Human Gene CPSF7 (ENST00000394888.8) Description and Page Index
  Description: Homo sapiens cleavage and polyadenylation specific factor 7 (CPSF7), transcript variant 2, mRNA. (from RefSeq NM_001136040)
RefSeq Summary (NM_001136040): Cleavage factor Im (CFIm) is one of six factors necessary for correct cleavage and polyadenylation of pre-mRNAs. CFIm is composed of three different subunits of 25, 59, and 68 kDa, and it functions as a heterotetramer, with a dimer of the 25 kDa subunit binding to two of the 59 or 68 kDa subunits. The protein encoded by this gene represents the 59 kDa subunit, which can interact with the splicing factor U2 snRNP Auxiliary Factor (U2AF) 65 to link the splicing and polyadenylation complexes. [provided by RefSeq, Oct 2016].
Gencode Transcript: ENST00000394888.8
Gencode Gene: ENSG00000149532.15
Transcript (Including UTRs)
   Position: hg38 chr11:61,402,649-61,430,031 Size: 27,383 Total Exon Count: 10 Strand: -
Coding Region
   Position: hg38 chr11:61,410,943-61,429,235 Size: 18,293 Coding Exon Count: 8 

Page IndexSequence and LinksUniProtKB CommentsCTDRNA-Seq ExpressionMicroarray Expression
RNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA DescriptionsPathways
Other NamesMethods
Data last updated: 2019-09-04

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr11:61,402,649-61,430,031)mRNA (may differ from genome)Protein (471 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsHGNC
LynxMGIneXtProtPubMedReactomeStanford SOURCE

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Cleavage and polyadenylation specificity factor subunit 7; AltName: Full=Cleavage and polyadenylation specificity factor 59 kDa subunit; Short=CFIm59; Short=CPSF 59 kDa subunit; AltName: Full=Pre-mRNA cleavage factor Im 59 kDa subunit;
FUNCTION: Component of the cleavage factor Im complex (CFIm) that plays a key role in pre-mRNA 3' processing. Binds to cleavage and polyadenylation RNA substrates.
SUBUNIT: Component of the cleavage factor Im (CFIm) complex, composed of, at least, 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.
INTERACTION: P54253:ATXN1; NbExp=2; IntAct=EBI-746909, EBI-930964;
SIMILARITY: Belongs to the RRM CPSF6/7 family.
SIMILARITY: Contains 1 RRM (RNA recognition motif) domain.
SEQUENCE CAUTION: Sequence=AAH18135.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=BAB14118.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=CAD97884.1; Type=Erroneous initiation; Note=Translation N-terminally shortened;

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 64.44 RPKM in Pituitary
Total median expression: 1525.86 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 -85.30173-0.493 Picture PostScript Text
3' UTR -677.102061-0.329 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)

Protein Data Bank (PDB) 3-D Structure
MuPIT help

- X-ray MuPIT

ModBase Predicted Comparative 3D Structure on Q8N684
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 BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
 Protein Sequence    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003676 nucleic acid binding
GO:0003723 RNA binding
GO:0005515 protein binding

Biological Process:
GO:0000398 mRNA splicing, via spliceosome
GO:0006369 termination of RNA polymerase II transcription
GO:0006397 mRNA processing
GO:0031124 mRNA 3'-end processing
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:0005737 cytoplasm
GO:0005847 mRNA cleavage and polyadenylation specificity factor complex
GO:0005849 mRNA cleavage factor complex
GO:0016020 membrane

