Cstf3 (cleavage stimulation factor subunit 3)

Gene: Cstf3 (cleavage stimulation factor subunit 3) Rattus norvegicus

Analyze

Symbol:

Cstf3

Name:

cleavage stimulation factor subunit 3

RGD ID:

1305901

Description:

Predicted to enable mRNA binding activity. Predicted to be involved in co-transcriptional mRNA 3'-end processing, cleavage and polyadenylation pathway. Predicted to be located in nucleoplasm. Predicted to be part of mRNA cleavage stimulating factor complex. Predicted to be active in nucleus. Orthologous to human CSTF3 (cleavage stimulation factor subunit 3); PARTICIPATES IN 3'-end pre-mRNA processing pathway; RNA polymerase II transcription termination pathway; mRNA decay pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,4,6-trinitrotoluene; 2,4-dinitrotoluene.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Previously known as:

cleavage stimulation factor, 3' pre-RNA, subunit 3; cleavage stimulation factor, 3' pre-RNA, subunit 3, 77kDa; LOC362178; MGC156746

RGD Orthologs

Alliance Genes

More Info

more info ...

More Info

Species	Gene symbol and name	Data Source	Assertion derived from	less info ...
Orthologs ¹				less info ...
Homo sapiens (human):	CSTF3 (cleavage stimulation factor subunit 3)	HGNC	Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, Treefam
Mus musculus (house mouse):	Cstf3 (cleavage stimulation factor, 3' pre-RNA, subunit 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Cstf3 (cleavage stimulation factor subunit 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	CSTF3 (cleavage stimulation factor subunit 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	CSTF3 (cleavage stimulation factor subunit 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Cstf3 (cleavage stimulation factor subunit 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	CSTF3 (cleavage stimulation factor subunit 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	CSTF3 (cleavage stimulation factor subunit 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Cstf3 (cleavage stimulation factor subunit 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Other homologs ²
Homo sapiens (human):	CSNK1G3 (casein kinase 1 gamma 3)	HGNC	OMA
Alliance orthologs ³
Homo sapiens (human):	CSTF3 (cleavage stimulation factor subunit 3)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Cstf3 (cleavage stimulation factor, 3' pre-RNA, subunit 3)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	cstf3 (cleavage stimulation factor, 3' pre-RNA, subunit 3)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|SonicParanoid)
Saccharomyces cerevisiae (baker's yeast):	RNA14	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)
Drosophila melanogaster (fruit fly):	su(f)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|SonicParanoid)
Caenorhabditis elegans (roundworm):	suf-1	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Xenopus tropicalis (tropical clawed frog):	cstf3	Alliance	DIOPT (Ensembl Compara\|OrthoFinder\|PANTHER\|PhylomeDB)
Xenopus tropicalis (tropical clawed frog):	smim15	Alliance	DIOPT (OMA\|OrthoFinder\|PhylomeDB)

Latest Assembly:

mRatBN7.2 - mRatBN7.2 Assembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	3	111,421,291 - 111,492,539 (+)	NCBI		GRCr8
mRatBN7.2	3	90,966,415 - 91,037,669 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	3	90,966,354 - 91,042,196 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	3	94,460,422 - 94,531,676 (+)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	3	103,059,495 - 103,130,743 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	3	100,889,656 - 100,960,806 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	3	94,530,586 - 94,603,378 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	3	94,530,586 - 94,607,588 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	3	101,156,169 - 101,228,401 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	3	89,919,376 - 89,991,676 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	3	89,815,940 - 89,892,116 (+)	NCBI
Celera	3	90,026,496 - 90,097,116 (+)	NCBI		Celera
Cytogenetic Map	3	q32	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

genetic disease (ISO)

intellectual disability (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2-dimethylhydrazine (ISO)

17alpha-ethynylestradiol (ISO)

2,2',4,4'-Tetrabromodiphenyl ether (ISO)

2,3,7,8-tetrachlorodibenzodioxine (EXP,ISO)

2,4,6-trinitrotoluene (EXP)

2,4-dinitrotoluene (EXP)

2,6-dinitrotoluene (EXP)

2-hydroxypropanoic acid (ISO)

2-methylcholine (ISO)

3-isobutyl-1-methyl-7H-xanthine (ISO)

4,4'-sulfonyldiphenol (ISO)

