Human Gene NFYC (ENST00000447388.8_6) from GENCODE V47lift37
  Description: nuclear transcription factor Y subunit gamma, transcript variant 2 (from RefSeq NM_014223.5)
Gencode Transcript: ENST00000447388.8_6
Gencode Gene: ENSG00000066136.21_15
Transcript (Including UTRs)
   Position: hg19 chr1:41,157,376-41,237,275 Size: 79,900 Total Exon Count: 10 Strand: +
Coding Region
   Position: hg19 chr1:41,204,516-41,236,500 Size: 31,985 Coding Exon Count: 9 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:41,157,376-41,237,275)mRNA (may differ from genome)Protein (335 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMGIOMIMPubMedReactomeUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: NFYC_HUMAN
DESCRIPTION: RecName: Full=Nuclear transcription factor Y subunit gamma; AltName: Full=CAAT box DNA-binding protein subunit C; AltName: Full=Nuclear transcription factor Y subunit C; Short=NF-YC; AltName: Full=Transactivator HSM-1/2;
FUNCTION: Stimulates the transcription of various genes by recognizing and binding to a CCAAT motif in promoters, for example in type 1 collagen, albumin and beta-actin genes.
SUBUNIT: Heterotrimeric transcription factor composed of three components, NF-YA, NF-YB and NF-YC. NF-YB and NF-YC must interact and dimerize for NF-YA association and DNA binding.
INTERACTION: P23511:NFYA; NbExp=3; IntAct=EBI-389755, EBI-389739; P25208:NFYB; NbExp=3; IntAct=EBI-389755, EBI-389728;
SUBCELLULAR LOCATION: Nucleus.
SIMILARITY: Belongs to the NFYC/HAP5 subunit family.

-  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


-  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: 18.55 RPKM in Spleen
Total median expression: 588.75 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 -59.30172-0.345 Picture PostScript Text
3' UTR -223.60775-0.289 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
IPR003958 - CBFA_NFYB_domain
IPR009072 - Histone-fold

Pfam Domains:
PF00125 - Core histone H2A/H2B/H3/H4
PF00808 - Histone-like transcription factor (CBF/NF-Y) and archaeal histone

SCOP Domains:
47113 - Histone-fold
89392 - Prokaryotic lipoproteins and lipoprotein localization factors

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1N1J - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q13952
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 orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
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-  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:0003700 transcription factor activity, sequence-specific DNA binding
GO:0003713 transcription coactivator activity
GO:0005515 protein binding
GO:0008134 transcription factor binding
GO:0044212 transcription regulatory region DNA binding
GO:0046982 protein heterodimerization activity
GO:0000980 RNA polymerase II distal enhancer sequence-specific DNA binding

Biological Process:
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006357 regulation of transcription from RNA polymerase II promoter
GO:0006366 transcription from RNA polymerase II promoter
GO:0006457 protein folding
GO:0045540 regulation of cholesterol biosynthetic process
GO:0045893 positive regulation of transcription, DNA-templated
GO:0045944 positive regulation of transcription from RNA polymerase II promoter

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0016602 CCAAT-binding factor complex
GO:0032993 protein-DNA complex
GO:0090575 RNA polymerase II transcription factor complex