-  Descriptions from all associated GenBank mRNAs
  AK307190 - Homo sapiens cDNA, FLJ97138.
BX537888 - Homo sapiens mRNA; cDNA DKFZp313F1311 (from clone DKFZp313F1311); complete cds.
AK096343 - Homo sapiens cDNA FLJ39024 fis, clone NT2RP7004428, highly similar to Cleavage and polyadenylation specificity factor 7.
AK022591 - Homo sapiens cDNA FLJ12529 fis, clone NT2RM4000156, weakly similar to H.sapiens HPBRII-7 gene.
AL512759 - Homo sapiens mRNA; cDNA DKFZp547I126 (from clone DKFZp547I126).
BC018135 - Homo sapiens pre-mRNA cleavage factor I, 59 kDa subunit, mRNA (cDNA clone MGC:9315 IMAGE:3913173), complete cds.
AL833332 - Homo sapiens mRNA; cDNA DKFZp686L0633 (from clone DKFZp686L0633).
AK092037 - Homo sapiens cDNA FLJ34718 fis, clone MESAN2005633, moderately similar to H.sapiens HPBRII-4 mRNA.
AL832667 - Homo sapiens mRNA; cDNA DKFZp313K1112 (from clone DKFZp313K1112).
AL832546 - Homo sapiens mRNA; cDNA DKFZp547I1017 (from clone DKFZp547I1017).
JD303400 - Sequence 284424 from Patent EP1572962.
JD299072 - Sequence 280096 from Patent EP1572962.
JD089862 - Sequence 70886 from Patent EP1572962.
JD314196 - Sequence 295220 from Patent EP1572962.
JD054321 - Sequence 35345 from Patent EP1572962.
JD124336 - Sequence 105360 from Patent EP1572962.
JD363895 - Sequence 344919 from Patent EP1572962.
JD219464 - Sequence 200488 from Patent EP1572962.
JD402796 - Sequence 383820 from Patent EP1572962.
JD340134 - Sequence 321158 from Patent EP1572962.
JD559453 - Sequence 540477 from Patent EP1572962.
JD234410 - Sequence 215434 from Patent EP1572962.
JD489886 - Sequence 470910 from Patent EP1572962.
JD279690 - Sequence 260714 from Patent EP1572962.
JD295295 - Sequence 276319 from Patent EP1572962.
JD305994 - Sequence 287018 from Patent EP1572962.
JD544334 - Sequence 525358 from Patent EP1572962.
JD254240 - Sequence 235264 from Patent EP1572962.
JD548816 - Sequence 529840 from Patent EP1572962.
JD177777 - Sequence 158801 from Patent EP1572962.
JD341481 - Sequence 322505 from Patent EP1572962.
JD235094 - Sequence 216118 from Patent EP1572962.
JD157159 - Sequence 138183 from Patent EP1572962.
JD435601 - Sequence 416625 from Patent EP1572962.
JD397385 - Sequence 378409 from Patent EP1572962.
JD557999 - Sequence 539023 from Patent EP1572962.
JD337220 - Sequence 318244 from Patent EP1572962.
JD285982 - Sequence 267006 from Patent EP1572962.
DQ589631 - Homo sapiens piRNA piR-56743, complete sequence.
JD448567 - Sequence 429591 from Patent EP1572962.
JD341209 - Sequence 322233 from Patent EP1572962.
JD328149 - Sequence 309173 from Patent EP1572962.
JD120424 - Sequence 101448 from Patent EP1572962.
JD344633 - Sequence 325657 from Patent EP1572962.
JD438195 - Sequence 419219 from Patent EP1572962.
JD317830 - Sequence 298854 from Patent EP1572962.
JD232949 - Sequence 213973 from Patent EP1572962.
JD121312 - Sequence 102336 from Patent EP1572962.
JD560459 - Sequence 541483 from Patent EP1572962.
AK294578 - Homo sapiens cDNA FLJ57877 complete cds, highly similar to Cleavage and polyadenylation specificity factor 7.
JD555193 - Sequence 536217 from Patent EP1572962.
AJ275970 - Homo sapiens mRNA for pre-mRNA cleavage factor I, 59 kDa subunit.
EU831912 - Synthetic construct Homo sapiens clone HAIB:100066941; DKFZo008A1223 pre-mRNA cleavage factor I, 59 kDa subunit protein (FLJ12529) gene, encodes complete protein.
KJ899581 - Synthetic construct Homo sapiens clone ccsbBroadEn_08975 CPSF7 gene, encodes complete protein.
EU832006 - Synthetic construct Homo sapiens clone HAIB:100067035; DKFZo004A1224 pre-mRNA cleavage factor I, 59 kDa subunit protein (FLJ12529) gene, encodes complete protein.
AB529084 - Synthetic construct DNA, clone: pF1KB4161, Homo sapiens CPSF7 gene for cleavage and polyadenylation specific factor 7, 59kDa, without stop codon, in Flexi system.
CU676198 - Synthetic construct Homo sapiens gateway clone IMAGE:100019556 5' read FLJ12529 mRNA.
DQ579794 - Homo sapiens piRNA piR-47906, complete sequence.
JD459081 - Sequence 440105 from Patent EP1572962.

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

Protein Q8N684 (Reactome details) participates in the following event(s):

R-HSA-72231 Cleavage and Polyadenylation
R-HSA-77591 Binding of Cleavage factors and Poly(A)Polymerase to the CstF:CPSF:Pre-mRNA Complex
R-HSA-72180 Cleavage of mRNA at the 3'-end
R-HSA-77592 Cleavage of Intronless Pre-mRNA at 3'-end
R-HSA-77593 Cleavage and polyadenylation of Intronless Pre-mRNA
R-HSA-72130 Formation of an intermediate Spliceosomal C (Bact) complex
R-HSA-72143 Lariat Formation and 5'-Splice Site Cleavage
R-HSA-72139 Formation of the active Spliceosomal C (B*) complex
R-HSA-8849157 TREX complex binds spliced, capped mRNA:CBC:EJC cotranscriptionally
R-HSA-156661 Formation of Exon Junction Complex
R-HSA-72163 mRNA Splicing - Major Pathway
R-HSA-77595 Processing of Intronless Pre-mRNAs
R-HSA-72187 mRNA 3'-end processing
R-HSA-109688 Cleavage of Growing Transcript in the Termination Region
R-HSA-72172 mRNA Splicing
R-HSA-75067 Processing of Capped Intronless Pre-mRNA
R-HSA-72203 Processing of Capped Intron-Containing Pre-mRNA
R-HSA-73856 RNA Polymerase II Transcription Termination
R-HSA-8953854 Metabolism of RNA
R-HSA-73857 RNA Polymerase II Transcription
R-HSA-74160 Gene expression (Transcription)

-  Other Names for This Gene
  Alternate Gene Symbols: B3KU04, C9K0Q4, CPSF7_HUMAN, NM_001136040, Q7Z3H9, Q8N684, Q9H025, Q9H9V1, uc001nrq.1, uc001nrq.2, uc001nrq.3, uc001nrq.4
UCSC ID: uc001nrq.4
RefSeq Accession: NM_001136040
Protein: Q8N684 (aka CPSF7_HUMAN)
CCDS: CCDS44619.1, CCDS44620.1

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