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Aliases for NFIX Gene

Aliases for NFIX Gene

  • Nuclear Factor I X 2 3 5
  • CCAAT-Box-Binding Transcription Factor 3 4
  • Nuclear Factor 1 X-Type 3 4
  • TGGCA-Binding Protein 3 4
  • Nuclear Factor 1/X 3 4
  • NF-I/X 3 4
  • NF1-X 3 4
  • CTF 3 4
  • Nuclear Factor I/X (CCAAT-Binding Transcription Factor) 2
  • CCAAT-Binding Transcription Factor 2
  • Nuclear Factor I/X 4
  • MRSHSS 3
  • SOTOS2 3
  • NFI-X 4
  • NF1A 3

External Ids for NFIX Gene

Previous GeneCards Identifiers for NFIX Gene

  • GC19P013468
  • GC19P012951
  • GC19P012967
  • GC19P013106
  • GC19P012710

Summaries for NFIX Gene

Entrez Gene Summary for NFIX Gene

  • The protein encoded by this gene is a transcription factor that binds the palindromic sequence 5'-TTGGCNNNNNGCCAA-3 in viral and cellular promoters. The encoded protein can also stimulate adenovirus replication in vitro. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2012]

GeneCards Summary for NFIX Gene

NFIX (Nuclear Factor I X) is a Protein Coding gene. Diseases associated with NFIX include Sotos Syndrome 2 and Marshall-Smith Syndrome. Among its related pathways are RNA Polymerase III Transcription Initiation and Oxidative Stress. Gene Ontology (GO) annotations related to this gene include DNA-binding transcription factor activity and transcription factor activity, RNA polymerase II distal enhancer sequence-specific binding. An important paralog of this gene is NFIA.

UniProtKB/Swiss-Prot for NFIX 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 NFIX Gene

Additional gene information for NFIX Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for NFIX Gene

Genomics for NFIX Gene

GeneHancer (GH) Regulatory Elements for NFIX Gene

Promoters and enhancers for NFIX 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
GH19J013011 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 616.3 +24.6 24587 17.2 ZNF473 ZNF652 SP1 ZFX CC2D1A ELF3 ZNF148 MLLT1 CEBPG RERE NFIX ZNF709 TRMT1 ZNF136 CCDC130 ZNF44 ZNF564 ZNF625 ZNF791 WDR83OS
GH19J012994 Promoter/Enhancer 1.7 Ensembl ENCODE dbSUPER 600.7 +1.2 1231 4.5 ZFX ELF3 ZNF148 MLLT1 GTF2F1 CDC5L MCM2 NCOA6 SP7 SP5 GC19M012993 NFIX ZNF20 RNASEH2A DCAF15 TRMT1 ZNF136 ZNF44 ENSG00000213293 ZNF799
GH19J012969 Promoter/Enhancer 1.1 EPDnew Ensembl 600.3 -26.0 -26007 0.8 PRDM10 ZIC2 EGR1 NCOR1 RCOR1 GLIS1 EGR2 CBFA2T3 DAND5 NFIX
GH19J013030 Promoter/Enhancer 2 FANTOM5 Ensembl ENCODE dbSUPER 13.1 +38.8 38818 8.2 CC2D1A CTCF CEBPG ZSCAN21 AHR TFE3 SP7 PPARG KLF14 PRDM1 TRMT1 ZNF844 ZNF791 ZNF442 ZNF136 ZNF625 RPS6P25 MRI1 STX10 ZNF433
GH19J013042 Enhancer 1.4 FANTOM5 Ensembl ENCODE dbSUPER 12 +48.8 48793 4 ZNF148 SP7 ZNF600 ZIC2 GATAD2A ZEB2 PATZ1 ZNF692 ZNF561 SCRT2 TRMT1 ZNF20 ZNF490 LYL1 NACC1 RNASEH2A NFIX DAND5 GADD45GIP1 DCAF15
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around NFIX on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the NFIX gene promoter:
  • AP-1
  • ATF-2
  • c-Fos
  • c-Jun
  • E47
  • Meis-1
  • Meis-1b
  • Pbx1a

Genomic Locations for NFIX Gene

Genomic Locations for NFIX Gene
chr19:12,995,608-13,098,796
(GRCh38/hg38)
Size:
103,189 bases
Orientation:
Plus strand
chr19:13,106,422-13,209,610
(GRCh37/hg19)
Size:
103,189 bases
Orientation:
Plus strand

Genomic View for NFIX Gene

Genes around NFIX on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for NFIX Gene

Proteins for NFIX Gene

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

    Protein Symbol:
    Q14938-NFIX_HUMAN
    Recommended name:
    Nuclear factor 1 X-type
    Protein Accession:
    Q14938
    Secondary Accessions:
    • B4DM25
    • O60413
    • Q0VG09
    • Q12859
    • Q13050
    • Q13052
    • Q5U094
    • Q9UPH1
    • Q9Y6R8

    Protein attributes for NFIX Gene

    Size:
    502 amino acids
    Molecular mass:
    55098 Da
    Quaternary structure:
    • Binds DNA as a homodimer.

    Alternative splice isoforms for NFIX Gene

neXtProt entry for NFIX Gene

Post-translational modifications for NFIX Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for NFIX Gene

Domains & Families for NFIX Gene

Gene Families for NFIX Gene

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

Suggested Antigen Peptide Sequences for NFIX Gene

GenScript: Design optimal peptide antigens:
  • Nuclear factor 1 (C9JSM5_HUMAN)
  • Nuclear factor 1 (C9JWJ8_HUMAN)
  • TGGCA-binding protein (NFIX_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q14938

UniProtKB/Swiss-Prot:

NFIX_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 NFIX: view

Function for NFIX Gene

Molecular function for NFIX 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 X,DNA binding protein

Phenotypes From GWAS Catalog for NFIX Gene

Gene Ontology (GO) - Molecular Function for NFIX Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific TAS,NAS 19274049
GO:0003677 DNA binding IEA --
GO:0003700 DNA-binding transcription factor activity TAS,IEA 7590749
GO:0005515 protein binding IPI 25416956
genes like me logo Genes that share ontologies with NFIX: view
genes like me logo Genes that share phenotypes with NFIX: view

Human Phenotype Ontology for NFIX Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for NFIX Gene

MGI Knock Outs for NFIX:

Animal Model Products

CRISPR Products

miRNA for NFIX Gene

miRTarBase miRNAs that target NFIX

Inhibitory RNA Products

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

Clone Products

  • Applied Biological Materials (abm): Clones for NFIX - Now 50% OFF >
  • * NFIX as ready-to-use vector or virus: ORF | Lenti- | Retro- | Adeno- | AAV- | Protein Vector - Browse All
  • * NFIX tags and reporters available: His, HA, Myc, Flag, GFP, RFP, Luciferase - Browse All

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

Localization for NFIX Gene

Subcellular locations from UniProtKB/Swiss-Prot for NFIX 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 NFIX gene
Compartment Confidence
nucleus 5

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for NFIX Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005622 intracellular IEA --
GO:0005634 nucleus IBA,IEA 21873635
GO:0005654 nucleoplasm IDA --
genes like me logo Genes that share ontologies with NFIX: view

Pathways & Interactions for NFIX Gene

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

SIGNOR curated interactions for NFIX Gene

Is activated by:
Is inactivated by:

Gene Ontology (GO) - Biological Process for NFIX Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription by RNA polymerase II IDA 19706729
GO:0006260 DNA replication IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006366 transcription by RNA polymerase II TAS 7937100
GO:0045944 positive regulation of transcription by RNA polymerase II IDA 19706729
genes like me logo Genes that share ontologies with NFIX: view

Drugs & Compounds for NFIX Gene

No Compound Related Data Available

Transcripts for NFIX Gene

Unigene Clusters for NFIX Gene

Nuclear factor I/X (CCAAT-binding transcription factor):
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

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

Clone Products

  • Applied Biological Materials (abm): Clones for NFIX - Now 50% OFF >
  • * NFIX as ready-to-use vector or virus: ORF | Lenti- | Retro- | Adeno- | AAV- | Protein Vector - Browse All
  • * NFIX tags and reporters available: His, HA, Myc, Flag, GFP, RFP, Luciferase - Browse All

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

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

Relevant External Links for NFIX Gene

GeneLoc Exon Structure for
NFIX
ECgene alternative splicing isoforms for
NFIX

Expression for NFIX Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for NFIX Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for NFIX Gene

This gene is overexpressed in Ovary (19.4), Fetal Brain (10.6), Fetal testis (10.3), and Serum (7.8).

