Cstf1 (cleavage stimulation factor subunit 1) - Rat Genome Database

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Gene: Cstf1 (cleavage stimulation factor subunit 1) Rattus norvegicus
Analyze
Symbol: Cstf1
Name: cleavage stimulation factor subunit 1
RGD ID: 1309267
Description: Predicted to be involved in mRNA 3'-end processing. Predicted to be located in nucleoplasm. Predicted to be part of mRNA cleavage stimulating factor complex. Orthologous to human CSTF1 (cleavage stimulation factor subunit 1); PARTICIPATES IN 3'-end pre-mRNA processing pathway; RNA polymerase II transcription termination pathway; mRNA decay pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; bisphenol A; C60 fullerene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: CF-1 50 kDa subunit; cleavage stimulation factor 50 kDa subunit; cleavage stimulation factor, 3' pre-RNA, subunit 1; cleavage stimulation factor, 3' pre-RNA, subunit 1, 50kDa; CSTF 50 kDa subunit; cstF-50; LOC311670; MGC109461
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.23161,144,533 - 161,156,294 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl3161,144,548 - 161,156,300 (+)Ensembl
Rnor_6.03170,380,413 - 170,392,162 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3170,380,719 - 170,392,160 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03176,456,203 - 176,467,944 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43163,287,021 - 163,298,464 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.13163,193,056 - 163,204,498 (+)NCBI
Celera3160,345,104 - 160,356,547 (+)NCBICelera
Cytogenetic Map3q42NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
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. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
6. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
7. GOA pipeline RGD automated data pipeline
8. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
9. Comprehensive gene review and curation RGD comprehensive gene curation
10. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
Additional References at PubMed
PMID:11459828   PMID:15489334   PMID:22658674   PMID:22681889  


