Cpsf6 (cleavage and polyadenylation specific factor 6) - Rat Genome Database

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Gene: Cpsf6 (cleavage and polyadenylation specific factor 6) Rattus norvegicus
Analyze
Symbol: Cpsf6
Name: cleavage and polyadenylation specific factor 6
RGD ID: 1304640
Description: Predicted to enable exon-exon junction complex binding activity; mRNA binding activity; and ribosomal large subunit binding activity. Predicted to contribute to RNA binding activity. Predicted to be involved in several processes, including mRNA alternative polyadenylation; pre-mRNA cleavage required for polyadenylation; and protein-containing complex assembly. Predicted to be located in cytoplasm and nuclear lumen. Predicted to be part of mRNA cleavage and polyadenylation specificity factor complex and ribonucleoprotein complex. Orthologous to human CPSF6 (cleavage and polyadenylation specific factor 6); PARTICIPATES IN 3'-end pre-mRNA processing pathway; RNA polymerase II transcription termination pathway; mRNA decay pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran; 2,4-dinitrotoluene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: cleavage and polyadenylation specific factor 6, 68kDa; cleavage and polyadenylation specificity factor subunit 6; LOC299811
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
mRatBN7.2752,956,589 - 53,001,783 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl752,956,589 - 52,988,122 (-)Ensembl
Rnor_6.0760,385,688 - 60,417,661 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl760,385,688 - 60,416,925 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0760,387,688 - 60,432,254 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4756,658,291 - 56,689,892 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1756,684,035 - 56,711,179 (-)NCBI
Celera749,730,420 - 49,761,230 (-)NCBICelera
Cytogenetic Map7q22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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. 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.
4. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
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
Additional References at PubMed
PMID:9659921   PMID:14690600   PMID:15169763   PMID:17267687   PMID:18032416   PMID:18809582   PMID:19864460   PMID:19946888   PMID:20695905   PMID:21295486   PMID:22658674   PMID:22681889  
PMID:23187700   PMID:29276085   PMID:30916345  


Genomics

Comparative Map Data
Cpsf6
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2752,956,589 - 53,001,783 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl752,956,589 - 52,988,122 (-)Ensembl
Rnor_6.0760,385,688 - 60,417,661 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl760,385,688 - 60,416,925 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0760,387,688 - 60,432,254 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4756,658,291 - 56,689,892 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1756,684,035 - 56,711,179 (-)NCBI
Celera749,730,420 - 49,761,230 (-)NCBICelera
Cytogenetic Map7q22NCBI
CPSF6
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381269,239,569 - 69,274,358 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl1269,239,569 - 69,274,358 (+)EnsemblGRCh38hg38GRCh38
GRCh371269,633,349 - 69,668,138 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361267,919,667 - 67,951,290 (+)NCBINCBI36hg18NCBI36
Build 341267,919,666 - 67,951,290NCBI
Celera1269,297,148 - 69,331,977 (+)NCBI
Cytogenetic Map12q15NCBI
HuRef1266,694,597 - 66,717,839 (+)NCBIHuRef
CHM1_11269,601,666 - 69,636,525 (+)NCBICHM1_1
T2T-CHM13v2.01269,218,652 - 69,253,462 (+)NCBI
Cpsf6
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3910117,180,572 - 117,212,903 (-)NCBIGRCm39mm39
GRCm39 Ensembl10117,180,578 - 117,215,920 (-)Ensembl
GRCm3810117,344,667 - 117,376,998 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl10117,344,673 - 117,380,015 (-)EnsemblGRCm38mm10GRCm38
MGSCv3710116,781,724 - 116,814,029 (-)NCBIGRCm37mm9NCBIm37
MGSCv3610116,752,317 - 116,781,059 (-)NCBImm8
Celera10119,287,703 - 119,311,036 (-)NCBICelera
Cytogenetic Map10D2NCBI
Cpsf6
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495545815,677,645 - 15,708,011 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495545815,684,040 - 15,708,011 (+)NCBIChiLan1.0ChiLan1.0
CPSF6
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11269,537,904 - 69,562,570 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1269,535,302 - 69,550,789 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01266,750,301 - 66,785,104 (+)NCBIMhudiblu_PPA_v0panPan3
CPSF6
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11011,265,044 - 11,297,395 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1011,262,265 - 11,292,832 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1011,192,974 - 11,229,102 (+)NCBI
ROS_Cfam_1.01011,384,373 - 11,420,547 (+)NCBI
UMICH_Zoey_3.11011,251,450 - 11,287,708 (+)NCBI
UNSW_CanFamBas_1.01011,498,596 - 11,534,738 (+)NCBI
UU_Cfam_GSD_1.01011,620,546 - 11,656,791 (+)NCBI
Cpsf6
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494547,032,412 - 47,064,888 (-)NCBI
SpeTri2.0NW_0049365457,045,043 - 7,077,710 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CPSF6
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl533,525,689 - 33,555,226 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1533,525,668 - 33,559,941 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2536,157,912 - 36,194,879 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CPSF6
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11164,859,701 - 64,894,144 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl1164,859,718 - 64,882,269 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_023666037180,805,605 - 180,840,076 (-)NCBIVero_WHO_p1.0
Cpsf6
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462494856,246 - 84,051 (-)EnsemblHetGla_female_1.0hetGla2
HetGla 1.0NW_00462494853,317 - 83,983 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
RH143542  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2752,970,933 - 52,971,048 (+)MAPPERmRatBN7.2
Rnor_6.0760,400,032 - 60,400,146NCBIRnor6.0
Rnor_5.0760,402,032 - 60,402,146UniSTSRnor5.0
RGSC_v3.4756,672,636 - 56,672,750UniSTSRGSC3.4
Celera749,744,763 - 49,744,877UniSTS
RH 3.4 Map7487.7UniSTS
Cytogenetic Map7q22UniSTS
BE115415  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2752,958,575 - 52,958,764 (+)MAPPERmRatBN7.2
Rnor_6.0760,387,674 - 60,387,862NCBIRnor6.0
Rnor_5.0760,389,674 - 60,389,862UniSTSRnor5.0
RGSC_v3.4756,660,277 - 56,660,465UniSTSRGSC3.4
Celera749,732,406 - 49,732,594UniSTS
RH 3.4 Map7480.9UniSTS
Cytogenetic Map7q22UniSTS
RH135054  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2752,959,300 - 52,959,497 (+)MAPPERmRatBN7.2
Rnor_6.0760,388,399 - 60,388,595NCBIRnor6.0
Rnor_5.0760,390,399 - 60,390,595UniSTSRnor5.0
RGSC_v3.4756,661,002 - 56,661,198UniSTSRGSC3.4
Celera749,733,131 - 49,733,327UniSTS
RH 3.4 Map7483.0UniSTS
Cytogenetic Map7q22UniSTS
RH140527  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2752,959,967 - 52,960,057 (+)MAPPERmRatBN7.2
Rnor_6.0760,389,066 - 60,389,155NCBIRnor6.0
Rnor_5.0760,391,066 - 60,391,155UniSTSRnor5.0
RGSC_v3.4756,661,669 - 56,661,758UniSTSRGSC3.4
Celera749,733,798 - 49,733,887UniSTS
RH 3.4 Map7483.0UniSTS
Cytogenetic Map7q22UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)7924703115097879Rat
2298547Neuinf5Neuroinflammation QTL 53.7nervous system integrity trait (VT:0010566)spinal cord Cd74 protein level (CMO:0002131)7946224658265113Rat
1643004Pain2Pain QTL 21mechanical nociception trait (VT:0002734)self mutilation severity score (CMO:0002145)7946224698011544Rat
1578652Bmd15Bone mineral density QTL 155.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)7986646760460686Rat
738033Anxrr6Anxiety related response QTL 64.1exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)71557388960573889Rat
2317059Aia15Adjuvant induced arthritis QTL 152.46joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)71700459862004598Rat
10755451Coatc11Coat color QTL 110coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)71794435762944357Rat
1300132Bp182Blood pressure QTL 1823.49arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)71965431784928080Rat
7411569Bw137Body weight QTL 1370.001body mass (VT:0001259)body weight gain (CMO:0000420)72192119566921195Rat
1641885Alcrsp9Alcohol response QTL 9alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)72409960669099606Rat
1549840Bss5Bone structure and strength QTL 59.8femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)72475184169751841Rat
70190Mcs6Mammary carcinoma susceptibility QTL 62.29mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)72673740163902784Rat
1300138Hrtrt9Heart rate QTL 94.72heart pumping trait (VT:2000009)heart rate (CMO:0000002)72940968353612950Rat
10402855Bp379Blood pressure QTL 3790.21arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)72940968374409683Rat
1300127Srn1Serum renin concentration QTL 13.87blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)72940968384928080Rat
10755453Coatc12Coat color QTL 120coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)73111283276112832Rat
7411605Foco14Food consumption QTL 1424.10.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)73429328279293282Rat
631534Lnnr1Liver neoplastic nodule remodeling QTL 13.850.001liver integrity trait (VT:0010547)liver remodeling tumorous lesion number to liver total tumorous lesion number ratio (CMO:0001705)73429328279293282Rat
631513Scl7Serum cholesterol level QTL 74.1blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)73796056982960569Rat
2303629Vencon3Ventilatory control QTL 37.25respiration trait (VT:0001943)respiration rate (CMO:0000289)74110969256793354Rat
61357Bp38Blood pressure QTL 381.60.052arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)741333674119109060Rat
634326Hc3Hypercalciuria QTL 32.1urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)74278731487787314Rat
10053722Scort27Serum corticosterone level QTL 272.410.0083blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)74322875088228750Rat
1358361Sradr5Stress Responsive Adrenal Weight QTL 55.55adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)743747012108555253Rat
1300179Kidm5Kidney mass QTL 53.51kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)743747012135012528Rat
1300149Cm6Cardiac mass QTL 64.09heart mass (VT:0007028)heart left ventricle weight to body weight ratio (CMO:0000530)743747099102228765Rat
631504Cm27Cardiac mass QTL 273.45heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)744421311118198041Rat
61428Scl3Serum cholesterol level QTL 33.2blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)74486753389867533Rat
738030Anxrr8Anxiety related response QTL 84.1exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)74659007091590070Rat
10059605Kidm47Kidney mass QTL 472.910.05kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)74725178365728867Rat
2293696Bmd32Bone mineral density QTL 325.10.0001femur strength trait (VT:0010010)femoral neck polar moment of inertia (CMO:0001670)74765143992651439Rat
2293707Bss32Bone structure and strength QTL 327.640.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)74765143992651439Rat
2300178Bmd54Bone mineral density QTL 545.30.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)74765143992651439Rat
2293644Bmd29Bone mineral density QTL 295.40.0001femur size trait (VT:1000369)femoral neck cross-sectional area (CMO:0001697)74765143992651439Rat
2293667Bss42Bone structure and strength QTL 427.250.0001lumbar vertebra size trait (VT:0010518)lumbar vertebra cross-sectional area (CMO:0001689)74765143992651439Rat
2293678Bss24Bone structure and strength QTL 246.710.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)74765143992651439Rat
2293685Bmd21Bone mineral density QTL 214.20.0003femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)74765143992651439Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:678
Count of miRNA genes:280
Interacting mature miRNAs:388
Transcripts:ENSRNOT00000008193
Prediction methods:Miranda, 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.


