Rbm28 (RNA binding motif protein 28)

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Gene: Rbm28 (RNA binding motif protein 28) Rattus norvegicus

Analyze

Symbol:

Rbm28

Name:

RNA binding motif protein 28

RGD ID:

1311336

Description:

Predicted to localize to nucleolus. Orthologous to human RBM28 (RNA binding motif protein 28); PARTICIPATES IN ribosome biogenesis pathway; INTERACTS WITH 2,4-dinitrotoluene; 2,6-dinitrotoluene; bisphenol A.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Also known as:

LOC312182; RNA-binding protein 28

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):	RBM28 (RNA binding motif protein 28)	HGNC	Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, Panther
Mus musculus (house mouse):	Rbm28 (RNA binding motif protein 28)	HGNC	NCBI, OMA, HomoloGene, Inparanoid, Panther, OrthoDB, Ensembl
Chinchilla lanigera (long-tailed chinchilla):	Rbm28 (RNA binding motif protein 28)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	RBM28 (RNA binding motif protein 28)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	RBM28 (RNA binding motif protein 28)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Rbm28 (RNA binding motif protein 28)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	RBM28 (RNA binding motif protein 28)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (African green monkey):	RBM28 (RNA binding motif protein 28)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Rbm28 (RNA binding motif protein 28)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	RBM28 (RNA binding motif protein 28)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector)
Mus musculus (house mouse):	Rbm28 (RNA binding motif protein 28)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector)
Danio rerio (zebrafish):	rbm28 (RNA binding motif protein 28)	Alliance	DIOPT (Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector)
Saccharomyces cerevisiae (baker's yeast):	NOP4	Alliance	DIOPT (Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER)
Drosophila melanogaster (fruit fly):	CG4806	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER)
Caenorhabditis elegans (roundworm):	rbm-28	Alliance	DIOPT (Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector)

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	4	57,722,223 - 57,761,935 (-)	NCBI
Rnor_6.0 Ensembl	4	56,398,769 - 56,438,465 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	4	56,398,769 - 56,438,442 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	4	56,165,550 - 56,205,238 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	4	55,995,621 - 56,034,994 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	4	56,247,944 - 56,286,518 (-)	NCBI
Celera	4	52,830,354 - 52,869,724 (-)	NCBI		Celera
Cytogenetic Map	4	q22	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

Alopecia, Neurologic Defects, and Endocrinopathy Syndrome (ISO)

microcephaly (ISO)

pleomorphic xanthoastrocytoma (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2-dimethylhydrazine (ISO)

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

2,4-dinitrotoluene (EXP)

2,6-dinitrotoluene (EXP)

4-hydroxyphenyl retinamide (ISO)

aflatoxin B1 (ISO)

benzo[a]pyrene (ISO)

bisphenol A (EXP,ISO)

cadmium dichloride (ISO)

carbon nanotube (ISO)

chromium(6+) (ISO)

copper atom (ISO)

copper(0) (ISO)

copper(II) sulfate (ISO)

cyclosporin A (ISO)

enzyme inhibitor (ISO)

folic acid (ISO)

hydrogen peroxide (ISO)

methamphetamine (ISO)

nickel atom (ISO)

paracetamol (ISO)

pentachlorophenol (ISO)

resveratrol (ISO)

tetrachloromethane (EXP)

thapsigargin (ISO)

thioacetamide (EXP)

titanium dioxide (ISO)

tungsten (ISO)

valproic acid (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Cellular Component

nucleolus (IEA,ISO)

ribonucleoprotein complex (IBA)

Molecular Function

RNA binding (IBA)

Molecular Pathway Annotations Click to see Annotation Detail View

ribosome biogenesis pathway (IEA,ISO)

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.	OMIM Disease Annotation Pipeline
3.	Pipeline to import KEGG annotations from KEGG into RGD
4.	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
5.	RGD automated import pipeline for gene-chemical interactions
6.	Sloan KE, etal., J Cell Biol. 2013 Mar 4;200(5):577-88. doi: 10.1083/jcb.201207131. Epub 2013 Feb 25.

Additional References at PubMed

PMID:22658674	PMID:22681889

Genomics

Comparative Map Data

Rbm28
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	4	57,722,223 - 57,761,935 (-)	NCBI
Rnor_6.0 Ensembl	4	56,398,769 - 56,438,465 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	4	56,398,769 - 56,438,442 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	4	56,165,550 - 56,205,238 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	4	55,995,621 - 56,034,994 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	4	56,247,944 - 56,286,518 (-)	NCBI
Celera	4	52,830,354 - 52,869,724 (-)	NCBI		Celera
Cytogenetic Map	4	q22	NCBI

