Ddx28 (DEAD-box helicase 28) - Rat Genome Database

Name: Ddx28
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

Gene: Ddx28 (DEAD-box helicase 28) Rattus norvegicus

Analyze

Symbol:

Ddx28

Name:

DEAD-box helicase 28

RGD ID:

1311976

Description:

Predicted to enable rRNA binding activity. Predicted to be involved in mitochondrial large ribosomal subunit assembly. Predicted to be located in several cellular components, including mitochondrial nucleoid; nuclear lumen; and ribonucleoprotein granule. Predicted to be active in mitochondrion. Orthologous to human DDX28 (DEAD-box helicase 28); INTERACTS WITH 1,3-dinitrobenzene; 2,4-dinitrotoluene; bisphenol A.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Previously known as:

DEAD (Asp-Glu-Ala-Asp) box polypeptide 28; LOC364995; probable ATP-dependent RNA helicase DDX28

RGD Orthologs

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):	DDX28 (DEAD-box helicase 28)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, PhylomeDB, Treefam
Mus musculus (house mouse):	Ddx28 (DEAD box helicase 28)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Ddx28 (DEAD-box helicase 28)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	LOC103785397 (probable ATP-dependent RNA helicase DDX28)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	DDX28 (DEAD-box helicase 28)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	LOC101964431 (probable ATP-dependent RNA helicase DDX28)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	DDX28 (DEAD-box helicase 28)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	DDX28 (DEAD-box helicase 28)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	DDX28 (DEAD-box helicase 28)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Ddx28 (DEAD box helicase 28)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	ddx28 (DEAD (Asp-Glu-Ala-Asp) box polypeptide 28)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Drosophila melanogaster (fruit fly):	Dbp21E2	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Saccharomyces cerevisiae (baker's yeast):	MRH4	Alliance	DIOPT (Ensembl Compara\|OrthoFinder)
Xenopus tropicalis (tropical clawed frog):	ddx28	Alliance	DIOPT (Ensembl Compara\|OMA\|OrthoFinder\|PANTHER\|PhylomeDB)

Latest Assembly:

mRatBN7.2 - mRatBN7.2 Assembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	19	50,819,643 - 50,821,573 (-)	NCBI		GRCr8
mRatBN7.2	19	33,909,799 - 33,911,729 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	19	33,909,801 - 33,911,742 (-)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	19	40,725,329 - 40,727,259 (-)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	19	41,378,646 - 41,380,576 (-)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	19	43,677,546 - 43,679,476 (-)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	19	37,988,423 - 37,990,353 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	19	37,988,423 - 37,990,353 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	19	48,855,409 - 48,857,339 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	19	35,856,545 - 35,858,475 (-)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	19	35,861,723 - 35,863,394 (-)	NCBI
Celera	19	33,337,342 - 33,339,272 (-)	NCBI		Celera
Cytogenetic Map	19	q12	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

autosomal dominant dyskeratosis congenita 6 (ISO)

genetic disease (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

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

1,2-dimethylhydrazine (ISO)

1,3-dinitrobenzene (EXP)

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

2,4-dinitrotoluene (EXP)

4,4'-diaminodiphenylmethane (ISO)

4,4'-sulfonyldiphenol (ISO)

5-aza-2'-deoxycytidine (ISO)

aflatoxin B1 (ISO)

antirheumatic drug (ISO)

atrazine (ISO)

benzo[a]pyrene (ISO)

bis(2-ethylhexyl) phthalate (ISO)

bisphenol A (EXP)

carbon nanotube (ISO)

CGP 52608 (ISO)

cisplatin (ISO)

copper(II) sulfate (ISO)

cyclosporin A (ISO)

cylindrospermopsin (ISO)

dibutyl phthalate (ISO)

dioxygen (ISO)

epoxiconazole (ISO)

flutamide (EXP)

folic acid (ISO)

formaldehyde (ISO)

gentamycin (EXP)

iron dichloride (ISO)

methotrexate (ISO)

nickel atom (ISO)

paracetamol (EXP,ISO)

perfluorooctane-1-sulfonic acid (ISO)

pirinixic acid (ISO)

silver atom (ISO)

silver(0) (ISO)

teriflunomide (ISO)

tetrachloromethane (ISO)

thioacetamide (EXP)

trimellitic anhydride (ISO)

urethane (ISO)

valproic acid (ISO)

vinclozolin (EXP)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

mitochondrial large ribosomal subunit assembly (IBA,ISO)