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 40 48 32 19 32 8 8 74 34 41 11 8
Low 3 9 9 9 3 1
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000008193   ⟹   ENSRNOP00000008193
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl752,956,589 - 52,988,100 (-)Ensembl
Rnor_6.0 Ensembl760,385,688 - 60,416,925 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000108117   ⟹   ENSRNOP00000094948
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl752,960,136 - 52,988,122 (-)Ensembl
RefSeq Acc Id: NM_001106785   ⟹   NP_001100255
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2752,956,589 - 52,988,100 (-)NCBI
Rnor_6.0760,385,688 - 60,416,925 (-)NCBI
Rnor_5.0760,387,688 - 60,432,254 (-)NCBI
RGSC_v3.4756,658,291 - 56,689,892 (-)RGD
Celera749,730,420 - 49,761,230 (-)RGD
Sequence:
RefSeq Acc Id: XM_006241372   ⟹   XP_006241434
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2752,957,207 - 52,988,143 (-)NCBI
Rnor_6.0760,386,308 - 60,416,957 (-)NCBI
Rnor_5.0760,387,688 - 60,432,254 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006241373   ⟹   XP_006241435
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2752,957,207 - 52,988,143 (-)NCBI
Rnor_6.0760,386,308 - 60,416,957 (-)NCBI
Rnor_5.0760,387,688 - 60,432,254 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006241374   ⟹   XP_006241436
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2752,957,207 - 52,988,143 (-)NCBI
Rnor_6.0760,386,308 - 60,416,957 (-)NCBI
Rnor_5.0760,387,688 - 60,432,254 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039078738   ⟹   XP_038934666
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2752,957,207 - 52,988,143 (-)NCBI
RefSeq Acc Id: XM_039078739   ⟹   XP_038934667
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2752,957,207 - 52,988,143 (-)NCBI
RefSeq Acc Id: XM_039078740   ⟹   XP_038934668
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2752,957,207 - 53,001,783 (-)NCBI
RefSeq Acc Id: XM_039078741   ⟹   XP_038934669
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2752,957,207 - 52,988,809 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_001100255   ⟸   NM_001106785
- UniProtKB: D3ZPL1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006241436   ⟸   XM_006241374
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006241434   ⟸   XM_006241372
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006241435   ⟸   XM_006241373
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000008193   ⟸   ENSRNOT00000008193
RefSeq Acc Id: XP_038934668   ⟸   XM_039078740
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038934669   ⟸   XM_039078741
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038934667   ⟸   XM_039078739
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038934666   ⟸   XM_039078738
- Peptide Label: isoform X3
RefSeq Acc Id: ENSRNOP00000094948   ⟸   ENSRNOT00000108117
Protein Domains
RRM

