Clp1 (cleavage factor polyribonucleotide kinase subunit 1) - Rat Genome Database

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Gene: Clp1 (cleavage factor polyribonucleotide kinase subunit 1) Rattus norvegicus
Analyze
Symbol: Clp1
Name: cleavage factor polyribonucleotide kinase subunit 1
RGD ID: 1307679
Description: Predicted to enable ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity and ATP-dependent polyribonucleotide 5'-hydroxyl-kinase activity. Predicted to be involved in RNA processing; cerebellar cortex development; and negative regulation of gene expression. Predicted to be located in cytosol and nucleoplasm. Predicted to be part of tRNA-intron endonuclease complex. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in pontocerebellar hypoplasia type 10. Orthologous to human CLP1 (cleavage factor polyribonucleotide kinase subunit 1); PARTICIPATES IN 3'-end pre-mRNA processing pathway; RNA polymerase II transcription termination pathway; tRNA maturation pathway; INTERACTS WITH 1-naphthyl isothiocyanate; 2,3,7,8-tetrachlorodibenzodioxine; 4,4'-diaminodiphenylmethane.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: ATP/GTP-binding protein; cleavage and polyadenylation factor I subunit 1; CLP1, cleavage and polyadenylation factor I subunit, homolog; CLP1, cleavage and polyadenylation factor I subunit, homolog (S. cerevisiae); Heab; LOC311166; MGC94928; polyadenylation factor Clp1; polynucleotide kinase Clp1; polyribonucleotide 5'-hydroxyl-kinase Clp1; pre-mRNA cleavage complex II protein Clp1; RGD1307679; similar to ATP/GTP-binding protein
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
GRCr8390,213,461 - 90,217,165 (-)NCBIGRCr8
mRatBN7.2369,806,774 - 69,818,633 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl369,806,778 - 69,810,421 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx373,188,581 - 73,192,284 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0381,787,243 - 81,790,946 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0379,546,170 - 79,549,873 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0372,125,269 - 72,137,122 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl372,125,273 - 72,128,973 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0378,645,908 - 78,657,782 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4367,934,068 - 67,937,772 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1367,830,439 - 67,834,144 (-)NCBI
Celera369,162,457 - 69,166,161 (-)NCBICelera
Cytogenetic Map3q24NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

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. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
6. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
7. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
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. Handling tRNA introns, archaeal way and eukaryotic way. Yoshihisa T Front Genet. 2014 Jul 10;5:213. doi: 10.3389/fgene.2014.00213. eCollection 2014.
Additional References at PubMed
PMID:12477932   PMID:17495927   PMID:24766809   PMID:24766810   PMID:25931508  


