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Gene: Clp1 (cleavage factor polyribonucleotide kinase subunit 1) Rattus norvegicus

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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 cerebellar cortex development; negative regulation of gene expression; and tRNA splicing, via endonucleolytic cleavage and ligation. 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

Alliance Orthologs

More Info

more info ...

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	90,213,461 - 90,217,165 (-)	NCBI		GRCr8
mRatBN7.2	3	69,806,774 - 69,818,633 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	3	69,806,778 - 69,810,421 (-)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	3	73,188,581 - 73,192,284 (-)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	3	81,787,243 - 81,790,946 (-)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	3	79,546,170 - 79,549,873 (-)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	3	72,125,269 - 72,137,122 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	3	72,125,273 - 72,128,973 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	3	78,645,908 - 78,657,782 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	3	67,934,068 - 67,937,772 (-)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	3	67,830,439 - 67,834,144 (-)	NCBI
Celera	3	69,162,457 - 69,166,161 (-)	NCBI		Celera
Cytogenetic Map	3	q24	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

Experimental Liver Cirrhosis (ISO)

genetic disease (ISO)

intellectual disability (ISO)

pontocerebellar hypoplasia (ISO)

pontocerebellar hypoplasia type 10 (ISO,ISS)

pontocerebellar hypoplasia type 1B (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(+)-catechin (ISO)

(-)-epigallocatechin 3-gallate (ISO)

(1->4)-beta-D-glucan (ISO)

1,2-dichloroethane (ISO)

1-naphthyl isothiocyanate (EXP)

17alpha-ethynylestradiol (ISO)

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

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

2,4-dibromophenyl 2,4,5-tribromophenyl ether (ISO)

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

4,4'-diaminodiphenylmethane (EXP,ISO)

acrylamide (ISO)

aflatoxin B1 (ISO)

antirheumatic drug (ISO)

aristolochic acid A (ISO)

arsane (ISO)

arsenic atom (ISO)

atrazine (ISO)

benzo[a]pyrene (ISO)

benzo[a]pyrene diol epoxide I (ISO)

beta-lapachone (ISO)

bisphenol A (EXP,ISO)

bisphenol F (ISO)

caffeine (ISO)

carbon nanotube (ISO)

chromium(6+) (ISO)

cisplatin (ISO)

clofibric acid (EXP)

copper atom (ISO)

copper(0) (ISO)

dexamethasone (ISO)

disulfiram (ISO)

dorsomorphin (ISO)

entinostat (ISO)

ethanol (ISO)

ethyl methanesulfonate (ISO)

flutamide (EXP)

formaldehyde (ISO)

fulvestrant (ISO)

gentamycin (EXP)

indometacin (ISO)

leflunomide (ISO)

methapyrilene (EXP)

methyl methanesulfonate (ISO)

N-nitrosodimethylamine (EXP)

panobinostat (ISO)

perfluorooctane-1-sulfonic acid (ISO)

phenylmercury acetate (ISO)

pirinixic acid (ISO)

potassium chromate (ISO)

potassium dichromate (ISO)

quercetin (ISO)

SB 431542 (ISO)

silicon dioxide (ISO)

sodium arsenite (ISO)

sulindac sulfide (ISO)

sunitinib (ISO)

tamoxifen (ISO)

thimerosal (ISO)

thioacetamide (EXP)

trichostatin A (ISO)

triphenyl phosphate (ISO)

tungsten (ISO)

valproic acid (ISO)

vinclozolin (EXP)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

biological_process (ND)

cerebellar cortex development (ISO,ISS)

global gene silencing by mRNA cleavage (ISO,ISS)

mRNA 3'-end processing (IEA)

RISC complex assembly (ISO,ISS)

tRNA splicing, via endonucleolytic cleavage and ligation (IBA,ISO,ISS)

Cellular Component

cytosol (IEA,ISO)

mRNA cleavage factor complex (IEA)

nucleoplasm (IEA,ISO)

nucleus (IBA,ISO)

tRNA-intron endonuclease complex (ISO,ISS)

Molecular Function

ATP binding (IEA)

ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity (ISO)