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZPL1-F1-model_v2 AlphaFold D3ZPL1 1-551 view protein structure

Transcriptome

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

Promoters
RGD ID:13695214
Promoter ID:EPDNEW_R5738
Type:initiation region
Name:Cpsf6_1
Description:cleavage and polyadenylation specific factor 6
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_6.0760,416,959 - 60,417,019EPDNEW

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)
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
DA/OlaHsd (2019)
Visual CSV TAB Printer
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)
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
FXLE16/Stm (2020)
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
FXLE18/Stm (2020)
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
GK/FarMcwi (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
HXB10/IpcvMcwi (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
HXB2/IpcvMcwi (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
HXB20/IpcvMcwi (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
HXB31/IpcvMcwi (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
HXB4/IpcvMcwi (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
LE/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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (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
LEXF10A/StmMcwi (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
LEXF11/Stm (2020)
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
LEXF1A/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
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)
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
LEXF4/Stm (2020)
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
LH/MavRrrcAek (2020)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
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
MR/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
MWF/Hsd (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
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)
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
SHRSP/A3NCrl (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
SR/JrHsd (2020)
Visual CSV TAB Printer
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)
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
WAG/RijCrl (2020)
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
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)
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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1304640 AgrOrtholog
BioCyc Gene G2FUF-34005 BioCyc
Ensembl Genes ENSRNOG00000005927 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000008193 ENTREZGENE
  ENSRNOP00000008193.6 UniProtKB/TrEMBL
  ENSRNOP00000094948 ENTREZGENE
  ENSRNOP00000094948.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000008193 ENTREZGENE
  ENSRNOT00000008193.7 UniProtKB/TrEMBL
  ENSRNOT00000108117 ENTREZGENE
  ENSRNOT00000108117.1 UniProtKB/TrEMBL
Gene3D-CATH 3.30.70.330 UniProtKB/TrEMBL
InterPro CPSF6 UniProtKB/TrEMBL
  CPSF6/7 UniProtKB/TrEMBL
  Nucleotide-bd_a/b_plait_sf UniProtKB/TrEMBL
  RBD_domain_sf UniProtKB/TrEMBL
  RRM_RNP1 UniProtKB/TrEMBL
KEGG Report rno:299811 UniProtKB/TrEMBL
NCBI Gene 299811 ENTREZGENE
PANTHER PTHR23204 UniProtKB/TrEMBL
  PTHR23204:SF3 UniProtKB/TrEMBL
Pfam RRM_1 UniProtKB/TrEMBL
PhenoGen Cpsf6 PhenoGen
PROSITE RRM UniProtKB/TrEMBL
SMART RRM UniProtKB/TrEMBL
Superfamily-SCOP SSF54928 UniProtKB/TrEMBL
UniProt A0A8I6AMJ9_RAT UniProtKB/TrEMBL
  D3ZPL1 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-11-19 Cpsf6  cleavage and polyadenylation specific factor 6  Cpsf6  cleavage and polyadenylation specific factor 6, 68kDa  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-01-10 Cpsf6  cleavage and polyadenylation specific factor 6, 68kDa  Cpsf6  cleavage and polyadenylation specific factor 6  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-03 Cpsf6  cleavage and polyadenylation specific factor 6  Cpsf6_predicted  cleavage and polyadenylation specific factor 6, 68kDa (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-12 Cpsf6_predicted  cleavage and polyadenylation specific factor 6, 68kDa (predicted)      Symbol and Name status set to approved 70820 APPROVED