4-amino-2,6-dinitrotoluene (EXP)

5-fluorouracil (ISO)

acrylamide (ISO)

all-trans-retinoic acid (ISO)

Aroclor 1254 (ISO)

atrazine (ISO)

benzo[a]pyrene (ISO)

benzo[a]pyrene diol epoxide I (ISO)

bis(2-ethylhexyl) phthalate (EXP)

bisphenol A (EXP,ISO)

bisphenol F (ISO)

cadmium sulfate (ISO)

caffeine (ISO)

carbamazepine (ISO)

carbon nanotube (ISO)

chlorpyrifos (ISO)

choline (ISO)

ciguatoxin CTX1B (ISO)

cisplatin (ISO)

copper atom (ISO)

copper(0) (ISO)

copper(II) sulfate (ISO)

cyclosporin A (ISO)

dexamethasone (ISO)

dibutyl phthalate (EXP,ISO)

diclofenac (ISO)

dicrotophos (ISO)

ethanol (ISO)

flutamide (EXP)

folic acid (ISO)

FR900359 (ISO)

furan (EXP,ISO)

gentamycin (EXP)

hydrogen peroxide (ISO)

indole-3-methanol (EXP)

indometacin (ISO)

ivermectin (ISO)

L-methionine (ISO)

ochratoxin A (EXP)

oxaliplatin (ISO)

paracetamol (ISO)

phenobarbital (ISO)

pirinixic acid (ISO)

rac-lactic acid (ISO)

silicon dioxide (ISO)

silver atom (ISO)

silver(0) (ISO)

sodium dichromate (EXP)

succimer (ISO)

tamoxifen (ISO)

tetrachloromethane (EXP,ISO)

tetraphene (ISO)

thioacetamide (EXP)

trichostatin A (ISO)

troglitazone (ISO)

urethane (ISO)

valproic acid (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

biological_process (ND)

co-transcriptional mRNA 3'-end processing, cleavage and polyadenylation pathway (ISO)

RNA 3'-end processing (IBA)

Cellular Component

mRNA cleavage stimulating factor complex (ISO)

nucleoplasm (IEA,ISO)

nucleus (IBA)

Molecular Function

mRNA binding (IBA)

protein binding (IPI,ISO)

Molecular Pathway Annotations Click to see Annotation Detail View

3'-end pre-mRNA processing pathway (ISO)

mRNA decay pathway (IEA)

RNA polymerase II transcription termination pathway (ISO)

References

References - curated

#	Reference Title	Reference Citation
1.	Pre-mRNA 3'-end processing complex assembly and function.	Chan S, etal., Wiley Interdiscip Rev RNA. 2011 May-Jun;2(3):321-35. doi: 10.1002/wrna.54. Epub 2010 Oct 18.
2.	Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
3.	Rat ISS GO annotations from GOA human gene data--August 2006	GOA data from the GO Consortium
4.	Means to an end: mechanisms of alternative polyadenylation of messenger RNA precursors.	Gruber AR, etal., Wiley Interdiscip Rev RNA. 2014 Mar-Apr;5(2):183-96. doi: 10.1002/wrna.1206. Epub 2013 Nov 14.
5.	KEGG Annotation Import Pipeline	Pipeline to import KEGG annotations from KEGG into RGD
6.	GOA pipeline	RGD automated data pipeline
7.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions
8.	Comprehensive gene review and curation	RGD comprehensive gene curation
9.	Polyadenylation site-specific differences in the activity of the neuronal betaCstF-64 protein in PC-12 cells.	Shankarling GS and MacDonald CC, Gene. 2013 Oct 25;529(2):220-7. doi: 10.1016/j.gene.2013.08.007. Epub 2013 Aug 12.

