Nfia nuclear factor I/A [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Nfiaprovided by MGI
Official Full Name: nuclear factor I/Aprovided by MGI
Primary source: MGI:MGI:108056
See related: Ensembl:ENSMUSG00000028565 AllianceGenome:MGI:108056
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: CTF; NF1A; NF1-A; 1110047K16Rik; 9430022M17Rik
Summary: Enables DNA binding activity and chromatin binding activity. Involved in several processes, including BMP signaling pathway; limb morphogenesis; and positive regulation of transcription by RNA polymerase II. Acts upstream of or within several processes, including exit from mitosis; nervous system development; and ureter development. Located in nucleus. Is expressed in several structures, including alimentary system; genitourinary system; nervous system; respiratory system; and sensory organ. 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, Jan 2025]
Expression: Ubiquitous expression in limb E14.5 (RPKM 8.7), CNS E14 (RPKM 7.7) and 27 other tissues See more
Orthologs: human all
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Genomic context

Location:: 4 C5- C6; 4 45.52 cM

Exon count:: 14

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	4	NC_000070.7 (97469534..98007113)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	4	NC_000070.6 (97578066..98118876)

Chromosome 4 - NC_000070.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Nuclear Factor I A and Nuclear Factor I B Are Jointly Required for Mouse Postnatal Neural Stem Cell Self-Renewal.
Title: Nuclear Factor I A and Nuclear Factor I B Are Jointly Required for Mouse Postnatal Neural Stem Cell Self-Renewal.
Nfia Is Critical for AII Amacrine Cell Production: Selective Bipolar Cell Dependencies and Diminished ERG.
Title: Nfia Is Critical for AII Amacrine Cell Production: Selective Bipolar Cell Dependencies and Diminished ERG.
An miRNA derived from amelogenin exon4 regulates expression of transcription factor Runx2 by directly targeting upstream activators Nfia and Prkch.
Title: An miRNA derived from amelogenin exon4 regulates expression of transcription factor Runx2 by directly targeting upstream activators Nfia and Prkch.
Expression and role of microRNA-212/nuclear factor I-A in depressive mice.
Title: Expression and role of microRNA-212/nuclear factor I-A in depressive mice.
miR-142a-5p promoted osteoblast differentiation via targeting nuclear factor IA.
Title: miR-142a-5p promoted osteoblast differentiation via targeting nuclear factor IA.
NFIA and NFIB function as tumour suppressors in high-grade glioma in mice.
Title: NFIA and NFIB function as tumour suppressors in high-grade glioma in mice.
Expression of NFIA and NFIB within the murine spinal cord.
Title: Expression of NFIA and NFIB within the murine spinal cord.
NFIA differentially controls adipogenic and myogenic gene program through distinct pathways to ensure brown and beige adipocyte differentiation.
Title: NFIA differentially controls adipogenic and myogenic gene program through distinct pathways to ensure brown and beige adipocyte differentiation.
Region-Specific Transcriptional Control of Astrocyte Function Oversees Local Circuit Activities.
Title: Region-Specific Transcriptional Control of Astrocyte Function Oversees Local Circuit Activities.
HuR promotes miRNA-mediated upregulation of NFI-A protein expression in MDSCs during murine sepsis.
Title: HuR promotes miRNA-mediated upregulation of NFI-A protein expression in MDSCs during murine sepsis.

Submit: New GeneRIF Correction See all GeneRIFs (39)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (1)
Targeted (4) 1 citation

General gene information

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Markers

D4Mit290 (e-PCR), detects polymorphism
- UniSTS:130082

NoName (e-PCR)
- UniSTS:488300

G35307 (e-PCR)
- UniSTS:61592

RH80440 (e-PCR)
- UniSTS:91041

D1S3419 (e-PCR)
- UniSTS:8877

Nfia (e-PCR), detects polymorphism
- UniSTS:507088

NoName (e-PCR)
- UniSTS:234965

AU022120 (e-PCR)
- UniSTS:167399

D4Ertd681e (e-PCR), detects polymorphism
- UniSTS:167410

Nfia (e-PCR), detects polymorphism
- UniSTS:502774

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables DNA binding	IDA Inferred from Direct Assay more info	PubMed
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, 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	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in BMP signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in DNA replication	IEA Inferred from Electronic Annotation more info
involved_in cartilage development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cell morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within cell quiescence	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within exit from mitosis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in gene expression	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within gene expression	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within generation of neurons	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within glial cell fate specification	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within glial cell proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in limb morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within neural precursor cell proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within neurogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within neuron fate specification	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
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
acts_upstream_of_or_within response to wounding	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within retina development in camera-type eye	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within synapse maturation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within ureter development	IMP Inferred from Mutant Phenotype more info	PubMed

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	IDA Inferred from Direct Assay more info	PubMed
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; 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_001122952.1 → NP_001116424.1 nuclear factor 1 A-type isoform 1

Status: VALIDATED

Description

Transcript Variant: This variant (1) encodes the longest isoform (1).

Source sequence(s)

AK052204, AK139357, AL670260, AW122288

UniProtKB/Swiss-Prot

P70250, P70251, Q02780, Q3UUZ2, Q61960, Q8VBT5, Q9R1G5

UniProtKB/TrEMBL

Q3UTK6

Conserved Domains (3) summary

cl00055
Location:91 → 195

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

pfam00859
Location:237 → 531

CTF_NFI; CTF/NF-I family transcription modulation region

pfam10524
Location:32 → 69

NfI_DNAbd_pre-N; Nuclear factor I protein pre-N-terminus
NM_001122953.1 → NP_001116425.1 nuclear factor 1 A-type isoform 3

Status: VALIDATED

Description

Transcript Variant: This variant (3) has an alternate 5' exon and lacks an internal coding exon, which does not affect the reading frame, as compared to variant 1. The resulting isoform (2) has a different and shorter N-terminus and lacks an internal segment, as compared to isoform 1.

Source sequence(s)

AL670195, AL670260, AL671238, AW122288, BC122878, BC122880

Consensus CDS

CCDS51234.1

UniProtKB/TrEMBL

B1AUB9

Related

ENSMUSP00000130032.2, ENSMUST00000092532.13

Conserved Domains (3) summary

cl00055
Location:68 → 172

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

pfam00859
Location:214 → 465

CTF_NFI; CTF/NF-I family transcription modulation region

pfam10524
Location:8 → 46

NfI_DNAbd_pre-N; Nuclear factor I protein pre-N-terminus
NM_010905.3 → NP_035035.1 nuclear factor 1 A-type isoform 2

Status: VALIDATED

Description

Transcript Variant: This variant (2) has an alternate 5' exon, as compared to variant 1. The resulting isoform (2) has a different and shorter N-terminus, as compared to isoform 1.

Source sequence(s)

AF326553, AL670195, AL670260, AL671238, AW122288

Consensus CDS

CCDS18373.1

UniProtKB/TrEMBL

B1AUB9

Related

ENSMUSP00000074899.7, ENSMUST00000075448.13

Conserved Domains (3) summary

cl00055
Location:68 → 172

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

pfam00859
Location:214 → 508

CTF_NFI; CTF/NF-I family transcription modulation region

pfam10524
Location:8 → 46

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

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCm39 C57BL/6J

Genomic

NC_000070.7 Reference GRCm39 C57BL/6J

Range

97469534..98007113

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006502841.5 → XP_006502904.1 nuclear factor 1 A-type isoform X1

UniProtKB/TrEMBL

Q3UTK6

Conserved Domains (3) summary

pfam00859
Location:237 → 496

CTF_NFI; CTF/NF-I family transcription modulation region

pfam10524
Location:33 → 69

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

cl00055
Location:91 → 195

MH1; N-terminal Mad Homology 1 (MH1) domain
XM_006502844.5 → XP_006502907.1 nuclear factor 1 A-type isoform X5

UniProtKB/TrEMBL

Q3UTK6

Conserved Domains (3) summary

pfam00859
Location:237 → 488

CTF_NFI; CTF/NF-I family transcription modulation region

pfam03165
Location:91 → 195

MH1; MH1 domain

pfam10524
Location:33 → 69

NfI_DNAbd_pre-N; Nuclear factor I protein pre-N-terminus
XM_036163811.1 → XP_036019704.1 nuclear factor 1 A-type isoform X6

UniProtKB/TrEMBL

Q3UTK6

Conserved Domains (3) summary

pfam10524
Location:33 → 69

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

pfam00859
Location:237 → 453

CTF_NFI; CTF/NF-I family transcription modulation region

cl00055
Location:91 → 195

MH1; N-terminal Mad Homology 1 (MH1) domain
XM_030253303.2 → XP_030109163.1 nuclear factor 1 A-type isoform X2

UniProtKB/TrEMBL

Q3UTK6

Conserved Domains (3) summary

pfam00859
Location:206 → 500

CTF_NFI; CTF/NF-I family transcription modulation region

pfam03165
Location:60 → 164

MH1; MH1 domain

pfam10524
Location:2 → 38

NfI_DNAbd_pre-N; Nuclear factor I protein pre-N-terminus
XM_036163810.1 → XP_036019703.1 nuclear factor 1 A-type isoform X4

UniProtKB/TrEMBL

Q69ZJ5

Conserved Domains (3) summary

pfam10524
Location:2 → 38

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

pfam00859
Location:206 → 465

CTF_NFI; CTF/NF-I family transcription modulation region

cl00055
Location:60 → 164

MH1; N-terminal Mad Homology 1 (MH1) domain
XM_006502842.4 → XP_006502905.1 nuclear factor 1 A-type isoform X2

UniProtKB/TrEMBL

Q3UTK6

Conserved Domains (3) summary

pfam00859
Location:206 → 500

CTF_NFI; CTF/NF-I family transcription modulation region

pfam03165
Location:60 → 164

MH1; MH1 domain

pfam10524
Location:2 → 38

NfI_DNAbd_pre-N; Nuclear factor I protein pre-N-terminus
XM_006502843.4 → XP_006502906.1 nuclear factor 1 A-type isoform X3

UniProtKB/TrEMBL

B1AUB9, B1AUC0

Related

ENSMUSP00000102677.3, ENSMUST00000107062.9

Conserved Domains (3) summary

pfam00859
Location:214 → 473

CTF_NFI; CTF/NF-I family transcription modulation region

pfam10524
Location:9 → 46

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

cl00055
Location:68 → 172

MH1; N-terminal Mad Homology 1 (MH1) domain
XM_006502845.4 → XP_006502908.1 nuclear factor 1 A-type isoform X7

UniProtKB/TrEMBL

B1AUB9, Q05B39

Conserved Domains (3) summary

pfam00859
Location:214 → 430

CTF_NFI; CTF/NF-I family transcription modulation region

pfam10524
Location:9 → 46

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

cl00055
Location:68 → 172

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