Cellular Component

cytosol (IEA,ISO)

mitochondrial nucleoid (ISO)

mitochondrion (IBA,ISO)

nucleolus (IEA,ISO)

nucleoplasm (IEA,ISO)

ribonucleoprotein granule (ISO)

Molecular Function

ATP binding (IEA)

hydrolase activity (IEA)

mRNA binding (IEA)

RNA helicase activity (IEA)

rRNA binding (ISO)

References

References - curated

#	Reference Title	Reference Citation
1.	Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2.	Rat ISS GO annotations from MGI mouse gene data--August 2006	MGD data from the GO Consortium
3.	GOA pipeline	RGD automated data pipeline
4.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions

Additional References at PubMed

PMID:18063578	PMID:18614015	PMID:22658674	PMID:22681889	PMID:25683715

Genomics

Comparative Map Data

Ddx28
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	19	50,819,643 - 50,821,573 (-)	NCBI		GRCr8
mRatBN7.2	19	33,909,799 - 33,911,729 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	19	33,909,801 - 33,911,742 (-)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	19	40,725,329 - 40,727,259 (-)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	19	41,378,646 - 41,380,576 (-)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	19	43,677,546 - 43,679,476 (-)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	19	37,988,423 - 37,990,353 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	19	37,988,423 - 37,990,353 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	19	48,855,409 - 48,857,339 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	19	35,856,545 - 35,858,475 (-)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	19	35,861,723 - 35,863,394 (-)	NCBI
Celera	19	33,337,342 - 33,339,272 (-)	NCBI		Celera
Cytogenetic Map	19	q12	NCBI

DDX28
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	16	68,020,916 - 68,023,232 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	16	68,020,916 - 68,023,232 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	16	68,054,819 - 68,057,135 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	16	66,612,675 - 66,615,460 (-)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	16	66,612,674 - 66,615,460	NCBI
Celera	16	52,563,630 - 52,566,223 (-)	NCBI		Celera
Cytogenetic Map	16	q22.1	NCBI
HuRef	16	53,928,754 - 53,931,347 (-)	NCBI		HuRef
CHM1_1	16	69,463,195 - 69,465,788 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	16	73,816,696 - 73,819,012 (-)	NCBI		T2T-CHM13v2.0

Ddx28
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	8	106,736,248 - 106,738,118 (-)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	8	106,736,253 - 106,738,514 (-)	Ensembl		GRCm39 Ensembl
GRCm38	8	106,009,616 - 106,011,486 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	8	106,009,621 - 106,011,882 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	8	108,533,516 - 108,535,386 (-)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	8	108,898,751 - 108,900,562 (-)	NCBI		MGSCv36	mm8
Celera	8	110,237,668 - 110,239,538 (-)	NCBI		Celera
Cytogenetic Map	8	D3	NCBI
cM Map	8	53.08	NCBI

Ddx28
(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	NW_004955484	8,609,895 - 8,612,309 (+)	NCBI	ChiLan1.0	ChiLan1.0

LOC103785397
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
NHGRI_mPanPan1-v2	18	77,547,560 - 77,549,510 (-)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	16	83,458,879 - 83,460,857 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	16	48,362,204 - 48,364,134 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	16	67,786,315 - 67,788,330 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	16	67,786,592 - 67,788,211 (-)	Ensembl	panpan1.1		panPan2

DDX28
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	5	81,489,718 - 81,491,760 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
Dog10K_Boxer_Tasha	5	81,479,630 - 81,481,674 (+)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	5	81,924,704 - 81,926,748 (+)	NCBI		ROS_Cfam_1.0
UMICH_Zoey_3.1	5	81,751,293 - 81,753,337 (+)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	5	81,433,517 - 81,435,561 (+)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	5	82,075,452 - 82,077,496 (+)	NCBI		UU_Cfam_GSD_1.0