ATP-dependent polyribonucleotide 5'-hydroxyl-kinase activity (ISO)

polynucleotide 5'-hydroxyl-kinase activity (IBA)

protein binding (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)

tRNA maturation 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.	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 Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	3	90,213,461 - 90,217,165 (-)	NCBI		GRCr8
mRatBN7.2	3	69,806,774 - 69,818,633 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	3	69,806,778 - 69,810,421 (-)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	3	73,188,581 - 73,192,284 (-)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	3	81,787,243 - 81,790,946 (-)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	3	79,546,170 - 79,549,873 (-)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	3	72,125,269 - 72,137,122 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	3	72,125,273 - 72,128,973 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	3	78,645,908 - 78,657,782 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	3	67,934,068 - 67,937,772 (-)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	3	67,830,439 - 67,834,144 (-)	NCBI
Celera	3	69,162,457 - 69,166,161 (-)	NCBI		Celera
Cytogenetic Map	3	q24	NCBI

CLP1
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	11	57,657,762 - 57,661,865 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	11	57,648,188 - 57,661,865 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	11	57,425,234 - 57,429,337 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	11	57,181,206 - 57,185,913 (+)	NCBI	NCBI36	Build 36	hg18	NCBI36
Celera	11	54,781,701 - 54,785,822 (+)	NCBI		Celera
Cytogenetic Map	11	q12.1	NCBI
HuRef	11	53,774,137 - 53,778,258 (+)	NCBI		HuRef
CHM1_1	11	57,291,424 - 57,295,545 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	11	57,607,935 - 57,612,038 (+)	NCBI		T2T-CHM13v2.0

Clp1
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	2	84,553,466 - 84,557,631 (-)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	2	84,552,448 - 84,557,694 (-)	Ensembl		GRCm39 Ensembl
GRCm38	2	84,723,122 - 84,727,287 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	2	84,722,104 - 84,727,350 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	2	84,563,279 - 84,567,425 (-)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	2	84,523,961 - 84,528,107 (-)	NCBI		MGSCv36	mm8
Celera	2	86,318,290 - 86,322,440 (-)	NCBI		Celera
Cytogenetic Map	2	D	NCBI
cM Map	2	49.45	NCBI

Clp1
(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_004955511	2,588,825 - 2,593,192 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955511	2,588,825 - 2,592,108 (+)	NCBI	ChiLan1.0	ChiLan1.0

CLP1
(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	58,794,718 - 58,818,214 (+)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	11	59,826,329 - 59,838,193 (+)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	11	52,898,181 - 52,902,656 (+)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	11	56,368,732 - 56,373,129 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	11	56,368,433 - 56,373,129 (+)	Ensembl	panpan1.1		panPan2

CLP1
(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	38,528,700 - 38,531,899 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	18	38,528,621 - 38,530,846 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	18	38,075,104 - 38,078,316 (-)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	18	39,210,508 - 39,213,726 (-)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	18	39,210,508 - 39,213,629 (-)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	18	38,793,608 - 38,796,826 (-)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	18	38,366,628 - 38,369,840 (-)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	18	38,997,368 - 39,000,586 (-)	NCBI		UU_Cfam_GSD_1.0

Clp1
(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	14,756,010 - 14,759,418 (-)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936581	4,869,686 - 4,873,217 (-)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936581	4,870,126 - 4,873,158 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

CLP1
(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	13,282,164 - 13,285,162 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	2	13,282,157 - 13,285,208 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	2	12,915,349 - 12,918,466 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

CLP1
(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	15,568,984 - 15,573,849 (-)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	1	15,568,976 - 15,573,082 (-)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666038	112,920,089 - 112,924,752 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Clp1
(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_004624864	3,063,555 - 3,067,051 (-)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624864	3,063,555 - 3,067,045 (-)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Variants

