Ublcp1 (ubiquitin-like domain containing CTD phosphatase 1)

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Gene: Ublcp1 (ubiquitin-like domain containing CTD phosphatase 1) Rattus norvegicus

Analyze

Symbol:

Ublcp1

Name:

ubiquitin-like domain containing CTD phosphatase 1

RGD ID:

1310386

Description:

Predicted to have protein serine/threonine phosphatase activity. Predicted to be involved in protein dephosphorylation. Predicted to localize to nucleolus and nucleoplasm. Orthologous to human UBLCP1 (ubiquitin like domain containing CTD phosphatase 1); INTERACTS WITH 2,4-dinitrotoluene; 2,6-dinitrotoluene; bisphenol A.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Also known as:

LOC360514; MGC105972; nuclear proteasome inhibitor UBLCP1; RGD1310386; similar to hypothetical protein MGC10067; ubiquitin-like domain-containing CTD phosphatase 1

RGD Orthologs

Human

Mouse

Chinchilla

Bonobo

Dog

Squirrel

Pig

Green Monkey

Naked Mole-Rat

Alliance Genes

More Info

more info ...

Latest Assembly:

Rnor_6.0 - RGSC Genome Assembly v6.0

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Rnor_6.0	10	30,103,607 - 30,118,945 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	10	30,103,613 - 30,118,873 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	10	29,936,811 - 29,952,143 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	10	29,612,055 - 29,627,325 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	10	29,613,103 - 29,628,374 (-)	NCBI
Celera	10	28,424,577 - 28,439,847 (-)	NCBI		Celera
Cytogenetic Map	10	q21	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

Breast Neoplasms (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2-dichloroethane (ISO)

1,2-dimethylhydrazine (ISO)

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

2,4-dinitrotoluene (EXP)

2,6-dinitrotoluene (EXP)

2-hydroxypropanoic acid (ISO)

aflatoxin M1 (ISO)

arsane (ISO)

arsenic atom (ISO)

atrazine (ISO)

benzo[a]pyrene (ISO)

benzo[a]pyrene diol epoxide I (ISO)

bisphenol A (EXP)

carbon nanotube (ISO)

clorgyline (ISO)

cobalt dichloride (ISO)

copper(II) sulfate (ISO)

dicrotophos (ISO)

doxorubicin (ISO)

enzyme inhibitor (ISO)

ethanol (ISO)

flutamide (EXP)

folic acid (ISO)

indometacin (ISO)

paracetamol (ISO)

perfluorooctane-1-sulfonic acid (ISO)

pirinixic acid (ISO)

rac-lactic acid (ISO)

sunitinib (ISO)

tungsten (ISO)

valproic acid (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

protein dephosphorylation (IBA,IEA,ISO)

Cellular Component

nucleolus (IEA,ISO)

nucleoplasm (IEA,ISO)

nucleus (IBA,ISO)

Molecular Function

protein binding (ISO)

protein serine phosphatase activity (IEA)

protein serine/threonine phosphatase activity (IBA,ISO)

protein threonine phosphatase activity (IEA)

References

References - curated


1.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2.	RGD automated data pipeline
3.	RGD automated import pipeline for gene-chemical interactions
4.	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:15489334	PMID:21949367

Genomics

Comparative Map Data

Ublcp1
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Rnor_6.0	10	30,103,607 - 30,118,945 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	10	30,103,613 - 30,118,873 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	10	29,936,811 - 29,952,143 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	10	29,612,055 - 29,627,325 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	10	29,613,103 - 29,628,374 (-)	NCBI
Celera	10	28,424,577 - 28,439,847 (-)	NCBI		Celera
Cytogenetic Map	10	q21	NCBI

UBLCP1
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	5	159,263,290 - 159,286,036 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	5	159,263,290 - 159,286,036 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	5	158,690,089 - 158,713,048 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	5	158,622,876 - 158,645,617 (+)	NCBI	NCBI36		hg18	NCBI36
Celera	5	154,720,940 - 154,743,899 (+)	NCBI
Cytogenetic Map	5	q33.3	NCBI
HuRef	5	153,784,215 - 153,807,159 (+)	NCBI		HuRef
CHM1_1	5	158,122,533 - 158,145,488 (+)	NCBI		CHM1_1

Ublcp1
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	11	44,345,398 - 44,361,540 (-)	NCBI	GRCm39		mm39
GRCm38	11	44,454,571 - 44,470,713 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	11	44,454,571 - 44,470,498 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	11	44,268,073 - 44,284,050 (-)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	11	44,297,996 - 44,313,868 (-)	NCBI			mm8
Celera	11	17,009,149 - 17,013,836 (-)	NCBI		Celera
Cytogenetic Map	11	B1.1	NCBI

Ublcp1
(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_004955408	13,259,328 - 13,279,574 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955408	13,259,328 - 13,279,509 (+)	NCBI	ChiLan1.0	ChiLan1.0

UBLCP1
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
PanPan1.1	5	161,271,839 - 161,294,639 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	5	161,271,844 - 161,294,643 (+)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	5	154,655,018 - 154,677,794 (+)	NCBI	Mhudiblu_PPA_v0		panPan3

UBLCP1
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1 Ensembl	4	51,218,928 - 51,234,198 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
CanFam3.1	4	51,218,471 - 51,237,661 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1

Ublcp1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
SpeTri2.0	NW_004936515	4,093,255 - 4,111,616 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

UBLCP1
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	16	64,178,935 - 64,205,675 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	16	64,182,918 - 64,205,684 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	16	70,006,436 - 70,029,004 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

UBLCP1
(Chlorocebus sabaeus - African green monkey)

Vervet Assembly	Chr	Position (strand)	Source	Genome Browsers
Vervet Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1 Ensembl	23	61,664,677 - 61,687,433 (+)	Ensembl
ChlSab1.1	23	61,664,467 - 61,686,874 (+)	NCBI

Ublcp1
(Heterocephalus glaber - naked mole-rat)

Molerat Assembly	Chr	Position (strand)	Source	Genome Browsers
Molerat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla 1.0	NW_004624733	30,166,045 - 30,202,081 (-)	NCBI

Position Markers

RH128834

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	12	3,558,005 - 3,558,214	NCBI	Rnor6.0
Rnor_6.0	10	30,103,682 - 30,103,889	NCBI	Rnor6.0
Rnor_5.0	12	5,700,413 - 5,700,622	UniSTS	Rnor5.0
Rnor_5.0	10	29,936,886 - 29,937,093	UniSTS	Rnor5.0
RGSC_v3.4	12	1,987,010 - 1,987,219	UniSTS	RGSC3.4
RGSC_v3.4	10	29,612,128 - 29,612,335	UniSTS	RGSC3.4
Celera	10	28,424,650 - 28,424,857	UniSTS
Celera	12	4,023,052 - 4,023,261	UniSTS
Cytogenetic Map	10	q21	UniSTS

QTLs in Region (Rnor_6.0)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
2293680	Bss40	Bone structure and strength QTL 40	5.66	0.0001	femur strength trait (VT:0010010)	femur total energy absorbed before break (CMO:0001677)	10	1	35538813	Rat
634327	Hc4	Hypercalciuria QTL 4	2.4		urine calcium amount (VT:0002985)	urine calcium excretion rate (CMO:0000763)	10	1	38594330	Rat
7411611	Foco17	Food consumption QTL 17	18.7	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	10	1	42669970	Rat
10401803	Kidm50	Kidney mass QTL 50			kidney mass (VT:0002707)	both kidneys wet weight (CMO:0000085)	10	1	44902893	Rat
631554	Bp133	Blood pressure QTL 133		0.005	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	764421	66221621	Rat
2298544	Neuinf9	Neuroinflammation QTL 9	4.6		nervous system integrity trait (VT:0010566)	spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)	10	5877536	64401490	Rat
8662860	Vetf10	Vascular elastic tissue fragility QTL 10			artery integrity trait (VT:0010639)	number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)	10	6229095	75983805	Rat
631660	Hcar1	Hepatocarcinoma resistance QTL 1	3.4	0.0001	liver integrity trait (VT:0010547)	volume of individual liver tumorous lesion (CMO:0001078)	10	6229289	36185929	Rat
61427	Cia16	Collagen induced arthritis QTL 16	3.2		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	6429075	99492409	Rat
1578761	Stresp21	Stress response QTL 21	3.3		thymus mass (VT:0004954)	thymus wet weight (CMO:0000855)	10	7521450	52521450	Rat
2303118	Mamtr7	Mammary tumor resistance QTL 7		0.003	mammary gland integrity trait (VT:0010552)	mammary tumor growth rate (CMO:0000344)	10	9841807	108540162	Rat
9590310	Scort19	Serum corticosterone level QTL 19	6.3	0.001	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	10	12639513	57639513	Rat
9590268	Scort13	Serum corticosterone level QTL 13	3.26	0.001	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	10	12639513	57639513	Rat
9589136	Insul27	Insulin level QTL 27	10.46	0.001	blood insulin amount (VT:0001560)	plasma insulin level (CMO:0000342)	10	12639513	57639513	Rat
2301967	Cm73	Cardiac mass QTL 73	4.55		heart left ventricle mass (VT:0007031)	heart left ventricle weight to body weight ratio (CMO:0000530)	10	14827894	92423564	Rat
631268	Cia21	Collagen induced arthritis QTL 21	3.1		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	14827894	107857673	Rat
2316949	Gluco60	Glucose level QTL 60	3.7		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	10	14827894	110992275	Rat
1354587	Kidm21	Kidney mass QTL 21	3.3		kidney mass (VT:0002707)	right kidney wet weight (CMO:0000082)	10	15375474	62469074	Rat
631564	Apr3	Acute phase response QTL 3	3.9		blood interleukin-6 amount (VT:0008595)	plasma interleukin-6 level (CMO:0001927)	10	16468736	61468736	Rat
6893350	Bw99	Body weight QTL 99	0.87	0.16	body mass (VT:0001259)	body weight (CMO:0000012)	1	17121542	62121542	Rat
6893352	Bw100	Body weight QTL 100	0.33	0.6	body mass (VT:0001259)	body weight (CMO:0000012)	1	17121542	62121542	Rat
631532	Cm50	Cardiac mass QTL 50	6.6		heart mass (VT:0007028)	calculated heart weight (CMO:0000073)	10	18246394	53637634	Rat
1598852	Anxrr19	Anxiety related response QTL 19	5.07		body movement coordination trait (VT:0005424)	number of rearing movements in an experimental apparatus (CMO:0001752)	10	19402814	64402814	Rat
1554317	Bmd4	Bone mineral density QTL 4	9.4	0.0001	lumbar vertebra mineral mass (VT:0010511)	volumetric bone mineral density (CMO:0001553)	10	20170031	102897474	Rat
70223	Bp57	Blood pressure QTL 57	5		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	21523906	83549467	Rat
70188	BpQTLcluster1	Blood pressure QTL cluster 1	4.864		arterial blood pressure trait (VT:2000000)	pulse pressure (CMO:0000292)	1	21523906	90312401	Rat
70188	BpQTLcluster1	Blood pressure QTL cluster 1	4.864		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	21523906	90312401	Rat
70188	BpQTLcluster1	Blood pressure QTL cluster 1	4.864		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	21523906	90312401	Rat
70188	BpQTLcluster1	Blood pressure QTL cluster 1	4.864		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	1	21523906	90312401	Rat
70198	BpQTLcluster9	Blood pressure QTL cluster 9	2.94		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	10	21523906	90312401	Rat
1581497	Esta1	Estrogen-induced thymic atrophy QTL 1			thymus mass (VT:0004954)	thymus wet weight (CMO:0000855)	10	21707766	64648311	Rat
631531	Iresp2	Immunoglobin response QTL2	6.3		blood immunoglobulin E amount (VT:0002492)	serum total immunoglobulin E level (CMO:0001542)	10	22402817	38204229	Rat
724556	Pur2	Proteinuria QTL 2	5.5		urine protein amount (VT:0005160)	urine protein level (CMO:0000591)	10	22901497	93886300	Rat
1331762	Rf40	Renal function QTL 40	3.873		kidney blood vessel physiology trait (VT:0100012)	absolute change in renal vascular resistance (CMO:0001900)	10	23861015	66539843	Rat
1331791	Cm31	Cardiac mass QTL 31	3.84606		heart mass (VT:0007028)	heart wet weight (CMO:0000069)	10	23861015	112626471	Rat
631267	Cia20	Collagen induced arthritis QTL 20	3.2		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	24483076	107857673	Rat
61325	Aia5	Adjuvant induced arthritis QTL 5		0.01	joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	24483076	107857673	Rat
61354	Pia10	Pristane induced arthritis QTL 10		0.01	joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	24483076	107857673	Rat
634329	Pia15	Pristane induced arthritis QTL 15	3.1		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	24884084	47487910	Rat
70224	Eae3	Experimental allergic encephalomyelitis QTL 3	4.1		nervous system integrity trait (VT:0010566)	experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)	10	27237530	64648311	Rat
1298069	Bp168	Blood pressure QTL 168	5.5		blood pressure trait (VT:0000183)	systolic blood pressure (CMO:0000004)	10	27237530	101482600	Rat
631542	Bp82	Blood pressure QTL 82	6.8		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	27237530	102427718	Rat
2300171	Bmd58	Bone mineral density QTL 58	4.9	0.0001	lumbar vertebra mineral mass (VT:0010511)	volumetric bone mineral density (CMO:0001553)	10	28789280	73789280	Rat
1600371	Mcs21	Mammary carcinoma susceptibility QTL 21	3		mammary gland integrity trait (VT:0010552)	mammary tumor growth rate (CMO:0000344)	10	30021354	54057745	Rat
2292441	Bp308	Blood pressure QTL 308			arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	10	30099909	75099909	Rat
10402859	Bp381	Blood pressure QTL 381		0.002	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	10	30099909	75099909	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	167
Count of miRNA genes:	121
Interacting mature miRNAs:	137
Transcripts:	ENSRNOT00000006063
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	43	55	39	19	39	8	10	74	35	40	11	8
Low			2	2		2		1			1
Below cutoff

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001014117	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_006246140	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AABR07029476	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AAHX01063522	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC089210	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473948	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ233702	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ233828	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ233841	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ235222	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000006063 ⟹ ENSRNOP00000006063

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	10	30,103,613 - 30,118,873 (-)	Ensembl

RefSeq Acc Id:

NM_001014117 ⟹ NP_001014139

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	10	30,103,609 - 30,118,879 (-)	NCBI
Rnor_5.0	10	29,936,811 - 29,952,143 (-)	NCBI
RGSC_v3.4	10	29,612,055 - 29,627,325 (-)	RGD
Celera	10	28,424,577 - 28,439,847 (-)	RGD

Sequence:

show sequence

CTTTTTCGTCCGCTGTAGCTGGTTCCGCCGCGCTCCAGGTGTTTTGTCTAGCAGGAAGCCGCTG
CTTCATATGCTTGAAGAATGTCACTCCCCATCATTGTGAAATGGGGTGGGCAGGAATACTCGGT
GACCACGCTCTCAGAGGATGACACTGTGCTGGATCTCAAGCAGTTCCTCAAGACCCTTACAGGA
GTGCTCCCAGAGCGCCAGAAATTACTAGGGCTCAAAGTAAAAGGCAAACCTGCAGAAAATGATG
TTAAGCTTGGAGCTCTCAAACTGAAACCAAATACTAAAATCATGATGATGGGAACTCGTGAGGA
GAGCTTGGAAGATGTCTTATGTCCTCCCCCTGACAATGATGATGTCATCAATGATTTTGACATT
GAAGATGAAGTAGTTGAAGTAGAAAATAGGGAAGAAAACCTATTGAAGATCTCTCGCAGGGTCA
AGGAGTACAAGGTGGAAGTGCTGAACCCTCCCAGGGAAGGGAAGAAGCTTCTGGTGCTGGATGT
TGATTATACGCTATTTGATCATAGGTCTTGTGCAGAGACTGGGGTAGAGTTAATGAGGCCATAT
CTTCATGAATTTCTAACATCTGCATATGAAGATTATGACATTGTTATTTGGTCTGCAACAAATA
TGAAGTGGATTGAAGCTAAAATGAAAGAGCTGGGAGTGAGCACTAATGCCAACTATAAGATTAC
CTTCATGCTAGACAGTGCCGCCATGATAACTGTGCACACACCACGGAGGGGGCTCATTGACGTG
AAGCCTCTTGGTGTCATTTGGGGAAAGTTTTCTGAATTCTACAGCAAAAAAAACACCATTATGT
TTGATGACATAGGAAGAAATTTTCTAATGAACCCACAAAATGGACTGAAGATACGGCCTTTCAT
GAAAGCTCATCTAAATCGTGATAAAGACAAGGAACTGGTGAAGCTCACTCAGTACCTCAAGGAG
ATAGCCAAGCTTGATGACTTCCTGGAGCTGAATCACAAGTACTGGGAACGGTATCTATCTAAGA
AGCAAGGACAGTAGTTACCAGTTACACTCACAGTTGAAGGTCCTTGAGGTCCATGGACCTTTTT
TTCTTTGCTAGGCATTACCATGTTTGTGCTGGACACTGAAGCAGATGCCAGGTTGCCTAGCTGT
GGTCTTCCAATGCTTTGTAAATTTAATTTTGTATTTTTTTGAAGATCATAACAAAGTGCTAAAA
AACAAAACAAAAAGTTCTCTTCCCTCTGTGTTAATTTACTCCTGAAGAAATGTTTTTGGGCATT
AATTATTGAGGTGTTTCCCAAACCCTCTAAACATGCAAAAAAGAAAGGAAAATGAAAAGTGGAG
AAAATATACCTACCAGTGTCATCCTGTGACTTTGGAAATGAGTTTTGTCTTATGCTTTTATGCT
TTTGTCTCCTTGTATAATCCGCTGCCTGAGTCTGAGACCAAATCTATCTTCAACTAGCTAGTGT
TCTCCCCCTTAAAACCAAAAGCAAAACCAAAAATCCCAGACCAGCTTTTAAGTAATGACCTGGT
TTGTTATGCTGAAAACTCCCAAGAGTTGTCTCCTTGTCAGAGTTTCTCTACTGCAGTCTTCCAG
GAAGATCTTGAAGCTGGAGTTGTCAGTGTTCTTTAAGAATGAAGGACATCTGTGTGATATGGCT
GTGCCCTAGATGACAGGGTAACAAGCAGACTGAAGTAACACTGCAGGACAAGAATATGTTTCTT
TTTGGTGGCTAAGTAGAAAAAGCCTTTCTGCCTACACTGTAGTCCTGAGCACAGCTTACCACAG
TAGTAAAAAGGCACCGTCACCAACTCCACTCTCAGAAGCATGGATAGCATTTCTGCCTACTCCA
CCTAGTGTCATTGTAACTGCTAACACCAAACATCTAGCCATGAGAGTAAAAAGATCTGTTACTT
GCAATGCTTAAGCCTTGTGCAAATATGTAATGTGACTATTGTTTTATGTTGACAGTATTGCTTT
ATACAGTTCTTGCATTGAAGGGAATTGCTCCTTTTAAATGAACATGGTGTACATTGTTCTTATG
GGACTATTTCAGTGGTGTAAATAATAAATATCTTTTCTTAAAAAAAAAAAAAAAAAAAAAAAAA
AGG

hide sequence

RefSeq Acc Id:

XM_006246140 ⟹ XP_006246202

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	10	30,103,607 - 30,118,945 (-)	NCBI
Rnor_5.0	10	29,936,811 - 29,952,143 (-)	NCBI

Sequence:

show sequence

CCGGTCCTCCCGCCGGTTCCGGTCCCGCCTCTCACTTCCGGTCTCCTTAGGTTCCGCTGCGGCC
GGCTTTTTCGTCCGCTGTAGCTGGTTCCGCCGCGCTCCAGGTGTTTTGTCTAGCAGGAAGCCGC
TGCTTCATATGCTTGAAGAATGTCACTCCCCATCATTGTGAAATGGGGTGGGCAGGAATACTCG
GTGACCACGCTCTCAGAGGATGACACTGTGCTGGATCTCAAGCAGTTCCTCAAGACCCTTACAG
GAGTGCTCCCAGAGCGCCAGAAATTACTAGGGCTCAAAGTAAAAGGCAAACCTGCAGAAAATGA
TGTTAAGCTTGGAGCTCTCAAACTGAAACCAAATACTAAAATCATGATGATGGGAACTCGTGAG
GAGAGCTTGGAAGATGTCTTATGTCCTCCCCCTGACAATGATGATGTCATCAATGATTTTGACA
TTGAAGATGAAGTAGTTGAAGTAGAAAATAGGGTCAAGGAGTACAAGGTGGAAGTGCTGAACCC
TCCCAGGGAAGGGAAGAAGCTTCTGGTGCTGGATGTTGATTATACGCTATTTGATCATAGGTCT
TGTGCAGAGACTGGGGTAGAGTTAATGAGGCCATATCTTCATGAATTTCTAACATCTGCATATG
AAGATTATGACATTGTTATTTGGTCTGCAACAAATATGAAGTGGATTGAAGCTAAAATGAAAGA
GCTGGGAGTGAGCACTAATGCCAACTATAAGATTACCTTCATGCTAGACAGTGCCGCCATGATA
ACTGTGCACACACCACGGAGGGGGCTCATTGACGTGAAGCCTCTTGGTGTCATTTGGGGAAAGT
TTTCTGAATTCTACAGCAAAAAAAACACCATTATGTTTGATGACATAGGAAGAAATTTTCTAAT
GAACCCACAAAATGGACTGAAGATACGGCCTTTCATGAAAGCTCATCTAAATCGTGATAAAGAC
AAGGAACTGGTGAAGCTCACTCAGTACCTCAAGGAGATAGCCAAGCTTGATGACTTCCTGGAGC
TGAATCACAAGTACTGGGAACGGTATCTATCTAAGAAGCAAGGACAGTAGTTACCAGTTACACT
CACAGTTGAAGGTCCTTGAGGTCCATGGACCTTTTTTTCTTTGCTAGGCATTACCATGTTTGTG
CTGGACACTGAAGCAGATGCCAGGTTGCCTAGCTGTGGTCTTCCAATGCTTTGTAAATTTAATT
TTGTATTTTTTTGAAGATCATAACAAAGTGCTAAAAAACAAAACAAAAAGTTCTCTTCCCTCTG
TGTTAATTTACTCCTGAAGAAATGTTTTTGGGCATTAATTATTGAGGTGTTTCCCAAACCCTCT
AAACATGCAAAAAAGAAAGGAAAATGAAAAGTGGAGAAAATATACCTACCAGTGTCATCCTGTG
ACTTTGGAAATGAGTTTTGTCTTATGCTTTTATGCTTTTGTCTCCTTGTATAATCCGCTGCCTG
AGTCTGAGACCAAATCTATCTTCAACTAGCTAGTGTTCTCCCCCTTAAAACCAAAAGCAAAACC
AAAAATCCCAGACCAGCTTTTAAGTAATGACCTGGTTTGTTATGCTGAAAACTCCCAAGAGTTG
TCTCCTTGTCAGAGTTTCTCTACTGCAGTCTTCCAGGAAGATCTTGAAGCTGGAGTTGTCAGTG
TTCTTTAAGAATGAAGGACATCTGTGTGATATGGCTGTGCCCTAGATGACAGGGTAACAAGCAG
ACTGAAGTAACACTGCAGGACAAGAATATGTTTCTTTTTGGTGGCTAAGTAGAAAAAGCCTTTC
TGCCTACACTGTAGTCCTGAGCACAGCTTACCACAGTAGTAAAAAGGCACCGTCACCAACTCCA
CTCTCAGAAGCATGGATAGCATTTCTGCCTACTCCACCTAGTGTCATTGTAACTGCTAACACCA
AACATCTAGCCATGAGAGTAAAAAGATCTGTTACTTGCAATGCTTAAGCCTTGTGCAAATATGT
AATGTGACTATTGTTTTATGTTGACAGTATTGCTTTATACAGTTCTTGCATTGAAGGGAATTGC
TCCTTTTAAATGAACATGGTGTACATTGTTCTTATGGGACTATTTCAGTGGTGTAAATAATAAA
TATCTTTTCTTAAAACA

hide sequence

Protein Sequences


Protein RefSeqs	NP_001014139	(Get FASTA)	NCBI Sequence Viewer
	XP_006246202	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAH89210	(Get FASTA)	NCBI Sequence Viewer
	EDM04148	(Get FASTA)	NCBI Sequence Viewer
	Q5FWT7	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_001014139 ⟸ NM_001014117

- UniProtKB:

Q5FWT7 (UniProtKB/Swiss-Prot)

- Sequence:

show sequence

MSLPIIVKWGGQEYSVTTLSEDDTVLDLKQFLKTLTGVLPERQKLLGLKVKGKPAENDVKLGAL
KLKPNTKIMMMGTREESLEDVLCPPPDNDDVINDFDIEDEVVEVENREENLLKISRRVKEYKVE
VLNPPREGKKLLVLDVDYTLFDHRSCAETGVELMRPYLHEFLTSAYEDYDIVIWSATNMKWIEA
KMKELGVSTNANYKITFMLDSAAMITVHTPRRGLIDVKPLGVIWGKFSEFYSKKNTIMFDDIGR
NFLMNPQNGLKIRPFMKAHLNRDKDKELVKLTQYLKEIAKLDDFLELNHKYWERYLSKKQGQ

hide sequence

RefSeq Acc Id:

XP_006246202 ⟸ XM_006246140

- Peptide Label:

isoform X1

- Sequence:

show sequence

MSLPIIVKWGGQEYSVTTLSEDDTVLDLKQFLKTLTGVLPERQKLLGLKVKGKPAENDVKLGAL
KLKPNTKIMMMGTREESLEDVLCPPPDNDDVINDFDIEDEVVEVENRVKEYKVEVLNPPREGKK
LLVLDVDYTLFDHRSCAETGVELMRPYLHEFLTSAYEDYDIVIWSATNMKWIEAKMKELGVSTN
ANYKITFMLDSAAMITVHTPRRGLIDVKPLGVIWGKFSEFYSKKNTIMFDDIGRNFLMNPQNGL
KIRPFMKAHLNRDKDKELVKLTQYLKEIAKLDDFLELNHKYWERYLSKKQGQ

hide sequence

RefSeq Acc Id:

ENSRNOP00000006063 ⟸ ENSRNOT00000006063

Protein Domains

FCP1 homology Ubiquitin-like

Transcriptome

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

Promoters

RGD ID:

13697120

Promoter ID:

EPDNEW_R7644

Type:

initiation region

Name:

Ublcp1_1

Description:

ubiquitin-like domain containing CTD phosphatase 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	10	30,118,912 - 30,118,972	EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)

ACI/EurMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

ACI/EurMcwi (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

ACI/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

BBDP/Wor (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

BN/SsN (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Buf/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

COP/CrCrl (MCW & UW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob) University of Wisconsin (Dr. James Shull)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Charles River Laboratories
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)

F344/NCrl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

F344/NRrrc (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

FHH/EurMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

FHH/EurMcwi (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

FHL/EurMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

FHL/EurMcwi (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

GH/OmrMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

GK/Ox (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LE/Stm (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LEW/Crl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LEW/NCrlBR (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LH/MavRrrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LL/MavRrrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LN/MavRrrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

M520/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

MHS/Gib (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

MNS/Gib (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

MR/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

SBH/Ygl (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	SBH/Ygl sequenced by MCW

SBH/Ygl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SBN/Ygl (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	SBN/Ygl sequenced by MCW

SBN/Ygl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SHR/NHsd (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SHRSP/Gcrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SR/JrHsd (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Harlan Laboratories
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

SR/JrHsd (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SS/Jr (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SS/JrHsdMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

SS/JrHsdMcwi (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WAG/Rij (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WKY/Gcrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WKY/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

WKY/NCrl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WKY/NHsd (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WN/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1310386	AgrOrtholog
Ensembl Genes	ENSRNOG00000004477	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000006063	ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000006063	ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH	3.40.50.1000	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE	IMAGE:7302690	IMAGE-MGC_LOAD
InterPro	FCP1_dom	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	HAD-like_sf	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	HAD-SF_hydro_IIID	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	HAD_sf	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Ubiquitin-like_dom	UniProtKB/TrEMBL
	Ubiquitin-like_domsf	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Ubiquitin_dom	UniProtKB/Swiss-Prot
KEGG Report	rno:360514	UniProtKB/Swiss-Prot
MGC_CLONE	MGC:105972	IMAGE-MGC_LOAD
NCBI Gene	360514	ENTREZGENE
Pfam	NIF	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	ubiquitin	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen	Ublcp1	PhenoGen
PROSITE	FCP1	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	UBIQUITIN_2	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART	CPDc	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	UBQ	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP	SSF54236	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	SSF56784	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGRFAMs	HAD_IIID1	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniGene	Rn.34113	ENTREZGENE
UniProt	A0A0H2UHC8_RAT	UniProtKB/TrEMBL
	Q5FWT7	ENTREZGENE, UniProtKB/Swiss-Prot

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2006-03-30	Ublcp1	ubiquitin-like domain containing CTD phosphatase 1	RGD1310386	similar to hypothetical protein MGC10067	Symbol and Name updated	1299863	APPROVED
2005-12-06	RGD1310386	similar to hypothetical protein MGC10067	RGD1310386_predicted	similar to hypothetical protein MGC10067 (predicted)	Symbol and Name updated	1559027	APPROVED
2005-01-20	RGD1310386_predicted	similar to hypothetical protein MGC10067 (predicted)	LOC360514_predicted		Symbol and Name status set to approved	1331353	APPROVED
2005-01-12	LOC360514_predicted	similar to hypothetical protein MGC10067 (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 - CTD