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Aliases for NFIA Gene

Aliases for NFIA Gene

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

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 Chromosome 1P32-P31 Deletion Syndrome. Among its related pathways are RNA Polymerase III Transcription Initiation and Gene Expression. 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 NFIB.

UniProtKB/Swiss-Prot 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 , fRNAdb sequence ontologies and piRNA Summary for NFIA Gene

Genomics for NFIA Gene

GeneHancer (GH) Regulatory Elements for NFIA Gene

Promoters and enhancers for NFIA Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH01I061076 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 558.6 +215.7 215725 9.9 FEZF1 DMAP1 YY1 ZNF213 E2F8 ZNF143 SP3 NFYC MEF2D ZNF610 NFIA ENSG00000271200 NFIA-AS1 GC01P061084 GC01P061077
GH01I060865 Enhancer 1.2 Ensembl ENCODE dbSUPER 550.8 +1.8 1787 2.5 INSM2 ZNF76 FEZF1 ZEB1 ZNF335 ZNF366 ZSCAN5C ZNF362 RXRA OVOL3 LOC101926964 NFIA NFIA-AS2
GH01I060866 Enhancer 0.8 UCNEbase dbSUPER 550.8 +0.1 71 0.3 POLR2A RCOR1 CHD2 NFIA LOC101926964
GH01I061048 Promoter/Enhancer 2.3 FANTOM5 Ensembl ENCODE dbSUPER 7.8 +188.5 188521 9.6 CLOCK FEZF1 DMAP1 YY1 ZNF213 ZNF143 SP3 MEF2D SSRP1 GLIS1 NFIA-AS2 NFIA-AS1 TM2D1 NFIA GC01P061077 GC01P060986
GH01I060893 Enhancer 1.2 UCNEbase ENCODE dbSUPER 11.7 +30.1 30132 4.6 TAL1 CBFA2T3 ZNF148 FOSL1 EGR1 VEZF1 NR2C1 CUX1 RCOR1 NR2C2 NFIA NFIA-AS2 RNU6-1177P LOC105378764 LOC101926964
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around NFIA on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the NFIA gene promoter:

Genomic Locations for NFIA Gene

Genomic Locations for NFIA Gene
chr1:60,865,259-61,462,793
(GRCh38/hg38)
Size:
597,535 bases
Orientation:
Plus strand
chr1:61,330,931-61,928,465
(GRCh37/hg19)

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 StructureGene Density

RefSeq DNA sequence for NFIA Gene

Proteins for NFIA Gene

  • 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=Translation N-terminally shortened.; Evidence={ECO:0000305};

    Alternative splice isoforms for NFIA Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for NFIA Gene

Post-translational modifications for NFIA Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for NFIA Gene

Domains & Families for NFIA Gene

Gene Families for NFIA Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Transcription factors

Graphical View of Domain Structure for InterPro Entry

Q12857

UniProtKB/Swiss-Prot:

NFIA_HUMAN :
  • Belongs to the CTF/NF-I family.
Family:
  • Belongs to the CTF/NF-I family.
genes like me logo Genes that share domains with NFIA: view

Function for NFIA Gene

Molecular function for NFIA Gene

GENATLAS Biochemistry:
nuclear transcription factor I A,DNA binding protein
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.

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:0001077 transcriptional activator activity, RNA polymerase II proximal promoter sequence-specific DNA binding IDA 17010934
GO:0003677 DNA binding IEA --
GO:0003682 chromatin binding IEA --
GO:0003700 DNA binding transcription factor activity NAS,IEA 7590749
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 Model Products

Clone Products

  • 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

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

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for NFIA Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005622 intracellular IEA --
GO:0005634 nucleus NAS,IEA 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

Gene Ontology (GO) - Biological Process for NFIA Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription by RNA polymerase II IBA --
GO:0006260 DNA replication IEA --
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated NAS,IEA 7590749
GO:0006366 transcription by RNA polymerase II IEA --
genes like me logo Genes that share ontologies with NFIA: view