LOC101964431
(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_024409349	41,235,307 - 41,237,203 (+)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936475	18,352,139 - 18,353,761 (-)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936475	18,351,924 - 18,353,793 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

DDX28
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	6	28,615,330 - 28,617,335 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	6	28,615,461 - 28,617,443 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	6	26,002,074 - 26,003,953 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

DDX28
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	5	59,412,602 - 59,415,170 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	5	59,413,265 - 59,414,905 (+)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666047	22,145,860 - 22,147,905 (+)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Variants

Variants in Ddx28
3 total Variants

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	139
Count of miRNA genes:	115
Interacting mature miRNAs:	123
Transcripts:	ENSRNOT00000026817
Prediction methods:	Microtar, Miranda, Rnahybrid, Targetscan
Result types:	miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.

QTLs in Region (mRatBN7.2)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
9590298	Uminl5	Urine mineral level QTL 5	3.59	0.001	urine mineral amount (VT:0015086)	urine electrolyte level (CMO:0000593)	19	1	36824771	Rat
8552935	Pigfal10	Plasma insulin-like growth factor 1 level QTL 10	5.7		blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	19	1	36824771	Rat
9590250	Scort11	Serum corticosterone level QTL 11	23.45	0.001	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	19	1	36824771	Rat
9590090	Insglur8	Insulin/glucose ratio QTL 8	10.81	0.001	blood insulin amount (VT:0001560)	calculated plasma insulin level (CMO:0002170)	19	1	36824771	Rat
9589102	Slep13	Serum leptin concentration QTL 13	4.63	0.001	blood leptin amount (VT:0005667)	plasma leptin level (CMO:0000781)	19	569374	45569374	Rat
8694186	Bw152	Body weight QTL 152	3.34	0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	19	569374	45569374	Rat
7247442	Uae39	Urinary albumin excretion QTL 39			urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	19	2187927	46708701	Rat
724566	Uae12	Urinary albumin excretion QTL 12	5		urine albumin amount (VT:0002871)	urine albumin level (CMO:0000130)	19	2187927	56457239	Rat
61447	Tcas1	Tongue tumor susceptibility QTL 1	6.08		tongue integrity trait (VT:0010553)	squamous cell carcinoma of the tongue maximum tumor diameter (CMO:0001875)	19	2316121	47316121	Rat
2317848	Alcrsp21	Alcohol response QTL 21	1.899999976158142	0.05	response to alcohol trait (VT:0010489)	duration of loss of righting reflex (CMO:0002289)	19	3204777	48204777	Rat
1331737	Uae29	Urinary albumin excretion QTL 29	5.5		urine albumin amount (VT:0002871)	urine albumin level (CMO:0000130)	19	4096155	55283277	Rat
724518	Uae19	Urinary albumin excretion QTL 19	5.5		urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	19	7457249	42983518	Rat
724565	Tcas5	Tongue tumor susceptibility QTL 5	10.04		tongue integrity trait (VT:0010553)	number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)	19	9977753	39654489	Rat
61423	Cia14	Collagen induced arthritis QTL 14	3		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	19	10827970	43544039	Rat
1558656	Prcs1	Prostate cancer susceptibility QTL 1	5		prostate integrity trait (VT:0010571)	percentage of study population developing ventral prostate tumorous lesions during a period of time (CMO:0000943)	19	15114598	34521833	Rat
7411549	Bw130	Body weight QTL 130	5	0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	19	15455860	57337602	Rat
1331788	Rf45	Renal function QTL 45	2.818		kidney blood vessel physiology trait (VT:0100012)	absolute change in renal blood flow rate (CMO:0001168)	19	15605023	46559041	Rat
1578764	Stresp19	Stress response QTL 19	3.6	0.001	blood renin amount (VT:0003349)	plasma renin activity level (CMO:0000116)	19	15630201	57337602	Rat
2298478	Eau8	Experimental allergic uveoretinitis QTL 8		0.0163	uvea integrity trait (VT:0010551)	experimental autoimmune uveitis score (CMO:0001504)	19	17154433	57337602	Rat
61350	Bp32	Blood pressure QTL 32		0.012	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	19	20483575	57337602	Rat
1549835	Tcas7	Tongue tumor susceptibility QTL 7		0.001	tongue integrity trait (VT:0010553)	squamous cell carcinoma of the head and neck tumor number (CMO:0001876)	19	24817978	39654489	Rat
1354600	Salc2	Saline consumption QTL 2	9.91	0.001	drinking behavior trait (VT:0001422)	saline drink intake rate (CMO:0001627)	19	27530207	37947399	Rat
1354607	Gmadr1	Adrenal mass QTL 1	5.83		adrenal gland mass (VT:0010420)	both adrenal glands wet weight (CMO:0000164)	19	27530207	37947399	Rat
1354633	Bw28	Body weight QTL 28	6.04		body mass (VT:0001259)	body weight (CMO:0000012)	19	27530207	37947399	Rat
724546	Kidm3	Kidney mass QTL 3	3.1		kidney mass (VT:0002707)	calculated kidney weight (CMO:0000160)	19	29322490	57337602	Rat
1358200	Insglur2	Insulin/glucose ratio QTL 2	4.1		blood glucose amount (VT:0000188)	serum insulin level (CMO:0000358)	19	33838214	55283146	Rat
1358200	Insglur2	Insulin/glucose ratio QTL 2	4.1		blood glucose amount (VT:0000188)	serum glucose level (CMO:0000543)	19	33838214	55283146	Rat

Markers in Region

RH140741

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	19	33,911,318 - 33,911,538 (+)	MAPPER	mRatBN7.2
Rnor_6.0	19	37,989,943 - 37,990,162	NCBI	Rnor6.0
Rnor_5.0	19	48,856,929 - 48,857,148	UniSTS	Rnor5.0
RGSC_v3.4	19	35,858,065 - 35,858,284	UniSTS	RGSC3.4
Celera	19	33,338,862 - 33,339,081	UniSTS
RH 3.4 Map	19	317.7	UniSTS
Cytogenetic Map	19	q12	UniSTS

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	2	8	31	17	18	17			66	25	41	11
Low	1	35	26	24	1	24	8	11	8	10			8
Below cutoff

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001108898	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC121465	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473972	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000019	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

RefSeq Acc Id:

ENSRNOT00000026817 ⟹ ENSRNOP00000026817

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	19	33,909,801 - 33,911,742 (-)	Ensembl
Rnor_6.0 Ensembl	19	37,988,423 - 37,990,353 (-)	Ensembl

RefSeq Acc Id:

NM_001108898 ⟹ NP_001102368

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	19	50,819,643 - 50,821,573 (-)	NCBI
mRatBN7.2	19	33,909,799 - 33,911,729 (-)	NCBI
Rnor_6.0	19	37,988,423 - 37,990,353 (-)	NCBI
Rnor_5.0	19	48,855,409 - 48,857,339 (-)	NCBI
RGSC_v3.4	19	35,856,545 - 35,858,475 (-)	RGD
Celera	19	33,337,342 - 33,339,272 (-)	RGD

Sequence:

show sequence

CAAGAGAAATATGGCTTTAGCCGGGCCAACGCGGCTATTATCATTAGCAGTCCGGTTGCTTCTG
GAACCTCGACGGAACATAGTGTTGCGCGGTTCCGACCAGTCCTTGCCTGTTGTGCGCATTCCGC
GGGCTCTGCAGCGACGGCAGGAACAGCGACGGAGCGACCGTGGGAGTTTCCAACGGCCGGTGCT
AGTGCAACCTGGTCCACTCCTGGTCTCGGCAAAGCGGCCAGAGTTGAACCAGCCCGCACGCCTC
ACGCTGGGCCGTTGGGAGCGGGCACCACTGGCTTCGCGTGGCTGGAAGCATCGGCGATCGCGTC
AGGACCATTTTTCCATAGAGCGAGTGCAGCAAGAGGCGCCCGCCATGAGGAACCTCTCGTCCCG
GGGCAACTTCGTGGACCTGGGTCTAGAACCCCGAGTACTGCTCGCGCTTCAGAAGGCTGTCCCC
GAAATTGTTCAGCCAACCTCCGTGCAGTCGAAAACCATTCCCCCACTGCTTCGCGGCCGCCACA
TCCTTTGCGCTGCTGAAACCGGTAGCGGCAAGACGCTTAGCTATCTACTGCCCCTATTTCAACG
GCTCCTAAAAGGGCCAGAGCTGGACTCCCGCAGTTCCACCGCTCCTCGAGGCTTGGTTCTGGTA
CCTTCCCGAGAATTAGCCGAACAGGTGCAGGCAGTGGCCCAGTCATTGGGTAGGTACTTGGACC
TGCAGGTTATAGAACTTGGCGGAGGCCTGGGAATGAATAGGCTCAAACTTCAGCTGGGTAAATG
GCCGTCAGCAGATGTGCTAGTGGCTACTCCAGGGGCGCTGTGGAAGGCTCTGAAAAGTCAACTG
ATCAGCTTACATCATCTTAACTTCATAGTGCTGGATGAAGTAGACACGCTGCTAGATGAAAGCT
TCGTGGAACTGGTGGACTACATCTTGGGAAAGAGCCCTATAGCAGAAAGTCCAGCTGAGTTAGA
AGACCCCTTTAATCCCAAAGCTCAGTTAGTGATGGTGGGAGCCACATTTCCAGAAGGCCTAAAC
CAATTGCTGAGTAAAGTCACCAGCCCAGACAGTCTGACCACCATCACCAGCTCCAAGCTCCACT
GCATCATGCCTCATGTCAGACAGACATTTATGAGACTAAAGGGAACAGAGAAGGTGACAGAACT
GATTCAGATCCTCAAACAGCATGACAAAGCAAATAAGGCAGAACCCTCGGGAACTGTCCTGGTA
TTCTGCAACAGCGCCAGCACCGTGAACTGGCTTGGGTACATTCTGGATGACCACAAAATCCAAC
ATTTAAGGCTGCAAGGGCAAATGCCAGCCTCAATGAGGGCAGGTATCTTCCAGAGTTTCCAGAA
GGGCTCCCAAAACATACTTGTCTGCACAGACATTGCCTCACGAGGCCTAGACAGCATCCACGTG
GAAATGGTTGTCAATTATGATTTTCCCCCTACTCTGCAGGATTACATCCACAGAGCAGGAAGGG
TGGGTCGAGTGGGCAGTGAAGTGCCGGGGACTGTTACCAGTTTTGTGACCCATCCCTGGGATGT
GAGCCTGGTTCAGAAAATTGAACTGGCAGCTCGTAGAAGGAGAAGCCTTCCAGGACTAACATCT
TCAGTGAGGGACCCATTGCCTCAACAAGACTGACTTTTTTGGCTGACTTAAACCTACAATAGAG
CAGGGATCTTCTTGGAGGTCCAGGAAAGTTGAACACTTGTCTTTTGATGACATTGGGTCATACC
AGCCCCTCGCCTCTCTGCAGTATAATGAATTGTTTCGAGATCTGAAAAATAAACTACTAGACAG
GAATGGAGAGTAACATTCAAACAATAAAGTGGGGGGTTGGGGATTTAGCTCAGTGGTAGAGCGC
TTGCCTAGCAAGTGCAAGGCCCTGGGTTCAGTCCCCAGCTCCGAAAAAATAAAAAATAAAGTGG
ATGTTGACTTT

hide sequence

Protein Sequences


Protein RefSeqs	NP_001102368	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	EDL92431	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSRNOP00000026817
	ENSRNOP00000026817.2

RefSeq Acc Id:

NP_001102368 ⟸ NM_001108898

- UniProtKB:

D4A7Q5 (UniProtKB/TrEMBL), A6IYV3 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MALAGPTRLLSLAVRLLLEPRRNIVLRGSDQSLPVVRIPRALQRRQEQRRSDRGSFQRPVLVQP
GPLLVSAKRPELNQPARLTLGRWERAPLASRGWKHRRSRQDHFSIERVQQEAPAMRNLSSRGNF
VDLGLEPRVLLALQKAVPEIVQPTSVQSKTIPPLLRGRHILCAAETGSGKTLSYLLPLFQRLLK
GPELDSRSSTAPRGLVLVPSRELAEQVQAVAQSLGRYLDLQVIELGGGLGMNRLKLQLGKWPSA
DVLVATPGALWKALKSQLISLHHLNFIVLDEVDTLLDESFVELVDYILGKSPIAESPAELEDPF
NPKAQLVMVGATFPEGLNQLLSKVTSPDSLTTITSSKLHCIMPHVRQTFMRLKGTEKVTELIQI
LKQHDKANKAEPSGTVLVFCNSASTVNWLGYILDDHKIQHLRLQGQMPASMRAGIFQSFQKGSQ
NILVCTDIASRGLDSIHVEMVVNYDFPPTLQDYIHRAGRVGRVGSEVPGTVTSFVTHPWDVSLV
QKIELAARRRRSLPGLTSSVRDPLPQQD

hide sequence

RefSeq Acc Id:

ENSRNOP00000026817 ⟸ ENSRNOT00000026817

Protein Domains

DEAD-box RNA helicase Q Helicase ATP-binding Helicase C-terminal

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-D4A7Q5-F1-model_v2	AlphaFold	D4A7Q5	1-540	view protein structure

Transcriptome

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

Promoters

RGD ID:

13701099

Promoter ID:

EPDNEW_R11623

Type:

initiation region

Name:

Ddx28_1

Description:

DEAD-box helicase 28

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	19	37,990,355 - 37,990,415	EPDNEW

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1311976	AgrOrtholog
BioCyc Gene	G2FUF-5792	BioCyc
Ensembl Genes	ENSRNOG00000019817	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000026817	ENTREZGENE
	ENSRNOT00000026817.4	UniProtKB/TrEMBL
Gene3D-CATH	3.40.50.300	UniProtKB/TrEMBL
InterPro	DEAD-like_N	UniProtKB/TrEMBL
	DNA/RNA_helicase_C	UniProtKB/TrEMBL
	DNA/RNA_helicase_DEAD/DEAH_N	UniProtKB/TrEMBL
	P-loop_NTPase	UniProtKB/TrEMBL
	RNA_helicase_DEAD_Q_motif	UniProtKB/TrEMBL
KEGG Report	rno:364995	UniProtKB/TrEMBL
NCBI Gene	364995	ENTREZGENE
PANTHER	DEAD-BOX ATP-DEPENDENT RNA HELICASE 50	UniProtKB/TrEMBL
	RNA HELICASE	UniProtKB/TrEMBL
Pfam	DEAD	UniProtKB/TrEMBL
	Helicase_C	UniProtKB/TrEMBL
PhenoGen	Ddx28	PhenoGen
PROSITE	HELICASE_ATP_BIND_1	UniProtKB/TrEMBL
	HELICASE_CTER	UniProtKB/TrEMBL
	Q_MOTIF	UniProtKB/TrEMBL
RatGTEx	ENSRNOG00000019817	RatGTEx
SMART	DEXDc	UniProtKB/TrEMBL
	HELICc	UniProtKB/TrEMBL
Superfamily-SCOP	SSF52540	UniProtKB/TrEMBL
UniProt	A6IYV3	ENTREZGENE, UniProtKB/TrEMBL
	D4A7Q5	ENTREZGENE, UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2016-01-13	Ddx28	DEAD-box helicase 28	Ddx28	DEAD (Asp-Glu-Ala-Asp) box polypeptide 28	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2008-04-30	Ddx28	DEAD (Asp-Glu-Ala-Asp) box polypeptide 28	Ddx28_predicted	DEAD (Asp-Glu-Ala-Asp) box polypeptide 28 (predicted)	'predicted' is removed	2292626	APPROVED
2005-01-12	Ddx28_predicted	DEAD (Asp-Glu-Ala-Asp) box polypeptide 28 (predicted)			Symbol and Name status set to approved	70820	APPROVED

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)

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