Genomics

Comparative Map Data
Clp1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8390,213,461 - 90,217,165 (-)NCBIGRCr8
mRatBN7.2369,806,774 - 69,818,633 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl369,806,778 - 69,810,421 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx373,188,581 - 73,192,284 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0381,787,243 - 81,790,946 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0379,546,170 - 79,549,873 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0372,125,269 - 72,137,122 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl372,125,273 - 72,128,973 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0378,645,908 - 78,657,782 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4367,934,068 - 67,937,772 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1367,830,439 - 67,834,144 (-)NCBI
Celera369,162,457 - 69,166,161 (-)NCBICelera
Cytogenetic Map3q24NCBI
CLP1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381157,657,762 - 57,661,865 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1157,648,188 - 57,661,865 (+)EnsemblGRCh38hg38GRCh38
GRCh371157,425,234 - 57,429,337 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361157,181,206 - 57,185,913 (+)NCBINCBI36Build 36hg18NCBI36
Celera1154,781,701 - 54,785,822 (+)NCBICelera
Cytogenetic Map11q12.1NCBI
HuRef1153,774,137 - 53,778,258 (+)NCBIHuRef
CHM1_11157,291,424 - 57,295,545 (+)NCBICHM1_1
T2T-CHM13v2.01157,607,935 - 57,612,038 (+)NCBIT2T-CHM13v2.0
Clp1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39284,553,466 - 84,557,631 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl284,552,448 - 84,557,694 (-)EnsemblGRCm39 Ensembl
GRCm38284,723,122 - 84,727,287 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl284,722,104 - 84,727,350 (-)EnsemblGRCm38mm10GRCm38
MGSCv37284,563,279 - 84,567,425 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36284,523,961 - 84,528,107 (-)NCBIMGSCv36mm8
Celera286,318,290 - 86,322,440 (-)NCBICelera
Cytogenetic Map2DNCBI
cM Map249.45NCBI
Clp1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555112,588,825 - 2,593,192 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555112,588,825 - 2,592,108 (+)NCBIChiLan1.0ChiLan1.0
CLP1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2958,794,718 - 58,818,214 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11159,826,329 - 59,838,193 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01152,898,181 - 52,902,656 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11156,368,732 - 56,373,129 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1156,368,433 - 56,373,129 (+)Ensemblpanpan1.1panPan2
CLP1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11838,528,700 - 38,531,899 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1838,528,621 - 38,530,846 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1838,075,104 - 38,078,316 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01839,210,508 - 39,213,726 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1839,210,508 - 39,213,629 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11838,793,608 - 38,796,826 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01838,366,628 - 38,369,840 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01838,997,368 - 39,000,586 (-)NCBIUU_Cfam_GSD_1.0
Clp1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494714,756,010 - 14,759,418 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365814,869,686 - 4,873,217 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365814,870,126 - 4,873,158 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CLP1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl213,282,164 - 13,285,162 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1213,282,157 - 13,285,208 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2212,915,349 - 12,918,466 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CLP1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1115,568,984 - 15,573,849 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl115,568,976 - 15,573,082 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666038112,920,089 - 112,924,752 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Clp1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248643,063,555 - 3,067,051 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248643,063,555 - 3,067,045 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Clp1
49 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:63
Count of miRNA genes:52
Interacting mature miRNAs:61
Transcripts:ENSRNOT00000009726
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.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2290452Scl56Serum cholesterol level QTL 562.26blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)3191609953Rat
1358905Hrtrt17Heart rate QTL 175.90.000014heart pumping trait (VT:2000009)heart rate (CMO:0000002)31086191289878372Rat
1358885Bp251Blood pressure QTL 2513.8arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)314489145121056321Rat
1358888Bp264Blood pressure QTL 2644.43arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)314489145121056321Rat
2298542Neuinf11Neuroinflammation QTL 113.9nervous system integrity trait (VT:0010566)spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)31500542276927699Rat
2302055Pia30Pristane induced arthritis QTL 303.50.001blood autoantibody amount (VT:0003725)serum immunoglobulin M-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002111)32793691972936919Rat
9590286Uminl1Urine mineral level QTL 13.50.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)32824968773249687Rat
8694196Abfw2Abdominal fat weight QTL 216.580.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)32824968773249687Rat
8694386Bw159Body weight QTL 1594.520.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)32824968773249687Rat
8552950Pigfal12Plasma insulin-like growth factor 1 level QTL 127.3blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)32824968773249687Rat
9590136Scort3Serum corticosterone level QTL 323.370.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)32824968773249687Rat
2303593Gluco46Glucose level QTL 463blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)32846857173468571Rat
1354590Despr11Despair related QTL 110.000031locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)32846857173468571Rat
737818Hcar12Hepatocarcinoma resistance QTL 122.6liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)329463235118376539Rat
61419Cia11Collagen induced arthritis QTL 115.6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)33035677398535386Rat
61356Bp37Blood pressure QTL 373blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)33068464275684642Rat
631647Bp122Blood pressure QTL 1226.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)33068464275684642Rat
70216Cm14Cardiac mass QTL 142.1heart mass (VT:0007028)heart wet weight (CMO:0000069)331172320163586636Rat
11565451Bw177Body weight QTL 1770.002body mass (VT:0001259)body weight (CMO:0000012)33142640370668733Rat
11565452Kidm57Kidney mass QTL 570.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)33142640370668733Rat
12879866Cm94Cardiac mass QTL 940.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)33142640370668733Rat
12879867Cm95Cardiac mass QTL 950.047heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)33142640370668733Rat
12879868Am6Aortic mass QTL 60.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)33142640370668733Rat
2301400Cm68Cardiac mass QTL 680.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)33142640370668733Rat
1354589Bw31Body weight QTL 313.3body mass (VT:0001259)body weight (CMO:0000012)33370334778196190Rat
1354604Bw36Body weight QTL 362.9body mass (VT:0001259)body weight (CMO:0000012)333703347104104347Rat
1358362Srcrt2Stress Responsive Cort QTL 22.78blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)338192233133483320Rat
738019Anxrr10Anxiety related response QTL 103.9exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)33851780383517803Rat
1331777Bw24Body weight QTL 243.503body mass (VT:0001259)body weight (CMO:0000012)33945463789115240Rat
1331795Rf30Renal function QTL 303.708urine potassium amount (VT:0010539)urine potassium level (CMO:0000128)33945463789115240Rat
1354597Kidm13Kidney mass QTL 132.9kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)341874578104104347Rat
2301970Bw81Body weight QTL 815.19body mass (VT:0001259)body weight (CMO:0000012)341874578155617519Rat
2301971Cm71Cardiac mass QTL 714.63heart left ventricle mass (VT:0007031)heart left ventricle weight (CMO:0000776)341874578155617519Rat
1300178Hrtrt4Heart rate QTL 43.74heart pumping trait (VT:2000009)heart rate (CMO:0000002)34382736490905114Rat
1581503Cm58Cardiac mass QTL 582.70.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)343827364121056321Rat
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
2292591Esta4Estrogen-induced thymic atrophy QTL 4thymus mass (VT:0004954)thymus wet weight (CMO:0000855)347233211147415807Rat
1358186Ept2Estrogen-induced pituitary tumorigenesis QTL 28.3pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)347233430110362260Rat
2292613Ept16Estrogen-induced pituitary tumorigenesis QTL 168.3pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)347233430110362260Rat
631665Bw8Body weight QTL 85.5body mass (VT:0001259)body weight (CMO:0000012)350437042119183768Rat
724523Tsu1Thymus enlargement suppressive QTL 13.84thymus mass (VT:0004954)thymus weight to body weight ratio (CMO:0000612)350437504115638231Rat
1582218Bw74Body weight QTL 743.90.0021body mass (VT:0001259)body weight (CMO:0000012)353184593115665732Rat
1582238Bw68Body weight QTL 683.20.0064body mass (VT:0001259)body weight (CMO:0000012)353184593115665732Rat
1582239Epfw1Epididymal fat weight QTL 14.50.0006epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)353184593115665732Rat
61377Edpm3Estrogen-dependent pituitary mass QTL 37.050.038pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)35318469289878207Rat
731180Bp152Blood pressure QTL 1520.03arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)35378111291609953Rat
731180Bp152Blood pressure QTL 1520.03arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)35378111291609953Rat
731180Bp152Blood pressure QTL 1520.03arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)35378111291609953Rat
1581568Rf53Renal function QTL 53urine total protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)356395968161299569Rat
8662816Vetf4Vascular elastic tissue fragility QTL 44renal artery integrity trait (VT:0010642)number of ruptures of the internal elastic lamina of the renal arteries (CMO:0002563)359242096157323038Rat
1300111Rf12Renal function QTL 123.78renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)361017749121056321Rat
631200Cm25Cardiac mass QTL 254.80.0001heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)36113434889115068Rat
1582210Bw71Body weight QTL 713.30.0012body mass (VT:0001259)body weight (CMO:0000012)364655305115665732Rat
1582221Kidm30Kidney mass QTL 303.50.0008kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)364655305115665732Rat