Genomics

Comparative Map Data
Cstf1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.23161,144,533 - 161,156,294 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl3161,144,548 - 161,156,300 (+)Ensembl
Rnor_6.03170,380,413 - 170,392,162 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3170,380,719 - 170,392,160 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03176,456,203 - 176,467,944 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43163,287,021 - 163,298,464 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.13163,193,056 - 163,204,498 (+)NCBI
Celera3160,345,104 - 160,356,547 (+)NCBICelera
Cytogenetic Map3q42NCBI
CSTF1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382056,392,379 - 56,406,362 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl2056,392,371 - 56,406,362 (+)EnsemblGRCh38hg38GRCh38
GRCh372054,967,435 - 54,981,418 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362054,400,834 - 54,412,989 (+)NCBINCBI36hg18NCBI36
Build 342054,401,025 - 54,412,514NCBI
Celera2051,707,860 - 51,720,014 (+)NCBI
Cytogenetic Map20q13.2-q13.31NCBI
HuRef2051,752,305 - 51,764,459 (+)NCBIHuRef
CHM1_12054,868,520 - 54,880,675 (+)NCBICHM1_1
T2T-CHM13v2.02058,169,873 - 58,183,854 (+)NCBI
Cstf1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm392172,212,565 - 172,224,369 (+)NCBIGRCm39mm39
GRCm39 Ensembl2172,212,601 - 172,224,368 (+)Ensembl
GRCm382172,370,645 - 172,382,449 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2172,370,681 - 172,382,448 (+)EnsemblGRCm38mm10GRCm38
MGSCv372172,196,503 - 172,206,586 (+)NCBIGRCm37mm9NCBIm37
MGSCv362172,062,208 - 172,072,291 (+)NCBImm8
Celera2178,330,185 - 178,340,378 (+)NCBICelera
Cytogenetic Map2H3NCBI
cM Map294.84NCBI
Cstf1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554452,816,732 - 2,830,306 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554452,816,986 - 2,830,971 (-)NCBIChiLan1.0ChiLan1.0
CSTF1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12054,017,362 - 54,029,296 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2054,017,435 - 54,033,230 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02052,730,646 - 52,744,635 (+)NCBIMhudiblu_PPA_v0panPan3
CSTF1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12441,604,988 - 41,615,988 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2441,605,447 - 41,615,671 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2440,852,695 - 40,863,729 (+)NCBI
ROS_Cfam_1.02442,315,943 - 42,326,976 (+)NCBI
ROS_Cfam_1.0 Ensembl2442,315,969 - 42,328,350 (+)Ensembl
UMICH_Zoey_3.12441,555,718 - 41,566,747 (+)NCBI
UNSW_CanFamBas_1.02441,694,756 - 41,705,804 (+)NCBI
UU_Cfam_GSD_1.02442,352,711 - 42,363,782 (+)NCBI
Cstf1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024408640183,767,547 - 183,775,478 (-)NCBI
SpeTri2.0NW_004936875310,491 - 319,027 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CSTF1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1756,972,248 - 56,985,813 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11756,972,202 - 56,984,065 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21764,083,832 - 64,095,600 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CSTF1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.127,717,974 - 7,729,974 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl27,715,595 - 7,726,770 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366605055,792,354 - 55,804,748 (-)NCBIVero_WHO_p1.0
Cstf1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624790132,023 - 144,363 (-)EnsemblHetGla_female_1.0hetGla2
HetGla 1.0NW_004624790133,872 - 143,762 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
RH137028  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23161,154,780 - 161,154,984 (+)MAPPERmRatBN7.2
Rnor_6.03170,390,649 - 170,390,852NCBIRnor6.0
Rnor_5.03176,466,431 - 176,466,634UniSTSRnor5.0
RGSC_v3.43163,296,951 - 163,297,154UniSTSRGSC3.4
Celera3160,355,034 - 160,355,237UniSTS
RH 3.4 Map31494.1UniSTS
Cytogenetic Map3q42UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2301411Bp320Blood pressure QTL 3200.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)3145925360166177555Rat
1576306Schws3Schwannoma susceptibility QTL 30.001nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)3118839124163839124Rat
1598877Bp285Blood pressure QTL 2851.50.03arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3120538241165538241Rat
1559282Emca5Estrogen-induced mammary cancer QTL 53.9mammary gland integrity trait (VT:0010552)percentage of study population developing mammary tumors during a period of time (CMO:0000948)343827364169034231Rat
631673Iddm13Insulin dependent diabetes mellitus QTL 131.30.663blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)3130193298161695983Rat
1331726Bp208Blood pressure QTL 2083.129arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)3141339013162184794Rat
1578653Vnigr3Vascular neointimal growth QTL 33.1artery morphology trait (VT:0002191)artery neointimal hyperplastic lesion area (CMO:0001414)3130656562169034231Rat
631541Bp81Blood pressure QTL 814arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3124122556169034231Rat
2302373Gluco39Glucose level QTL 395.01blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)398535386161695835Rat
8552952Pigfal13Plasma insulin-like growth factor 1 level QTL 13blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)3138799500169034231Rat
8552791Vie2Viral induced encephalitis QTL 24.1brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)3145956084169034231Rat
70216Cm14Cardiac mass QTL 142.1heart mass (VT:0007028)heart wet weight (CMO:0000069)331172320163586636Rat
12879876Bw182Body weight QTL 1820.003body mass (VT:0001259)body weight (CMO:0000012)3145925360166177555Rat
1598854Memor10Memory QTL 102exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)3145956084161299569Rat
1298068Bp167Blood pressure QTL 1670.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3141074471169034231Rat
10755461Coatc16Coat color QTL 16coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)3122438700167438700Rat
1581568Rf53Renal function QTL 53total urine protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)356395968161299569Rat
2312673Scl63Serum cholesterol level QTL 630.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)398535255168026850Rat
9589106Insul23Insulin level QTL 2313.860.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)3131635904169034231Rat
1578656Vnigr2Vascular neointimal growth QTL 24.2artery morphology trait (VT:0002191)lesioned artery residual lumen area (CMO:0001417)3130656562169034231Rat
1578666Vnigr1Vascular neointimal growth QTL 14.6artery morphology trait (VT:0002191)artery lumen area (CMO:0001409)3149040888168026850Rat
2298477Eau4Experimental allergic uveoretinitis QTL 40.0011uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)3137398739169034231Rat
2312659Slep7Serum leptin concentration QTL 70.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)398535255168026850Rat
2312670Bw94Body weight QTL 940.01inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)398535255168026850Rat
2303620Vencon4Ventilatory control QTL 43.9respiration trait (VT:0001943)tidal volume (CMO:0000222)3127162703168026850Rat
2317883Alcrsp26Alcohol response QTL 261.80.63response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)3145526770169034231Rat
12879872Cm97Cardiac mass QTL 970.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)3145925360166177555Rat
12879873Cm96Cardiac mass QTL 960.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)3145925360166177555Rat
12879875Kidm64Kidney mass QTL 640.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)3145925360166177555Rat
12879874Cm98Cardiac mass QTL 980.005heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)3145925360166177555Rat
12879871Am7Aortic mass QTL 70.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)3145925360166177555Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:929
Count of miRNA genes:306
Interacting mature miRNAs:390
Transcripts:ENSRNOT00000055101
Prediction methods:Microtar, Miranda, Rnahybrid
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.


