Human Gene NFIA (uc001czw.3) Description and Page Index
  Description: Homo sapiens nuclear factor I/A (NFIA), transcript variant 1, mRNA.
RefSeq Summary (NM_001134673): 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].
Transcript (Including UTRs)
   Position: hg19 chr1:61,547,980-61,928,460 Size: 380,481 Total Exon Count: 11 Strand: +
Coding Region
   Position: hg19 chr1:61,548,464-61,920,992 Size: 372,529 Coding Exon Count: 11 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsOther NamesGeneReviewsModel InformationMethods
Data last updated: 2013-06-15

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:61,547,980-61,928,460)mRNA (may differ from genome)Protein (509 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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OMIMPubMedReactomeStanford SOURCEUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: NFIA_HUMAN
DESCRIPTION: RecName: Full=Nuclear factor 1 A-type; Short=NF1-A; Short=Nuclear factor 1/A; AltName: Full=CCAAT-box-binding transcription factor; Short=CTF; AltName: Full=Nuclear factor I/A; Short=NF-I/A; Short=NFI-A; AltName: Full=TGGCA-binding protein;
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.
SUBUNIT: Binds DNA as a homodimer.
SUBCELLULAR LOCATION: Nucleus.
PTM: Phosphorylated upon DNA damage, probably by ATM or ATR.
SIMILARITY: Belongs to the CTF/NF-I family.
SIMILARITY: Contains 1 CTF/NF-I DNA-binding domain.
SEQUENCE CAUTION: Sequence=BAA92677.1; Type=Erroneous initiation;

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): NFIA
CDC HuGE Published Literature: NFIA
Positive Disease Associations: Body Height , Body Mass Index , Body Weight , Celiac disease , Echocardiography , Heart Function Tests , Heart Rate , Natriuretic Peptide, Brain , Stroke
Related Studies:
  1. Body Height
    , , . [PubMed 0]
  2. Body Mass Index
    , , . [PubMed 0]
  3. Body Mass Index
    , , . [PubMed 0]
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: NFIA
Diseases sorted by gene-association score: brain malformations and urinary tract defects* (944), chromosome 1p32-p31 deletion syndrome (18), hydrocephalus (7), leukemia, acute promyelocytic, somatic (2)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 17.55 RPKM in Brain - Cerebellar Hemisphere
Total median expression: 339.02 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -208.70484-0.431 Picture PostScript Text
3' UTR -1975.177468-0.264 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR000647 - CTF/NFI
IPR020604 - CTF/NFI_DNA-bd-dom
IPR019739 - CTF/NFI_DNA-bd_CS
IPR019548 - CTF/NFI_DNA-bd_N
IPR003619 - MAD_homology1_Dwarfin-type

Pfam Domains:
PF00859 - CTF/NF-I family transcription modulation region
PF03165 - MH1 domain
PF10524 - Nuclear factor I protein pre-N-terminus

ModBase Predicted Comparative 3D Structure on Q12857
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserGenome BrowserNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGDEnsembl   
 Protein SequenceProtein Sequence   
 AlignmentAlignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000978 RNA polymerase II core promoter proximal region sequence-specific DNA binding
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0001077 transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding
GO:0003677 DNA binding
GO:0003682 chromatin binding
GO:0003700 transcription factor activity, sequence-specific DNA binding
GO:0005515 protein binding
GO:0008134 transcription factor binding

Biological Process:
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0006260 DNA replication
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006366 transcription from RNA polymerase II promoter
GO:0019079 viral genome replication
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0060074 synapse maturation
GO:0072189 ureter development

Cellular Component:
GO:0005622 intracellular
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0030054 cell junction


