Dpcd (deleted in primary ciliary dyskinesia)

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Gene: Dpcd (deleted in primary ciliary dyskinesia) Rattus norvegicus

Analyze

Symbol:

Dpcd

Name:

deleted in primary ciliary dyskinesia

RGD ID:

1307648

Description:

Predicted to be involved in several processes, including flagellated sperm motility; left/right pattern formation; and ventricular system development. Predicted to localize to extracellular region. Orthologous to human DPCD (deleted in primary ciliary dyskinesia homolog (mouse)); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; acrylamide; bisphenol A.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Also known as:

LOC294004; RGD1307648; similar to CG13901-PA

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
mRatBN7.2	1	244,408,710 - 244,426,891 (+)	NCBI
Rnor_6.0 Ensembl	1	265,298,868 - 265,317,860 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	1	265,298,872 - 265,318,521 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	1	272,738,421 - 272,756,536 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	1	250,726,987 - 250,746,864 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	1	250,987,555 - 251,007,430 (+)	NCBI
Celera	1	240,217,583 - 240,235,755 (+)	NCBI		Celera
Cytogenetic Map	1	q54	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

hydrocephalus (ISS)

primary ciliary dyskinesia (ISS)

split hand-foot malformation (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2-dichloroethane (ISO)

1,2-dimethylhydrazine (ISO)

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

2-hydroxypropanoic acid (ISO)

acrylamide (EXP)

atrazine (ISO)

benzo[e]pyrene (ISO)

bisphenol A (EXP,ISO)

carbon nanotube (ISO)

copper(II) sulfate (ISO)

crocidolite asbestos (ISO)

cyclosporin A (ISO)

dibutyl phthalate (ISO)

doxorubicin (ISO)

flutamide (EXP)

methapyrilene (ISO)

methyl methanesulfonate (ISO)

methylmercury chloride (ISO)

rac-lactic acid (ISO)

silver atom (ISO)

silver(0) (ISO)

titanium dioxide (ISO)

urethane (ISO)

valproic acid (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

determination of left/right symmetry (ISO)

epithelial cilium movement involved in extracellular fluid movement (ISO)

flagellated sperm motility (ISO)

lateral ventricle development (ISO)

left/right pattern formation (ISO)

spermatogenesis (ISO)

third ventricle development (ISO)

ventricular system development (ISO)

Cellular Component

extracellular region (IEA)

Molecular Function

protein binding (ISO)

References

References - curated


1.	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
2.	RGD automated import pipeline for gene-chemical interactions
3.	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:20080492	PMID:21630459	PMID:21746835

Genomics

Comparative Map Data

Dpcd
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	1	244,408,710 - 244,426,891 (+)	NCBI
Rnor_6.0 Ensembl	1	265,298,868 - 265,317,860 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	1	265,298,872 - 265,318,521 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	1	272,738,421 - 272,756,536 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	1	250,726,987 - 250,746,864 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	1	250,987,555 - 251,007,430 (+)	NCBI
Celera	1	240,217,583 - 240,235,755 (+)	NCBI		Celera
Cytogenetic Map	1	q54	NCBI

DPCD
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	10	101,570,560 - 101,609,662 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	10	101,588,321 - 101,609,662 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	10	103,348,078 - 103,369,419 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	10	103,338,079 - 103,359,400 (+)	NCBI	NCBI36		hg18	NCBI36
Celera	10	97,086,875 - 97,108,196 (+)	NCBI
Cytogenetic Map	10	q24.32	NCBI
HuRef	10	96,978,686 - 96,999,706 (+)	NCBI		HuRef
CHM1_1	10	103,631,745 - 103,653,089 (+)	NCBI		CHM1_1

Dpcd
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	19	45,549,018 - 45,566,728 (+)	NCBI	GRCm39		mm39
GRCm39 Ensembl	19	45,549,054 - 45,568,202 (+)	Ensembl
GRCm38	19	45,560,583 - 45,578,289 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	19	45,560,615 - 45,579,763 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	19	45,635,105 - 45,652,777 (+)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	19	45,613,926 - 45,631,598 (+)	NCBI			mm8
Celera	19	46,328,265 - 46,345,935 (+)	NCBI		Celera
Cytogenetic Map	19	C3	NCBI