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



Protein tissue co-expression partners for NFIX Gene

NURSA nuclear receptor signaling pathways regulating expression of NFIX Gene:

NFIX

SOURCE GeneReport for Unigene cluster for NFIX Gene:

Hs.257970

mRNA Expression by UniProt/SwissProt for NFIX Gene:

Q14938-NFIX_HUMAN
Tissue specificity: Widely expressed.

Evidence on tissue expression from TISSUES for NFIX Gene

  • Nervous system(4.8)
  • Liver(4.3)
  • Muscle(2.9)
  • Lung(2)

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

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • integumentary
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
Regions:
Head and neck:
  • brain
  • cheek
  • chin
  • ear
  • epiglottis
  • eye
  • eyelid
  • face
  • forehead
  • head
  • jaw
  • larynx
  • lip
  • mandible
  • maxilla
  • middle ear
  • mouth
  • neck
  • nose
  • outer ear
  • pharynx
  • skull
  • tongue
  • tooth
  • vocal cord
Thorax:
  • bronchus
  • chest wall
  • clavicle
  • heart
  • heart valve
  • lung
  • rib
  • rib cage
  • scapula
  • sternum
  • trachea
Abdomen:
  • abdominal wall
  • intestine
  • large intestine
  • liver
  • small intestine
Pelvis:
  • pelvis
Limb:
  • ankle
  • arm
  • digit
  • elbow
  • femur
  • fibula
  • finger
  • foot
  • forearm
  • hand
  • hip
  • humerus
  • knee
  • lower limb
  • radius
  • shin
  • shoulder
  • thigh
  • tibia
  • toe
  • ulna
  • upper limb
  • wrist
General:
  • blood
  • blood vessel
  • hair
  • skin
  • spinal column
  • vertebrae
genes like me logo Genes that share expression patterns with NFIX: view

No data available for mRNA differential expression in normal tissues for NFIX Gene

Orthologs for NFIX Gene

This gene was present in the common ancestor of animals.

Orthologs for NFIX Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia NFIX 35 34
  • 97.83 (n)
OneToOne
dog
(Canis familiaris)
Mammalia NFIX 35 34
  • 97.71 (n)
OneToOne
cow
(Bos Taurus)
Mammalia NFIX 35 34
  • 97.52 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Nfix 17 35 34
  • 95.4 (n)
rat
(Rattus norvegicus)
Mammalia Nfix 34
  • 94.78 (n)
oppossum
(Monodelphis domestica)
Mammalia NFIX 35
  • 91 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia NFIX 35
  • 80 (a)
OneToOne
chicken
(Gallus gallus)
Aves NFIX 34
  • 78.7 (n)
lizard
(Anolis carolinensis)
Reptilia NFIX 35
  • 81 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia nfix 34
  • 79.41 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.1096 34
zebrafish
(Danio rerio)
Actinopterygii nfixa 35 34
  • 78.4 (n)
OneToMany
nfixb 35
  • 67 (a)
OneToMany
Dr.12642 34
fruit fly
(Drosophila melanogaster)
Insecta CG2380 36
  • 46 (a)
NfI 35
  • 25 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea nfi-1 35 36
  • 18 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 36 (a)
OneToMany
Species where no ortholog for NFIX was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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 NFIX Gene

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

Paralogs for NFIX Gene

Paralogs for NFIX Gene

(6) SIMAP similar genes for NFIX Gene using alignment to 8 proteins:

  • NFIX_HUMAN
  • C9JWJ8_HUMAN
  • K7EJB0_HUMAN
  • K7EKH0_HUMAN
  • K7EMQ5_HUMAN
  • K7EN08_HUMAN
  • K7EPU2_HUMAN
  • K7ESG9_HUMAN
genes like me logo Genes that share paralogs with NFIX: view

