Nfib nuclear factor I/B [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Nfibprovided by RGD
Official Full Name: nuclear factor I/Bprovided by RGD
Primary source: RGD:62015
See related: EnsemblRapid:ENSRNOG00000009795 AllianceGenome:RGD:62015
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: Enables double-stranded DNA binding activity. Involved in positive regulation of DNA-templated transcription. Predicted to be located in cerebellar mossy fiber; fibrillar center; and nucleoplasm. Predicted to be active in nucleus. Orthologous to human NFIB (nuclear factor I B). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Heart (RPKM 413.1), Lung (RPKM 373.9) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 5q31

Exon count:: 14

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	5	NC_086023.1 (101805168..102020618, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	5	NC_051340.1 (96759208..96974001, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	5	NC_005104.4 (100436343..100647962, complement)

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?

Inhibition of microRNA-495 inhibits hypoxia-induced apoptosis in H9c2 cells via targeting NFIB.
Title: Inhibition of microRNA-495 inhibits hypoxia-induced apoptosis in H9c2 cells via targeting NFIB.
Inhibition of microRNA-346 inhibits myocardial inflammation and apoptosis after myocardial infarction via targeting NFIB.
Title: Inhibition of microRNA-346 inhibits myocardial inflammation and apoptosis after myocardial infarction via targeting NFIB.
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

RH132021 (e-PCR)
- UniSTS:215304

D5Got128 (e-PCR)
- UniSTS:114699

Nfib (e-PCR), detects polymorphism
- UniSTS:527449

RH143568 (e-PCR)
- UniSTS:232814

AU028248 (e-PCR)
- UniSTS:112511

RH138459 (e-PCR)
- UniSTS:220546

Nfib (e-PCR), detects polymorphism
- UniSTS:515976

MARC_17865-17866:1025013775:1 (e-PCR)
- UniSTS:268427

D9S2012 (e-PCR)
- UniSTS:82852

RH80854 (e-PCR)
- UniSTS:89539

RH142928 (e-PCR)
- UniSTS:232175

d5rat149 (e-PCR)
- UniSTS:122098

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables DNA binding	IDA Inferred from Direct Assay more info	PubMed
NOT enables DNA binding	ISO Inferred from Sequence Orthology more info
enables DNA binding	ISO Inferred from Sequence Orthology more info
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 DNA-binding transcription factor activity, RNA polymerase II-specific	ISO Inferred from Sequence Orthology more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	ISS Inferred from Sequence or Structural Similarity 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 double-stranded DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables sequence-specific double-stranded DNA binding	ISO Inferred from Sequence Orthology more info
enables transcription regulator inhibitor activity	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in DNA replication	IEA Inferred from Electronic Annotation more info
involved_in anterior commissure morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in anterior commissure morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in brain development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cell differentiation involved in salivary gland development	ISO Inferred from Sequence Orthology more info
acts_upstream_of cell population proliferation	ISO Inferred from Sequence Orthology more info
involved_in cell proliferation in forebrain	ISO Inferred from Sequence Orthology more info
involved_in chondrocyte differentiation	ISO Inferred from Sequence Orthology more info
involved_in chondrocyte differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in club cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in club cell differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in commissural neuron axon guidance	ISO Inferred from Sequence Orthology more info
involved_in commissural neuron axon guidance	ISS Inferred from Sequence or Structural Similarity 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
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
acts_upstream_of_or_within glandular epithelial cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in glial cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in glial cell differentiation	ISS Inferred from Sequence or Structural Similarity 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
acts_upstream_of_or_within hindbrain development	ISO Inferred from Sequence Orthology more info
involved_in lung ciliated cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in lung ciliated cell differentiation	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within lung development	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of DNA-templated transcription	TAS Traceable Author Statement more info	PubMed
involved_in negative regulation of epithelial cell proliferation involved in lung morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of epithelial cell proliferation involved in lung morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of mesenchymal cell proliferation involved in lung development	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of mesenchymal cell proliferation involved in lung development	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of miRNA transcription	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of stem cell proliferation	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
acts_upstream_of_or_within neurogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within neuron fate specification	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of DNA-templated transcription	TAS Traceable Author Statement more info	PubMed
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
involved_in positive regulation of transcription by RNA polymerase II	ISS Inferred from Sequence or Structural Similarity more info
involved_in principal sensory nucleus of trigeminal nerve development	ISO Inferred from Sequence Orthology more info
involved_in principal sensory nucleus of trigeminal nerve development	ISS Inferred from Sequence or Structural Similarity 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 bacterium	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within 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
acts_upstream_of_or_within salivary gland cavitation	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 stem cell proliferation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within tissue homeostasis	ISO Inferred from Sequence Orthology more info
involved_in type I pneumocyte differentiation	ISO Inferred from Sequence Orthology more info
involved_in type I pneumocyte differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in type II pneumocyte differentiation	ISO Inferred from Sequence Orthology more info
involved_in type II pneumocyte differentiation	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
located_in cerebellar mossy fiber	ISO Inferred from Sequence Orthology more info
located_in cerebellar mossy fiber	ISS Inferred from Sequence or Structural Similarity more info
located_in fibrillar center	ISO Inferred from Sequence Orthology 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 nucleus	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: nuclear factor 1 B-type

