mutLBSgeneDB

mutLBSgeneDB
mutated Ligand Binding Site gene DataBase

Home

	Gene Summary
	Ligand Binding Site Mutation Information
	Protein Structure Related Information
	Gene Expression and Gene-Gene Network
	Phenotype Information
	Pharmacological Information
	Conservation Information for LBS

Gene summary for CPSF3

Gene summary

Basic gene Info.	Gene symbol	CPSF3
	Gene name	cleavage and polyadenylation specific factor 3, 73kDa
	Synonyms	CPSF-73\|CPSF73
	Cytomap	UCSC genome browser: 2p25.1
	Type of gene	protein-coding
	RefGenes	NM_016207.3,
	Description	cleavage and polyadenylation specificity factor subunit 3mRNA 3'-end-processing endonuclease CPSF-73
	Modification date	20141207
dbXrefs	MIM : 606029
	HGNC : HGNC
	Ensembl : ENSG00000119203
	HPRD : 05825
	Vega : OTTHUMG00000090415
Protein	UniProt: Q9UKF6 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_CPSF3
	BioGPS: 51692
Pathway	NCI Pathway Interaction Database: CPSF3
	KEGG: CPSF3
	REACTOME: CPSF3
	Pathway Commons: CPSF3
Context	iHOP: CPSF3
	ligand binding site mutation search in PubMed: CPSF3
	UCL Cancer Institute: CPSF3
Assigned class in mutLBSgeneDB	C: This gene just belongs to mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez

GO ID	GO Term	PubMed ID
GO:0006398	histone mRNA 3'-end processing	18688255

Top

Ligand binding site mutations for CPSF3

Lollipop-style diagram of mutations at LBS in amino-acid sequence.
We represented ligand binding site mutations only. (You can see big image via clicking.)

: non-synonymous mutation on LBS, Circle size denotes number of samples.

Cancer type specific mutLBS sorted by frequency

LBS	AAchange of nsSNV	Cancer type	# samples
D75,H73	L74S	COAD	1
H158	H158L	KIRC	1
D179	G178R	SKCM	1

cf) Cancer type abbreviation. BLCA: Bladder urothelial carcinoma, BRCA: Breast invasive carcinoma, CESC: Cervical squamous cell carcinoma and endocervical adenocarcinoma, COAD: Colon adenocarcinoma, GBM: Glioblastoma multiforme, LGG: Brain lower grade glioma, HNSC: Head and neck squamous cell carcinoma, KICH: Kidney chromophobe, KIRC: Kidney renal clear cell carcinoma, KIRP: Kidney renal papillary cell carcinoma, LAML: Acute myeloid leukemia, LUAD: Lung adenocarcinoma, LUSC: Lung squamous cell carcinoma, OV: Ovarian serous cystadenocarcinoma, PAAD: Pancreatic adenocarcinoma, PRAD: Prostate adenocarcinoma, SKCM: Skin cutaneous melanoma, STAD: Stomach adenocarcinoma, THCA: Thyroid carcinoma, UCEC: Uterine corpus endometrial carcinoma.

Top

Protein structure related information for CPSF3

Relative protein structure stability change (ΔΔE) using Mupro 1.1
Mupro score denotes assessment of the effect of mutations on thermodynamic stability.
(ΔΔE<0: mutation decreases stability, ΔΔE>0: mutation increases stability)

: nsSNV at non-LBS

: nsSNV at LBS

nsSNVs sorted by the relative stability change of protein structure by each mutation
Blue: mutations of positive stability change. and red : the most recurrent mutation for this gene.

LBS	AAchange of nsSNV	Relative stability change
H158	H158L	0.3390007
H73	L74S	-1.2640073
D75	L74S	-1.2640073
D179	G178R	-0.87651524

(MuPro1.1: Jianlin Cheng et al., Prediction of Protein Stability Changes for Single-Site Mutations Using Support Vector Machines, PROTEINS: Structure, Function, and Bioinformatics. 2006, 62:1125-1132)

Structure image for CPSF3 from PDB

Top

Differential gene expression and gene-gene network for CPSF3

Differential gene expression between mutated and non-mutated LBS samples in all 16 major cancer types

Differential co-expressed gene network based on protein-protein interaction data (CePIN)

* Left PPI network was created from samples with mutations in the LBS of CPSF3 and the right PPI network was created from samples without mutations in the LBS of CPSF3. Only genes with p-value < 0.05 are shown.
Red circle: input gene. Orange circle: LBSgene. Blue circle: other gene.