RBM28
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	7	128,297,685 - 128,343,908 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	7	128,297,685 - 128,343,915 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	7	127,937,738 - 127,983,962 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	7	127,737,673 - 127,771,198 (-)	NCBI	NCBI36		hg18	NCBI36
Build 34	7	127,544,387 - 127,577,913	NCBI
Celera	7	122,753,554 - 122,787,084 (-)	NCBI
Cytogenetic Map	7	q32.1	NCBI
HuRef	7	122,311,644 - 122,345,174 (-)	NCBI		HuRef
CHM1_1	7	127,884,083 - 127,917,597 (-)	NCBI		CHM1_1
CRA_TCAGchr7v2	7	127,333,546 - 127,367,073 (-)	NCBI

Rbm28
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	6	29,123,572 - 29,164,975 (-)	NCBI	GRCm39		mm39
GRCm39 Ensembl	6	29,123,575 - 29,165,005 (-)	Ensembl
GRCm38	6	29,123,573 - 29,164,724 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	6	29,123,576 - 29,165,006 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	6	29,073,573 - 29,114,724 (-)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	6	29,075,028 - 29,108,210 (-)	NCBI			mm8
Celera	6	29,129,031 - 29,170,032 (-)	NCBI		Celera
Cytogenetic Map	6	A3.3	NCBI

Rbm28
(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_004955479	9,319,555 - 9,350,141 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955479	9,319,132 - 9,350,261 (-)	NCBI	ChiLan1.0	ChiLan1.0

RBM28
(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	7	132,955,078 - 132,988,576 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	7	132,955,078 - 132,988,576 (-)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	7	120,211,198 - 120,335,079 (-)	NCBI	Mhudiblu_PPA_v0		panPan3

RBM28
(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	14	8,043,197 - 8,074,145 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
CanFam3.1	14	8,043,159 - 8,074,174 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1

Rbm28
(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_004936479	15,451,583 - 15,483,496 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

RBM28
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	18	20,034,334 - 20,072,966 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	18	20,034,305 - 20,069,159 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1

RBM28
(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	21	97,111,801 - 97,143,721 (-)	NCBI
ChlSab1.1 Ensembl	21	97,112,215 - 97,143,669 (-)	Ensembl

Rbm28
(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_004624783	7,628,968 - 7,659,772 (+)	NCBI

