NFIA Gene (Protein Coding)

Nuclear Factor I A

GC01P060865
GIFtS:
46
This gene encodes a member of the NF1 (nuclear factor 1) family of transcription factors. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2011] See more...

Aliases for NFIA Gene

Aliases for NFIA Gene

  • Nuclear Factor I A 2 3 5
  • CCAAT-Box-Binding Transcription Factor 3 4
  • Nuclear Factor 1 A-Type 3 4
  • TGGCA-Binding Protein 3 4
  • Nuclear Factor I/A 2 4
  • KIAA1439 2 4
  • NF-I/A 3 4
  • NF1-A 3 4
  • NFI-A 3 4
  • NFI-L 2 3
  • CTF 3 4
  • Nuclear Factor 1/A 4
  • BRMUTD 3
  • NFIA 5

External Ids for NFIA Gene

Previous GeneCards Identifiers for NFIA Gene

  • GC01P061481
  • GC01P060471
  • GC01P060905
  • GC01P060917
  • GC01P060918
  • GC01P061260
  • GC01P061103
  • GC01P059635

Summaries for NFIA Gene

Entrez Gene Summary for NFIA Gene

  • This gene encodes a member of the NF1 (nuclear factor 1) family of transcription factors. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2011]

GeneCards Summary for NFIA Gene

NFIA (Nuclear Factor I A) is a Protein Coding gene. Diseases associated with NFIA include Brain Malformations With Or Without Urinary Tract Defects and Cleft Palate, Isolated. Among its related pathways are RNA Polymerase III Transcription Initiation and Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3. Gene Ontology (GO) annotations related to this gene include DNA-binding transcription factor activity and RNA polymerase II proximal promoter sequence-specific DNA binding. An important paralog of this gene is NFIX.

UniProtKB/Swiss-Prot Summary for NFIA Gene

  • Recognizes and binds the palindromic sequence 5'-TTGGCNNNNNGCCAA-3' present in viral and cellular promoters and in the origin of replication of adenovirus type 2. These proteins are individually capable of activating transcription and replication.

Gene Wiki entry for NFIA Gene

Additional gene information for NFIA Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for NFIA Gene

Genomics for NFIA Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for NFIA Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around NFIA on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for NFIA

Top Transcription factor binding sites by QIAGEN in the NFIA gene promoter:
  • C/EBPalpha
  • E2F-5

Genomic Locations for NFIA Gene

Latest Assembly
chr1:60,865,259-61,462,788
(GRCh38/hg38)
Size:
597,530 bases
Orientation:
Plus strand

Previous Assembly
chr1:61,542,899-61,928,460
(GRCh37/hg19 by Entrez Gene)
Size:
385,562 bases
Orientation:
Plus strand

chr1:61,330,931-61,928,465
(GRCh37/hg19 by Ensembl)
Size:
597,535 bases
Orientation:
Plus strand

Genomic View for NFIA Gene

Genes around NFIA on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
NFIA Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for NFIA Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for NFIA Gene

Proteins for NFIA Gene

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  • Protein details for NFIA Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q12857-NFIA_HUMAN
    Recommended name:
    Nuclear factor 1 A-type
    Protein Accession:
    Q12857
    Secondary Accessions:
    • B4DRJ3
    • B4DS53
    • F5H0R0
    • F8W8W3
    • Q8TA97
    • Q9H3X9
    • Q9P2A9

    Protein attributes for NFIA Gene

    Size:
    509 amino acids
    Molecular mass:
    55944 Da
    Quaternary structure:
    • Binds DNA as a homodimer.
    SequenceCaution:
    • Sequence=BAA92677.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};

    Alternative splice isoforms for NFIA Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for NFIA Gene

Protein Expression for NFIA Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for NFIA Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for NFIA Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for NFIA Gene

Domains & Families for NFIA Gene

Gene Families for NFIA Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins
  • Transcription factors

Protein Domains for NFIA Gene

InterPro:
Blocks:
  • CTF/NF-I family
ProtoNet:

Suggested Antigen Peptide Sequences for NFIA Gene

GenScript: Design optimal peptide antigens:
  • Nuclear factor 1 (B1AKN5_HUMAN)
  • Nuclear factor 1 (B1AKN6_HUMAN)
  • Nuclear factor 1 (B1AKN7_HUMAN)
  • Nuclear factor 1 (B1AKN8_HUMAN)
  • Nuclear factor 1 (E2QRI7_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q12857