Top

Phenotype information for CPSF3

Gene level disease information (DisGeNet)

Disease ID

Disease name

# PubMed

Association type

Mutation level pathogenic information (ClinVar annotation)

Allele ID

AA change

Clinical significance

Origin

Phenotype IDs

Top

Pharmacological information for CPSF3

Drug information targeting mutLBSgene (Approved drugs only)

Drug status

DrugBank ID

Name

Type

Drug structure

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of CPSF3 go to BioLip

Ligand ID	Ligand short name	Ligand long name	PDB ID	PDB name	mutLBS
ZN		ZINC(2+)	2i7t	A	D75 D179
ZN		ZINC(2+)	2i7v	A	D75 D179
SO4		SULFATE	2i7t	A	H73 D75 H158 D179
SO4		SULFATE	2i7v	A	H73 D75 H158 D179
ZN		ZINC(2+)	2i7t	A	H73 H158 D179
ZN		ZINC(2+)	2i7v	A	H73 H158 D179

Top

Conservation information for LBS of CPSF3

Multiple alignments for Q9UKF6 in multiple species

LBS	AA sequence	# species	Species
D179	LLYTGDFSRQE	3	Homo sapiens, Mus musculus, Bos taurus
D179	VLFTGDYSREV	2	Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
D179	IFFTGDYSREE	1	Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
D179	ILFTGDYSREE	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
D179	ILFTGDYSREL	1	Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056)
D179	ILYTGDYSREE	1	Arabidopsis thaliana
D179	ILYTGDFSRQE	1	Drosophila melanogaster
D75	SHFHLDHCGAL	4	Homo sapiens, Drosophila melanogaster, Mus musculus, Bos taurus
D75	SHFHLDHAASL	3	Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37), Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056)
D75	SHFHIDHAASL	1	Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
D75	SHFHLDHVASL	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
D75	THFHIDHAASL	1	Arabidopsis thaliana
E262	WQNHPEL---H	3	Homo sapiens, Mus musculus, Bos taurus
E262	WGKHAEY---Q	1	Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
E262	WNNHLDL---R	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
E262	WSQHADELGGG	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
E262	WQNHKEELGNG	1	Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
E262	WSQHAEQLGNG	1	Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056)
E262	WANHPDL---H	1	Arabidopsis thaliana
E262	WSQNPDL---H	1	Drosophila melanogaster
E436	LIREYEDND--	3	Homo sapiens, Mus musculus, Bos taurus
E436	LLSLNATKE--	1	Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
E436	LASKFHNRK--	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
E436	LLSNFASLKGT	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
E436	LLSNFSSLKDT	1	Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
E436	LLSNFSSLKGT	1	Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056)
E436	LLTEFPDGN--	1	Arabidopsis thaliana
E436	LQREYEADA--	1	Drosophila melanogaster
H158	CYHAGHVLGAA	3	Homo sapiens, Mus musculus, Bos taurus
H158	AFHAGHVLGAA	2	Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
H158	PYPAGHVLGAA	1	Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
H158	PYHAGHVLGAC	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
H158	AYHAGHVLGAA	1	Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056)
H158	CYTAGHVLGAA	1	Arabidopsis thaliana
H158	AYIAGHVLGAA	1	Drosophila melanogaster
H260	EYWQNHPEL--	3	Homo sapiens, Mus musculus, Bos taurus
H260	EYWGKHAEY--	1	Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
H260	EYWNNHLDL--	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
H260	EYWSQHADELG	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
H260	EYWQNHKEELG	1	Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
H260	EYWSQHAEQLG	1	Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056)
H260	EYWANHPDL--	1	Arabidopsis thaliana
H260	EFWSQNPDL--	1	Drosophila melanogaster
H396	ISFSAHTDYQQ	4	Homo sapiens, Drosophila melanogaster, Mus musculus, Bos taurus
H396	FSFAAHVDGVE	1	Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
H396	LSFAAHVDYLQ	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
H396	ISFAAHVDFQE	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
H396	ITFAAHVDFRE	1	Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
H396	ISFAAHVDFRE	1	Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056)
H396	ISFSAHADYAQ	1	Arabidopsis thaliana
H418	HVILVHGEQNE	3	Homo sapiens, Mus musculus, Bos taurus
H418	NIILVHGESNP	2	Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37), Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056)
H418	VVILVHGEVHN	1	Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
H418	HIILVHGEQTN	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
H418	NIILVHGEANP	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
H418	NIILVHGEANE	1	Arabidopsis thaliana
H418	HVVLVHGEQNE	1	Drosophila melanogaster
H442	D--EVHIEVHN	3	Homo sapiens, Mus musculus, Bos taurus
H442	E---HKVKVFS	1	Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
H442	K---VDVKVYT	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
H442	KGTDNEVHVFN	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
H442	KDTENEVHVFN	1	Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
H442	KGTEDEVRVYN	1	Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056)
H442	N-----TKIMT	1	Arabidopsis thaliana
H442	A--STDIKFYN	1	Drosophila melanogaster
H71	LLLISHFHLDH	4	Homo sapiens, Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37), Mus musculus, Bos taurus
H71	VLLISHFHLDH	2	Schizosaccharomyces pombe (strain 972 / ATCC 24843), Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056)
H71	VLLISHFHIDH	1	Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
H71	ILLISHFHLDH	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
H71	VLLITHFHIDH	1	Arabidopsis thaliana
H71	LLFISHFHLDH	1	Drosophila melanogaster
H73	LISHFHLDHCG	3	Homo sapiens, Mus musculus, Bos taurus
H73	LISHFHLDHAA	3	Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37), Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056)
H73	LISHFHIDHAA	1	Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
H73	LISHFHLDHVA	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
H73	LITHFHIDHAA	1	Arabidopsis thaliana
H73	FISHFHLDHCG	1	Drosophila melanogaster
H76	HFHLDHCGALP	4	Homo sapiens, Drosophila melanogaster, Mus musculus, Bos taurus
H76	HFHLDHAASLP	3	Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37), Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056)
H76	HFHIDHAASLP	2	Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987), Arabidopsis thaliana
H76	HFHLDHVASLP	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)