Dpcd
(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_004955485	8,670,261 - 8,691,541 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955485	8,670,261 - 8,691,545 (-)	NCBI	ChiLan1.0	ChiLan1.0

DPCD
(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	10	101,663,384 - 101,684,812 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	10	101,663,384 - 101,684,812 (+)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	10	98,190,415 - 98,212,857 (+)	NCBI	Mhudiblu_PPA_v0		panPan3

DPCD
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	28	14,201,302 - 14,219,121 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	28	14,201,351 - 14,219,121 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	28	14,370,021 - 14,387,849 (+)	NCBI
ROS_Cfam_1.0	28	14,669,462 - 14,687,299 (+)	NCBI
UMICH_Zoey_3.1	28	14,214,203 - 14,232,016 (+)	NCBI
UNSW_CanFamBas_1.0	28	14,255,724 - 14,273,535 (+)	NCBI
UU_Cfam_GSD_1.0	28	14,387,841 - 14,405,674 (+)	NCBI

Dpcd
(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_024407213	32,559,777 - 32,581,811 (-)	NCBI
SpeTri2.0	NW_004936600	4,163,002 - 4,185,013 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

DPCD
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	14	112,617,398 - 112,637,948 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	14	112,617,338 - 112,637,397 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	14	122,360,728 - 122,380,767 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

DPCD
(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	9	94,612,383 - 94,633,729 (+)	NCBI
ChlSab1.1 Ensembl	9	94,612,460 - 94,633,537 (+)	Ensembl

Dpcd
(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_004624831	1,087,270 - 1,107,197 (+)	NCBI

Position Markers

RH129979

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	1	265,318,561 - 265,318,772	NCBI	Rnor6.0
Rnor_5.0	1	272,756,576 - 272,756,787	UniSTS	Rnor5.0
RGSC_v3.4	1	250,746,904 - 250,747,115	UniSTS	RGSC3.4
Celera	1	240,235,795 - 240,236,006	UniSTS
RH 3.4 Map	1	1624.0	UniSTS
Cytogenetic Map	1	q54	UniSTS

AA956318

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	1	265,317,559 - 265,317,665	NCBI	Rnor6.0
Rnor_5.0	1	272,755,574 - 272,755,680	UniSTS	Rnor5.0
RGSC_v3.4	1	250,745,902 - 250,746,008	UniSTS	RGSC3.4
Celera	1	240,234,793 - 240,234,899	UniSTS
RH 3.4 Map	1	1621.7	UniSTS
Cytogenetic Map	1	q54	UniSTS