-  Descriptions from all associated GenBank mRNAs
  AK299289 - Homo sapiens cDNA FLJ59397 complete cds, highly similar to Nuclear factor 1 A-type.
AK299579 - Homo sapiens cDNA FLJ59746 complete cds, highly similar to Nuclear factor 1 A-type.
AB037860 - Homo sapiens KIAA1439 mRNA for KIAA1439 protein.
AK299356 - Homo sapiens cDNA FLJ61358 complete cds, highly similar to Nuclear factor 1 A-type.
BC022264 - Homo sapiens nuclear factor I/A, mRNA (cDNA clone MGC:22317 IMAGE:4270934), complete cds.
AB384210 - Synthetic construct DNA, clone: pF1KSDA1439, Homo sapiens NFIA gene for nuclear factor 1 A-type, complete cds, without stop codon, in Flexi system.
DQ893250 - Synthetic construct clone IMAGE:100005880; FLH195620.01X; RZPDo839E05152D nuclear factor I/A (NFIA) gene, encodes complete protein.
DQ896579 - Synthetic construct Homo sapiens clone IMAGE:100011039; FLH195616.01L; RZPDo839E05151D nuclear factor I/A (NFIA) gene, encodes complete protein.
KJ905238 - Synthetic construct Homo sapiens clone ccsbBroadEn_14712 NFIA gene, encodes complete protein.
CU692518 - Synthetic construct Homo sapiens gateway clone IMAGE:100022319 5' read NFIA mRNA.
U07809 - Human nuclear factor 1 A-type mRNA, partial cds.
JD104032 - Sequence 85056 from Patent EP1572962.
JD451862 - Sequence 432886 from Patent EP1572962.
JD514513 - Sequence 495537 from Patent EP1572962.
JD501231 - Sequence 482255 from Patent EP1572962.
JD555623 - Sequence 536647 from Patent EP1572962.
JD167054 - Sequence 148078 from Patent EP1572962.
JD379329 - Sequence 360353 from Patent EP1572962.
JD461547 - Sequence 442571 from Patent EP1572962.
BX648791 - Homo sapiens mRNA; cDNA DKFZp686E23184 (from clone DKFZp686E23184).
AK024964 - Homo sapiens cDNA: FLJ21311 fis, clone COL02167.
AL133665 - Homo sapiens mRNA; cDNA DKFZp434L0422 (from clone DKFZp434L0422).
JD303508 - Sequence 284532 from Patent EP1572962.
JD039970 - Sequence 20994 from Patent EP1572962.
JD506660 - Sequence 487684 from Patent EP1572962.
JD443729 - Sequence 424753 from Patent EP1572962.
JD249383 - Sequence 230407 from Patent EP1572962.
JD355132 - Sequence 336156 from Patent EP1572962.
JD361714 - Sequence 342738 from Patent EP1572962.
JD404293 - Sequence 385317 from Patent EP1572962.
JD305463 - Sequence 286487 from Patent EP1572962.
JD314825 - Sequence 295849 from Patent EP1572962.
JD560313 - Sequence 541337 from Patent EP1572962.
JD298704 - Sequence 279728 from Patent EP1572962.
JD049935 - Sequence 30959 from Patent EP1572962.
JD562595 - Sequence 543619 from Patent EP1572962.
JD091604 - Sequence 72628 from Patent EP1572962.
JD553767 - Sequence 534791 from Patent EP1572962.
JD244769 - Sequence 225793 from Patent EP1572962.
JD153781 - Sequence 134805 from Patent EP1572962.
JD359756 - Sequence 340780 from Patent EP1572962.
JD298739 - Sequence 279763 from Patent EP1572962.
BX537823 - Homo sapiens mRNA; cDNA DKFZp686J23256 (from clone DKFZp686J23256).
AK096483 - Homo sapiens cDNA FLJ39164 fis, clone OCBBF2002656.
AF086381 - Homo sapiens full length insert cDNA clone ZD69D05.

-  Other Names for This Gene
  Alternate Gene Symbols: KIAA1439, NFIA_HUMAN, NM_001134673, NP_001128145, Q12857, Q8TA97, Q9H3X9, Q9P2A9
UCSC ID: uc001czw.3
RefSeq Accession: NM_001134673
Protein: Q12857 (aka NFIA_HUMAN)
CCDS: CCDS44156.1, CCDS53321.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene NFIA:
nfia-dis (NFIA-Related Disorder)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001134673.3
exon count: 11CDS single in 3' UTR: no RNA size: 9495
ORF size: 1530CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3166.00frame shift in genome: no % Coverage: 99.86
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 453# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.