Variants in Clp1
50 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.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
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
2298542	Neuinf11	Neuroinflammation QTL 11	3.9		nervous system integrity trait (VT:0010566)	spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)	3	15005422	76927699	Rat
1358362	Srcrt2	Stress Responsive Cort QTL 2	2.78		blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	3	38192233	133483320	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
1582218	Bw74	Body weight QTL 74	3.9	0.0021	body mass (VT:0001259)	body weight (CMO:0000012)	3	53184593	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
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
1582210	Bw71	Body weight QTL 71	3.3	0.0012	body mass (VT:0001259)	body weight (CMO:0000012)	3	64655305	115665732	Rat
9590286	Uminl1	Urine mineral level QTL 1	3.5	0.001	urine mineral amount (VT:0015086)	urine electrolyte level (CMO:0000593)	3	28249687	73249687	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
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
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
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
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
731180	Bp152	Blood pressure QTL 152		0.03	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	3	53781112	91609953	Rat
631200	Cm25	Cardiac mass QTL 25	4.8	0.0001	heart left ventricle mass (VT:0007031)	heart left ventricle wet weight (CMO:0000071)	3	61134348	89115068	Rat
61356	Bp37	Blood pressure QTL 37	3		blood pressure trait (VT:0000183)	systolic blood pressure (CMO:0000004)	3	30684642	75684642	Rat
1358905	Hrtrt17	Heart rate QTL 17	5.9	0.000014	heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	3	10861912	89878372	Rat
8694196	Abfw2	Abdominal fat weight QTL 2	16.58	0.001	visceral adipose mass (VT:0010063)	abdominal fat pad weight to body weight ratio (CMO:0000095)	3	28249687	73249687	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
1358885	Bp251	Blood pressure QTL 251	3.8		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	3	14489145	121056321	Rat
2301970	Bw81	Body weight QTL 81	5.19		body mass (VT:0001259)	body weight (CMO:0000012)	3	41874578	155617519	Rat
2290452	Scl56	Serum cholesterol level QTL 56	2.26		blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	3	1	91609953	Rat
12879868	Am6	Aortic mass QTL 6		0.001	aorta mass (VT:0002845)	aorta weight to aorta length to body weight ratio (CMO:0002722)	3	31426403	70668733	Rat
11565451	Bw177	Body weight QTL 177		0.002	body mass (VT:0001259)	body weight (CMO:0000012)	3	31426403	70668733	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
11565452	Kidm57	Kidney mass QTL 57		0.001	kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	3	31426403	70668733	Rat
12879866	Cm94	Cardiac mass QTL 94		0.001	heart left ventricle mass (VT:0007031)	heart left ventricle weight to body weight ratio (CMO:0000530)	3	31426403	70668733	Rat
12879867	Cm95	Cardiac mass QTL 95		0.047	heart right ventricle mass (VT:0007033)	heart right ventricle weight to body weight ratio (CMO:0000914)	3	31426403	70668733	Rat
1300178	Hrtrt4	Heart rate QTL 4	3.74		heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	3	43827364	90905114	Rat
61377	Edpm3	Estrogen-dependent pituitary mass QTL 3	7.05	0.038	pituitary gland mass (VT:0010496)	pituitary gland wet weight (CMO:0000853)	3	53184692	89878207	Rat
2302055	Pia30	Pristane induced arthritis QTL 30	3.5	0.001	blood autoantibody amount (VT:0003725)	serum immunoglobulin M-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002111)	3	27936919	72936919	Rat
1331795	Rf30	Renal function QTL 30	3.708		urine potassium amount (VT:0010539)	urine potassium level (CMO:0000128)	3	39454637	89115240	Rat
70216	Cm14	Cardiac mass QTL 14	2.1		heart mass (VT:0007028)	heart wet weight (CMO:0000069)	3	31172320	163586636	Rat
1354589	Bw31	Body weight QTL 31	3.3		body mass (VT:0001259)	body weight (CMO:0000012)	3	33703347	78196190	Rat
2303593	Gluco46	Glucose level QTL 46	3		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	3	28468571	73468571	Rat
1354590	Despr11	Despair related QTL 11		0.000031	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	3	28468571	73468571	Rat
2292591	Esta4	Estrogen-induced thymic atrophy QTL 4			thymus mass (VT:0004954)	thymus wet weight (CMO:0000855)	3	47233211	147415807	Rat
1331777	Bw24	Body weight QTL 24	3.503		body mass (VT:0001259)	body weight (CMO:0000012)	3	39454637	89115240	Rat
631647	Bp122	Blood pressure QTL 122	6.2		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	3	30684642	75684642	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
738019	Anxrr10	Anxiety related response QTL 10	3.9		exploratory behavior trait (VT:0010471)	number of entries into a discrete space in an experimental apparatus (CMO:0000960)	3	38517803	83517803	Rat
9590136	Scort3	Serum corticosterone level QTL 3	23.37	0.001	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	3	28249687	73249687	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
1354597	Kidm13	Kidney mass QTL 13	2.9		kidney mass (VT:0002707)	right kidney wet weight (CMO:0000082)	3	41874578	104104347	Rat
8552950	Pigfal12	Plasma insulin-like growth factor 1 level QTL 12	7.3		blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	3	28249687	73249687	Rat
8694386	Bw159	Body weight QTL 159	4.52	0.001	body lean mass (VT:0010483)	lean tissue morphological measurement (CMO:0002184)	3	28249687	73249687	Rat
1354604	Bw36	Body weight QTL 36	2.9		body mass (VT:0001259)	body weight (CMO:0000012)	3	33703347	104104347	Rat
631665	Bw8	Body weight QTL 8	5.5		body mass (VT:0001259)	body weight (CMO:0000012)	3	50437042	119183768	Rat
2301400	Cm68	Cardiac mass QTL 68		0.001	heart mass (VT:0007028)	heart wet weight to body weight ratio (CMO:0002408)	3	31426403	70668733	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

Markers in Region

RH128883

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	3	69,806,899 - 69,807,079 (+)	MAPPER	mRatBN7.2
Rnor_6.0	3	72,125,395 - 72,125,574	NCBI	Rnor6.0
Rnor_5.0	3	78,646,034 - 78,646,213	UniSTS	Rnor5.0
RGSC_v3.4	3	67,934,194 - 67,934,373	UniSTS	RGSC3.4
Celera	3	69,162,583 - 69,162,762	UniSTS
Cytogenetic Map	3	q24	UniSTS

RH144001

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	3	69,809,376 - 69,809,622 (+)	MAPPER	mRatBN7.2
Rnor_6.0	3	72,127,872 - 72,128,117	NCBI	Rnor6.0
Rnor_5.0	3	78,648,511 - 78,648,756	UniSTS	Rnor5.0
RGSC_v3.4	3	67,936,671 - 67,936,916	UniSTS	RGSC3.4
Celera	3	69,165,060 - 69,165,305	UniSTS
Cytogenetic Map	3	q24	UniSTS

RH139104

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	3	69,808,993 - 69,809,158 (+)	MAPPER	mRatBN7.2
Rnor_6.0	3	72,127,489 - 72,127,653	NCBI	Rnor6.0
Rnor_5.0	3	78,648,128 - 78,648,292	UniSTS	Rnor5.0
RGSC_v3.4	3	67,936,288 - 67,936,452	UniSTS	RGSC3.4
Celera	3	69,164,677 - 69,164,841	UniSTS
Cytogenetic Map	3	q24	UniSTS

Expression

RNA-SEQ Expression

Click on a value in the shaded box below the category label to view a detailed expression data table for that system.

Download All Expressed Objects for this Gene

alimentary part of gastrointestinal system	appendage	circulatory system	ectoderm	endocrine system	endoderm	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	mesenchyme	mesoderm	nervous system	renal system	reproductive system	respiratory system
9	11	49	113	91	90	59	25	59	6	218	97	93	45	60	31

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001009599	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_017591708	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC096003	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC087130	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473949	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ231160	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000003	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSRNOT00000009726 ⟹ ENSRNOP00000009726

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	3	69,806,778 - 69,810,421 (-)	Ensembl
Rnor_6.0 Ensembl	3	72,125,273 - 72,128,973 (-)	Ensembl

RefSeq Acc Id:

NM_001009599 ⟹ NP_001009599

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	3	90,213,461 - 90,217,165 (-)	NCBI
mRatBN7.2	3	69,806,774 - 69,810,478 (-)	NCBI
Rnor_6.0	3	72,125,269 - 72,128,973 (-)	NCBI
Rnor_5.0	3	78,645,908 - 78,657,782 (-)	NCBI
RGSC_v3.4	3	67,934,068 - 67,937,772 (-)	RGD
Celera	3	69,162,457 - 69,166,161 (-)	RGD

Sequence:

show sequence

CACGTCCCAAAATGCATCACGCGACCGCGTCTCCTACTACCGCGCAAGAGCGGAACCGCCTTTG
CTTTCCGGCTAGTATTTAGGCACAGCAGCTCAACAGAAAAGATGAGTGAGGAATCCAATGATGA
CAAGAAGCCAACGACCAAGTTTGAACTAGAGCGAGAAACAGAGCTTCGATTTGAGGTGGAGGCA
TCTCAGTCAGTTCAGTTGGAGTTGCTGGCTGGCATGGCAGAGATCTTTGGCACAGAACTGACCA
GAAACAAGAAATTCACCTTTGATGCTGGTGCCAAGGTGGCTGTTTTCACTTGGCATGGCTGTTC
TCTGCAGTTGAGTGGCCGGACCGAGGTGGCTTATGTCTCTAAGGACACCCCTATGTTGCTTTAC
CTTAACACTCATACAGCCTTGGAGCAGATGCGGAGGCAGGCAGAAAAGGAAGAAGAGAGAGGCC
CCCGAGTGATGGTTGTGGGTCCTACTGATGTGGGCAAGTCCACGGTGTGCCGGCTGCTACTCAA
CTACGCAGTGCGTTTGGGCCGACGTCCTACTTACGTGGAGTTGGATGTAGGGCAGGGCTCTGTG
TCCATTCCTGGTACCATGGGGGCCCTGTACATTGAGCGACCCGCAGATGTGGAAGAAGGTTTCT
CCATCCAGGCACCTCTTGTGTATCATTTTGGCTCCACCACTCCTGGCACCAACATCAAGCTTTA
CAACAAGATTACATCTCGTTTAGCAGATGTGTTCAACCAAAGGTGTGAAGTGAATAGAAGAGCT
TCTGTGAGTGGCTGTGTCATCAACACCTGTGGCTGGGTCAAGGGTTATGGTTACCAGGCCCTGG
TGCACGCAGCTTCAGCCTTTGAGGTGGATGTGGTTGTGGTTCTGGATCAAGAACGACTGTACAA
CGAGTTGAAAAGGGACCTGCCTCATTTTGTTCGAACTGTGCTGCTCCCAAAATCAGGGGGTGTG
GTAGAACGCTCCAAGGACTTCCGGCGGGAATGTAGGGATGAACGTATCCGTGAATATTTCTATG
GATTCCGAGGCTGTTTCTATCCCCATGCCTTCAATGTCAAATTTTCTGATGTGAAAATCTACAA
AGTTGGGGCACCCACCATCCCAGACTCGTGTTTACCTCTGGGCATGTCTCAGGAAGACAATCAG
CTCAAGTTAGTACCTGTCACCCCTGGTAGAGATATGGTGCACCATCTCCTGAGTGTCAGCACTG
CTGAGGGCACAGAAGAGAACCTTTCTGAGACAAGTGTGGCTGGATTCATTGTTGTGACCAGTGT
GGACGTGGAACACCAGGTGTTTACTGTCTTGTCTCCAGCCCCCCGCCCACTGCCTAAGAACTTT
CTTCTCATCATGGATATCCGGTTCATGGATCTCAAGTAGTGATTAGCAAGGAGCCTCACTTTCT
GCGCCCTAGAGTTCTGACCATCACCAAAGCAGATGGAATGAGCTCTGGCAGTCTTACTAAGTCA
ACTGACAAGGCCCAACTAGCAGAGAGCACATCCTCTACCTCTTGAAACAGTGGCAGTAGCCAGA
GTCCTGGCTATTATTTGGTTCATTTACCTGGAACCAAAAGGAGAGCGCTCAAAAAGAAAATCTG
AATATTTTTTTAAGATCGCCTAAGGTACCATTTTAAAGATTCCAAGACCCTAGAGAACTCCATG
TCTTCCTATGCTACCATGTAGGTTTTCTTGTTATCATTTTCTACTGTCTCGGTATAGTATTTGT
TATATTATTTAACCAGGACGGACGTGAGAAAGAGTTCAAACTTTAAAACAATTAATTTTAATAA
ATATTATTGTCATAGAAAAAAAAAAAAAAAAAAAAAAAAAAAA

hide 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:

show sequence

MSEESNDDKKPTTKFELERETELRFEVEASQSVQLELLAGMAEIFGTELTRNKKFTFDAGAKVA
VFTWHGCSLQLSGRTEVAYVSKDTPMLLYLNTHTALEQMRRQAEKEEERGPRVMVVGPTDVGKS
TVCRLLLNYAVRLGRRPTYVELDVGQGSVSIPGTMGALYIERPADVEEGFSIQAPLVYHFGSTT
PGTNIKLYNKITSRLADVFNQRCEVNRRASVSGCVINTCGWVKGYGYQALVHAASAFEVDVVVV
LDQERLYNELKRDLPHFVRTVLLPKSGGVVERSKDFRRECRDERIREYFYGFRGCFYPHAFNVK
FSDVKIYKVGAPTIPDSCLPLGMSQEDNQLKLVPVTPGRDMVHHLLSVSTAEGTEENLSETSVA
GFIVVTSVDVEHQVFTVLSPAPRPLPKNFLLIMDIRFMDLK

hide sequence

Ensembl 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 Assembly	Chr	Position (strand)	Source
Rnor_6.0	3	72,128,910 - 72,128,970	EPDNEW

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1307679	AgrOrtholog
BioCyc Gene	G2FUF-49166	BioCyc
Ensembl Genes	ENSRNOG00000007416	Ensembl, 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

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)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
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

Imported Disease Annotations - CTD

Imported Disease Annotations - MGI

Imported Disease Annotations - OMIM

RGD Manual Annotations

Imported Annotations - KEGG (archival)

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Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

Imported Disease Annotations - MGI

Imported Disease Annotations - OMIM

RGD Manual Annotations

Imported Annotations - KEGG (archival)