Additional References at PubMed

PMID:12477932	PMID:22681889

Genomics

Comparative Map Data

Cstf3
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	3	111,421,291 - 111,492,539 (+)	NCBI		GRCr8
mRatBN7.2	3	90,966,415 - 91,037,669 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	3	90,966,354 - 91,042,196 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	3	94,460,422 - 94,531,676 (+)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	3	103,059,495 - 103,130,743 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	3	100,889,656 - 100,960,806 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	3	94,530,586 - 94,603,378 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	3	94,530,586 - 94,607,588 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	3	101,156,169 - 101,228,401 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	3	89,919,376 - 89,991,676 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	3	89,815,940 - 89,892,116 (+)	NCBI
Celera	3	90,026,496 - 90,097,116 (+)	NCBI		Celera
Cytogenetic Map	3	q32	NCBI

CSTF3
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	11	33,084,584 - 33,161,480 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	11	33,077,188 - 33,162,371 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	11	33,106,130 - 33,183,026 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	11	33,062,706 - 33,139,613 (-)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	11	33,062,727 - 33,139,578	NCBI
Celera	11	33,252,825 - 33,329,726 (-)	NCBI		Celera
Cytogenetic Map	11	p13	NCBI
HuRef	11	32,800,798 - 32,877,697 (-)	NCBI		HuRef
CHM1_1	11	33,105,588 - 33,182,478 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	11	33,220,126 - 33,297,015 (-)	NCBI		T2T-CHM13v2.0

Cstf3
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	2	104,420,829 - 104,495,770 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	2	104,420,868 - 104,495,774 (+)	Ensembl		GRCm39 Ensembl
GRCm38	2	104,590,484 - 104,665,425 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	2	104,590,523 - 104,665,429 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	2	104,430,641 - 104,505,582 (+)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	2	104,391,362 - 104,466,264 (+)	NCBI		MGSCv36	mm8
Celera	2	105,828,672 - 105,903,653 (+)	NCBI		Celera
Cytogenetic Map	2	E2	NCBI
cM Map	2	54.84	NCBI

Cstf3
(Chinchilla lanigera - long-tailed chinchilla)

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0 Ensembl	NW_004955422	13,050,088 - 13,123,784 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955422	13,049,908 - 13,124,274 (+)	NCBI	ChiLan1.0	ChiLan1.0

CSTF3
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
NHGRI_mPanPan1-v2	9	35,307,998 - 35,386,385 (-)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	11	35,312,687 - 35,391,781 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	11	33,061,237 - 33,137,911 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	11	32,945,428 - 33,022,079 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	11	32,945,934 - 33,021,885 (-)	Ensembl	panpan1.1		panPan2

CSTF3
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	18	34,493,922 - 34,563,899 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	18	34,493,980 - 34,568,326 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	18	34,105,542 - 34,175,542 (+)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	18	35,105,023 - 35,175,020 (+)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	18	35,104,999 - 35,175,017 (+)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	18	34,673,600 - 34,743,514 (+)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	18	34,257,453 - 34,327,428 (+)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	18	34,892,507 - 34,962,475 (+)	NCBI		UU_Cfam_GSD_1.0

Cstf3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024404947	31,629,531 - 31,707,483 (+)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936533	4,754,514 - 4,831,769 (+)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936533	4,754,335 - 4,832,278 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

CSTF3
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	2	27,769,421 - 27,850,382 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	2	27,769,457 - 27,850,382 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	2	30,402,895 - 30,418,796 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

CSTF3
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	1	32,083,831 - 32,106,704 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
Vero_WHO_p1.0	NW_023666038	129,218,549 - 129,295,945 (+)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Cstf3
(Heterocephalus glaber - naked mole-rat)

Naked Mole-Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Naked Mole-Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla_female_1.0 Ensembl	NW_004624767	14,071,392 - 14,144,258 (+)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624767	14,071,196 - 14,144,758 (+)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Variants

Variants in Cstf3
216 total Variants

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	19
Count of miRNA genes:	15
Interacting mature miRNAs:	19
Transcripts:	ENSRNOT00000016318
Prediction methods:	Miranda, Rnahybrid, Targetscan
Result types:	miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.