UniProtKB/Swiss-Prot:

NFIA_HUMAN :
  • The 9aaTAD motif is a transactivation domain present in a large number of yeast and animal transcription factors.
  • Belongs to the CTF/NF-I family.
Domain:
  • The 9aaTAD motif is a transactivation domain present in a large number of yeast and animal transcription factors.
Family:
  • Belongs to the CTF/NF-I family.
genes like me logo Genes that share domains with NFIA: view

Function for NFIA Gene

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  6. Cell Lines for research

Molecular function for NFIA Gene

UniProtKB/Swiss-Prot Function:
Recognizes and binds the palindromic sequence 5'-TTGGCNNNNNGCCAA-3' present in viral and cellular promoters and in the origin of replication of adenovirus type 2. These proteins are individually capable of activating transcription and replication.
GENATLAS Biochemistry:
nuclear transcription factor I A,DNA binding protein

Phenotypes From GWAS Catalog for NFIA Gene

Gene Ontology (GO) - Molecular Function for NFIA Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000978 RNA polymerase II proximal promoter sequence-specific DNA binding IDA 17010934
GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific ISA --
GO:0001228 DNA-binding transcription activator activity, RNA polymerase II-specific IDA 17010934
GO:0003677 DNA binding IEA --
GO:0003682 chromatin binding IEA --
genes like me logo Genes that share ontologies with NFIA: view
genes like me logo Genes that share phenotypes with NFIA: view

Human Phenotype Ontology for NFIA Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for NFIA Gene

MGI Knock Outs for NFIA:

Animal Models for research

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for NFIA

Clone products for research

  • Addgene plasmids for NFIA

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for NFIA Gene

Localization for NFIA Gene

Subcellular locations from UniProtKB/Swiss-Prot for NFIA Gene

Nucleus.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for NFIA gene
Compartment Confidence
nucleus 5
extracellular 2
cytoskeleton 2
plasma membrane 1
mitochondrion 1
peroxisome 1
endoplasmic reticulum 1
endosome 1
cytosol 1
lysosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoplasm (4)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for NFIA Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000785 chromatin ISA --
GO:0005634 nucleus IEA,NAS 7590749
GO:0005654 nucleoplasm IDA --
GO:0030054 cell junction IDA --
genes like me logo Genes that share ontologies with NFIA: view

Pathways & Interactions for NFIA Gene

genes like me logo Genes that share pathways with NFIA: view

SIGNOR curated interactions for NFIA Gene

Is activated by:

Gene Ontology (GO) - Biological Process for NFIA Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006260 DNA replication IEA --
GO:0006355 regulation of transcription, DNA-templated IEA,NAS 7590749
GO:0006357 regulation of transcription by RNA polymerase II IBA 21873635
GO:0019079 viral genome replication NAS 7590749
GO:0045944 positive regulation of transcription by RNA polymerase II IDA 17010934
genes like me logo Genes that share ontologies with NFIA: view

Drugs & Compounds for NFIA Gene

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(1) Additional Compounds for NFIA Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with NFIA: view

Transcripts for NFIA Gene

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mRNA/cDNA for NFIA Gene

4 REFSEQ mRNAs :
18 NCBI additional mRNA sequence :
22 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for NFIA

Clone products for research

  • Addgene plasmids for NFIA

Alternative Splicing Database (ASD) splice patterns (SP) for NFIA Gene

ExUns: 1 ^ 2a · 2b ^ 3 ^ 4a · 4b ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10a · 10b ^ 11 ^ 12 ^ 13
SP1: - -
SP2: - - -
SP3:
SP4: -
SP5:

Relevant External Links for NFIA Gene

GeneLoc Exon Structure for
NFIA

Expression for NFIA Gene

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  1. Primer products for research
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mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for NFIA Gene

mRNA expression in normal human tissues for NFIA Gene
mRNA expression by BioGPS for NFIA GenemRNA expression by GTEx for NFIA Gene

Protein differential expression in normal tissues from HIPED for NFIA Gene

This gene is overexpressed in Fetal gut (14.9), Fetal testis (10.9), and Pancreas (6.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for NFIA Gene



Protein tissue co-expression partners for NFIA Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for NFIA

