Nfia nuclear factor I/A [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Nfiaprovided by RGD
Official Full Name: nuclear factor I/Aprovided by RGD
Primary source: RGD:3170
See related: EnsemblRapid:ENSRNOG00000006966 AllianceGenome:RGD:3170
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
Summary: Enables DNA binding activity. Involved in positive regulation of DNA-templated transcription and response to organic cyclic compound. Predicted to be located in cell junction and nucleoplasm. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in NFIA-related disorder. Orthologous to human NFIA (nuclear factor I A). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Heart (RPKM 292.9), Lung (RPKM 205.8) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 5q33

Exon count:: 15

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	5	NC_086023.1 (117359006..117897391)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	5	NC_051340.1 (112436655..112781878)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	5	NC_005104.4 (116421895..116750381)

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
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?

NFIA has a role in the transcriptional activation of CYP2A3
Title: Transcriptional regulation of rat CYP2A3 by nuclear factor 1: identification of a novel NFI-A isoform, and evidence for tissue-selective interaction of NFI with the CYP2A3 promoter in vivo.
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.
Data suggest that activation of UDP-glucuronosyltransferase 1A2 (UGT1A2) by nuclear factor I (NFI)-A1 is suppressed by NFI-C1 in the liver, and culture-associated expression of UGT1A2 is triggered by disappearance of NFI-C1 in cultured hepatocytes.
Title: Transcriptional enhancement of UDP-glucuronosyltransferase form 1A2 (UGT1A2) by nuclear factor I-A (NFI-A) in rat hepatocytes.

Submit: New GeneRIF Correction

General gene information

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Markers

RH143730 (e-PCR)
- UniSTS:232976

RH80440 (e-PCR)
- UniSTS:91041

BI288968 (e-PCR)
- UniSTS:246438

D5Wox18 (e-PCR)
- UniSTS:117986

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables DNA binding	ISO Inferred from Sequence Orthology more info
enables DNA-binding transcription activator activity, RNA polymerase II-specific	IEA Inferred from Electronic Annotation 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	IEA Inferred from Electronic Annotation 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 binding	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription factor binding	ISO Inferred from Sequence Orthology 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	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables chromatin binding	IEA Inferred from Electronic Annotation more info
enables chromatin binding	ISO Inferred from Sequence Orthology more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in BMP signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in BMP signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in DNA replication	IEA Inferred from Electronic Annotation more info
involved_in cartilage development	IEA Inferred from Electronic Annotation more info
involved_in cartilage development	ISO Inferred from Sequence Orthology more info
involved_in cell morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in cell morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in exit from mitosis	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within exit from mitosis	ISO Inferred from Sequence Orthology more info
involved_in gene expression	IEA Inferred from Electronic Annotation 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 fate specification	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within glial cell fate specification	ISO Inferred from Sequence Orthology more info
involved_in glial cell proliferation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within glial cell proliferation	ISO Inferred from Sequence Orthology more info
involved_in limb morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in limb morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in neural precursor cell proliferation	IEA Inferred from Electronic Annotation 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
involved_in neuron fate specification	IEA Inferred from Electronic Annotation 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	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation 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
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in response to organic cyclic compound	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to wounding	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within response to wounding	ISO Inferred from Sequence Orthology more info
involved_in retina development in camera-type eye	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within retina development in camera-type eye	ISO Inferred from Sequence Orthology more info
involved_in synapse maturation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within synapse maturation	ISO Inferred from Sequence Orthology more info
involved_in ureter development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within ureter development	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in cell junction	IEA Inferred from Electronic Annotation more info
located_in cell junction	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 nucleus	IEA Inferred from Electronic Annotation more info
located_in nucleus	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: nuclear factor 1 A-type

Names: CCAAT-box-binding transcription factor; CTF; NF-I/A; NF1-A; NFI-A; TGGCA-binding protein; nuclear factor 1/A

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_012988.2 → NP_037120.1 nuclear factor 1 A-type

See identical proteins and their annotated locations for NP_037120.1

Status: PROVISIONAL

Source sequence(s)

D78017

UniProtKB/Swiss-Prot

P09414, Q54A99, Q63782

UniProtKB/TrEMBL

A0A8I6G968

Related

ENSRNOP00000073066.3, ENSRNOT00000086628.3

Conserved Domains (3) summary

pfam10524
Location:9 → 46

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

pfam00859
Location:214 → 508

CTF_NFI; CTF/NF-I family transcription modulation region

cl00055
Location:68 → 172

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

117359006..117897391

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063287182.1 → XP_063143252.1 nuclear factor 1 A-type isoform X2

UniProtKB/TrEMBL

A6JRJ7
XM_063287181.1 → XP_063143251.1 nuclear factor 1 A-type isoform X1

UniProtKB/TrEMBL

Q9QY90

Related

ENSRNOP00000004017.9, ENSRNOT00000004017.9
XM_063287183.1 → XP_063143253.1 nuclear factor 1 A-type isoform X3

UniProtKB/TrEMBL

A6JRJ9
XM_039109300.2 → XP_038965228.1 nuclear factor 1 A-type isoform X4

UniProtKB/TrEMBL

A0A8I6AR84, A0A8I6G968

Related

ENSRNOP00000097022.1, ENSRNOT00000117135.2

Conserved Domains (3) summary

pfam10524
Location:2 → 38

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

pfam00859
Location:206 → 500

CTF_NFI; CTF/NF-I family transcription modulation region

pfam03165
Location:60 → 164

MH1; MH1 domain
XM_063287184.1 → XP_063143254.1 nuclear factor 1 A-type isoform X6
XM_063287185.1 → XP_063143255.1 nuclear factor 1 A-type isoform X7

UniProtKB/TrEMBL

F1LRV0, Q63783

Related

ENSRNOP00000082237.2, ENSRNOT00000106921.2
XM_039109301.2 → XP_038965229.1 nuclear factor 1 A-type isoform X5

UniProtKB/TrEMBL

A0A0G2K5I9, A0A8I6G968, Q63573

Related

ENSRNOP00000073444.2, ENSRNOT00000087089.3

Conserved Domains (3) summary

pfam10524
Location:9 → 46

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

pfam00859
Location:214 → 473

CTF_NFI; CTF/NF-I family transcription modulation region

cl00055
Location:68 → 172

MH1; N-terminal Mad Homology 1 (MH1) domain
XM_039109303.2 → XP_038965231.1 nuclear factor 1 A-type isoform X9

UniProtKB/TrEMBL

Q63785

Conserved Domains (1) summary

pfam00859
Location:60 → 354

CTF_NFI; CTF/NF-I family transcription modulation region
XM_039109302.2 → XP_038965230.1 nuclear factor 1 A-type isoform X8

Conserved Domains (1) summary

pfam00859
Location:72 → 366

CTF_NFI; CTF/NF-I family transcription modulation region