TISIDB

Summary
Symbol	CPSF7
Name	cleavage and polyadenylation specific factor 7, 59kDa
Aliases	FLJ12529; pre mRNA cleavage factor I, 59 kDa subunit; cleavage factor Im complex 59 kDa subunit; CFIm59; CPS ......
Chromosomal Location	11q12.2
External Links	HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content	Basic function annotation. > Subcellular Location, Domain and Function > Gene Ontology > KEGG and Reactome Pathway

> Subcellular Location, Domain and Function [ TOP ]
Subcellular Location	Nucleus Cytoplasm Note=Shuttles between the nucleus and the cytoplasm in a transcription- and XPO1/CRM1-independent manner, most probably in complex with the cleavage factor Im complex (CFIm) (PubMed:19864460).
Domain	PF00076 RNA recognition motif. (a.k.a. RRM
Function	Component of the cleavage factor Im (CFIm) complex that functions as an activator of the pre-mRNA 3'-end cleavage and polyadenylation processing required for the maturation of pre-mRNA into functional mRNAs (PubMed:8626397, PubMed:17024186, PubMed:29276085). CFIm contributes to the recruitment of multiprotein complexes on specific sequences on the pre-mRNA 3'-end, so called cleavage and polyadenylation signals (pA signals) (PubMed:8626397, PubMed:17024186). Most pre-mRNAs contain multiple pA signals, resulting in alternative cleavage and polyadenylation (APA) producing mRNAs with variable 3'-end formation (PubMed:23187700, PubMed:29276085). The CFIm complex acts as a key regulator of cleavage and polyadenylation site choice during APA through its binding to 5'-UGUA-3' elements localized in the 3'-untranslated region (UTR) for a huge number of pre-mRNAs (PubMed:20695905, PubMed:29276085). CPSF7 activates directly the mRNA 3'-processing machinery (PubMed:29276085). Binds to pA signals in RNA substrates (PubMed:8626397, PubMed:17024186).

> Gene Ontology [ TOP ]
Biological Process	GO:0000375 RNA splicing, via transesterification reactions GO:0000377 RNA splicing, via transesterification reactions with bulged adenosine as nucleophile GO:0000398 mRNA splicing, via spliceosome GO:0006353 DNA-templated transcription, termination GO:0006369 termination of RNA polymerase II transcription GO:0006397 mRNA processing GO:0008380 RNA splicing GO:0031123 RNA 3'-end processing GO:0031124 mRNA 3'-end processing GO:0051259 protein oligomerization GO:0051262 protein tetramerization
Molecular Function	-
Cellular Component	GO:0005849 mRNA cleavage factor complex

> KEGG and Reactome Pathway [ TOP ]
KEGG	hsa03015 mRNA surveillance pathway
Reactome	R-HSA-109688: Cleavage of Growing Transcript in the Termination Region R-HSA-74160: Gene Expression R-HSA-112296: Post-Elongation Processing of Intron-Containing pre-mRNA R-HSA-112297: Post-Elongation Processing of Intronless pre-mRNA R-HSA-76044: Post-Elongation Processing of the Transcript R-HSA-72203: Processing of Capped Intron-Containing Pre-mRNA R-HSA-75067: Processing of Capped Intronless Pre-mRNA R-HSA-77595: Processing of Intronless Pre-mRNAs R-HSA-73857: RNA Polymerase II Transcription R-HSA-73856: RNA Polymerase II Transcription Termination R-HSA-72187: mRNA 3'-end processing R-HSA-72172: mRNA Splicing R-HSA-72163: mRNA Splicing - Major Pathway

> KEGG and Reactome Pathway

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KEGG

hsa03015 mRNA surveillance pathway

Reactome

R-HSA-109688: Cleavage of Growing Transcript in the Termination Region
R-HSA-74160: Gene Expression
R-HSA-112296: Post-Elongation Processing of Intron-Containing pre-mRNA
R-HSA-112297: Post-Elongation Processing of Intronless pre-mRNA
R-HSA-76044: Post-Elongation Processing of the Transcript
R-HSA-72203: Processing of Capped Intron-Containing Pre-mRNA
R-HSA-75067: Processing of Capped Intronless Pre-mRNA
R-HSA-77595: Processing of Intronless Pre-mRNAs
R-HSA-73857: RNA Polymerase II Transcription
R-HSA-73856: RNA Polymerase II Transcription Termination
R-HSA-72187: mRNA 3'-end processing
R-HSA-72172: mRNA Splicing
R-HSA-72163: mRNA Splicing - Major Pathway

