Nuclear factor I protein pre-N-terminus

pfam00859
Location:213 → 418

CTF_NFI; CTF/NF-I family transcription modulation region

cl00055
Location:68 → 170

MH1; N-terminal Mad Homology 1 (MH1) domain

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_086037.1 Reference GRCr8

Range

40259873..40356966

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063278304.1 → XP_063134374.1 nuclear factor 1 X-type isoform X6
XM_063278302.1 → XP_063134372.1 nuclear factor 1 X-type isoform X4
XM_063278307.1 → XP_063134377.1 nuclear factor 1 X-type isoform X8
XM_063278308.1 → XP_063134378.1 nuclear factor 1 X-type isoform X10
XM_063278305.1 → XP_063134375.1 nuclear factor 1 X-type isoform X8
XM_063278303.1 → XP_063134373.1 nuclear factor 1 X-type isoform X5

UniProtKB/TrEMBL

A0A0G2K1B6
XM_063278301.1 → XP_063134371.1 nuclear factor 1 X-type isoform X2
XM_039098011.2 → XP_038953939.1 nuclear factor 1 X-type isoform X1

Conserved Domains (3) summary

pfam10524
Location:82 → 118

NfI_DNAbd_pre-N; Nuclear factor I protein pre-N-terminus

pfam00859
Location:285 → 574

CTF_NFI; CTF/NF-I family transcription modulation region

cl00055
Location:140 → 242

MH1; N-terminal Mad Homology 1 (MH1) domain
XM_039098013.2 → XP_038953941.1 nuclear factor 1 X-type isoform X3

UniProtKB/TrEMBL

A6IY74

Conserved Domains (3) summary

pfam10524
Location:6 → 42

NfI_DNAbd_pre-N; Nuclear factor I protein pre-N-terminus

pfam00859
Location:209 → 414

CTF_NFI; CTF/NF-I family transcription modulation region

cl00055
Location:64 → 166

MH1; N-terminal Mad Homology 1 (MH1) domain
XM_039098017.2 → XP_038953945.1 nuclear factor 1 X-type isoform X7

UniProtKB/TrEMBL

A6IY74

Related

ENSRNOP00000096564.1

Conserved Domains (3) summary

pfam10524
Location:6 → 42

NfI_DNAbd_pre-N; Nuclear factor I protein pre-N-terminus

pfam00859
Location:209 → 373

CTF_NFI; CTF/NF-I family transcription modulation region

cl00055
Location:64 → 166

MH1; N-terminal Mad Homology 1 (MH1) domain
XM_063278306.1 → XP_063134376.1 nuclear factor 1 X-type isoform X9