QTLs in Region (mRatBN7.2)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
2290452	Scl56	Serum cholesterol level QTL 56	2.26		blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	3	1	91609953	Rat
1358885	Bp251	Blood pressure QTL 251	3.8		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	3	14489145	121056321	Rat
1358888	Bp264	Blood pressure QTL 264	4.43		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	3	14489145	121056321	Rat
737818	Hcar12	Hepatocarcinoma resistance QTL 12	2.6		liver integrity trait (VT:0010547)	volume of individual liver tumorous lesion (CMO:0001078)	3	29463235	118376539	Rat
61419	Cia11	Collagen induced arthritis QTL 11	5.6		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	3	30356773	98535386	Rat
70216	Cm14	Cardiac mass QTL 14	2.1		heart mass (VT:0007028)	heart wet weight (CMO:0000069)	3	31172320	163586636	Rat
1354604	Bw36	Body weight QTL 36	2.9		body mass (VT:0001259)	body weight (CMO:0000012)	3	33703347	104104347	Rat
1358362	Srcrt2	Stress Responsive Cort QTL 2	2.78		blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	3	38192233	133483320	Rat
1354597	Kidm13	Kidney mass QTL 13	2.9		kidney mass (VT:0002707)	right kidney wet weight (CMO:0000082)	3	41874578	104104347	Rat
2301970	Bw81	Body weight QTL 81	5.19		body mass (VT:0001259)	body weight (CMO:0000012)	3	41874578	155617519	Rat
2301971	Cm71	Cardiac mass QTL 71	4.63		heart left ventricle mass (VT:0007031)	heart left ventricle weight (CMO:0000776)	3	41874578	155617519	Rat
1581503	Cm58	Cardiac mass QTL 58	2.7	0.05	heart left ventricle mass (VT:0007031)	heart left ventricle weight to body weight ratio (CMO:0000530)	3	43827364	121056321	Rat
1559282	Emca5	Estrogen-induced mammary cancer QTL 5	3.9		mammary gland integrity trait (VT:0010552)	percentage of study population developing mammary tumors during a period of time (CMO:0000948)	3	43827364	169034231	Rat
2292591	Esta4	Estrogen-induced thymic atrophy QTL 4			thymus mass (VT:0004954)	thymus wet weight (CMO:0000855)	3	47233211	147415807	Rat
1358186	Ept2	Estrogen-induced pituitary tumorigenesis QTL 2	8.3		pituitary gland mass (VT:0010496)	pituitary gland wet weight (CMO:0000853)	3	47233430	110362260	Rat
2292613	Ept16	Estrogen-induced pituitary tumorigenesis QTL 16	8.3		pituitary gland mass (VT:0010496)	pituitary gland wet weight (CMO:0000853)	3	47233430	110362260	Rat
631665	Bw8	Body weight QTL 8	5.5		body mass (VT:0001259)	body weight (CMO:0000012)	3	50437042	119183768	Rat
724523	Tsu1	Thymus enlargement suppressive QTL 1	3.84		thymus mass (VT:0004954)	thymus weight to body weight ratio (CMO:0000612)	3	50437504	115638231	Rat
1582218	Bw74	Body weight QTL 74	3.9	0.0021	body mass (VT:0001259)	body weight (CMO:0000012)	3	53184593	115665732	Rat
1582238	Bw68	Body weight QTL 68	3.2	0.0064	body mass (VT:0001259)	body weight (CMO:0000012)	3	53184593	115665732	Rat
1582239	Epfw1	Epididymal fat weight QTL 1	4.5	0.0006	epididymal fat pad mass (VT:0010421)	epididymal fat pad weight to body weight ratio (CMO:0000658)	3	53184593	115665732	Rat
731180	Bp152	Blood pressure QTL 152		0.03	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	3	53781112	91609953	Rat
731180	Bp152	Blood pressure QTL 152		0.03	arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	3	53781112	91609953	Rat
731180	Bp152	Blood pressure QTL 152		0.03	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	3	53781112	91609953	Rat
1581568	Rf53	Renal function QTL 53			urine total protein amount (VT:0000032)	urine protein excretion rate to body weight ratio (CMO:0001099)	3	56395968	161299569	Rat
8662816	Vetf4	Vascular elastic tissue fragility QTL 4	4		renal artery integrity trait (VT:0010642)	number of ruptures of the internal elastic lamina of the renal arteries (CMO:0002563)	3	59242096	157323038	Rat
1300111	Rf12	Renal function QTL 12	3.78		renal blood flow trait (VT:2000006)	absolute change in renal blood flow rate (CMO:0001168)	3	61017749	121056321	Rat
1582210	Bw71	Body weight QTL 71	3.3	0.0012	body mass (VT:0001259)	body weight (CMO:0000012)	3	64655305	115665732	Rat
1582221	Kidm30	Kidney mass QTL 30	3.5	0.0008	kidney mass (VT:0002707)	both kidneys wet weight (CMO:0000085)	3	64655305	115665732	Rat
12879848	Bw181	Body weght QTL 181		0.015	body mass (VT:0001259)	body weight (CMO:0000012)	3	70348525	121056321	Rat
2301414	Kidm37	Kidney mass QTL 37		0.001	kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	3	70653097	121056321	Rat
1600376	Arunc5	Aerobic running capacity QTL 5		0.21	exercise endurance trait (VT:0002332)	maximum distance run on treadmill (CMO:0001406)	3	73376539	118376539	Rat
1581546	Pur13	Proteinuria QTL 13	2.93	0.0335	urine total protein amount (VT:0000032)	urine protein excretion rate (CMO:0000759)	3	78196190	146592722	Rat
2302273	Gluco35	Glucose level QTL 35	5.3	0.001	blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	3	80800231	114297550	Rat
631649	Bp123	Blood pressure QTL 123	3.2		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	3	89772419	134772419	Rat