Variants for NFIX Gene

Sequence variations from dbSNP and Humsavar for NFIX Gene

SNP ID Clin Chr 19 pos Variation AA Info Type
rs1135401802 pathogenic, Sotos syndrome 2 13,025,066(+) G/ coding_sequence_variant, frameshift
rs1555696597 likely-pathogenic, Sotos syndrome 2 13,025,330(+) A/G coding_sequence_variant, missense_variant
rs1555696603 likely-pathogenic, Marshall-Smith syndrome 13,025,339(+) C/T coding_sequence_variant, missense_variant
rs1555696606 likely-pathogenic, Marshall-Smith syndrome 13,025,341(+) G/A coding_sequence_variant, synonymous_variant
rs1555696611 pathogenic, Marshall-Smith syndrome, Sotos syndrome 2 13,025,350(+) CC/C coding_sequence_variant, frameshift

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

Variant ID Type Subtype PubMed ID
esv275430 CNV gain+loss 21479260
nsv1055900 CNV gain 25217958
nsv1071912 CNV deletion 25765185
nsv1133444 CNV deletion 24896259
nsv2422 CNV insertion 18451855
nsv474735 CNV novel sequence insertion 20440878
nsv578635 CNV loss 21841781
nsv828444 CNV loss 20364138
nsv828445 CNV gain 20364138
nsv828446 CNV loss 20364138
nsv828447 CNV gain 20364138
nsv833754 CNV loss 17160897
nsv953977 CNV deletion 24416366
nsv953978 CNV deletion 24416366

Variation tolerance for NFIX Gene

Residual Variation Intolerance Score: 13.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.04; 0.85% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for NFIX Gene

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

SNP Genotyping and Copy Number Assay Products

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

Disorders for NFIX Gene

MalaCards: The human disease database

(5) MalaCards diseases for NFIX Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
sotos syndrome 2
  • sotos2
marshall-smith syndrome
  • mss
chromosome 19p13.13 deletion syndrome
  • chromosome 19p13.13 duplication syndrome
sotos syndrome 1
  • sotos1
scoliosis
- elite association - COSMIC cancer census association via MalaCards
Search NFIX in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

NFIX_HUMAN
  • Sotos syndrome 2 (SOTOS2) [MIM:614753]: A form of Sotos syndrome, a childhood overgrowth syndrome characterized by prenatal and postnatal overgrowth, developmental delay, mental retardation, advanced bone age, and abnormal craniofacial morphology. SOTOS2 patients have macrocephaly, long narrow face, high forehead, slender habitus, scoliosis, and unusual behavior characterized especially by anxiety. {ECO:0000269 PubMed:20673863, ECO:0000269 PubMed:22301465, ECO:0000269 PubMed:26193383, ECO:0000269 PubMed:26200704}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Marshall-Smith syndrome (MRSHSS) [MIM:602535]: A distinct malformation syndrome characterized by accelerated skeletal maturation, relative failure to thrive, respiratory difficulties, mental retardation, and unusual facies, including prominent forehead, shallow orbits, blue sclerae, depressed nasal bridge, and micrognathia. Additional skeletal findings include long and thin tubular bones, broad middle phalanges with relatively narrow distal phalanges, and scoliosis. {ECO:0000269 PubMed:20673863, ECO:0000269 PubMed:26200704}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for NFIX

genes like me logo Genes that share disorders with NFIX: view

No data available for Genatlas for NFIX Gene

Publications for NFIX 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 58
  2. Cloning and functional analysis of spliced isoforms of human nuclear factor I-X: interference with transcriptional activation by NFI/CTF in a cell-type specific manner. (PMID: 7937100) Apt D … Bernard HU (Nucleic acids research 1994) 3 4 23 58
  3. Localisation of the human nuclear factor I/X (NFI/X) gene to chromosome 19p13 and detection of five other related loci at 1p21-22, 1q42-43, 5q15, 11p13 and 20q13 by FISH. (PMID: 8340106) Seisenberger C … Scherthan H (Human genetics 1993) 2 3 23 58
  4. Novel mutations of NFIX gene causing Marshall-Smith syndrome or Sotos-like syndrome: one gene, two phenotypes. (PMID: 26200704) Martinez F … Orellana C (Pediatric research 2015) 3 4 58
  5. Missense mutations in the DNA-binding/dimerization domain of NFIX cause Sotos-like features. (PMID: 22301465) Yoneda Y … Matsumoto N (Journal of human genetics 2012) 3 4 58

Products for NFIX Gene

Sources for NFIX Gene

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