No data available for SIGNOR curated interactions for NFIA Gene

Drugs & Compounds for NFIA Gene

(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

Unigene Clusters for NFIA Gene

Nuclear factor I/A:
Representative Sequences:

Clone Products

  • 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
ECgene alternative splicing isoforms for
NFIA

Expression for NFIA Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE 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, PaxDb, MaxQB, and MOPED for NFIA Gene



Protein tissue co-expression partners for NFIA Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of NFIA Gene:

NFIA

SOURCE GeneReport for Unigene cluster for NFIA Gene:

Hs.744898

Evidence on tissue expression from TISSUES for NFIA Gene

  • Nervous system(4.8)
  • Liver(4.4)
  • Muscle(4.3)
  • Lung(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

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 33 34
  • 99.88 (n)
cow
(Bos Taurus)
Mammalia NFIA 33 34
  • 96.25 (n)
dog
(Canis familiaris)
Mammalia NFIA 33 34
  • 96.22 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia NFIA 34
  • 96 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Nfia 33 16 34
  • 94.04 (n)
oppossum
(Monodelphis domestica)
Mammalia NFIA 34
  • 94 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Nfia 33
  • 93.32 (n)
chicken
(Gallus gallus)
Aves NFIA 33
  • 91.55 (n)
CNFI-A4 34
  • 80 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia -- 34
  • 97 (a)
OneToMany
-- 34
  • 95 (a)
OneToMany
tropical clawed frog
(Silurana tropicalis)
Amphibia nfia 33
  • 88.54 (n)
zebrafish
(Danio rerio)
Actinopterygii nfia 33 34
  • 78.1 (n)
Dr.15268 33
fruit fly
(Drosophila melanogaster)
Insecta CG2380 35
  • 44 (a)
NfI 34
  • 30 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea nfi-1 34
  • 22 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 39 (a)
OneToMany
Species where no ortholog for NFIA was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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 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)

Paralogs for NFIA Gene

Paralogs for NFIA Gene

Pseudogenes.org Pseudogenes for NFIA Gene

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

Variants for NFIA Gene

Sequence variations from dbSNP and Humsavar for NFIA Gene

SNP ID Clin Chr 01 pos Variation AA Info Type
rs1057518992 likely-pathogenic, Cleft palate, Macrocephaly 61,359,232(+) GG/G coding_sequence_variant, frameshift
rs1060505054 pathogenic, Brain malformations and urinary tract defects 61,404,121(+) CC/C coding_sequence_variant, frameshift
rs886039429 pathogenic, not provided 61,088,482(+) C/T coding_sequence_variant, genic_upstream_transcript_variant, missense_variant
rs1064794841 likely-pathogenic, not provided 61,088,191(+) C/T coding_sequence_variant, genic_upstream_transcript_variant, stop_gained
rs1064796492 likely-pathogenic, not provided 61,088,429(+) G/C coding_sequence_variant, genic_upstream_transcript_variant, missense_variant

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 Assay Products

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

Disorders for NFIA Gene

MalaCards: The human disease database

(4) MalaCards diseases for NFIA Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
brain malformations with or without urinary tract defects
  • brmutd
chromosome 1p32-p31 deletion syndrome
  • 1p31p32 microdeletion syndrome
hydrocephalus
  • hydrocephalus, nonsyndromic, autosomal recessive 1
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 and 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 mutations affecting the gene represented in this entry.

Additional Disease Information for NFIA

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
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 22 58
  2. Truncating mutation in NFIA causes brain malformation and urinary tract defects. (PMID: 27081522) Negishi Y … Saitoh S (Human genome variation 2015) 3 4 58
  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 58
  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 44 58
  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 44 58

Products for NFIA Gene

  • Addgene plasmids for NFIA

Sources for NFIA Gene

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