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 29 50 34 19 34 1 2 71 34 41 11 1
Low 14 7 7 7 7 9 3 1 7
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000055101   ⟹   ENSRNOP00000051976
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3161,144,548 - 161,156,300 (+)Ensembl
Rnor_6.0 Ensembl3170,380,719 - 170,392,160 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000118376   ⟹   ENSRNOP00000076939
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3161,144,828 - 161,154,999 (+)Ensembl
RefSeq Acc Id: NM_001013161   ⟹   NP_001013179
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23161,144,851 - 161,156,294 (+)NCBI
Rnor_6.03170,380,719 - 170,392,162 (+)NCBI
Rnor_5.03176,456,203 - 176,467,944 (+)NCBI
RGSC_v3.43163,287,021 - 163,298,464 (+)RGD
Celera3160,345,104 - 160,356,547 (+)RGD
Sequence:
RefSeq Acc Id: XM_006235681   ⟹   XP_006235743
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23161,144,715 - 161,156,294 (+)NCBI
Rnor_6.03170,380,599 - 170,392,162 (+)NCBI
Rnor_5.03176,456,203 - 176,467,944 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006235682   ⟹   XP_006235744
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23161,144,746 - 161,156,294 (+)NCBI
Rnor_6.03170,380,667 - 170,392,162 (+)NCBI
Rnor_5.03176,456,203 - 176,467,944 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006235683   ⟹   XP_006235745
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23161,144,553 - 161,156,294 (+)NCBI
Rnor_6.03170,380,413 - 170,392,162 (+)NCBI
Rnor_5.03176,456,203 - 176,467,944 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006235684   ⟹   XP_006235746
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23161,144,533 - 161,156,294 (+)NCBI
Rnor_6.03170,380,414 - 170,392,162 (+)NCBI
Rnor_5.03176,456,203 - 176,467,944 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006235685   ⟹   XP_006235747
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23161,144,538 - 161,156,294 (+)NCBI
Rnor_6.03170,380,413 - 170,392,162 (+)NCBI
Rnor_5.03176,456,203 - 176,467,944 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006235686   ⟹   XP_006235748
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23161,144,550 - 161,156,294 (+)NCBI
Rnor_6.03170,380,413 - 170,392,162 (+)NCBI
Rnor_5.03176,456,203 - 176,467,944 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039105145   ⟹   XP_038961073
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23161,144,553 - 161,156,294 (+)NCBI
RefSeq Acc Id: XM_039105146   ⟹   XP_038961074
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23161,144,551 - 161,156,294 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_001013179   ⟸   NM_001013161
- UniProtKB: Q5BJQ6 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006235745   ⟸   XM_006235683
- Peptide Label: isoform X2
- UniProtKB: Q5BJQ6 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006235746   ⟸   XM_006235684
- Peptide Label: isoform X2
- UniProtKB: Q5BJQ6 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006235747   ⟸   XM_006235685
- Peptide Label: isoform X2
- UniProtKB: Q5BJQ6 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006235748   ⟸   XM_006235686
- Peptide Label: isoform X2
- UniProtKB: Q5BJQ6 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006235743   ⟸   XM_006235681
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006235744   ⟸   XM_006235682
- Peptide Label: isoform X2
- UniProtKB: Q5BJQ6 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000051976   ⟸   ENSRNOT00000055101
RefSeq Acc Id: XP_038961074   ⟸   XM_039105146
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038961073   ⟸   XM_039105145
- Peptide Label: isoform X2
RefSeq Acc Id: ENSRNOP00000076939   ⟸   ENSRNOT00000118376

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q5BJQ6-F1-model_v2 AlphaFold Q5BJQ6 1-431 view protein structure

Transcriptome

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

Promoters
RGD ID:13692706
Promoter ID:EPDNEW_R3230
Type:initiation region
Name:Cstf1_1
Description:cleavage stimulation factor subunit 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.03170,380,675 - 170,380,735EPDNEW

Strain Variation

Strain Sequence Variants (mRatBN7.2)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BUF/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
DA/OlaHsd (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE16/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/FarMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB10/IpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF10A/StmMcwi (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrcAek (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrcAek (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrcAek (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/NRrrcMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MWF/Hsd (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHR/OlalpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WAG/RijCrl (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1309267 AgrOrtholog
BioCyc Gene G2FUF-46540 BioCyc
Ensembl Genes ENSRNOG00000004775 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000051976 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000076939 ENTREZGENE
  ENSRNOP00000076939.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000055101 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000118376 ENTREZGENE
  ENSRNOT00000118376.1 UniProtKB/TrEMBL
Gene3D-CATH 1.20.960.50 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  2.130.10.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7320917 IMAGE-MGC_LOAD
InterPro CstF1-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CSTF1_dimer UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CSTF1_dimer_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  WD40/YVTN_repeat-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  WD40_repeat UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  WD40_repeat_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  WD40_repeat_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:311670 UniProtKB/Swiss-Prot
MGC_CLONE MGC:109461 IMAGE-MGC_LOAD
NCBI Gene 311670 ENTREZGENE
PANTHER PTHR44133 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam CSTF1_dimer UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  WD40 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Cstf1 PhenoGen
PROSITE WD_REPEATS_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  WD_REPEATS_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  WD_REPEATS_REGION UniProtKB/Swiss-Prot
SMART WD40 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF50978 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A8I5Y796_RAT UniProtKB/TrEMBL
  CSTF1_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-04-13 Cstf1  cleavage stimulation factor subunit 1  Cstf1  cleavage stimulation factor, 3' pre-RNA, subunit 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2015-11-19 Cstf1  cleavage stimulation factor, 3' pre-RNA, subunit 1  Cstf1  cleavage stimulation factor, 3' pre-RNA, subunit 1, 50kDa  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-01-10 Cstf1  cleavage stimulation factor, 3' pre-RNA, subunit 1, 50kDa  Cstf1  cleavage stimulation factor, 3' pre-RNA, subunit 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-12-06 Cstf1  cleavage stimulation factor, 3' pre-RNA, subunit 1  Cstf1_predicted  cleavage stimulation factor, 3' pre-RNA, subunit 1 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Cstf1_predicted  cleavage stimulation factor, 3' pre-RNA, subunit 1 (predicted)      Symbol and Name status set to approved 70820 APPROVED