Human Gene CPSF6 (ENST00000435070.7_11) from GENCODE V47lift37
  Description: cleavage and polyadenylation specific factor 6, transcript variant 1 (from RefSeq NM_007007.3)
Gencode Transcript: ENST00000435070.7_11
Gencode Gene: ENSG00000111605.18_15
Transcript (Including UTRs)
   Position: hg19 chr12:69,633,349-69,668,138 Size: 34,790 Total Exon Count: 10 Strand: +
Coding Region
   Position: hg19 chr12:69,633,427-69,656,339 Size: 22,913 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 (chr12:69,633,349-69,668,138)mRNA (may differ from genome)Protein (551 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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HGNCMGIOMIMPubMedReactomeUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CPSF6_HUMAN
DESCRIPTION: RecName: Full=Cleavage and polyadenylation specificity factor subunit 6; AltName: Full=Cleavage and polyadenylation specificity factor 68 kDa subunit; Short=CFIm68; Short=CPSF 68 kDa subunit; AltName: Full=Pre-mRNA cleavage factor Im 68 kDa subunit; AltName: Full=Protein HPBRII-4/7;
FUNCTION: Component of the cleavage factor Im complex (CFIm) that plays a key role in pre-mRNA 3'-processing. Involved in association with NUDT21/CPSF5 in pre-MRNA 3'-end poly(A) site cleavage and poly(A) addition. CPSF6 binds to cleavage and polyadenylation RNA substrates and promotes RNA looping.
SUBUNIT: Component of the cleavage factor Im (CFIm) complex, composed at least of NUDT21/CPSF5 and CPSF6 or CPSF7. Within the cleavage factor Im complex, the NUDT21/CPSF5 homodimer is at the core of a heterotetramer, and is clasped by two additional subunits (CPSF6 or CPSF7). Interacts with NUDT21/CPSF5, SFRS3, SFRS7, SNRNP70 and TRA2B/SFRS10.
INTERACTION: O15162:PLSCR1; NbExp=2; IntAct=EBI-358410, EBI-740019; Q9H0M0:WWP1; NbExp=3; IntAct=EBI-358410, EBI-742157;
SUBCELLULAR LOCATION: Nucleus. Note=In punctate subnuclear structures localized adjacent to nuclear speckles, called paraspeckles.
PTM: Phosphorylated upon DNA damage, probably by ATM or ATR.
SIMILARITY: Belongs to the RRM CPSF6/7 family.
SIMILARITY: Contains 1 RRM (RNA recognition motif) 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


-  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: 33.55 RPKM in Ovary
Total median expression: 691.55 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 -45.7078-0.586 Picture PostScript Text
3' UTR -1126.804850-0.232 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
IPR012677 - Nucleotide-bd_a/b_plait
IPR000504 - RRM_dom

Pfam Domains:
PF00076 - RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)

SCOP Domains:
54928 - RNA-binding domain, RBD

Protein Data Bank (PDB) 3-D Structure
MuPIT help
3P5T - X-ray MuPIT 3P6Y - X-ray MuPIT 3Q2S - X-ray MuPIT 3Q2T - X-ray MuPIT 4B4N - X-ray


ModBase Predicted Comparative 3D Structure on Q16630
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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:0003676 nucleic acid binding
GO:0003723 RNA binding
GO:0003729 mRNA binding
GO:0005515 protein binding
GO:0043023 ribosomal large subunit binding
GO:1990448 exon-exon junction complex binding

Biological Process:
GO:0006378 mRNA polyadenylation
GO:0006397 mRNA processing
GO:0046833 positive regulation of RNA export from nucleus
GO:0051262 protein tetramerization
GO:0051290 protein heterotetramerization
GO:0098789 pre-mRNA cleavage required for polyadenylation
GO:1990120 messenger ribonucleoprotein complex assembly

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005726 perichromatin fibrils
GO:0005737 cytoplasm
GO:0005847 mRNA cleavage and polyadenylation specificity factor complex
GO:0005849 mRNA cleavage factor complex
GO:0016020 membrane
GO:0016607 nuclear speck
GO:0035061 interchromatin granule
GO:0042382 paraspeckles
GO:1990904 ribonucleoprotein complex