Summary
Symbol	CPSF7
Name	cleavage and polyadenylation specific factor 7, 59kDa
Aliases	FLJ12529; pre mRNA cleavage factor I, 59 kDa subunit; cleavage factor Im complex 59 kDa subunit; CFIm59; CPS ......
Chromosomal Location	11q12.2
External Links	HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content	Literatures that report relations between CPSF7 and anti-tumor immunity. The specific mechanism were also collected if the literature reports that a gene specifically promotes or inhibits the infiltration or function of T/NK cells.

> Text Mining [ TOP ]
There is no record.

Summary
Symbol	CPSF7
Name	cleavage and polyadenylation specific factor 7, 59kDa
Aliases	FLJ12529; pre mRNA cleavage factor I, 59 kDa subunit; cleavage factor Im complex 59 kDa subunit; CFIm59; CPS ......
Chromosomal Location	11q12.2
External Links	HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content	High-throughput screening data (e.g. CRISPR-Cas9, shRNA and RNAi) for T cell-mediated killing. Genetic screen techniques can identify mechanisms of tumor cell resistance (e.g., PTPN2) and sensitivity (e.g., APLNR) to killing by cytotoxic T cells, the central effectors of anti-tumor immunity. After comprehensively searching, eight groups of screening data sets were collected in the current database. In this tab, users can check whether their selected genes cause resistance or increase sensitivity to T cell-mediated killing in various data sets.

> High-throughput Screening

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Statistical results of CPSF7 in screening data sets for detecting immune reponses.

PMID	Screening System	Cancer Type	Cell Line	Data Set	Statistical Results	Relation to immunity
29301958	CRISPR-Cas9	melanoma	B16F10	Pmel-1 T cell	NA/NS	NA/NS
29301958	CRISPR-Cas9	melanoma	B16F10	OT-1 T cell	NA/NS	NA/NS
28783722	CRISPR-Cas9	melanoma	Mel624	2CT-CRISPR	Second most enriched score: 0.5	Sensitive to T cell-mediated killing
28723893	CRISPR-Cas9	melanoma	B16	GVAX+Anti-PD1	NA/NS	NA/NS
28723893	CRISPR-Cas9	melanoma	B16	GVAX	NA/NS	NA/NS
25691366	RNAi	Breast cancer	MCF7	Luc-CTL assay	NA/NS	NA/NS
24476824	shRNA	melanoma	B16	Primary screen	NA/NS	NA/NS
24476824	shRNA	melanoma	B16	Secondary screen	NA/NS	NA/NS

Summary
Symbol	CPSF7
Name	cleavage and polyadenylation specific factor 7, 59kDa
Aliases	FLJ12529; pre mRNA cleavage factor I, 59 kDa subunit; cleavage factor Im complex 59 kDa subunit; CFIm59; CPS ......
Chromosomal Location	11q12.2
External Links	HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content	Transcriptomic and genomic profiling of pre-treated tumor biopsies from responders and non-responders to immunotherapy. These data were used to identify signatures and mechanisms of response to checkpoint blockade (e.g., anti-PDL1 and anti-PD1). One example is that mutations in the gene PBRM1 benefit clinical survival of patients with clear cell renal cell carcinoma. After comprehensively searching, we collected 5 and 6 of transcriptomic and genomic data sets, respectively. In this tab, users can check whether their selected genes have significant difference of expression or mutation between responders and non-responders in various data sets. > Expression difference between responders and non-responders > Mutation difference between responders and non-responders

> Expression difference between responders and non-responders

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Points in the above scatter plot represent the expression difference of CPSF7 in various data sets.