Names: olfactory epithelium nuclear factor I-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_001398938.2 → NP_001385867.1 nuclear factor 1 B-type isoform 1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000005

UniProtKB/TrEMBL

F1LLY9, O70185

Conserved Domains (3) summary

pfam10524
Location:10 → 47

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

pfam00859
Location:209 → 489

CTF_NFI; CTF/NF-I family transcription modulation region

cl00055
Location:69 → 173

MH1; N-terminal Mad Homology 1 (MH1) domain
NM_001398939.2 → NP_001385868.1 nuclear factor 1 B-type isoform 3

Status: VALIDATED

Source sequence(s)

JAXUCZ010000005

UniProtKB/TrEMBL

A0A8I5ZX78, O70187

Conserved Domains (3) summary

pfam10524
Location:10 → 47

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

pfam00859
Location:209 → 415

CTF_NFI; CTF/NF-I family transcription modulation region

cl00055
Location:69 → 173

MH1; N-terminal Mad Homology 1 (MH1) domain
NM_001429567.1 → NP_001416496.1 nuclear factor 1 B-type isoform 4

Status: VALIDATED

Source sequence(s)

JAXUCZ010000005

UniProtKB/TrEMBL

A0A8I6AFY4
NM_001429568.1 → NP_001416497.1 nuclear factor 1 B-type isoform 5

Status: VALIDATED

Source sequence(s)

JAXUCZ010000005
NM_001429569.1 → NP_001416498.1 nuclear factor 1 B-type isoform 6

Status: VALIDATED

Source sequence(s)

JAXUCZ010000005
NM_001429570.1 → NP_001416499.1 nuclear factor 1 B-type isoform 7

Status: VALIDATED

Source sequence(s)

JAXUCZ010000005

UniProtKB/TrEMBL

A0A8J8YK50
NM_001429571.1 → NP_001416500.1 nuclear factor 1 B-type isoform 8

Status: VALIDATED

Source sequence(s)

JAXUCZ010000005
NM_001429572.1 → NP_001416501.1 nuclear factor 1 B-type isoform 9

Status: VALIDATED

Source sequence(s)

JAXUCZ010000005

UniProtKB/TrEMBL

A6J836
NM_001429573.1 → NP_001416502.1 nuclear factor 1 B-type isoform 10

Status: VALIDATED

Source sequence(s)

JAXUCZ010000005
NM_001429574.1 → NP_001416503.1 nuclear factor 1 B-type isoform 11

Status: VALIDATED

Source sequence(s)

JAXUCZ010000005
NM_001429575.1 → NP_001416504.1 nuclear factor 1 B-type isoform 12

Status: VALIDATED

Source sequence(s)

JAXUCZ010000005
NM_031566.3 → NP_113754.1 nuclear factor 1 B-type isoform 2

See identical proteins and their annotated locations for NP_113754.1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000005

UniProtKB/TrEMBL

F7F711, O70186

Related

ENSRNOP00000063791.3, ENSRNOT00000067538.5

Conserved Domains (3) summary

pfam10524
Location:10 → 47

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

pfam00859
Location:209 → 493

CTF_NFI; CTF/NF-I family transcription modulation region

cl00055
Location:69 → 173

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_086023.1 Reference GRCr8

Range

101805168..102020618 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039109355.2 → XP_038965283.1 nuclear factor 1 B-type isoform X8

Related

ENSRNOP00000111591.1, ENSRNOT00000134746.1

Conserved Domains (4) summary

PRK15127
Location:385 → 475

PRK15127; multidrug efflux RND transporter permease subunit AcrB

pfam10524
Location:10 → 47

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

pfam00859
Location:209 → 416

CTF_NFI; CTF/NF-I family transcription modulation region

cl00055
Location:69 → 173

MH1; N-terminal Mad Homology 1 (MH1) domain
XM_063287247.1 → XP_063143317.1 nuclear factor 1 B-type isoform X7
XM_006238335.5 → XP_006238397.1 nuclear factor 1 B-type isoform X3

Related

ENSRNOP00000108916.1, ENSRNOT00000149928.1

Conserved Domains (3) summary

pfam10524
Location:10 → 47

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

pfam00859
Location:209 → 498

CTF_NFI; CTF/NF-I family transcription modulation region

cl00055
Location:69 → 173

MH1; N-terminal Mad Homology 1 (MH1) domain
XM_008763762.4 → XP_008761984.2 nuclear factor 1 B-type isoform X2
XM_017593197.3 → XP_017448686.2 nuclear factor 1 B-type isoform X1
XM_017593199.3 → XP_017448688.2 nuclear factor 1 B-type isoform X5
XM_017593198.3 → XP_017448687.2 nuclear factor 1 B-type isoform X4
XM_039109354.2 → XP_038965282.2 nuclear factor 1 B-type isoform X6
XM_017593200.3 → XP_017448689.2 nuclear factor 1 B-type isoform X9

Related

ENSRNOP00000109289.1, ENSRNOT00000148312.1
XM_063287249.1 → XP_063143319.1 nuclear factor 1 B-type isoform X11
XM_039109357.2 → XP_038965285.1 nuclear factor 1 B-type isoform X10

Conserved Domains (1) summary

pfam00859
Location:39 → 328

CTF_NFI; CTF/NF-I family transcription modulation region