Markers in Region

D3Got46

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	3	90,992,393 - 90,992,693 (+)	MAPPER	mRatBN7.2
Rnor_6.0	3	94,557,269 - 94,557,568	NCBI	Rnor6.0
Rnor_5.0	3	101,182,355 - 101,182,654	UniSTS	Rnor5.0
RGSC_v3.4	3	89,945,874 - 89,946,172	RGD	RGSC3.4
RGSC_v3.4	3	89,945,875 - 89,946,174	UniSTS	RGSC3.4
RGSC_v3.1	3	89,842,302 - 89,842,600	RGD
Celera	3	90,052,416 - 90,052,715	UniSTS
RH 3.4 Map	3	722.2	UniSTS
RH 3.4 Map	3	722.2	RGD
RH 2.0 Map	3	470.3	RGD
Cytogenetic Map	3	q32	UniSTS

RH144362

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	3	91,037,486 - 91,037,681 (+)	MAPPER	mRatBN7.2
Rnor_6.0	3	94,603,196 - 94,603,390	NCBI	Rnor6.0
Rnor_5.0	3	101,228,219 - 101,228,413	UniSTS	Rnor5.0
RGSC_v3.4	3	89,991,494 - 89,991,688	UniSTS	RGSC3.4
Celera	3	90,096,934 - 90,097,128	UniSTS
RH 3.4 Map	3	732.0	UniSTS
Cytogenetic Map	3	q32	UniSTS

RH142661

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	3	91,041,937 - 91,042,118 (+)	MAPPER	mRatBN7.2
Rnor_6.0	3	94,607,647 - 94,607,827	NCBI	Rnor6.0
Rnor_5.0	3	101,232,670 - 101,232,850	UniSTS	Rnor5.0
RGSC_v3.4	3	89,995,945 - 89,996,125	UniSTS	RGSC3.4
Celera	3	90,101,385 - 90,101,565	UniSTS
RH 3.4 Map	3	731.7	UniSTS
Cytogenetic Map	3	q32	UniSTS

BF406428

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	3	90,970,936 - 90,971,075 (+)	MAPPER	mRatBN7.2
Rnor_6.0	3	94,535,110 - 94,535,248	NCBI	Rnor6.0
Rnor_5.0	3	101,160,693 - 101,160,831	UniSTS	Rnor5.0
RGSC_v3.4	3	89,923,858 - 89,923,996	UniSTS	RGSC3.4
Celera	3	90,031,019 - 90,031,157	UniSTS
Cytogenetic Map	3	q32	UniSTS

RH139617

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	3	90,998,886 - 90,999,067 (+)	MAPPER	mRatBN7.2
Rnor_6.0	3	94,563,733 - 94,563,913	NCBI	Rnor6.0
Rnor_5.0	3	101,188,819 - 101,188,999	UniSTS	Rnor5.0
RGSC_v3.4	3	89,952,789 - 89,952,969	UniSTS	RGSC3.4
Celera	3	90,058,596 - 90,058,776	UniSTS
RH 3.4 Map	3	724.2	UniSTS
Cytogenetic Map	3	q32	UniSTS

RH126683

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	3	91,041,887 - 91,042,104 (+)	MAPPER	mRatBN7.2
Rnor_6.0	3	94,607,597 - 94,607,813	NCBI	Rnor6.0
Rnor_5.0	3	101,232,620 - 101,232,836	UniSTS	Rnor5.0
RGSC_v3.4	3	89,995,895 - 89,996,111	UniSTS	RGSC3.4
Celera	3	90,101,335 - 90,101,551	UniSTS
Cytogenetic Map	3	q32	UniSTS

Expression

RNA-SEQ Expression

High: > 1000 TPM value Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM Below Cutoff: < 0.5 TPM

	alimentary part of gastrointestinal system	circulatory system	endocrine system	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	musculoskeletal system	nervous system	renal system	reproductive system	respiratory system	appendage
High
Medium	3	26	28	18	19	18			74	26	41	11
Low		17	29	23		23	8	11		9			8
Below cutoff

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001077672	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	BC127520	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473949	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ223256	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000003	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

RefSeq Acc Id:

ENSRNOT00000016318 ⟹ ENSRNOP00000016318

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	3	90,966,354 - 91,042,182 (+)	Ensembl
Rnor_6.0 Ensembl	3	94,549,180 - 94,607,588 (+)	Ensembl

RefSeq Acc Id:

ENSRNOT00000067860 ⟹ ENSRNOP00000061864

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	3	94,530,586 - 94,548,554 (+)	Ensembl

RefSeq Acc Id:

ENSRNOT00000076438 ⟹ ENSRNOP00000068083

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	3	94,596,197 - 94,603,378 (+)	Ensembl

RefSeq Acc Id:

ENSRNOT00000076762 ⟹ ENSRNOP00000068217

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	3	90,966,354 - 91,042,196 (+)	Ensembl
Rnor_6.0 Ensembl	3	94,585,873 - 94,592,142 (+)	Ensembl

RefSeq Acc Id:

NM_001077672 ⟹ NP_001071140

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	3	111,421,291 - 111,492,539 (+)	NCBI
mRatBN7.2	3	90,966,415 - 91,037,669 (+)	NCBI
Rnor_6.0	3	94,530,586 - 94,603,378 (+)	NCBI
Rnor_5.0	3	101,156,169 - 101,228,401 (+)	NCBI
RGSC_v3.4	3	89,919,376 - 89,991,676 (+)	RGD
Celera	3	90,026,496 - 90,097,116 (+)	RGD

Sequence:

show sequence

GGCGATTTTTGCGGCGGCTCTGGCTCCGAGGGACAAGGGGTAGCGTTACTGGTTTTGGTGGGGT
TGTTTTTAGTTTAAAATTTTCCTTTCTAGCTTCCCATTGCCGGCCCGTGTGTACGTTGTAATCC
TCTGAGGCCATGTCAGGAGACGCAGCCGCGGAGCAGGCAGCTGAATATGTCCCAGAGAAGGTGA
AGAAAGCGGAAAAGAAATTAGAAGAAAATCCATATGACCTTGATGCTTGGAGCATTCTCATTCG
AGAGGCACAGAATCAACCTATAGACAAAGCACGGAAGACTTACGAACGCCTTGTTGCCCAGTTC
CCCAGTTCTGGCAGATTCTGGAAACTGTACATTGAAGCAGAGATTAAAGCTAAAAATTATGACA
AGGTTGAAAAGCTATTTCAAAGATGCCTTATGAAGGTTTTGCACATTGATTTATGGAAGTGTTA
TCTTTCATACGTCAGAGAAACCAAGGGTAAACTGCCAAGTTACAAAGAAAAAATGGCTCAAGCT
TATGACTTTGCACTGGATAAAATTGGAATGGAAATTATGTCCTATCAGATTTGGGTGGATTACA
TCAATTTCTTAAAAGGCGTGGAAGCTGTAGGATCTTATGCAGAAAATCAGAGAATAACTGCTGT
CCGAAGAGTTTATCAACGAGGTTGTGTTAATCCAATGATCAACATTGAACAACTCTGGAGAGAC
TACAACAAGTATGAAGAGGGTATCAATATTCATTTAGCTAAAAAGATGATTGAAGATCGAAGTA
GAGACTACATGAATGCTAGACGTGTAGCAAAGGAATACGAGACAGTGATGAAAGGTTTGGACCG
CAATGCCCCTTCAGTGCCCCCTCAGAATACCCCTCAAGAAGCTCAGCAAGTAGACATGTGGAAG
AAGTACATCCAGTGGGAGAAGAGCAACCCCCTGCGTACCGAGGACCAGACCCTCATAACAAAGC
GAGTTATGTTTGCCTATGAACAGTGCCTACTTGTGCTGGGCCATCACCCTGATATCTGGTATGA
AGCTGCCCAGTATCTGGAACAGTCGAGTAAGCTGCTCGCAGAAAAGGGGGATATGAACAATGCC
AAATTATTTAGTGATGAAGCTGCTAATATATATGAACGAGCCATCAGCACTTTATTAAAGAAGA
ACATGCTCCTTTACTTTGCATATGCAGATTATGAAGAGAGTCGCATGAAGTACGAGAAAGTTCA
CAGTATATATAACAGACTGCTGGCAATTGAGGACATTGACCCCACCTTGGTATATATCCAATAT
ATGAAATTTGCAAGGAGAGCAGAAGGTATCAAATCTGGAAGAATGATATTTAAAAAGGCAAGAG
AGGATGCGAGAACCCGTCATCACGTCTATGTGACCGCAGCGCTCATGGAGTATTACTGCAGTAA
GGACAAATCTGTTGCCTTTAAGATTTTTGAATTGGGACTAAAGAAATATGGAGATATTCCAGAG
TATGTTTTGGCTTATATTGACTATCTCTCTCACCTCAATGAGGACAATAACACCCGAGTTCTGT
TTGAAAGAGTCTTGACGTCTGGAAGCCTTCCTCCCGAGAAGTCCGGAGAAATCTGGGCTCGGTT
TCTAGCTTTTGAAAGCAACATTGGTGATTTAGCTAGTATTCTCAAAGTGGAGAAAAGACGCTTT
ACAGCGTTCAGAGAAGAGTATGAAGGCAAAGAAACAGCTTTATTGGTAGACAGATACAAGTTTA
TGGATTTATACCCTTGTTCTGCAAGTGAACTCAAAGCACTGGGCTACAAGGTATGTACTCAGCA
GCAAGATGGCCGCAGTGTTCCCCTTCCCCTACGGTTTCAGGAGTCCATGCACTGCACAGTTTTC
ATTCTACGGTCAATTCTTTACTCTGTTGCTACTAAGACAAAAATATTTCATTGACTTTATTTAT
TTTGTTGTTGTTTATGGAAATCACAAGTAACAAAAAAATGGAAATTAAACATTTGAGAGCAAAT
AAATGCTTCCATTGTGTGAAAAAAAAAAAAAAAAAAAAAAAAAA

hide sequence

Protein Sequences


Protein RefSeqs	NP_001071140	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAI27521	(Get FASTA)	NCBI Sequence Viewer
	EDL79694	(Get FASTA)	NCBI Sequence Viewer
	EDL79695	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSRNOP00000016318.7
	ENSRNOP00000068217
	ENSRNOP00000068217.2

RefSeq Acc Id:

NP_001071140 ⟸ NM_001077672

- UniProtKB:

A0JPN7 (UniProtKB/TrEMBL), A0A096MJQ0 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MSGDAAAEQAAEYVPEKVKKAEKKLEENPYDLDAWSILIREAQNQPIDKARKTYERLVAQFPSS
GRFWKLYIEAEIKAKNYDKVEKLFQRCLMKVLHIDLWKCYLSYVRETKGKLPSYKEKMAQAYDF
ALDKIGMEIMSYQIWVDYINFLKGVEAVGSYAENQRITAVRRVYQRGCVNPMINIEQLWRDYNK
YEEGINIHLAKKMIEDRSRDYMNARRVAKEYETVMKGLDRNAPSVPPQNTPQEAQQVDMWKKYI
QWEKSNPLRTEDQTLITKRVMFAYEQCLLVLGHHPDIWYEAAQYLEQSSKLLAEKGDMNNAKLF
SDEAANIYERAISTLLKKNMLLYFAYADYEESRMKYEKVHSIYNRLLAIEDIDPTLVYIQYMKF
ARRAEGIKSGRMIFKKAREDARTRHHVYVTAALMEYYCSKDKSVAFKIFELGLKKYGDIPEYVL
AYIDYLSHLNEDNNTRVLFERVLTSGSLPPEKSGEIWARFLAFESNIGDLASILKVEKRRFTAF
REEYEGKETALLVDRYKFMDLYPCSASELKALGYKVCTQQQDGRSVPLPLRFQESMHCTVFILR
SILYSVATKTKIFH

hide sequence

RefSeq Acc Id:

ENSRNOP00000061864 ⟸ ENSRNOT00000067860

RefSeq Acc Id:

ENSRNOP00000016318 ⟸ ENSRNOT00000016318

RefSeq Acc Id:

ENSRNOP00000068217 ⟸ ENSRNOT00000076762

RefSeq Acc Id:

ENSRNOP00000068083 ⟸ ENSRNOT00000076438

Protein Domains

Suppressor of forked

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-F1M4W7-F1-model_v2	AlphaFold	F1M4W7	1-625	view protein structure

Transcriptome

eQTL		View at Phenogen
WGCNA		View at Phenogen
Tissue/Strain Expression		View at Phenogen

Promoters

RGD ID:

13692266

Promoter ID:

EPDNEW_R2786

Type:

initiation region

Name:

Cstf3_1

Description:

cleavage stimulation factor subunit 3

SO ACC ID:

SO:0000170

Source:

EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)

Experiment Methods:

Single-end sequencing.

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	3	94,530,564 - 94,530,624	EPDNEW

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1305901	AgrOrtholog
BioCyc Gene	G2FUF-48533	BioCyc
Ensembl Genes	ENSRNOG00000012089	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000016318.8	UniProtKB/TrEMBL
	ENSRNOT00000076762	ENTREZGENE
	ENSRNOT00000076762.2	UniProtKB/TrEMBL
Gene3D-CATH	1.25.40.1040	UniProtKB/TrEMBL
IMAGE_CLONE	IMAGE:7110287	IMAGE-MGC_LOAD
InterPro	HAT	UniProtKB/TrEMBL
	Rna14-like	UniProtKB/TrEMBL
	Suf	UniProtKB/TrEMBL
	TPR-like_helical_dom	UniProtKB/TrEMBL
KEGG Report	rno:362178	UniProtKB/TrEMBL
MGC_CLONE	MGC:156746	IMAGE-MGC_LOAD
NCBI Gene	362178	ENTREZGENE
PANTHER	CLEAVAGE STIMULATION FACTOR SUBUNIT 3	UniProtKB/TrEMBL
	PTHR19980	UniProtKB/TrEMBL
Pfam	Suf	UniProtKB/TrEMBL
PhenoGen	Cstf3	PhenoGen
RatGTEx	ENSRNOG00000012089	RatGTEx
SMART	HAT	UniProtKB/TrEMBL
Superfamily-SCOP	SSF48452	UniProtKB/TrEMBL
UniProt	A0A096MJQ0	ENTREZGENE, UniProtKB/TrEMBL
	A0JPN7	ENTREZGENE, UniProtKB/TrEMBL
	F1M4W7_RAT	UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2016-04-13	Cstf3	cleavage stimulation factor subunit 3	Cstf3	cleavage stimulation factor, 3' pre-RNA, subunit 3	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2015-11-19	Cstf3	cleavage stimulation factor, 3' pre-RNA, subunit 3	Cstf3	cleavage stimulation factor, 3' pre-RNA, subunit 3, 77kDa	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2012-01-10	Cstf3	cleavage stimulation factor, 3' pre-RNA, subunit 3, 77kDa	Cstf3	cleavage stimulation factor, 3' pre-RNA, subunit 3	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2008-04-30	Cstf3	cleavage stimulation factor, 3' pre-RNA, subunit 3	Cstf3_predicted	cleavage stimulation factor, 3' pre-RNA, subunit 3 (predicted)	'predicted' is removed	2292626	APPROVED
2006-03-30	Cstf3_predicted	cleavage stimulation factor, 3' pre-RNA, subunit 3 (predicted)		cleavage stimulation factor, 3' pre-RNA, subunit 3, 77kDa (predicted)	Name updated	1299863	APPROVED
2005-01-12	Cstf3_predicted	cleavage stimulation factor, 3' pre-RNA, subunit 3, 77kDa (predicted)			Symbol and Name status set to approved	70820	APPROVED

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

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InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

Imported Disease Annotations - ClinVar

RGD Manual Annotations

Imported Annotations - KEGG (archival)

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Imported Disease Annotations - ClinVar

RGD Manual Annotations

Imported Annotations - KEGG (archival)