SOURCE GeneReport for Unigene cluster for NFIA Gene:

Hs.744898

Evidence on tissue expression from TISSUES for NFIA Gene

  • Nervous system(4.9)
  • Liver(4.5)
  • Muscle(4.5)
  • Heart(2.6)
  • Lung(2.5)
  • Spleen(2.3)
  • Kidney(2.3)
  • Thyroid gland(2.2)
  • Blood(2.2)
  • Bone marrow(2.1)
  • Skin(2.1)

Phenotype-based relationships between genes and organs from Gene ORGANizer for NFIA Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • integumentary
  • nervous
  • skeletal muscle
  • skeleton
  • urinary
Regions:
Head and neck:
  • brain
  • chin
  • ear
  • face
  • forehead
  • head
  • lip
  • mouth
  • nose
  • outer ear
  • skull
Abdomen:
  • abdominal wall
  • intestine
  • kidney
Pelvis:
  • ureter
  • urinary bladder
General:
  • blood
  • blood vessel
  • skin
  • spinal cord
genes like me logo Genes that share expression patterns with NFIA: view

Primer products for research

No data available for mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for NFIA Gene

Orthologs for NFIA Gene

This gene was present in the common ancestor of animals.

Orthologs for NFIA Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia NFIA 30 31
  • 99.88 (n)
 OneToOne
Cow
(Bos Taurus)
 Mammalia NFIA 30 31
  • 96.25 (n)
 OneToOne
Dog
(Canis familiaris)
 Mammalia NFIA 30 31
  • 96.22 (n)
 OneToOne
Platypus
(Ornithorhynchus anatinus)
 Mammalia NFIA 31
  • 96 (a)
 OneToOne
Mouse
(Mus musculus)
 Mammalia Nfia 30 17 31
  • 94.04 (n)
 OneToOne
Oppossum
(Monodelphis domestica)
 Mammalia NFIA 31
  • 94 (a)
 OneToOne
Rat
(Rattus norvegicus)
 Mammalia Nfia 30
  • 93.32 (n)
Chicken
(Gallus gallus)
 Aves NFIA 30
  • 91.55 (n)
CNFI-A4 31
  • 80 (a)
 OneToOne
Lizard
(Anolis carolinensis)
 Reptilia -- 31
  • 97 (a)
 OneToMany
-- 31
  • 95 (a)
 OneToMany
Tropical Clawed Frog
(Silurana tropicalis)
 Amphibia nfia 30
  • 88.54 (n)
Zebrafish
(Danio rerio)
 Actinopterygii nfia 30 31
  • 78.1 (n)
 OneToOne
Dr.15268 30
Fruit Fly
(Drosophila melanogaster)
 Insecta CG2380 32
  • 44 (a)
NfI 31
  • 30 (a)
 OneToMany
Worm
(Caenorhabditis elegans)
 Secernentea nfi-1 31
  • 22 (a)
 OneToMany
Sea Squirt
(Ciona savignyi)
 Ascidiacea -- 31
  • 39 (a)
 OneToMany
Species where no ortholog for NFIA was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for NFIA Gene

ENSEMBL:
Gene Tree for NFIA (if available)
TreeFam:
Gene Tree for NFIA (if available)
Aminode:
Evolutionary constrained regions (ECRs) for NFIA: view image

Paralogs for NFIA Gene

Paralogs for NFIA Gene

(7) SIMAP similar genes for NFIA Gene using alignment to 10 proteins:

  • NFIA_HUMAN
  • B1AKN5_HUMAN
  • B1AKN6_HUMAN
  • B1AKN7_HUMAN
  • B1AKN8_HUMAN
  • S4R308_HUMAN
  • S4R3K4_HUMAN
  • S4R3K5_HUMAN
  • S4R3W2_HUMAN
  • S4R3W6_HUMAN

Pseudogenes.org Pseudogenes for NFIA Gene

genes like me logo Genes that share paralogs with NFIA: view

Variants for NFIA Gene

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Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for NFIA Gene