-  Descriptions from all associated GenBank mRNAs
  AK299928 - Homo sapiens cDNA FLJ58421 complete cds, highly similar to Cleavage and polyadenylation specificity factor 6.
AK223568 - Homo sapiens mRNA for cleavage and polyadenylation specific factor 6, 68 kD subunit variant, clone: FCC128H10.
BC005000 - Homo sapiens cleavage and polyadenylation specific factor 6, 68kDa, mRNA (cDNA clone MGC:4425 IMAGE:2958189), complete cds.
BC000714 - Homo sapiens cleavage and polyadenylation specific factor 6, 68kDa, mRNA (cDNA clone MGC:1242 IMAGE:3506481), complete cds.
JD217639 - Sequence 198663 from Patent EP1572962.
X67337 - H.sapiens HPBRII-4 mRNA.
AK292024 - Homo sapiens cDNA FLJ78600 complete cds, highly similar to Homo sapiens cleavage and polyadenylation specific factor 6, 68kDa (CPSF6), mRNA.
CU674352 - Synthetic construct Homo sapiens gateway clone IMAGE:100017722 5' read CPSF6 mRNA.
CU678850 - Synthetic construct Homo sapiens gateway clone IMAGE:100017348 5' read CPSF6 mRNA.
EU176688 - Synthetic construct Homo sapiens clone IMAGE:100011463; FLH183563.01L; RZPDo839A04255D cleavage and polyadenylation specific factor 6, 68kDa (CPSF6) gene, encodes complete protein.
DQ892159 - Synthetic construct clone IMAGE:100004789; FLH183564.01X; RZPDo839E01142D cleavage and polyadenylation specific factor 6, 68kDa (CPSF6) gene, encodes complete protein.
KJ902191 - Synthetic construct Homo sapiens clone ccsbBroadEn_11585 CPSF6 gene, encodes complete protein.
KJ902192 - Synthetic construct Homo sapiens clone ccsbBroadEn_11586 CPSF6 gene, encodes complete protein.
MG715502 - Homo sapiens cleavage and polyadenylation specific factor 6/retinoic acid receptor gamma fusion protein (CPSF6/RARG fusion) mRNA, partial cds.
MG715503 - Homo sapiens cleavage and polyadenylation specific factor 6/retinoic acid receptor gamma fusion protein (CPSF6/RARG fusion) mRNA, partial cds.
AK093765 - Homo sapiens cDNA FLJ36446 fis, clone THYMU2013051.
JD352132 - Sequence 333156 from Patent EP1572962.
JD338447 - Sequence 319471 from Patent EP1572962.
JD087487 - Sequence 68511 from Patent EP1572962.
JD313018 - Sequence 294042 from Patent EP1572962.
JD260758 - Sequence 241782 from Patent EP1572962.
JD061409 - Sequence 42433 from Patent EP1572962.
JD503819 - Sequence 484843 from Patent EP1572962.
JD244782 - Sequence 225806 from Patent EP1572962.
JD202412 - Sequence 183436 from Patent EP1572962.
JD139609 - Sequence 120633 from Patent EP1572962.
JD506577 - Sequence 487601 from Patent EP1572962.
JD562539 - Sequence 543563 from Patent EP1572962.
JD560420 - Sequence 541444 from Patent EP1572962.
JD281761 - Sequence 262785 from Patent EP1572962.
JD041809 - Sequence 22833 from Patent EP1572962.
JD061608 - Sequence 42632 from Patent EP1572962.
JD548354 - Sequence 529378 from Patent EP1572962.
JD298877 - Sequence 279901 from Patent EP1572962.
AK098338 - Homo sapiens cDNA FLJ41019 fis, clone UTERU2019096.
AK021833 - Homo sapiens cDNA FLJ11771 fis, clone HEMBA1005822.
AK021534 - Homo sapiens cDNA FLJ11472 fis, clone HEMBA1001711.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q16630 (Reactome details) participates in the following event(s):

R-HSA-1839031 Dimerization of cytosolic FGFR1 fusion proteins
R-HSA-1839039 Tyrosine kinase inhibitors bind and inhibit cytosolic FGFR1 fusion dimer phosphorylation
R-HSA-1839065 Phosphorylation of cytosolic FGFR1 fusion dimers
R-HSA-1839080 Activated cytosolic FGFR1 fusions bind PIK3CA
R-HSA-1839094 Activated FGFR1 mutants and fusions bind PLCG1
R-HSA-1839100 p-4Y- PLCG1 dissociates from activated FGFR1 mutants and fusions
R-HSA-1839091 Cytosolic FGFR1 fusion protein-associated PI3K phosphorylates PIP2 to PIP3
R-HSA-1839098 Activated FGFR1 mutants and fusions phosphorylate PLCG1
R-HSA-1839117 Signaling by cytosolic FGFR1 fusion mutants
R-HSA-1839124 FGFR1 mutant receptor activation
R-HSA-5655302 Signaling by FGFR1 in disease
R-HSA-1226099 Signaling by FGFR in disease
R-HSA-5663202 Diseases of signal transduction
R-HSA-1643685 Disease

-  Other Names for This Gene
  Alternate Gene Symbols: A8K7K9, CFIM68 , CPSF6 , CPSF6_HUMAN, ENST00000435070.1, ENST00000435070.2, ENST00000435070.3, ENST00000435070.4, ENST00000435070.5, ENST00000435070.6, NM_007007, Q16630, Q53ES1, Q9BSJ7, Q9BW18, uc320dny.1, uc320dny.2
UCSC ID: ENST00000435070.7_11
RefSeq Accession: NM_007007.3
Protein: Q16630 (aka CPSF6_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.