Markers in Region
RH128883  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2369,806,899 - 69,807,079 (+)MAPPERmRatBN7.2
Rnor_6.0372,125,395 - 72,125,574NCBIRnor6.0
Rnor_5.0378,646,034 - 78,646,213UniSTSRnor5.0
RGSC_v3.4367,934,194 - 67,934,373UniSTSRGSC3.4
Celera369,162,583 - 69,162,762UniSTS
Cytogenetic Map3q24UniSTS
RH144001  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2369,809,376 - 69,809,622 (+)MAPPERmRatBN7.2
Rnor_6.0372,127,872 - 72,128,117NCBIRnor6.0
Rnor_5.0378,648,511 - 78,648,756UniSTSRnor5.0
RGSC_v3.4367,936,671 - 67,936,916UniSTSRGSC3.4
Celera369,165,060 - 69,165,305UniSTS
Cytogenetic Map3q24UniSTS
RH139104  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2369,808,993 - 69,809,158 (+)MAPPERmRatBN7.2
Rnor_6.0372,127,489 - 72,127,653NCBIRnor6.0
Rnor_5.0378,648,128 - 78,648,292UniSTSRnor5.0
RGSC_v3.4367,936,288 - 67,936,452UniSTSRGSC3.4
Celera369,164,677 - 69,164,841UniSTS
Cytogenetic Map3q24UniSTS


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 12 24 16 19 16 49 20 41 11
Low 31 33 25 25 8 11 25 15 8
Below cutoff