No	PMID	Cancer type	Group	Drug	# Res	# NRes	Log2 (Fold Change)	P value
1	26997480	Melanoma	all	Anti-PD-1 (pembrolizumab and nivolumab)	14	12	0.301	0.0965
2	26997480	Melanoma	MAPKi	Anti-PD-1 (pembrolizumab and nivolumab)	6	5	0.466	0.816
3	26997480	Melanoma	non-MAPKi	Anti-PD-1 (pembrolizumab and nivolumab)	8	7	0.178	0.905
4	28552987	Urothelial cancer	all	Anti-PD-L1 (atezolizumab)	9	16	0.179	0.484
5	28552987	Urothelial cancer	smoking	Anti-PD-L1 (atezolizumab)	5	9	0.06	0.976
6	28552987	Urothelial cancer	non-smoking	Anti-PD-L1 (atezolizumab)	4	7	0.332	0.9
7	29033130	Melanoma	all	Anti-PD-1 (nivolumab)	26	23	-0.035	0.925
8	29033130	Melanoma	NIV3-PROG	Anti-PD-1 (nivolumab)	15	11	0.118	0.947
9	29033130	Melanoma	NIV3-NAIVE	Anti-PD-1 (nivolumab)	11	12	-0.181	0.926
10	29301960	Clear cell renal cell carcinoma (ccRCC)	all	Anti-PD-1 (nivolumab)	4	8	0.524	0.748
11	29301960	Clear cell renal cell carcinoma (ccRCC)	VEGFRi	Anti-PD-1 (nivolumab)	2	0	0	1
12	29301960	Clear cell renal cell carcinoma (ccRCC)	non-VEGFRi	Anti-PD-1 (nivolumab)	2	8	1.386	0.549
13	29443960	Urothelial cancer	all	Anti-PD-L1 (atezolizumab)	68	230	0.052	0.248

> Mutation difference between responders and non-responders

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Points in the above scatter plot represent the mutation difference of CPSF7 in various data sets.

No	PMID	Cancer type	Group	Drug	# Res	# NRes	% Mut/Res	% Mut/NRes	% Diff (R vs NR)	Pval
1	25765070	Non-small cell lung cancer (NSCLC)	all	Anti-PD-1 (pembrolizumab)	14	17	0	0	0	1
2	25765070	Non-small cell lung cancer (NSCLC)	smoking	Anti-PD-1 (pembrolizumab)	10	3	0	0	0	1
3	25765070	Non-small cell lung cancer (NSCLC)	non-smoking	Anti-PD-1 (pembrolizumab)	4	14	0	0	0	1
4	26359337	Melanoma	all	Anti-CTLA-4 (ipilimumab)	27	73	11.1	1.4	9.7	0.0589
5	26359337	Melanoma	BRAFi	Anti-CTLA-4 (ipilimumab)	0	14	0	0	0	1
6	26359337	Melanoma	non-BRAFi	Anti-CTLA-4 (ipilimumab)	27	59	11.1	1.7	9.4	0.0895
7	26997480	Melanoma	all	Anti-PD-1 (pembrolizumab and nivolumab)	21	17	4.8	5.9	-1.1	1
8	26997480	Melanoma	MAPKi	Anti-PD-1 (pembrolizumab and nivolumab)	8	6	0	0	0	1
9	26997480	Melanoma	non-MAPKi	Anti-PD-1 (pembrolizumab and nivolumab)	13	11	7.7	9.1	-1.4	1
10	28552987	Urothelial cancer	all	Anti-PD-L1 (atezolizumab)	9	16	11.1	6.2	4.9	1
11	28552987	Urothelial cancer	smoking	Anti-PD-L1 (atezolizumab)	5	9	0	11.1	-11.1	1
12	28552987	Urothelial cancer	non-smoking	Anti-PD-L1 (atezolizumab)	4	7	25	0	25	0.364
13	29033130	Melanoma	all	Anti-PD-1 (nivolumab)	38	27	0	3.7	-3.7	0.415
14	29033130	Melanoma	NIV3-PROG	Anti-PD-1 (nivolumab)	22	13	0	0	0	1
15	29033130	Melanoma	NIV3-NAIVE	Anti-PD-1 (nivolumab)	16	14	0	7.1	-7.1	0.467
16	29301960	Clear cell renal cell carcinoma (ccRCC)	all	Anti-PD-1 (nivolumab)	11	13	0	0	0	1
17	29301960	Clear cell renal cell carcinoma (ccRCC)	VEGFRi	Anti-PD-1 (nivolumab)	6	1	0	0	0	1
18	29301960	Clear cell renal cell carcinoma (ccRCC)	non-VEGFRi	Anti-PD-1 (nivolumab)	5	12	0	0	0	1

Summary
Symbol	CPSF7
Name	cleavage and polyadenylation specific factor 7, 59kDa
Aliases	FLJ12529; pre mRNA cleavage factor I, 59 kDa subunit; cleavage factor Im complex 59 kDa subunit; CFIm59; CPS ......
Chromosomal Location	11q12.2
External Links	HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content	Relations between abundance of tumor-infiltrating lymphocytes (TILs) and expression, copy number, methylation, or mutation of CPSF7. The immune-related signatures of 28 TIL types from Charoentong's study, which can be viewed in the download page. For each cancer type, the relative abundance of TILs were inferred by using gene set variation analysis (GSVA) based on gene expression profile. In this tab, users can examine which kinds of TILs might be regulated by the current gene.

> Lymphocyte [ TOP ]

Summary
Symbol	CPSF7
Name	cleavage and polyadenylation specific factor 7, 59kDa
Aliases	FLJ12529; pre mRNA cleavage factor I, 59 kDa subunit; cleavage factor Im complex 59 kDa subunit; CFIm59; CPS ......
Chromosomal Location	11q12.2
External Links	HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content	Relations between three kinds of immunomodulators and expression, copy number, methylation, or mutation of CPSF7. These immunomo-dulators were collected from Charoentong's study. In this tab, users can examine which immunomodulators might be regulated by CPSF7. > Immunoinhibitor > Immunostimulator > MHC molecule

> Immunoinhibitor [ TOP ]

> Immunostimulator [ TOP ]

> MHC molecule [ TOP ]

Summary
Symbol	CPSF7
Name	cleavage and polyadenylation specific factor 7, 59kDa
Aliases	FLJ12529; pre mRNA cleavage factor I, 59 kDa subunit; cleavage factor Im complex 59 kDa subunit; CFIm59; CPS ......
Chromosomal Location	11q12.2
External Links	HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content	Relations between chemokines (or receptors) and expression, copy number, methylation, or mutation of CPSF7. In this tab, users can examine which chemokines (or receptors) might be regulated by the current gene. > Chemokine > Receptor

> Chemokine [ TOP ]

> Receptor [ TOP ]

Summary
Symbol	CPSF7
Name	cleavage and polyadenylation specific factor 7, 59kDa
Aliases	FLJ12529; pre mRNA cleavage factor I, 59 kDa subunit; cleavage factor Im complex 59 kDa subunit; CFIm59; CPS ......
Chromosomal Location	11q12.2
External Links	HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content	Distribution of CPSF7 expression across immune and molecular subtypes. > Immune subtype > Molecular subtype

> Immune subtype [ TOP ]

> Molecular subtype [ TOP ]

Summary
Symbol	CPSF7
Name	cleavage and polyadenylation specific factor 7, 59kDa
Aliases	FLJ12529; pre mRNA cleavage factor I, 59 kDa subunit; cleavage factor Im complex 59 kDa subunit; CFIm59; CPS ......
Chromosomal Location	11q12.2
External Links	HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content	Associations between CPSF7 and clinical features. > Overall survival analysis > Cancer stage > Tumor grade

> Overall survival [ TOP ]

> Stage [ TOP ]

> Grade [ TOP ]

Summary
Symbol	CPSF7
Name	cleavage and polyadenylation specific factor 7, 59kDa
Aliases	FLJ12529; pre mRNA cleavage factor I, 59 kDa subunit; cleavage factor Im complex 59 kDa subunit; CFIm59; CPS ......
Chromosomal Location	11q12.2
External Links	HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content	Drugs targeting CPSF7 collected from DrugBank database.

> Drugs from DrugBank database [ TOP ]
There is no record.

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