BE106000

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	1	265,318,307 - 265,318,457	NCBI	Rnor6.0
Rnor_5.0	1	272,756,322 - 272,756,472	UniSTS	Rnor5.0
RGSC_v3.4	1	250,746,650 - 250,746,800	UniSTS	RGSC3.4
Celera	1	240,235,541 - 240,235,691	UniSTS
RH 3.4 Map	1	1621.9	UniSTS
Cytogenetic Map	1	q54	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
70211	Niddm24	Non-insulin dependent diabetes mellitus QTL 24	3.79		blood glucose amount (VT:0000188)	blood glucose level area under curve (AUC) (CMO:0000350)	1	236795785	281795785	Rat
631215	Stl8	Serum triglyceride level QTL 8	9.27	0.0001	blood triglyceride amount (VT:0002644)	serum triglyceride level (CMO:0000360)	1	245529606	282763074	Rat
2302040	Pia35	Pristane induced arthritis QTL 35	3.8	0.001	blood immunoglobulin amount (VT:0002460)	serum immunoglobulin G1 level (CMO:0002115)	1	236265430	281265430	Rat
2302378	Insul11	Insulin level QTL 11	3.25		blood insulin amount (VT:0001560)	serum insulin level (CMO:0000358)	1	156446196	274977688	Rat
724531	Uae5	Urinary albumin excretion QTL 5	4		urine albumin amount (VT:0002871)	urine albumin level (CMO:0000130)	1	161321152	273792054	Rat
724533	Rf51	Renal function QTL 51	5.3	0.0002	kidney plasma flow trait (VT:0005524)	renal plasma flow (CMO:0001914)	1	238830534	278228767	Rat
724538	Kidm1	Kidney mass QTL 1	3.2		kidney mass (VT:0002707)	calculated kidney weight (CMO:0000160)	1	233663100	273792054	Rat
724552	Glom2	Glomerulus QTL 2	3.3	0.0001	kidney glomerulus morphology trait (VT:0005325)	count of superficial glomeruli directly contacting the kidney surface (CMO:0001001)	1	243272341	282763074	Rat
734767	Niddm57	Non-insulin dependent diabetes mellitus QTL 57			body mass (VT:0001259)	body weight (CMO:0000012)	1	244401175	282365384	Rat
734768	Niddm59	Non-insulin dependent diabetes mellitus QTL 59			body mass (VT:0001259)	body weight (CMO:0000012)	1	235850810	280850810	Rat
734769	Niddm58	Non-insulin dependent diabetes mellitus QTL 58			body mass (VT:0001259)	body weight (CMO:0000012)	1	244992467	282365384	Rat
631669	Iddm9	Insulin dependent diabetes mellitus QTL 9	2.8	0.039	blood glucose amount (VT:0000188)	plasma glucose level (CMO:0000042)	1	252955158	280632620	Rat
631690	Scl5	Serum cholesterol level QTL 5	2.1		blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	1	258132568	282763074	Rat
1354580	Scort1	Serum corticosterone level QTL 1	3.4		blood corticosterone amount (VT:0005345)	blood corticosterone level (CMO:0001172)	1	167394665	278228889	Rat
1581544	Rf52	Renal function QTL 52		0.05	total urine protein amount (VT:0000032)	urine protein excretion rate to body weight ratio (CMO:0001099)	1	252948438	281795785	Rat
731175	Uae20	Urinary albumin excretion QTL 20	3.5	0.0018	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	1	241482188	281795785	Rat
738032	Hcas5	Hepatocarcinoma susceptibility QTL 5	3.12		liver integrity trait (VT:0010547)	liver tumorous lesion number (CMO:0001068)	1	191825895	279986079	Rat
631536	Lnnr2	Liver neoplastic nodule remodeling QTL 2	2.9	0.0005	liver integrity trait (VT:0010547)	liver remodeling tumorous lesion number to liver total tumorous lesion number ratio (CMO:0001705)	1	255728828	282763074	Rat
1598821	Rf55	Renal function QTL 55	6.3		renal blood flow trait (VT:2000006)	ratio of change in renal blood flow to change in renal perfusion pressure (CMO:0001239)	1	238824734	279986079	Rat
2300175	Bmd40	Bone mineral density QTL 40	15.4	0.0001	femur mineral mass (VT:0010011)	bone mineral density (CMO:0001226)	1	221901238	266901238	Rat
2293655	Bss36	Bone structure and strength QTL 36	10.66	0.0001	femur strength trait (VT:0010010)	femur ultimate force (CMO:0001675)	1	221901238	266901238	Rat
2293674	Bss39	Bone structure and strength QTL 39	7.1	0.0001	femur strength trait (VT:0010010)	femur total energy absorbed before break (CMO:0001677)	1	221901238	266901238	Rat
2293694	Bss38	Bone structure and strength QTL 38	7.05	0.0001	femur strength trait (VT:0010010)	femur stiffness (CMO:0001674)	1	221901238	266901238	Rat
631836	Stl31	Serum triglyceride level QTL 31	4.64	0.00000487	blood triglyceride amount (VT:0002644)	plasma triglyceride level (CMO:0000548)	1	259295704	282763074	Rat
631837	Niddm35	Non-insulin dependent diabetes mellitus QTL 35		0.01	blood insulin amount (VT:0001560)	serum insulin level (CMO:0000358)	1	258709726	281795785	Rat
631843	Bw116	Body weight QTL 116	4.1	0.016	abdominal adipose amount (VT:1000220)	abdominal fat pad weight (CMO:0000088)	1	244401175	282365384	Rat
634313	Niddm43	Non-insulin dependent diabetes mellitus QTL 43			blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	1	217054291	281795785	Rat
1357399	Bw45	Body weight QTL 45	3.05		body mass (VT:0001259)	body mass index (BMI) (CMO:0000105)	1	225689973	270689973	Rat
1357404	Bw42	Body weight QTL 42	4.49	0.0001	body mass (VT:0001259)	body weight (CMO:0000012)	1	225689973	270689973	Rat
1600388	Niddm67	Non-insulin dependent diabetes mellitus QTL 67	5.84	0.000004	blood glucose amount (VT:0000188)	blood glucose level area under curve (AUC) (CMO:0000350)	1	213476630	278978026	Rat
1600392	Bw123	Body weight QTL 123		0.001	body mass (VT:0001259)	body weight (CMO:0000012)	1	244087148	282763074	Rat
1600395	Niddm69	Non-insulin dependent diabetes mellitus QTL 69	4.14	0.0002	blood insulin amount (VT:0001560)	plasma insulin level (CMO:0000342)	1	213476630	278978026	Rat
1600396	Niddm68	Non-insulin dependent diabetes mellitus QTL 68	4.97	0.0003	blood glucose amount (VT:0000188)	blood glucose level area under curve (AUC) (CMO:0000350)	1	213476630	278978026	Rat
1600397	Edcs4	Endometrial carcinoma susceptibility QTL 4	2.2		uterus morphology trait (VT:0001120)	percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)	1	226706329	271706329	Rat
1578759	Uae30	Urinary albumin excretion QTL 30	3.3	0.003	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	1	161321256	273791893	Rat
1578763	Kidm29	Kidney mass QTL 29	3.3	0.0001	kidney mass (VT:0002707)	both kidneys wet weight (CMO:0000085)	1	196395041	282763074	Rat
1578778	Pur4	Proteinuria QTL 4	3.3	0.003	total urine protein amount (VT:0000032)	urine total protein excretion rate (CMO:0000756)	1	161321256	273791893	Rat
1300108	Rf8	Renal function QTL 8	3.75		renal blood flow trait (VT:2000006)	absolute change in renal vascular resistance (CMO:0001900)	1	249206242	281795785	Rat
1354610	Bw34	Body weight QTL 34	4.1		body mass (VT:0001259)	body weight (CMO:0000012)	1	161784169	278228889	Rat
1354624	Cm35	Cardiac mass QTL35	5.7		heart left ventricle mass (VT:0007031)	calculated heart weight (CMO:0000073)	1	192639698	278228889	Rat
1354646	Kidm18	Kidney mass QTL 18	5.7		kidney mass (VT:0002707)	calculated kidney weight (CMO:0000160)	1	161784169	278228889	Rat
1354652	Kidm20	Kidney mass QTL 20	4.3		kidney mass (VT:0002707)	calculated kidney weight (CMO:0000160)	1	192639698	278228889	Rat
1354661	Bw33	Body weight QTL 33	5.2		body mass (VT:0001259)	body weight (CMO:0000012)	1	161784169	278228889	Rat
1549910	Bw54	Body weight QTL 54		0.05	body mass (VT:0001259)	body weight (CMO:0000012)	1	236795785	281795785	Rat
2316896	Gluco57	Glucose level QTL 57	7.2		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	1	249607907	266793958	Rat
1549837	Hcar15	Hepatocarcinoma resistance QTL 15		0.05	liver integrity trait (VT:0010547)	liver tumorous lesion number (CMO:0001068)	1	163796316	282763074	Rat
1358890	Bp259	Blood pressure QTL 259	3.06		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	230420627	282645769	Rat
1358898	Bp255	Blood pressure QTL 255	3.6		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	208517798	266948272	Rat
61327	Eae7	Experimental allergic encephalomyelitis QTL 7	5.6		body mass (VT:0001259)	change in body weight (CMO:0002045)	1	236265430	281265430	Rat
61400	Niddm1	Non-insulin dependent diabetes mellitus QTL 1	11		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	1	238830408	266793958	Rat
7394701	Uae46	Urinary albumin excretion QTL 46	3.6	0.0056	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	1	221901238	266901238	Rat
7387289	Uae45	Urinary albumin excretion QTL 45	2.86	0.0021	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	1	244148899	282763074	Rat
10053715	Scort24	Serum corticosterone level QTL 24	2.13	0.0088	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	1	242302911	282763074	Rat
10059587	Bw173	Body weight QTL 173	3.23	0.025	body mass (VT:0001259)	body weight (CMO:0000012)	1	222492538	267492538	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	101
Count of miRNA genes:	80
Interacting mature miRNAs:	94
Transcripts:	ENSRNOT00000023278
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.

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	32	47	37	13	37		1	74	35	41	11
Low		11	10	4	6	4	8	10					8
Below cutoff

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001013905	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_006231450	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC109672	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC078988	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473986	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ226696	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000054	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000023278 ⟹ ENSRNOP00000023278

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	1	265,298,868 - 265,317,860 (+)	Ensembl

RefSeq Acc Id:

NM_001013905 ⟹ NP_001013927

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	1	244,408,775 - 244,426,891 (+)	NCBI
Rnor_6.0	1	265,298,910 - 265,318,521 (+)	NCBI
Rnor_5.0	1	272,738,421 - 272,756,536 (+)	NCBI
RGSC_v3.4	1	250,726,987 - 250,746,864 (+)	RGD
Celera	1	240,217,583 - 240,235,755 (+)	RGD

Sequence:

show sequence

GCCAGGCGCGTTGCTGGGCGGAGGGAAGATGGCGGTGACTAGCTGGCTGGAGATTTTGCGGTCG
GCCGAGAAGACGGCACTGCTGCAGGATGGGAAGAGGATGGTGCACTATTTGTTCCCAGACGGGA
AGGAAATGGCGGAAGAATATGATGAGAAGACCAGTGAACTCCTTGTGAGAAAGTGGCGTGTGAA
AAATGCCCTGGGAGCCTTGGGCCAGTGGCAGCTCGAAGTGGGAGAACCAATGCCCTCAGGAGCT
GGGAGCCTGGGATCCGAGCTCATCAAGGAAACCCATCTTCATGCGCAAGGACACCAAAACAAGT
TTCCAGTGGCGGATTCGAAATCTCCCCTACCCAAAGGATGTCTACAGTGTGTCAGTGGCCCAGA
AGGAGCGCTGTGTCATTGTTAGAACGACAAACAAAAAGTACTACAAGAAGTTCTCCATTCCTGA
CTTAGACAGACACCAGCTTCCTCTGGAAGATTCTGCACTGAGCTTTGCTCACGCCAACTGCACC
CTGATAATCTCCTATCAGAAGCCAAAGGAGGTCATGGCAGCTGAATCAGAGCTACAGAAGGAGT
TAAAGAAGGTAAAGACAGCGCACAGCAGTGATGGGGACTGCAAGACGCAGTAGCTACTGAGCCT
CGCACCTCCAGTGTGGAGGAAACTGAGAGACGTCCAGACTTGGGTTTTATGCACAGGCAGCCTC
TTCTCTTCTAAGAACTACAGAGTCCCCAGAACTGGCCCTTGGGGCACAGCTTGCTCCCACCTGT
GGTTTTATCCTGAGTAAAGTCATTTGCAGTTGTTCTGGAAGGACTGACTGCCTTTTTCTCTGAT
GGCCCGTCCCTGGATGCCTTGGCCTTCCTCACCCCACCTTCCCATCCTGAGGACCTTCCACACA
GGCCTTCCAGCTAAAGGGGGAGAAAAGTGGGAACAGGGCTGGGTGTCTTGTAAACTCCTGTGTG
CTGGCTTGCCTTATATGAGTAGCTCAGGGAAAACTCCTCTGAGGCAGGTATGGGCAAAGGAGAA
GTTTAAAAATTTAGCTGTCTTGGAAACAGCACAGAATGTTAGGACACTGGTTAAAAGAGCATGG
CTACAGTATTGTCAAAGGTGTGTGTATGGTGGGACAGAGCGAAAGGTCACCCAGCTCAGCACCT
AGAGCCCTCTGACCGTTAGTTCCTTATCTGCGCCCCAAAGAGGTAGAAGAAACCTTTTTGTTCT
CGGGGGCACAGCCATGGGTTTGTCCTTCCCCTGTACACATTCCTGAGTTTAAATGTGATACTCT
GCCTTCCTGGAGCCTCTTAGAATACCTAACCAGGGCTGGAGAGATAGCTCAGAGTACCAACTGC
TCTCCCAGAGGTCCCGAGTTCAATTCCTAATAACTACATGTGGCTCACAGCCATCTGTAATGGG
ATCTGGTGTGTCTGAAGACAGCTGCAGTGTACGCATATACATTAAATAAATCTTAAAAAAAAAA
TGACCTAACCATCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

hide sequence

RefSeq Acc Id:

XM_006231450 ⟹ XP_006231512

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	1	244,408,710 - 244,426,883 (+)	NCBI
Rnor_6.0	1	265,298,872 - 265,318,513 (+)	NCBI
Rnor_5.0	1	272,738,421 - 272,756,536 (+)	NCBI

Sequence:

show sequence

CGGAAGTGATCATCGGTCGGGTAGTTGCCATGGCAGTGGCCAGGCGCGTTGCTGGGCGGAGGGA
AGATGGCGGTGACTAGCTGGCTGGAGATTTTGCGGTCGGCCGAGAAGACGGCACTGCTGCAGGA
TGGGAAGAGGATGGTGCACTATTTGTTCCCAGACGGGAAGGAAATGGCGGAAGAATATGATGAG
AAGACCAGTGAACTCCTTGTGAGAAAGTGGCGTGTGAAAAATGCCCTGGGAGCCTTGGGCCAGT
GGCAGCTCGAAGTGGGAGAACCAATGCCCTCAGGAGCTGGGAGCCTGGGATCCGAGCTCATCAA
GGAAAGTAATGCCAATCCCATCTTCATGCGCAAGGACACCAAAACAAGTTTCCAGTGGCGGATT
CGAAATCTCCCCTACCCAAAGGATGTCTACAGTGTGTCAGTGGCCCAGAAGGAGCGCTGTGTCA
TTGTTAGAACGACAAACAAAAAGTACTACAAGAAGTTCTCCATTCCTGACTTAGACAGACACCA
GCTTCCTCTGGAAGATTCTGCACTGAGCTTTGCTCACGCCAACTGCACCCTGATAATCTCCTAT
CAGAAGCCAAAGGAGGTCATGGCAGCTGAATCAGAGCTACAGAAGGAGTTAAAGAAGGTAAAGA
CAGCGCACAGCAGTGATGGGGACTGCAAGACGCAGTAGCTACTGAGCCTCGCACCTCCAGTGTG
GAGGAAACTGAGAGACGTCCAGACTTGGGTTTTATGCACAGGCAGCCTCTTCTCTTCTAAGAAC
TACAGAGTCCCCAGAACTGGCCCTTGGGGCACAGCTTGCTCCCACCTGTGGTTTTATCCTGAGT
AAAGTCATTTGCAGTTGTTCTGGAAGGACTGACTGCCTTTTTCTCTGATGGCCCGTCCCTGGAT
GCCTTGGCCTTCCTCACCCCACCTTCCCATCCTGAGGACCTTCCACACAGGCCTTCCAGCTAAA
GGGGGAGAAAAGTGGGAACAGGGCTGGGTGTCTTGTAAACTCCTGTGTGCTGGCTTGCCTTATA
TGAGTAGCTCAGGGAAAACTCCTCTGAGGCAGGTATGGGCAAAGGAGAAGTTTAAAAATTTAGC
TGTCTTGGAAACAGCACAGAATGTTAGGACACTGGTTAAAAGAGCATGGCTACAGTATTGTCAA
AGGTGTGTGTATGGTGGGACAGAGCGAAAGGTCACCCAGCTCAGCACCTAGAGCCCTCTGACCG
TTAGTTCCTTATCTGCGCCCCAAAGAGGTAGAAGAAACCTTTTTGTTCTCGGGGGCACAGCCAT
GGGTTTGTCCTTCCCCTGTACACATTCCTGAGTTTAAATGTGATACTCTGCCTTCCTGGAGCCT
CTTAGAATACCTAACCAGGGCTGGAGAGATAGCTCAGAGTACCAACTGCTCTCCCAGAGGTCCC
GAGTTCAATTCCTAATAACTACATGTGGCTCACAGCCATCTGTAATGGGATCTGGTGTGTCTGA
AGACAGCTGCAGTGTACGCATATACATTAAATAAATCTTAAAAAAAAAATGACCTAA

hide sequence

Protein Sequences


Protein RefSeqs	NP_001013927	(Get FASTA)	NCBI Sequence Viewer
	XP_006231512	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAH78988	(Get FASTA)	NCBI Sequence Viewer
	EDL94310	(Get FASTA)	NCBI Sequence Viewer
	Q6AYM4	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:	NP_001013927 ⟸ NM_001013905
- UniProtKB:	Q6AYM4 (UniProtKB/Swiss-Prot)
- Sequence:	show sequence MPWEPWASGSSKWENQCPQELGAWDPSSSRKPIFMRKDTKTSFQWRIRNLPYPKDVYSVSVAQK ERCVIVRTTNKKYYKKFSIPDLDRHQLPLEDSALSFAHANCTLIISYQKPKEVMAAESELQKEL KKVKTAHSSDGDCKTQ hide sequence

RefSeq Acc Id:	XP_006231512 ⟸ XM_006231450
- Peptide Label:	isoform X1
- UniProtKB:	Q6AYM4 (UniProtKB/Swiss-Prot)
- Sequence:	show sequence MAVTSWLEILRSAEKTALLQDGKRMVHYLFPDGKEMAEEYDEKTSELLVRKWRVKNALGALGQW QLEVGEPMPSGAGSLGSELIKESNANPIFMRKDTKTSFQWRIRNLPYPKDVYSVSVAQKERCVI VRTTNKKYYKKFSIPDLDRHQLPLEDSALSFAHANCTLIISYQKPKEVMAAESELQKELKKVKT AHSSDGDCKTQ hide sequence

RefSeq Acc Id:

ENSRNOP00000023278 ⟸ ENSRNOT00000023278

Transcriptome

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

Promoters

RGD ID:

13690951

Promoter ID:

EPDNEW_R1475

Type:

initiation region

Name:

Dpcd_1

Description:

deleted in primary ciliary dyskinesia

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	1	265,298,922 - 265,298,982	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:1307648	AgrOrtholog
Ensembl Genes	ENSRNOG00000017241	Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein	ENSRNOP00000023278	ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript	ENSRNOT00000023278	UniProtKB/Swiss-Prot
IMAGE_CLONE	IMAGE:7112530	IMAGE-MGC_LOAD
InterPro	DPCD	UniProtKB/Swiss-Prot
KEGG Report	rno:294004	UniProtKB/Swiss-Prot
MGC_CLONE	MGC:93886	IMAGE-MGC_LOAD
NCBI Gene	294004	ENTREZGENE
PANTHER	PTHR31921	UniProtKB/Swiss-Prot
Pfam	DPCD	UniProtKB/Swiss-Prot
PhenoGen	Dpcd	PhenoGen
PRINTS	PROTEINDPCD	UniProtKB/Swiss-Prot
UniProt	DPCD_RAT	UniProtKB/Swiss-Prot, ENTREZGENE

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2010-12-02	Dpcd	deleted in primary ciliary dyskinesia	RGD1307648	similar to CG13901-PA	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2005-12-06	RGD1307648	similar to CG13901-PA	RGD1307648_predicted	similar to CG13901-PA (predicted)	Symbol and Name updated	1559027	APPROVED
2005-01-20	RGD1307648_predicted	similar to CG13901-PA (predicted)	LOC294004_predicted		Symbol and Name status set to approved	1331353	APPROVED
2005-01-12	LOC294004_predicted	similar to CG13901-PA (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 - MGI

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Imported Disease Annotations - ClinVar

Imported Disease Annotations - MGI