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
619616	Bp79	Blood pressure QTL 79		0.0292	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	4	3043231	79575658	Rat
2303168	Bp330	Blood pressure QTL 330	4.25	0.017	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	4	3043231	145254791	Rat
1358203	Stl19	Serum triglyceride level QTL 19	2.8	0.002	blood triglyceride amount (VT:0002644)	serum triglyceride level (CMO:0000360)	4	3044017	64915903	Rat
631261	Tcas3	Tongue tumor susceptibility QTL 3	6.88		tongue integrity trait (VT:0010553)	number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)	4	7342404	92484039	Rat
2316958	Gluco58	Glucose level QTL 58	10		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	4	7850904	182171018	Rat
2303585	Bw86	Body weight QTL 86	4		body mass (VT:0001259)	body weight (CMO:0000012)	4	12638974	57638974	Rat
7387227	Uae40	Urinary albumin excretion QTL 40	2.9	0.0052	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	4	16149941	61149941	Rat
61412	Pia2	Pristane induced arthritis QTL 2	3.9		joint integrity trait (VT:0010548)	post-insult time to onset of experimental arthritis (CMO:0001450)	4	18222187	61039065	Rat
10755501	Bp390	Blood pressure QTL 390	2.5		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	4	23850384	169318094	Rat
6909122	Insul22	Insulin level QTL 22	4.63		blood insulin amount (VT:0001560)	plasma insulin level (CMO:0000342)	4	23991721	76238799	Rat
6909128	Pancm4	Pancreatic morphology QTL 4	11.35		pancreas mass (VT:0010144)	pancreas wet weight (CMO:0000626)	4	23991721	76238799	Rat
1578655	Bmd11	Bone mineral density QTL 11	11		femur mineral mass (VT:0010011)	total volumetric bone mineral density (CMO:0001728)	4	24631874	69631874	Rat
8655906	Rf60	Renal function QTL 60	3.8		blood creatinine amount (VT:0005328)	creatinine clearance (CMO:0000765)	4	26654749	81874227	Rat
12798520	Anxrr55	Anxiety related response QTL 55	4.45	0.01	locomotor behavior trait (VT:0001392)	number of rearing movements with lid-pushing in an experimental apparatus (CMO:0002715)	4	29549895	112807890	Rat
8552782	Vie1	Viral induced encephalitis QTL 1	26.4		brain integrity trait (VT:0010579)	encephalitis incidence/prevalence measurement (CMO:0002361)	4	31825560	83531021	Rat
8552801	Bw143	Body weight QTL 143	7.3		body mass (VT:0001259)	change in body weight to body weight ratio (CMO:0002216)	4	31825560	83531021	Rat
8552809	Vie5	Viral induced encephalitis QTL 5	25.3		brain integrity trait (VT:0010579)	encephalitis incidence/prevalence measurement (CMO:0002361)	4	31825560	83531021	Rat
2313401	Anxrr27	Anxiety related response QTL 27			aggression-related behavior trait (VT:0015014)	tameness/aggressiveness composite score (CMO:0002136)	4	33637803	61708341	Rat
8655961	Kidm43	Kidney mass QTL 43	18		kidney mass (VT:0002707)	both kidneys wet weight (CMO:0000085)	4	34277932	99067150	Rat
1358352	Srcrt3	Stress Responsive Cort QTL 3	2.29		blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	4	36615599	145611886	Rat
61475	Aia2	Adjuvant induced arthritis QTL 2	5.8		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	4	37685175	73066691	Rat
1331807	Rf31	Renal function QTL 31	2.988		urine potassium amount (VT:0010539)	urine potassium level (CMO:0000128)	4	37703272	75345433	Rat
1300139	Hrtrt6	Heart rate QTL 6	2.85		heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	4	37703272	115372927	Rat
61445	Strs3	Sensitivity to stroke QTL 3	3		cerebrum integrity trait (VT:0010549)	post-insult time to onset of cerebrovascular lesion (CMO:0002343)	4	39208222	84208222	Rat
8694439	Bw168	Body weight QTL 168	9.57	0.001	retroperitoneal fat pad mass (VT:0010430)	retroperitoneal fat pad weight to body weight ratio (CMO:0000635)	4	39208247	84208247	Rat
6893678	Bw108	Body weight QTL 108	2.6	0.006	body mass (VT:0001259)	body weight (CMO:0000012)	4	42415777	87415777	Rat
1576305	Emca6	Estrogen-induced mammary cancer QTL 6	5.8		mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	4	43414605	155469929	Rat
1354660	Salc1	Saline consumption QTL 1	11.26		drinking behavior trait (VT:0001422)	saline drink intake rate (CMO:0001627)	4	43414792	146942075	Rat
1354612	Foco1	Food consumption QTL 1	8.87		eating behavior trait (VT:0001431)	food intake rate (CMO:0000427)	4	43414792	146942075	Rat
1298082	Stresp4	Stress response QTL 4			blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	4	46898276	145611886	Rat
2312567	Glom19	Glomerulus QTL 19	1.9	0.006	kidney glomerulus morphology trait (VT:0005325)	index of glomerular damage (CMO:0001135)	4	49906054	145611886	Rat
4889969	Bss96	Bone structure and strength QTL 96	4.9		tibia size trait (VT:0100001)	tibia cortical bone volume (CMO:0001725)	4	55324857	79575658	Rat
4889972	Bss97	Bone structure and strength QTL 97	5.6		tibia size trait (VT:0100001)	tibia total bone volume (CMO:0001724)	4	55324857	79575658	Rat
5685009	Bmd86	Bone mineral density QTL 86	3.7		tibia mineral mass (VT:1000283)	bone mineral density (CMO:0001226)	4	55324857	79575658	Rat
5685012	Bmd87	Bone mineral density QTL 87	5.1		tibia mineral mass (VT:1000283)	bone mineral content (CMO:0001554)	4	55324857	79575658	Rat
70200	Alc18	Alcohol consumption QTL 18	9.2		drinking behavior trait (VT:0001422)	ethanol intake volume to total fluid intake volume ratio (CMO:0001591)	4	55324953	148360954	Rat
1641833	Alc21	Alcohol consumption QTL 21	8.6	0.0001	drinking behavior trait (VT:0001422)	ethanol drink intake rate (CMO:0001407)	4	55375865	125671711	Rat
634311	Sach7	Saccharin preference QTL 7			taste sensitivity trait (VT:0001986)	saccharin intake volume to total fluid intake volume ratio (CMO:0001601)	4	55791564	82134846	Rat
631546	Bp86	Blood pressure QTL 86	3.2		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	4	55791564	92484312	Rat
61336	Bp21	Blood pressure QTL 21	4.6		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	4	55791834	79557856	Rat
1578657	Bss12	Bone structure and strength QTL 12	8.9		femur morphology trait (VT:0000559)	femoral neck cross-sectional area (CMO:0001697)	4	56092756	101092756	Rat
1578658	Bss13	Bone structure and strength QTL 13	8		femur strength trait (VT:0010010)	femoral neck polar moment of inertia (CMO:0001670)	4	56092756	101092756	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	276
Count of miRNA genes:	175
Interacting mature miRNAs:	201
Transcripts:	ENSRNOT00000064007
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.

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	20	20	14	12	14			66	27	38	7
Low	1	23	37	27	7	27	8	11	8	8	3	4	8
Below cutoff

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001107850	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_006236190	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039107509	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039107510	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC096035	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473959	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ211470	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ221399	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000141	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000064007 ⟹ ENSRNOP00000059579

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	4	56,399,494 - 56,438,465 (-)	Ensembl

RefSeq Acc Id:

ENSRNOT00000077079 ⟹ ENSRNOP00000069435

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	4	56,398,769 - 56,438,142 (-)	Ensembl

RefSeq Acc Id:

NM_001107850 ⟹ NP_001101320

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	4	57,722,223 - 57,761,595 (-)	NCBI
Rnor_6.0	4	56,398,769 - 56,438,142 (-)	NCBI
Rnor_5.0	4	56,165,550 - 56,205,238 (-)	NCBI
RGSC_v3.4	4	55,995,621 - 56,034,994 (-)	RGD
Celera	4	52,830,354 - 52,869,724 (-)	RGD

Sequence:

show sequence

GGGTTTCCTGCCAGAGCTCAACCCAGCGGTCGCTCGCGCCGGTGCTGGTTGCGCGTGGTCTCAC
ACGCTTGTTTCTCGGTCTCATGGCCGGTCTGACTCTATTCGTGGGCCGTCTCCCGCCCTCCGCT
CGCAGTGATCAGCTGGAAGAGCTGTTCAGTCAGGTGGGTCCGGTGAAACAGTGCTTCGTGGTGA
CAGAGAAAGGGAGTAAAGCATGCCGGGGCTTTGGCTATGTGACCTTCTCCATGCTGGAAGATGT
TCAGAGGGCCCTTAAGGAGATCACTACCTTCGAAGGTTGCAAGATCAATGTGACCATTGCCAAG
AAAAAACTGAAGAACAAGTCCAAGGAAACAAGGAAAAATGAAAATTCAGAGTCCCCAAAAAAGG
AGCCAAAGCACAAAAAAGCCAAAGTGGCAGATAAGAAAGCCAGATTAATTATCCGGAACCTCAG
CTTTAAGTGTTCAGAAGATGACTTGAAATCAGTATTTACTCACTATGGAACTGTTCTGGAAGTG
AATATCCCAAGGAAACCAGATGGAAAGATGCGTGGTTTTGCTTTTATTCAATTCAAAAACCTCC
TTGAAGCAGGAAAAGCTCTCAAAGGCGCAAATATGAAAGAGATAAAAGGGCGGACTGTGGCTGT
GGACTGGGCTGTGGCCAAGGACAAATACAAAGATGCCCAGCATACTTCTGTCTCAGGTGGAAAG
AAGAGCAGCGAGCGTAAGCCTAAGGAGTCGAGTAAGAAGAGCTGCAGGGTGGAAGAGCAAGTAG
AAGATGATGATGATGATGGTGAAGATGAAGAAGATGATGATACCCAAGATGATGAGGACGAAAG
TAGAGACTCGACGGTAGCTTCTCCTGTGAGCGTGCGGAAGAGAGCAGTCAAGAGAGCAGCTCCC
GAGGAAAGCACCGAGGAAGACACTTACGATGACAGCGATCTGGAGGAAGGGAGCAGCTCCTACG
GCGACGGGACGGCACACAGCGAGAGCAGCACTGAAGAGCTGGAGGACGAAGATGTTCCAGTCTC
AAAGAAAAAGAAGAGGAAGTTACCCTCCGATGTGACTGAAGGGAAAACTGTCTTCATCAGAAAT
CTTTCATTTGACTCAGAAGAGGAAGCGCTTGGGGAGGTCCTCCAGCAATTTGGTGATCTTAAGT
ATGTCCGGATTGTCTTGCATCCAGACACAGAGCATTCTAAAGGTTGTGCATTTGCACAATTCGT
GACTCAGGAAGCAGCTCAGAAATGCCTTGCAGCAGCTTCTCCAGAGACCGAGGGTGGTGGGCTT
AAACTGGATGGCCGGCAGCTCAAGGTCGACTTGGCTGTGACCCGTGATGAGGCAGCAAAGCTTC
AGACAAAGAAGGTGAAGAAGCCAACTGGAACGCGGAACCTCTATCTGGCCCGAGAAGGCTTGAT
CCGCGCTGGGACGAAGGCTGCTGAGGGTGTGAGTGCCGCAGACATGGCCAAACGCGAGCGGTGT
AGAGTGATGCGAGACCTAAAGGCAGTTCATGGAAAAATGAAGGGTCAGTCCCTGGGCTATGCCT
TTGTGGAGTTCCAAAAGCATGAGCATGCCCTCCGAGCCCTCCGCCACTTCAACAACAACCCGGA
GACCTTTGGGCCCCAGAAGAGACCAATAGTGGAGTTCTCTTTAGAAGATCGAAGGAAACTTAAA
GTAAAGGAGCTGAGAATCCAGCGCAGCCTGCAAAAAATGGGATCTAAGCCTGTGACCAGTAAGC
CCCAAAAGGAACAGAAAGAACAAGGAAAAGACAAGCAACAGAAAGCAGCTCAGGGCGGCACGCG
GGATCAGAGTAAGGCGCCTGGAGAGCAGGGGAAGGGCCGCTGCACCTCGTGGACAGGGTTCCAG
ACCAAGGCCGAGGTGGAGCAGGTGGAGCTCCCCGACGGGACAAGGAGAAGAAAGGTCCTGGCGC
TCCCTTCACACCGAGGCCCCAAAGTGAGGCTGCGGGACAGAGGCAAAGTGAAGTCCCTTCCTTC
TAAGAAGCCAAAGCCCCAGATGGGCCAGCGGAAGCAAAAGAAGCAGCAGTCAGCTTCTTCCCTG
CAGGCACCTAAGAAAAAAGCTAAAGAAAGTAAGGCAGAAGCCCACTTCAACCGACTGGTTGAAC
AATATAAGCAGAAGTTGTTGGGCCCTTCTAAAGGAGCATCCCTTGTGAAGAGAAGCAAATGGTT
TGACAGCTGATCGTGCCTGCAGCCTGTAAGAAAGCCATGTCTTTCACTGAGGAAAGGATCCTAG
ATGATACCCACTTTCTTGGGGACTCTGTGGGTTGTCTACATTCTTGGTCCGTTCTCCAGTGTGG
TGTTTGTTAGCCACAAGGAAACACCTGAAAAGCACCATGAAGGTTTCTAACTTAACCGTCTTAG
TGCTAAATCTGCACATGTAATTGCAACTGATTTCTAATCTCTTCTCAGATGGAAACTATTGTAA
AGAGTGTCCCAGAGTACTGAATTTTAAAGATGCATATTTTGTTATGGAGTCTGTAAGTGAGAAA
TTGTGACTTTTTGGATGTGTCTCATTTTTAATATACACAAATATATTATTTATGAGTTTTTCTA
AAAGAACCTTTTTAACATTTTTAATCGGTTACAGAGTTTGCACAACTAGGAGCAGAGAAAATGC
TTACTAAAGTAGTCTTGAGTGCTGGAGATGCCAGGGAAGGACTGAAGGCCGTCCGTCTGGCATC
AGGCAGCACCTGAGAACTGTCTGTCCCTGGCGGAGGGGCTAACTGGAGATATGGTTGCGGGCTG
GGCACCAGCCTGACCACACATGGCCCAGATGTGCCCCTCAGCACCTTCTCCCAGGGACTGAGCT
CTCTGGTGAGGGAAGGCAGTGGGCACGAGGCTCTGACCTATGGGCCTGAAGTCTTACCTGGTCC
TGCAAAATAAACAGTTTAACCACATGGACTCCCGGCTCTTCCCTGCACTACATACTTTTAAACA
TTCTTTCTACCTGTACTTTGTCTTGTCTACAGAAAGCTGGCCATGGAGGGTGACTTAGAGTCAG
GGTCCACACGGATTCTGACACTATGGAGAGTAGGCCCTTGGGAAAGAAGATCACGGGAGATAAG
CAAAGCCCCGTGCTGTATAACTCTGATACACAATGTGGAGTACGTTGATTTCTGCCCCCTCAGA
GCCTTGTGCCTGCCCCGTCTCCTTAGGATCTTGTTCCTCAGATCTCCACTGAGCCATCAGCACT
TCTGCTGTTTCTTCAGTATCTGAAGTAGGGCTCCTCATACCTCCCCACTTCTGACTCCTGACTG
GATTCTCAGATCCTGTTTGTTTCCTCTTGGCACTAATCACTATCTAAAATTGTCTCCCCATTAA
AACATCTGCTTTGAGACTTCCTCTTGTTTGCCCTTACATAGTGGGTGTGGAATAAATATTTACT
GAATGAAAAAAAAAAAAACAAAAACCAATAACAAAGGAACAGGAGCAGTGGTAGTCTGTAGAAA
GGAAAAGGCTGAGAACTTAGCTTGCTTGGTTGCTGGCCTAATGTACTACTTTAAAGGATGCTAT
CCCAGAATATCGCTGAGCTGTTTTATCGCAGTGTCTTGGGAAAACCAACTAGCGCTCCAGAAAG
CCCTTAATAGTTTAGAGATAGTGAAGGAAAAGTCATGAAAACTTTAG

hide sequence

RefSeq Acc Id:

XM_006236190 ⟹ XP_006236252

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	4	57,722,946 - 57,761,935 (-)	NCBI
Rnor_6.0	4	56,399,492 - 56,438,442 (-)	NCBI
Rnor_5.0	4	56,165,550 - 56,205,238 (-)	NCBI

Sequence:

show sequence

AAACTTATTGAACACCCACTCTATGTCAGATGAGGGCAGGCTTAGGGGGAAAATGACTTCTGCC
TGCTTTGGTGAATTTGGGGTCGAGTTCCTAAATGAAAGATTTTAAGAGAGGTTTGCGTTTCCTC
CCGGACTCTTTTGAGCAACGAGTACTTCTTGAATTTCCCGGCACGGGTTTCCTGCCAGAGCTCA
ACCCAGCGGTCGCTCGCGCCGGTGCTGGTTGCGCGTGGTCTCACACGCTTGTTTCTCGGTCTCA
TGGCCGGTCTGACTCTATTCGTGGGCCGTCTCCCGCCCTCCGCTCGCAGTGATCAGCTGGAAGA
GCTGTTCAGTCAGGTGGGTCCGGTGAAACAGTGCTTCGTGGTGACAGAGAAAGGGAGTAAAGCA
TGCCGGGGCTTTGGCTATGTGACCTTCTCCATGCTGGAAGATGTTCAGAGGGCCCTTAAGGAGA
TCACTACCTTCGAAGGTTGCAAGATCAATGTGACCATTGCCAAGAAAAAACTGAAGAACAAGTC
CAAGGAAACAAGGAAAAATGAAAATTCAGAGTCCCCAAAAAAGGAGCCAAAGCACAAAAAAGCC
AAAGTGGCAGATAAGAAAGCCAGATTAATTATCCGGAACCTCAGCTTTAAGTGTTCAGAAGATG
ACTTGAAATCAGTATTTACTCACTATGGAACTGTTCTGGAAGTGAATATCCCAAGGAAACCAGA
TGGAAAGATGCGTGGTTTTGCTTTTATTCAATTCAAAAACCTCCTTGAAGCAGGAAAAGCTCTC
AAAGGCGCAAATATGAAAGAGATAAAAGGGCGGACTGTGGCTGTGGACTGGGCTGTGGCCAAGG
ACAAATACAAAGATGCCCAGCATACTTCTGTCTCAGGTGGAAAGAAGAGCAGCGAGCGTAAGCC
TAAGGAGTCGAGTAAGAAGAGCTGCAGGGTGGAAGAGCAAGTAGAAGATGATGATGATGATGGT
GAAGATGAAGAAGATGATGATACCCAAGATGATGAGGACGAAAGTAGAGACTCGACGGTAGCTT
CTCCTGTGAGCGTGCGGAAGAGAGCAGTCAAGAGAGCAGCTCCCGAGGAAAGCACCGAGGAAGA
CACTTACGATGACAGCGATCTGGAGGAAGGGAGCAGCTCCTACGGCGACGGGACGGCACACAGC
GAGAGCAGCACTGAAGAGCTGGAGGACGAAGATGTTCCAGTCTCAAAGAAAAAGAAGAGGAAGT
TACCCTCCGATGTGACTGAAGGGAAAACTGTCTTCATCAGAAATCTTTCATTTGACTCAGAAGA
GGAAGCGCTTGGGGAGGTCCTCCAGCAATTTGGTGATCTTAAGTATGTCCGGATTGTCTTGCAT
CCAGACACAGAGCATTCTAAAGGTTGTGCATTTGCACAATTCGTGACTCAGGAAGCAGCTCAGA
AATGCCTTGCAGCAGCTTCTCCAGAGACCGAGGGTGGTGGGCTTAAACTGGATGGCCGGCAGCT
CAAGGTCGACTTGGCTGTGACCCGTGATGAGGCAGCAAAGCTTCAGACAAAGAAGGTGAAGAAG
CCAACTGGAACGCGGAACCTCTATCTGGCCCGAGAAGGCTTGATCCGCGCTGGGACGAAGGCTG
CTGAGGGTGTGAGTGCCGCAGACATGGCCAAACGCGAGCGGTTTGAGCTACTGAAACATCAGAA
ACTCAAGAACCAGAATATCTTTGTCTCCCAGACCAGGCTTTGCCTGCACAACCTCCCGAAGTCA
GTGGATGATAAACAGCTAAGGAAGCTGCTGCTGCAGGCCACTGGAGGAGAGAAGGGGGTTCGCA
TTAAGGAGTGTAGAGTGATGCGAGACCTAAAGGCAGTTCATGGAAAAATGAAGGGTCAGTCCCT
GGGCTATGCCTTTGTGGAGTTCCAAAAGCATGAGCATGCCCTCCGAGCCCTCCGCCACTTCAAC
AACAACCCGGAGACCTTTGGGCCCCAGAAGAGACCAATAGTGGAGTTCTCTTTAGAAGATCGAA
GGAAACTTAAAGTAAAGGAGCTGAGAATCCAGCGCAGCCTGCAAAAAATGGGATCTAAGCCTGT
GACCAGTAAGCCCCAAAAGGAACAGAAAGAACAAGGAAAAGACAAGCAACAGAAAGCAGCTCAG
GGCGGCACGCGGGATCAGAGTAAGGCGCCTGGAGAGCAGGGGAAGGGCCGCTGCACCTCGTGGA
CAGGGTTCCAGACCAAGGCCGAGGTGGAGCAGGTGGAGCTCCCCGACGGGACAAGGAGAAGAAA
GGTCCTGGCGCTCCCTTCACACCGAGGCCCCAAAGTGAGGCTGCGGGACAGAGGCAAAGTGAAG
TCCCTTCCTTCTAAGAAGCCAAAGCCCCAGATGGGCCAGCGGAAGCAAAAGAAGCAGCAGTCAG
CTTCTTCCCTGCAGGCACCTAAGAAAAAAGCTAAAGAAAGTAAGGCAGAAGCCCACTTCAACCG
ACTGGTTGAACAATATAAGCAGAAGTTGTTGGGCCCTTCTAAAGGAGCATCCCTTGTGAAGAGA
AGCAAATGGTTTGACAGCTGATCGTGCCTGCAGCCTGTAAGAAAGCCATGTCTTTCACTGAGGA
AAGGATCCTAGATGATACCCACTTTCTTGGGGACTCTGTGGGTTGTCTACATTCTTGGTCCGTT
CTCCAGTGTGGTGTTTGTTAGCCACAAGGAAACACCTGAAAAGCACCATGAAGGTTTCTAACTT
AACCGTCTTAGTGCTAAATCTGCACATGTAATTGCAACTGATTTCTAATCTCTTCTCAGATGGA
AACTATTGTAAAGAGTGTCCCAGAGTACTGAATTTTAAAGATGCATATTTTGTTATGGAGTCTG
TAAGTGAGAAATTGTGACTTTTTGGATGTGTCTCATTTTTAATATACACAAATATATTATTTAT
GAGTTTTTCTAAAAGAACCTTTTTAACATTTTTAATCGGTTACAGAGTTTGCACAACTAGGAGC
AGAGAAAATGCTTACTAAAGTAGTCTTGAGTGCTGGAGATGCCAGGGAAGGACTGAAGGCCGTC
CGTCTGGCATCAGGCAGCACCTGAGAACTGTCTGTCCCTGGCGGAGGGGCTAACTGGAGATATG
GTTGCGGGCTGGGCACCAGCCTGACCACACATGGCCCAGATGTGCCCCTCAGCACCTTCTCCCA
GGGACTGAGCTCTCTGGTGAGGGAAGGCAGTGGGCACGAGGCTCTGACCTATGGGCCTGAAGTC
TTACCTGGTCCTGCAAAATAAACAGTTTAACCACATGGA

hide sequence

RefSeq Acc Id:

XM_039107509 ⟹ XP_038963437

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	4	57,722,946 - 57,761,935 (-)	NCBI

RefSeq Acc Id:

XM_039107510 ⟹ XP_038963438

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	4	57,722,946 - 57,761,935 (-)	NCBI

Protein Sequences


Protein RefSeqs	NP_001101320	(Get FASTA)	NCBI Sequence Viewer
	XP_006236252	(Get FASTA)	NCBI Sequence Viewer
	XP_038963437	(Get FASTA)	NCBI Sequence Viewer
	XP_038963438	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	EDM15204	(Get FASTA)	NCBI Sequence Viewer
	EDM15205	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_001101320 ⟸ NM_001107850

- UniProtKB:

A0A0G2JVD0 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MAGLTLFVGRLPPSARSDQLEELFSQVGPVKQCFVVTEKGSKACRGFGYVTFSMLEDVQRALKE
ITTFEGCKINVTIAKKKLKNKSKETRKNENSESPKKEPKHKKAKVADKKARLIIRNLSFKCSED
DLKSVFTHYGTVLEVNIPRKPDGKMRGFAFIQFKNLLEAGKALKGANMKEIKGRTVAVDWAVAK
DKYKDAQHTSVSGGKKSSERKPKESSKKSCRVEEQVEDDDDDGEDEEDDDTQDDEDESRDSTVA
SPVSVRKRAVKRAAPEESTEEDTYDDSDLEEGSSSYGDGTAHSESSTEELEDEDVPVSKKKKRK
LPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRIVLHPDTEHSKGCAFAQFVTQEAAQ
KCLAAASPETEGGGLKLDGRQLKVDLAVTRDEAAKLQTKKVKKPTGTRNLYLAREGLIRAGTKA
AEGVSAADMAKRERCRVMRDLKAVHGKMKGQSLGYAFVEFQKHEHALRALRHFNNNPETFGPQK
RPIVEFSLEDRRKLKVKELRIQRSLQKMGSKPVTSKPQKEQKEQGKDKQQKAAQGGTRDQSKAP
GEQGKGRCTSWTGFQTKAEVEQVELPDGTRRRKVLALPSHRGPKVRLRDRGKVKSLPSKKPKPQ
MGQRKQKKQQSASSLQAPKKKAKESKAEAHFNRLVEQYKQKLLGPSKGASLVKRSKWFDS