Sequence


RefSeq Acc Id: ENSRNOT00000009726   ⟹   ENSRNOP00000009726
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl369,806,778 - 69,810,421 (-)Ensembl
Rnor_6.0 Ensembl372,125,273 - 72,128,973 (-)Ensembl
RefSeq Acc Id: NM_001009599   ⟹   NP_001009599
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8390,213,461 - 90,217,165 (-)NCBI
mRatBN7.2369,806,774 - 69,810,478 (-)NCBI
Rnor_6.0372,125,269 - 72,128,973 (-)NCBI
Rnor_5.0378,645,908 - 78,657,782 (-)NCBI
RGSC_v3.4367,934,068 - 67,937,772 (-)RGD
Celera369,162,457 - 69,166,161 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001009599 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH87130 (Get FASTA)   NCBI Sequence Viewer  
  EDL79312 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000009726.4
  ENSRNOP00055028402
  ENSRNOP00060014251
  ENSRNOP00065030052
GenBank Protein Q5PQL4 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_001009599   ⟸   NM_001009599
- UniProtKB: Q5PQL4 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000009726   ⟸   ENSRNOT00000009726

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q5PQL4-F1-model_v2 AlphaFold Q5PQL4 1-425 view protein structure

Transcriptome

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

Promoters
RGD ID:13692181
Promoter ID:EPDNEW_R2706
Type:multiple initiation site
Name:Clp1_1
Description:cleavage and polyadenylation factor I 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_6.0372,128,910 - 72,128,970EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1307679 AgrOrtholog
BioCyc Gene G2FUF-49166 BioCyc
Ensembl Genes ENSRNOG00000007416 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOG00055020512 UniProtKB/Swiss-Prot
  ENSRNOG00060010798 UniProtKB/Swiss-Prot
  ENSRNOG00065021886 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000009726.6 UniProtKB/Swiss-Prot
  ENSRNOT00055035007 UniProtKB/Swiss-Prot
  ENSRNOT00060018291 UniProtKB/Swiss-Prot
  ENSRNOT00065037245 UniProtKB/Swiss-Prot
Gene3D-CATH 2.40.30.330 UniProtKB/Swiss-Prot
  2.60.120.1030 UniProtKB/Swiss-Prot
  3.40.50.300 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7112583 IMAGE-MGC_LOAD
InterPro Clp1 UniProtKB/Swiss-Prot
  Clp1/Grc3 UniProtKB/Swiss-Prot
  Clp1_C UniProtKB/Swiss-Prot
  Clp1_C_sf UniProtKB/Swiss-Prot
  Clp1_N UniProtKB/Swiss-Prot
  Clp1_N_sf UniProtKB/Swiss-Prot
  CLP1_P UniProtKB/Swiss-Prot
  P-loop_NTPase UniProtKB/Swiss-Prot
KEGG Report rno:311166 UniProtKB/Swiss-Prot
MGC_CLONE MGC:94928 IMAGE-MGC_LOAD
NCBI Gene 311166 ENTREZGENE
PANTHER POLYRIBONUCLEOTIDE 5'-HYDROXYL-KINASE CLP1 UniProtKB/Swiss-Prot
  PTHR12755 UniProtKB/Swiss-Prot
Pfam Clp1 UniProtKB/Swiss-Prot
  CLP1_N UniProtKB/Swiss-Prot
  CLP1_P UniProtKB/Swiss-Prot
PhenoGen Clp1 PhenoGen
RatGTEx ENSRNOG00000007416 RatGTEx
  ENSRNOG00055020512 RatGTEx
  ENSRNOG00060010798 RatGTEx
  ENSRNOG00065021886 RatGTEx
Superfamily-SCOP SSF52540 UniProtKB/Swiss-Prot
UniProt CLP1_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2019-11-11 Clp1  cleavage factor polyribonucleotide kinase subunit 1  Clp1  cleavage and polyadenylation factor I subunit 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-10-11 Clp1  cleavage and polyadenylation factor I subunit 1  Clp1  CLP1, cleavage and polyadenylation factor I subunit, homolog (S. cerevisiae)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-07 Clp1  CLP1, cleavage and polyadenylation factor I subunit, homolog (S. cerevisiae)  RGD1307679  similar to ATP/GTP-binding protein  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-12-06 RGD1307679  similar to ATP/GTP-binding protein  RGD1307679_predicted  similar to ATP/GTP-binding protein (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-20 RGD1307679_predicted  similar to ATP/GTP-binding protein (predicted)  LOC311166_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC311166_predicted  similar to ATP/GTP-binding protein (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL