Ddx1 (DEAD-box helicase 1) - Rat Genome Database

Name: Ddx1
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

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Gene: Ddx1 (DEAD-box helicase 1) Rattus norvegicus

Analyze

Symbol:

Ddx1

Name:

DEAD-box helicase 1

RGD ID:

619903

Description:

Predicted to have several functions, including RNA binding activity; helicase activity; and transcription coregulator activity. Predicted to be involved in several processes, including nucleic acid metabolic process; positive regulation of myeloid dendritic cell cytokine production; and protein localization to cytoplasmic stress granule. Predicted to localize to several cellular components, including cleavage body; cytoplasmic stress granule; and tRNA-splicing ligase complex. Orthologous to human DDX1 (DEAD-box helicase 1); INTERACTS WITH (+)-schisandrin B; 2,4-dinitrotoluene; 2,6-dinitrotoluene.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Also known as:

ATP-dependent RNA helicase DDX1; DEAD (Asp-Glu-Ala-Asp) box helicase 1; DEAD (Asp-Glu-Ala-Asp) box polypeptide 1; DEAD box protein 1; DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 1; DEAD/H-box helicase 1

RGD Orthologs

Human

Mouse

Chinchilla

Bonobo

Dog

Squirrel

Pig

Green Monkey

Naked Mole-Rat

Alliance Genes

More Info

more info ...

More Info

Species	Gene symbol and name	Data Source	Assertion derived from	less info ...
Orthologs ¹				less info ...
Homo sapiens (human):	DDX1 (DEAD-box helicase 1)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, PhylomeDB, Treefam
Mus musculus (house mouse):	Ddx1 (DEAD box helicase 1)	HGNC	Treefam, EggNOG, OrthoMCL, NCBI, OMA, HomoloGene, Inparanoid, Panther, PhylomeDB, OrthoDB, Ensembl
Chinchilla lanigera (long-tailed chinchilla):	Ddx1 (DEAD-box helicase 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	DDX1 (DEAD-box helicase 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	DDX1 (DEAD-box helicase 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Ddx1 (DEAD-box helicase 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	DDX1 (DEAD-box helicase 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (African green monkey):	DDX1 (DEAD-box helicase 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Ddx1 (DEAD-box helicase 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	DDX1 (DEAD-box helicase 1)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Mus musculus (house mouse):	Ddx1 (DEAD box helicase 1)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Danio rerio (zebrafish):	ddx1 (DEAD (Asp-Glu-Ala-Asp) box helicase 1)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Drosophila melanogaster (fruit fly):	Ddx1	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Caenorhabditis elegans (roundworm):	Y55F3BR.1	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)

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	6	35,996,469 - 36,027,340 (-)	NCBI
Rnor_6.0 Ensembl	6	38,422,888 - 38,453,797 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	6	38,422,892 - 38,453,762 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	6	47,188,697 - 47,219,567 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	6	36,794,602 - 36,825,473 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	6	36,812,356 - 36,818,005 (-)	NCBI
Celera	6	35,359,044 - 35,389,916 (-)	NCBI		Celera
Cytogenetic Map	6	q15	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

amenorrhea (ISO)

endometrial hyperplasia (ISO)

optic atrophy (ISO)

schizophrenia (ISO)

substance-related disorder (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(+)-schisandrin B (EXP)

1,2-dimethylhydrazine (ISO)

17alpha-ethynylestradiol (ISO)

17beta-hydroxy-17-methylestra-4,9,11-trien-3-one (ISO)

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

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

2,4-dinitrotoluene (EXP)

2,6-dinitrotoluene (EXP)

2-hydroxypropanoic acid (ISO)

4,4'-diaminodiphenylmethane (ISO)

ammonium chloride (EXP)

antirheumatic drug (ISO)

Aroclor 1254 (ISO)

arsenous acid (ISO)

atrazine (ISO)

benzo[a]pyrene (ISO)

bisphenol A (ISO)

buspirone (EXP)

C60 fullerene (EXP)

cadmium sulfate (ISO)

diarsenic trioxide (ISO)

dicrotophos (ISO)

enzyme inhibitor (ISO)

ethanol (ISO)

finasteride (EXP)

flutamide (EXP)

fumonisin B1 (ISO)

gentamycin (EXP)

hydrogen peroxide (ISO)

ibuprofen (ISO)

isoflavones (EXP)

lead(0) (ISO)

lead(2+) (ISO)

menadione (ISO)

N-methyl-4-phenylpyridinium (ISO)

okadaic acid (ISO)

oxaliplatin (EXP)

paracetamol (ISO)

pentachlorophenol (ISO)

pirinixic acid (ISO)

propiconazole (ISO)

rac-lactic acid (ISO)

resveratrol (ISO)

sodium arsenite (EXP)

sulindac (EXP)

tetrachloromethane (EXP,ISO)

topotecan (EXP)

trimellitic anhydride (ISO)

troglitazone (ISO)

trovafloxacin (EXP)

valproic acid (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

defense response to virus (IEA)

DNA duplex unwinding (ISO,ISS)

double-strand break repair (ISO,ISS)

innate immune response (IEA)

mRNA processing (IEA)

multicellular organism development (ISO)

nucleic acid phosphodiester bond hydrolysis (ISO)

positive regulation of I-kappaB kinase/NF-kappaB signaling (ISO,ISS)

positive regulation of myeloid dendritic cell cytokine production (ISO)

protein localization to cytoplasmic stress granule (ISO)

regulation of transcription, DNA-templated (IEA)

response to exogenous dsRNA (ISO)

response to virus (ISO)

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

Cellular Component

cleavage body (ISO,ISS)

cytoplasm (ISO,ISS)

cytoplasmic stress granule (ISO,ISS)

cytosol (ISO,ISS)

mitochondrion (ISO,ISS)

nucleoplasm (ISO)

nucleus (ISO,ISS)

ribonucleoprotein complex (ISO)

tRNA-splicing ligase complex (ISO,ISS)

Molecular Function

ATP binding (IEA)

chromatin binding (ISO,ISS)

DNA binding (IEA)

DNA/RNA helicase activity (ISO,ISS)

double-stranded RNA binding (ISO)

exonuclease activity (IEA)

helicase activity (ISO,ISS)

nuclease activity (ISO,ISS)

poly(A) binding (ISO,ISS)

protein binding (ISO)

RNA helicase activity (IEA,ISO)

transcription coregulator activity (ISO,ISS)

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.	GOA data from the GO Consortium
3.	Karlsson A, etal., Genes Chromosomes Cancer 2001 Aug;31(4):345-56.
4.	MGD data from the GO Consortium
5.	NCBI rat LocusLink and RefSeq merged data July 26, 2002
6.	RGD automated data pipeline
7.	RGD automated import pipeline for gene-chemical interactions

Additional References at PubMed

PMID:7689221	PMID:11598190	PMID:12183465	PMID:12477932	PMID:15489334	PMID:18335541	PMID:18710941	PMID:18809582	PMID:19058135	PMID:19946888	PMID:21311021	PMID:21703541
PMID:21933836	PMID:22658674	PMID:22681889	PMID:24608264	PMID:24870230	PMID:24965446	PMID:28259758	PMID:28755400	PMID:30295850

Genomics

Comparative Map Data

Ddx1
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	6	35,996,469 - 36,027,340 (-)	NCBI
Rnor_6.0 Ensembl	6	38,422,888 - 38,453,797 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	6	38,422,892 - 38,453,762 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	6	47,188,697 - 47,219,567 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	6	36,794,602 - 36,825,473 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	6	36,812,356 - 36,818,005 (-)	NCBI
Celera	6	35,359,044 - 35,389,916 (-)	NCBI		Celera
Cytogenetic Map	6	q15	NCBI

DDX1
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	2	15,591,178 - 15,634,346 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh38.p13 Ensembl	2	15,591,178 - 15,631,111 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	2	15,591,868 - 15,631,101 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	2	15,731,992 - 15,771,225 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	2	15,649,221 - 15,688,676 (+)	NCBI	NCBI36		hg18	NCBI36
Build 34	2	15,682,367 - 15,721,823	NCBI
Celera	2	15,649,490 - 15,688,945 (+)	NCBI
Cytogenetic Map	2	p24.3	NCBI
HuRef	2	15,583,004 - 15,622,496 (+)	NCBI		HuRef
CHM1_1	2	15,661,598 - 15,701,093 (+)	NCBI		CHM1_1

Ddx1
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	12	13,269,308 - 13,299,175 (-)	NCBI	GRCm39		mm39
GRCm39 Ensembl	12	13,266,974 - 13,299,214 (-)	Ensembl
GRCm38	12	13,219,307 - 13,249,174 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	12	13,216,973 - 13,249,213 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	12	13,226,113 - 13,255,980 (-)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	12	13,245,295 - 13,275,162 (-)	NCBI			mm8
Celera	12	13,565,291 - 13,593,111 (-)	NCBI		Celera
Cytogenetic Map	12	A1.1	NCBI

Ddx1
(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_004955487	9,085,918 - 9,119,979 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955487	9,085,950 - 9,117,599 (+)	NCBI	ChiLan1.0	ChiLan1.0

DDX1
(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	2A	15,716,044 - 15,753,482 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	2A	15,716,044 - 15,753,623 (+)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	2A	15,582,499 - 15,619,751 (+)	NCBI	Mhudiblu_PPA_v0		panPan3

DDX1
(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	17	11,432,136 - 11,466,990 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
CanFam3.1	17	11,432,060 - 11,467,000 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1

Ddx1
(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_004936493	14,884,532 - 14,918,621 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

DDX1
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	3	121,818,406 - 121,853,958 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	3	121,818,400 - 121,856,667 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	3	130,448,196 - 130,480,756 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

DDX1
(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	14	92,007,446 - 92,045,414 (-)	NCBI
ChlSab1.1 Ensembl	14	92,007,036 - 92,045,190 (-)	Ensembl

Ddx1
(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_004624865	898,850 - 927,375 (-)	NCBI

Position Markers

RH127887

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	6	38,423,017 - 38,423,207	NCBI	Rnor6.0
Rnor_5.0	6	47,188,822 - 47,189,012	UniSTS	Rnor5.0
RGSC_v3.4	6	36,794,727 - 36,794,917	UniSTS	RGSC3.4
Celera	6	35,359,169 - 35,359,359	UniSTS
Cytogenetic Map	6	q15-q16	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
1331743	Uae28	Urinary albumin excretion QTL 28	4.5		urine albumin amount (VT:0002871)	urine albumin level (CMO:0000130)	6	1	41917988	Rat
9589048	Scfw3	Subcutaneous fat weight QTL 3	4.57	0.001	subcutaneous adipose mass (VT:1000472)	abdominal subcutaneous fat pad weight (CMO:0002069)	6	1	42388212	Rat
9589129	Insul24	Insulin level QTL 24	19.06	0.001	blood insulin amount (VT:0001560)	plasma insulin level (CMO:0000342)	6	1	42388212	Rat
7411603	Foco13	Food consumption QTL 13	5.5	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	6	1	42388212	Rat
7411542	Bw127	Body weight QTL 127	5.5	0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	6	1	42388212	Rat
8552962	Pigfal16	Plasma insulin-like growth factor 1 level QTL 16	9.4		blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	6	1	42388212	Rat
2293709	Bss23	Bone structure and strength QTL 23	5.18	0.0001	femur morphology trait (VT:0000559)	femur cross-sectional area (CMO:0001661)	6	1	43665660	Rat
2293650	Bss31	Bone structure and strength QTL 31	5.05	0.0001	femur strength trait (VT:0010010)	femur midshaft polar moment of inertia (CMO:0001669)	6	1	43665660	Rat
2293656	Bss28	Bone structure and strength QTL 28	6.79	0.0001	femur morphology trait (VT:0000559)	femur midshaft cortical cross-sectional area (CMO:0001663)	6	1	43665660	Rat
7411584	Foco4	Food consumption QTL 4	4.3	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	6	1	44015370	Rat
738024	Sach5	Saccharine consumption QTL 5	3.9	0.00039	consumption behavior trait (VT:0002069)	saccharin intake volume to total fluid intake volume ratio (CMO:0001601)	6	1	44570292	Rat
2301972	Bp325	Blood pressure QTL 325	4.8		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	6	1	75623393	Rat
2292589	Emca10	Estrogen-induced mammary cancer QTL 10		0.048	mammary gland integrity trait (VT:0010552)	post-insult time to mammary tumor formation (CMO:0000345)	6	1120393	46120393	Rat
1354664	Slep2	Serum leptin concentration QTL 2	4.49		blood leptin amount (VT:0005667)	serum leptin level (CMO:0000780)	6	1120393	75023446	Rat
1576309	Emca7	Estrogen-induced mammary cancer QTL 7	4		mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	6	2537030	111715717	Rat
1578665	Bss16	Bone structure and strength QTL 16	4.4		femur morphology trait (VT:0000559)	bone trabecular cross-sectional area (CMO:0002311)	6	6161722	76002731	Rat
1578668	Bmd14	Bone mineral density QTL 14	3.8		femur mineral mass (VT:0010011)	total volumetric bone mineral density (CMO:0001728)	6	6161722	76002731	Rat
4145119	Mcs25	Mammary carcinoma susceptibility QTL 25		0.0001	mammary gland integrity trait (VT:0010552)	ratio of deaths to total study population during a period of time (CMO:0001023)	6	7009971	115379601	Rat
634322	Bw12	Body weight QTL 12	0		body mass (VT:0001259)	body weight (CMO:0000012)	7	10173862	55173862	Rat
1300164	Rf15	Renal function QTL 15	3.12		renal blood flow trait (VT:2000006)	absolute change in renal blood flow rate (CMO:0001168)	6	13122958	57516539	Rat
10401812	Kidm54	Kidney mass QTL 54			kidney mass (VT:0002707)	both kidneys wet weight (CMO:0000085)	6	16810107	61810107	Rat
10401800	Kidm49	Kidney mass QTL 49			kidney mass (VT:0002707)	both kidneys wet weight (CMO:0000085)	6	16810107	61810107	Rat
8552910	Pigfal5	Plasma insulin-like growth factor 1 level QTL 5	4.3		blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	6	19417887	64417887	Rat
1641898	Colcr4	Colorectal carcinoma resistance QTL4	3.71	0.0007	intestine integrity trait (VT:0010554)	well differentiated malignant colorectal tumor surface area measurement (CMO:0002077)	6	21515302	65784818	Rat
2293839	Kiddil2	Kidney dilation QTL 2	4.8		kidney pelvis morphology trait (VT:0004194)	hydronephrosis severity score (CMO:0001208)	6	22042854	84763421	Rat
2293841	Kiddil4	Kidney dilation QTL 4	4.4		kidney pelvis morphology trait (VT:0004194)	hydronephrosis severity score (CMO:0001208)	6	22042854	84763421	Rat
8693632	Alc27	Alcohol consumption QTL 27	2.2	0.791	drinking behavior trait (VT:0001422)	calculated ethanol drink intake rate (CMO:0001615)	6	34257766	53855198	Rat
1300143	Rf14	Renal function QTL 14	2.92		renal blood flow trait (VT:2000006)	absolute change in renal blood flow rate (CMO:0001168)	6	34367436	80490628	Rat
1331779	Rf38	Renal function QTL 38	2.876		kidney blood vessel physiology trait (VT:0100012)	absolute change in renal vascular resistance (CMO:0001900)	6	34995656	75623393	Rat
634318	Bw118	Body weight QTL 118	3.55		abdominal fat pad mass (VT:1000711)	abdominal fat pad weight (CMO:0000088)	6	36260288	60606186	Rat
6893340	Cm77	Cardiac mass QTL 77	0.26	0.57	heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	6	36260288	84763275	Rat
1354632	Scl29	Serum cholesterol level QTL 29	3.74		blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	6	37608980	75023446	Rat
634307	Bp141	Blood pressure QTL 141	4		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	6	38106308	83106308	Rat
70199	Coreg1	Compensatory renal growth QTL 1	11.8		kidney mass (VT:0002707)	compensatory renal growth score (CMO:0001894)	6	38196412	60606431	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	21
Count of miRNA genes:	21
Interacting mature miRNAs:	21
Transcripts:	ENSRNOT00000009100
Prediction methods:	Miranda, Rnahybrid
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	57	41	19	41	8	11	74	35	41	11	8
Low
Below cutoff

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_053414	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AH009557	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC082049	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473947	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ226373	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ227615	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000164	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000009100 ⟹ ENSRNOP00000009100

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	6	38,422,888 - 38,453,797 (-)	Ensembl

RefSeq Acc Id:

NM_053414 ⟹ NP_445866

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	6	35,996,469 - 36,027,340 (-)	NCBI
Rnor_6.0	6	38,422,892 - 38,453,762 (-)	NCBI
Rnor_5.0	6	47,188,697 - 47,219,567 (-)	NCBI
RGSC_v3.4	6	36,794,602 - 36,825,473 (-)	RGD
Celera	6	35,359,044 - 35,389,916 (-)	RGD

Sequence:

show sequence

CTGGAAGGAGGGATCGACCGGGCCGGCAGCGGAGGAGTGCGGGAAGATGGCGGCCTTCTCCGAA
ATGGGTGTTATGCCCGAGATTGCACAAGCCGTGGAGGAGATGGATTGGCTTCTACCCACTGATA
TCCAGGCAGAATCTATCCCATTGATCCTAGGAGGAGGTGATGTACTTATGGCTGCAGAAACGGG
AAGTGGAAAAACTGGTGCATTTAGTATTCCAGTTATCCAGATAGTGTATGAGACTCTGAAAGAC
CAACAGGAAGGAAAGAAAGGGAAAGCAACTATTAAAACTGGTGCTTCTGTGCTCAACAAGTGGC
AGATGAACCCATATGATAGAGGGTCTGCTTTTGCAATTGGGTCAGATGGTCTGTGTTGTCAGAG
CAGAGAGGTGAAGGAGTGGCATGGGTGCAGAGCGACTAGAGGACTGCTGAGAGGGAAGCACTAC
TACGAAGTATCCTGTCATGACCAAGGGCTGTGCAGAGTTGGGTGGTCCACCATGCAGGCTTCCT
TAGACCTGGGTACTGACAAGTTTGGATTTGGCTTCGGTGGAACAGGAAAGAAATCTCATAATAA
ACAATTTGATAATTATGGAGAGGAATTCACTATGCATGACACCATTGGATGTTACTTAGACATC
GATAAAGGGCACGTGAAGTTCTCTAAGAATGGAAAAGACCTTGGTCTGGCATTTGAAATACCTG
CACACATAAAAAACCAAGCCCTCTTCCCTGCCTGTGTTTTGAAGAATGCTGAATTGAAATTTAA
CTTTGGTGAAGAAGAATTTAAGTTTCCACCAAAAGATGGTTTTGTTGCTCTTTCCAAGGCCCCT
GATAGTTACGTCGTCAAATCGCAGCACACAGGTAATGCACAGGTGTCACAAACAAAATTTCTCC
CTAATGCTCCAAAAGCTCTTATTGTGGAACCCTCCAGAGAGTTAGCTGAGCAAACCTTGAACAA
TGTGAAACAGTTTAAGAAGTACATCGATAATCCTAAATTGCGGGAGCTTCTCATAATTGGTGGC
GTTGCAGCTCGGGATCAGCTCTCCGTTCTGGATAATGGGGTTGATATTGTCGTCGGTACTCCAG
GAAGATTAGATGATTTGGTGTCAACTGGAAAGCTCAACTTGTCTCAAGTTAGATTCCTGGTCCT
GGATGAAGCAGATGGGCTTCTCTCTCAAGGTTATTCTGACTTTATTAACAGGATGCACAACCAG
ATTCCTCAGATTACTTCTGATGGGAAAAGACTTCAGGTGATTGTTTGCTCTGCTACTCTGCATT
CTTTTGATGTAAAGAAACTATCTGAGAAGATAATGCATTTTCCCACGTGGGTGGATTTGAAAGG
AGAAGATTCTGTTCCTGATACTGTGCATCATGTCGTTGTTCCTGTGAACCCAAAAACTGACAGG
CTCTGGGAAAGGCTGGGGAAGAACCACATTCGAACCGATGATGTCCATGCAAAGGATAACACAA
GACCTGGTGCCAACAGTCCAGAGATGTGGTCTGAAGCTATTAAAATACTGAAGGGGGAGTATGC
TGTCCGAGCAATCAAGGAGCACAAGATGGATCAAGCAATTATCTTCTGTAGAACGAAAATTGAC
TGTGACAACTTGGAGCAGTACTTTATGCAGCAAGGAGGAGGACCTGATAAAAAAGGACACCAAT
TCTCATGTGTATGTCTTCATGGTGACAGAAAGCCTCACGAGAGAAAGCAGAACTTGGAACGATT
TAAGAAAGGAGACGTAAGATTCCTGATTTGCACAGACGTAGCTGCCAGAGGAATTGACATCCAC
GGTGTTCCTTATGTTATTAATGTCACCCTGCCTGATGAAAAGCAGAATTATGTGCACCGGATTG
GCAGAGTGGGGCGAGCTGAAAGGATGGGCCTGGCTATTTCCCTGGTGGCAACAGAGAAAGAAAA
GGTTTGGTATCACGTATGCAGCAACCGTGGGAAGGGATGCTATAACACTAGACTCAAGGAAGAT
GGCGGCTGTACTATCTGGTACAATGAAATGCAGCTACTTTCTGAGATAGAAGAACACCTGAACT
GTACCATTTCCCAGGTTGAGCCAGATATAAAGGTTCCAGTGGATGAGTTTGATGGGAAAGTTAC
ATATGGTCAGAAAAGAGCTGCTGGCGGTGGGAACTATAAAGGCCATGTGGACATCCTGGCACCT
ACCGTTCAAGAGTTGGCTGCCCTTGAAAAGGAAGCACAGACATCTTTCCTACACCTTGGCTACC
TTCCCAACCAGCTGTTCAGAACCTTCTGATTTCATGTAGATGGAGAAGGATTGGAGTAATCGCG
TCTGTAGTCTTAACTTAACGTGGTGGTGCTTCTGAGCACAGTGTTTACAGTAGCTGAACTATTA
CTGCTAACTCTGCATGTCGGCAAACACAAATCTTAGGAGTTCTTCATAAAATGGCCGCCTAATG
AAAATAAATTGGACAACTATATTTTCATGAAAAAAAAAAAAAAAAAAAAAAAAAA

hide sequence

Protein Sequences


Protein RefSeqs	NP_445866	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAF81015	(Get FASTA)	NCBI Sequence Viewer
	AAF81016	(Get FASTA)	NCBI Sequence Viewer
	AAH82049	(Get FASTA)	NCBI Sequence Viewer
	EDM03114	(Get FASTA)	NCBI Sequence Viewer
	EDM03115	(Get FASTA)	NCBI Sequence Viewer
	EDM03116	(Get FASTA)	NCBI Sequence Viewer
	Q641Y8	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_445866 ⟸ NM_053414

- UniProtKB:

Q641Y8 (UniProtKB/Swiss-Prot)

- Sequence:

show sequence

MAAFSEMGVMPEIAQAVEEMDWLLPTDIQAESIPLILGGGDVLMAAETGSGKTGAFSIPVIQIV
YETLKDQQEGKKGKATIKTGASVLNKWQMNPYDRGSAFAIGSDGLCCQSREVKEWHGCRATRGL
LRGKHYYEVSCHDQGLCRVGWSTMQASLDLGTDKFGFGFGGTGKKSHNKQFDNYGEEFTMHDTI
GCYLDIDKGHVKFSKNGKDLGLAFEIPAHIKNQALFPACVLKNAELKFNFGEEEFKFPPKDGFV
ALSKAPDSYVVKSQHTGNAQVSQTKFLPNAPKALIVEPSRELAEQTLNNVKQFKKYIDNPKLRE
LLIIGGVAARDQLSVLDNGVDIVVGTPGRLDDLVSTGKLNLSQVRFLVLDEADGLLSQGYSDFI
NRMHNQIPQITSDGKRLQVIVCSATLHSFDVKKLSEKIMHFPTWVDLKGEDSVPDTVHHVVVPV
NPKTDRLWERLGKNHIRTDDVHAKDNTRPGANSPEMWSEAIKILKGEYAVRAIKEHKMDQAIIF
CRTKIDCDNLEQYFMQQGGGPDKKGHQFSCVCLHGDRKPHERKQNLERFKKGDVRFLICTDVAA
RGIDIHGVPYVINVTLPDEKQNYVHRIGRVGRAERMGLAISLVATEKEKVWYHVCSNRGKGCYN
TRLKEDGGCTIWYNEMQLLSEIEEHLNCTISQVEPDIKVPVDEFDGKVTYGQKRAAGGGNYKGH
VDILAPTVQELAALEKEAQTSFLHLGYLPNQLFRTF

hide sequence

RefSeq Acc Id:

ENSRNOP00000009100 ⟸ ENSRNOT00000009100

Protein Domains

B30.2/SPRY DEAD Helicase ATP-binding Helicase C-terminal

Transcriptome

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

Promoters

RGD ID:

13694499

Promoter ID:

EPDNEW_R5024

Type:

initiation region

Name:

Ddx1_1

Description:

DEAD-box helicase 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	6	38,453,750 - 38,453,810	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

Damaging Variants

Assembly: RGSC_v3.4

Chromosome	Start Pos	End Pos	Reference Nucleotide	Variant Nucleotide	Variant Type	Strain
6	36804954	36804955	T	G	snv	HCR/1Mco (UMich)

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:619903	AgrOrtholog
Ensembl Genes	ENSRNOG00000006652	Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein	ENSRNOP00000009100	ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript	ENSRNOT00000009100	ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH	2.60.120.920	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE	IMAGE:7131804	IMAGE-MGC_LOAD
InterPro	B30.2/SPRY	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	B30.2/SPRY_sf	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	ConA-like_dom_sf	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	DEAD/DEAH_box_helicase_dom	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Helicase_ATP-bd	UniProtKB/Swiss-Prot
	Helicase_C	UniProtKB/Swiss-Prot
	P-loop_NTPase	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	RNA_helicase_DEAD_Q_motif	UniProtKB/Swiss-Prot
	SPRY_dom	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report	rno:84474	UniProtKB/Swiss-Prot
MGC_CLONE	MGC:95195	IMAGE-MGC_LOAD
NCBI Gene	84474	ENTREZGENE
Pfam	DEAD	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Helicase_C	UniProtKB/Swiss-Prot
	SPRY	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen	Ddx1	PhenoGen
PROSITE	B302_SPRY	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	HELICASE_ATP_BIND_1	UniProtKB/Swiss-Prot
	HELICASE_CTER	UniProtKB/Swiss-Prot
	Q_MOTIF	UniProtKB/Swiss-Prot
SMART	DEXDc	UniProtKB/Swiss-Prot
	HELICc	UniProtKB/Swiss-Prot
	SPRY	UniProtKB/Swiss-Prot
Superfamily-SCOP	SSF49899	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	SSF52540	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt	DDX1_RAT	UniProtKB/Swiss-Prot, ENTREZGENE
	Q9JIJ7_RAT	UniProtKB/TrEMBL
	Q9JIJ8_RAT	UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2016-10-05	Ddx1	DEAD-box helicase 1	Ddx1	DEAD/H-box helicase 1	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2016-01-13	Ddx1	DEAD/H-box helicase 1	Ddx1	DEAD (Asp-Glu-Ala-Asp) box helicase 1	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2012-07-16	Ddx1	DEAD (Asp-Glu-Ala-Asp) box helicase 1	Ddx1	DEAD (Asp-Glu-Ala-Asp) box polypeptide 1	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2004-09-10	Ddx1	DEAD (Asp-Glu-Ala-Asp) box polypeptide 1		DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 1	Name updated	1299863	APPROVED
2002-08-07	Ddx1	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 1			Symbol and Name status set to provisional	70820	PROVISIONAL

RGD Curation Notes

Note Type	Note	Reference
gene_regulation	expression is amplified in estrogen-dependent endometrial adenocarcinoma	632515

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