-  Descriptions from all associated GenBank mRNAs
  AK301215 - Homo sapiens cDNA FLJ52977 complete cds, highly similar to Nuclear transcription factor Y subunit gamma.
AK301385 - Homo sapiens cDNA FLJ52978 complete cds, highly similar to Nuclear transcription factor Y subunit gamma.
Z70024 - H.sapiens mRNA for CCAAT binding factor subunit gamma.
Z74792 - H.sapiens mRNA for CCAAT transcription binding factor subunit gamma.
BC005003 - Homo sapiens nuclear transcription factor Y, gamma, mRNA (cDNA clone MGC:792 IMAGE:3502903), complete cds.
AB208975 - Homo sapiens mRNA for nuclear transcription factor Y, gamma variant protein.
AK300774 - Homo sapiens cDNA FLJ58328 complete cds, highly similar to Nuclear transcription factor Y subunit gamma.
JD389457 - Sequence 370481 from Patent EP1572962.
D85425 - Homo sapiens mRNA for transactivator HSM-1, complete cds.
D89986 - Homo sapiens mRNA for HSM-2, complete cds.
JD462748 - Sequence 443772 from Patent EP1572962.
U78774 - Human NFY-C mRNA, complete cds.
JD198702 - Sequence 179726 from Patent EP1572962.
AK127677 - Homo sapiens cDNA FLJ45775 fis, clone NETRP2004017, highly similar to Nuclear transcription factor Y subunit gamma.
AK000346 - Homo sapiens cDNA FLJ20339 fis, clone HEP12350.
JD227470 - Sequence 208494 from Patent EP1572962.
AF191744 - Homo sapiens NFY-C variant DS2.8 mRNA, complete cds.
AB385526 - Synthetic construct DNA, clone: pF1KB3423, Homo sapiens NFYC gene for nuclear transcription factor Y subunit gamma, complete cds, without stop codon, in Flexi system.
BT020081 - Homo sapiens nuclear transcription factor Y, gamma mRNA, complete cds.
KJ891701 - Synthetic construct Homo sapiens clone ccsbBroadEn_01095 NFYC gene, encodes complete protein.
U62296 - Human transcription factor NF-YC subunit mRNA, complete cds.
S74703 - histone H1 transcription factor large subunit 2A=glutamine-rich CCAAT-binding transcription factor [human, HeLa cells, mRNA, 1862 nt].
AK055329 - Homo sapiens cDNA FLJ30767 fis, clone FEBRA2000690.
AL713771 - Homo sapiens mRNA; cDNA DKFZp667G242 (from clone DKFZp667G242).
AK126386 - Homo sapiens cDNA FLJ44422 fis, clone UTERU2003456.
AK093786 - Homo sapiens cDNA FLJ36467 fis, clone THYMU2015441.
JD460663 - Sequence 441687 from Patent EP1572962.
JD098342 - Sequence 79366 from Patent EP1572962.
JD253120 - Sequence 234144 from Patent EP1572962.
JD261742 - Sequence 242766 from Patent EP1572962.
JD430794 - Sequence 411818 from Patent EP1572962.
JD276725 - Sequence 257749 from Patent EP1572962.
JD066870 - Sequence 47894 from Patent EP1572962.
JD189105 - Sequence 170129 from Patent EP1572962.
JD326221 - Sequence 307245 from Patent EP1572962.
JD298334 - Sequence 279358 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  BioCarta from NCI Cancer Genome Anatomy Project
h_tercPathway - Overview of telomerase RNA component gene hTerc Transcriptional Regulation

Reactome (by CSHL, EBI, and GO)

Protein Q13952 (Reactome details) participates in the following event(s):

R-HSA-2065966 SREBP1A,1C,2 binds the TM7SF2 promoter
R-HSA-2426146 SREBP1A,1C,2 binds the FDFT1 promoter
R-HSA-2426147 SREBP1A,1C,2 binds the FDPS promoter
R-HSA-2426148 SREBP1A,1C binds the FASN promoter
R-HSA-2426150 SREBP1A,1C,2 binds the HMGCS1 promoter
R-HSA-2426151 SREBP1A,2 binds the SQLE promoter
R-HSA-2426152 SREBP1A,2 binds the IDI1 promoter
R-HSA-2426155 SREBP1A,2 binds the DHCR7 promoter
R-HSA-2426156 SREBP1A,2 binds the PMVK promoter
R-HSA-2426157 SREBP1A,2 binds the MVK promoter
R-HSA-2426158 SREBP1A,1C binds the GPAM promoter
R-HSA-2426161 SREBP1A,2 binds the GGPS1 promoter
R-HSA-2426162 SREBP1A,2 binds the HMGCR promoter
R-HSA-2426163 SREBP1A,2 binds the CYP51A1 promoter
R-HSA-2426164 SREBP1A,2 binds the SC5DL promoter
R-HSA-2426168 Activation of gene expression by SREBF (SREBP)
R-HSA-1655829 Regulation of cholesterol biosynthesis by SREBP (SREBF)
R-HSA-8957322 Metabolism of steroids
R-HSA-556833 Metabolism of lipids
R-HSA-1430728 Metabolism

-  Other Names for This Gene
  Alternate Gene Symbols: B4DUS6, B4DW63, D3DPV9, ENST00000447388.1, ENST00000447388.2, ENST00000447388.3, ENST00000447388.4, ENST00000447388.5, ENST00000447388.6, ENST00000447388.7, F8VWM3, NFYC_HUMAN, NM_014223, Q13952, Q59GY4, Q5T6K8, Q5T6K9, Q5T6L1, Q5TZR6, Q92869, Q9HBX1, Q9NXB5, Q9UM67, Q9UML0, Q9UMT7, uc320ozz.1, uc320ozz.2
UCSC ID: ENST00000447388.8_6
RefSeq Accession: NM_014223.5
Protein: Q13952 (aka NFYC_HUMAN)

-  Gene Model Information
  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.