Human Gene NFIC (ENST00000395111.7) from GENCODE V44
  Description: Homo sapiens nuclear factor I C (NFIC), transcript variant 4, mRNA. (from RefSeq NM_001245005)
RefSeq Summary (NM_001245005): The protein encoded by this gene belongs to the CTF/NF-I family. These are dimeric DNA-binding proteins, and function as cellular transcription factors and as replication factors for adenovirus DNA replication. Alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Oct 2011].
Gencode Transcript: ENST00000395111.7
Gencode Gene: ENSG00000141905.19
Transcript (Including UTRs)
   Position: hg38 chr19:3,359,647-3,463,142 Size: 103,496 Total Exon Count: 10 Strand: +
Coding Region
   Position: hg38 chr19:3,359,683-3,456,600 Size: 96,918 Coding Exon Count: 9 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr19:3,359,647-3,463,142)mRNA (may differ from genome)Protein (430 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
HGNCHPRDLynxMalacardsMGIneXtProt
OMIMPubMedReactomeUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: NFIC_HUMAN
DESCRIPTION: RecName: Full=Nuclear factor 1 C-type; Short=NF1-C; Short=Nuclear factor 1/C; AltName: Full=CCAAT-box-binding transcription factor; Short=CTF; AltName: Full=Nuclear factor I/C; Short=NF-I/C; Short=NFI-C; 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.
SIMILARITY: Belongs to the CTF/NF-I family.
SIMILARITY: Contains 1 CTF/NF-I DNA-binding domain.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: NFIC
Diseases sorted by gene-association score: common wart (2), marshall-smith syndrome (2), peripheral nervous system neoplasm (2)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene
  • D000082 Acetaminophen
  • D001564 Benzo(a)pyrene
  • D013749 Tetrachlorodibenzodioxin
  • C023514 2,6-dinitrotoluene
  • C548651 2-(1'H-indolo-3'-carbonyl)thiazole-4-carboxylic acid methyl ester
  • C012796 2-butenal
  • C009505 4,4'-diaminodiphenylmethane
  • C027576 4-hydroxy-2-nonenal
  • C012606 4-vinyl-1-cyclohexene dioxide
  • D015123 7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide
          more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 55.20 RPKM in Muscle - Skeletal
Total median expression: 1096.49 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 -11.9036-0.331 Picture PostScript Text
3' UTR -117.40426-0.276 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 P08651
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
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGD    
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:0000987 core promoter proximal region sequence-specific DNA binding
GO:0001077 transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding
GO:0003677 DNA binding
GO:0003690 double-stranded DNA binding
GO:0003700 transcription factor activity, sequence-specific DNA 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:0042475 odontogenesis of dentin-containing tooth
GO:0045892 negative regulation of transcription, DNA-templated
GO:0045944 positive regulation of transcription from RNA polymerase II promoter

Cellular Component:
GO:0001650 fibrillar center
GO:0005622 intracellular
GO:0005634 nucleus


-  Descriptions from all associated GenBank mRNAs
  X12492 - Human mRNA for CAAT-box binding transcription factor CTF-1 (syn. CTF/NFI or CTF or NF-I or NF-1).
AK304816 - Homo sapiens cDNA FLJ51687 complete cds, highly similar to Nuclear factor 1 C-type.
AK289885 - Homo sapiens cDNA FLJ75592 complete cds, highly similar to Homo sapiens nuclear factor I/C (CCAAT-binding transcription factor) (NFIC), transcript variant 2, mRNA.
BC012120 - Homo sapiens nuclear factor I/C (CCAAT-binding transcription factor), mRNA (cDNA clone MGC:20153 IMAGE:4554661), complete cds.
AK297867 - Homo sapiens cDNA FLJ60130 complete cds, highly similar to Nuclear factor 1 C-type.
AK297825 - Homo sapiens cDNA FLJ58543 complete cds, highly similar to Nuclear factor 1 C-type.
X92857 - H.sapiens mRNA for NFI/CAAT-binding transcription factor 5 (CTF5).
CU680224 - Synthetic construct Homo sapiens gateway clone IMAGE:100017653 5' read NFIC mRNA.
KJ897242 - Synthetic construct Homo sapiens clone ccsbBroadEn_06636 NFIC gene, encodes complete protein.
AB590220 - Synthetic construct DNA, clone: pFN21AE1374, Homo sapiens NFIC gene for nuclear factor I/C, without stop codon, in Flexi system.
DQ895795 - Synthetic construct Homo sapiens clone IMAGE:100010255; FLH187715.01L; RZPDo839C05149D nuclear factor I/C (CCAAT-binding transcription factor) (NFIC) gene, encodes complete protein.
DQ893655 - Synthetic construct clone IMAGE:100006285; FLH187719.01X; RZPDo839C05150D nuclear factor I/C (CCAAT-binding transcription factor) (NFIC) gene, encodes complete protein.
CR536507 - Homo sapiens full open reading frame cDNA clone RZPDo834G1221D for gene NFIC, nuclear factor I/C (CCAAT-binding transcription factor); complete cds, incl. stopcodon.
JD504279 - Sequence 485303 from Patent EP1572962.
JD163740 - Sequence 144764 from Patent EP1572962.
JD391325 - Sequence 372349 from Patent EP1572962.
JD251505 - Sequence 232529 from Patent EP1572962.
JD074056 - Sequence 55080 from Patent EP1572962.
JD422325 - Sequence 403349 from Patent EP1572962.
JD037869 - Sequence 18893 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: A8K1H0, B7Z9C3, ENST00000395111.1, ENST00000395111.2, ENST00000395111.3, ENST00000395111.4, ENST00000395111.5, ENST00000395111.6, NFI, NFIC_HUMAN, NM_001245005, P08651, P08652, Q14932, Q9UPJ3, Q9UPJ9, Q9UPK0, Q9UPK1, uc010xhh.1, uc010xhh.2, uc010xhh.3
UCSC ID: ENST00000395111.7
RefSeq Accession: NM_001245005
Protein: P08651 (aka NFIC_HUMAN)
CCDS: CCDS12107.1, CCDS59331.1, CCDS58640.1

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