SNP ID Clinical significance and condition Chr 01 pos Variation AA Info Type
916098 Likely Pathogenic: not provided 61,088,227(+) C/TGAACCTGTATTGA
NM_001134673.4(NFIA):c.106delinsTGAACCTGTATTGAAGTATTT (p.Arg36Ter) 		NONSENSE
931857 Likely Pathogenic: Brain malformations and urinary tract defects 61,404,256(+) C/T
NM_001134673.4(NFIA):c.1228C>T (p.Gln410Ter) 		NONSENSE
976669 Pathogenic: Brain malformations and urinary tract defects 61,088,147(+) A/G
NM_001134673.4(NFIA):c.28-2A>G 		SPLICE_ACCEPTOR
985113 Pathogenic: Inborn genetic diseases 61,088,493(+) TAA/T
NM_001134673.4(NFIA):c.374_375del (p.Lys125fs) 		FRAMESHIFT
986014 Uncertain Significance: Inborn genetic diseases 61,088,681(+) G/T
NM_001134673.4(NFIA):c.559+1G>T 		SPLICE_DONOR

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for NFIA Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for NFIA Gene

Variant ID Type Subtype PubMed ID
dgv296n54 CNV gain 21841781
esv25296 CNV loss 19812545
esv2678784 CNV deletion 23128226
esv2748941 CNV deletion 23290073
esv275289 CNV gain+loss 21479260
esv3310487 CNV novel sequence insertion 20981092
esv3339821 CNV insertion 20981092
esv3352599 CNV duplication 20981092
esv3382326 CNV insertion 20981092
esv3577891 CNV loss 25503493
esv3586213 CNV loss 21293372
nsv1008634 CNV loss 25217958
nsv1010797 CNV gain 25217958
nsv1012657 CNV gain 25217958
nsv1065 CNV insertion 18451855
nsv1077 CNV insertion 18451855
nsv1077873 CNV deletion 25765185
nsv1112535 CNV deletion 24896259
nsv1133858 CNV deletion 24896259
nsv473789 CNV novel sequence insertion 20440878
nsv479652 CNV novel sequence insertion 20440878
nsv480302 CNV novel sequence insertion 20440878
nsv481479 CNV novel sequence insertion 20440878
nsv512741 CNV insertion 21212237

Variation tolerance for NFIA Gene

Residual Variation Intolerance Score: 17.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.47; 10.25% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for NFIA Gene

Human Gene Mutation Database (HGMD)
NFIA
SNPedia medical, phenotypic, and genealogical associations of SNPs for
NFIA

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for NFIA Gene

Disorders for NFIA Gene

MalaCards: The human disease database

(6) MalaCards diseases for NFIA Gene - From: OMI, CVR, ORP, COP, and GCD

Disorder Aliases PubMed IDs
brain malformations with or without urinary tract defects
  • brmutd
cleft palate, isolated
  • cpi
hydrocephalus
  • hydrocephalus, nonsyndromic, autosomal recessive
marshall-smith syndrome
  • mrshss
acute promyelocytic leukemia
  • apl
- elite association - COSMIC cancer census association via MalaCards
Search NFIA in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

NFIA_HUMAN
  • Brain malformations with or without urinary tract defects (BRMUTD) [MIM:613735]: A syndrome characterized by corpus callosum hypoplasia or agenesis, hydrocephalus or ventricular enlargement, developmental delay, and urinary tract defects. {ECO:0000269 PubMed:24462883, ECO:0000269 PubMed:27081522}. Note=The disease is caused by variants affecting the gene represented in this entry.

Additional Disease Information for NFIA

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with NFIA: view

No data available for Genatlas for NFIA Gene

Publications for NFIA Gene

  1. Chromosomal localization of the four genes (NFIA, B, C, and X) for the human transcription factor nuclear factor I by FISH. (PMID: 7590749) Qian F … Sippel AE (Genomics 1995) 2 3 4 23
  2. Truncating mutation in NFIA causes brain malformation and urinary tract defects. (PMID: 27081522) Negishi Y … Saitoh S (Human genome variation 2015) 3 4 74
  3. An intragenic deletion of the NFIA gene in a patient with a hypoplastic corpus callosum, craniofacial abnormalities and urinary tract defects. (PMID: 24462883) Rao A … Goel H (European journal of medical genetics 2014) 3 4
  4. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 41
  5. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PMID: 20628086) Bailey SD … DREAM investigators (Diabetes care 2010) 3 41

ExternalLinks

View latest publications for NFIA gene in Mastermind

Products for NFIA Gene

  • Addgene plasmids for NFIA

Sources for NFIA Gene