hide sequence

RefSeq Acc Id:	XP_006236252 ⟸ XM_006236190
- Peptide Label:	isoform X1
- UniProtKB:	D4A5K7 (UniProtKB/TrEMBL)
- Sequence:	show sequence MAGLTLFVGRLPPSARSDQLEELFSQVGPVKQCFVVTEKGSKACRGFGYVTFSMLEDVQRALKE ITTFEGCKINVTIAKKKLKNKSKETRKNENSESPKKEPKHKKAKVADKKARLIIRNLSFKCSED DLKSVFTHYGTVLEVNIPRKPDGKMRGFAFIQFKNLLEAGKALKGANMKEIKGRTVAVDWAVAK DKYKDAQHTSVSGGKKSSERKPKESSKKSCRVEEQVEDDDDDGEDEEDDDTQDDEDESRDSTVA SPVSVRKRAVKRAAPEESTEEDTYDDSDLEEGSSSYGDGTAHSESSTEELEDEDVPVSKKKKRK LPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRIVLHPDTEHSKGCAFAQFVTQEAAQ KCLAAASPETEGGGLKLDGRQLKVDLAVTRDEAAKLQTKKVKKPTGTRNLYLAREGLIRAGTKA AEGVSAADMAKRERFELLKHQKLKNQNIFVSQTRLCLHNLPKSVDDKQLRKLLLQATGGEKGVR IKECRVMRDLKAVHGKMKGQSLGYAFVEFQKHEHALRALRHFNNNPETFGPQKRPIVEFSLEDR RKLKVKELRIQRSLQKMGSKPVTSKPQKEQKEQGKDKQQKAAQGGTRDQSKAPGEQGKGRCTSW TGFQTKAEVEQVELPDGTRRRKVLALPSHRGPKVRLRDRGKVKSLPSKKPKPQMGQRKQKKQQS ASSLQAPKKKAKESKAEAHFNRLVEQYKQKLLGPSKGASLVKRSKWFDS hide sequence

RefSeq Acc Id:

ENSRNOP00000069435 ⟸ ENSRNOT00000077079

RefSeq Acc Id:

ENSRNOP00000059579 ⟸ ENSRNOT00000064007

RefSeq Acc Id:	XP_038963438 ⟸ XM_039107510
- Peptide Label:	isoform X3

RefSeq Acc Id:	XP_038963437 ⟸ XM_039107509
- Peptide Label:	isoform X2

Protein Domains

RRM

Transcriptome

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

Promoters

RGD ID:

13692916

Promoter ID:

EPDNEW_R3441

Type:

multiple initiation site

Name:

Rbm28_1

Description:

RNA binding motif protein 28

SO ACC ID:

SO:0000170

Source:

EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)

Alternative Promoters:

null; see alsoEPDNEW_R3442

Experiment Methods:

Single-end sequencing.

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	4	56,438,123 - 56,438,183	EPDNEW

RGD ID:

13692924

Promoter ID:

EPDNEW_R3442

Type:

multiple initiation site

Name:

Rbm28_2

Description:

RNA binding motif protein 28

SO ACC ID:

SO:0000170

Source:

EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)

Alternative Promoters:

null; see alsoEPDNEW_R3441

Experiment Methods:

Single-end sequencing.

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	4	56,438,436 - 56,438,496	EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)

ACI/EurMcwi (MCW)

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CSV

TAB

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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)

Visual

CSV

TAB

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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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CSV

TAB

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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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CSV

TAB

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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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CSV

TAB

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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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CSV

TAB

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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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CSV

TAB

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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)

Visual

CSV

TAB

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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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CSV

TAB

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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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CSV

TAB

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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)

Visual

CSV

TAB

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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)

Visual

CSV

TAB

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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)

Visual

CSV

TAB

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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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CSV

TAB

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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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CSV

TAB

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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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CSV

TAB

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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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CSV

TAB

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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)

Visual

CSV

TAB

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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)

Visual

CSV

TAB

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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)

Visual

CSV

TAB

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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)

Visual

CSV

TAB

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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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CSV

TAB

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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)

Visual

CSV

TAB

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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)

Visual

CSV

TAB

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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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CSV

TAB

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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: Rnor_5.0

Chromosome	Start Pos	End Pos	Reference Nucleotide	Variant Nucleotide	Variant Type	Strain
4	56173567	56173568	C	T	snv	COP/CrCrl (MCW & UW), LEW/Crl (KNAW), SDLEF7/Barth (UDEL), WN/N (KNAW), LEW/NCrl (KNAW)

Assembly: Rnor_6.0

Chromosome	Start Pos	End Pos	Reference Nucleotide	Variant Nucleotide	Variant Type	Strain
4	56406786	56406787	C	T	snv	COP/CrCrl (MCW & UW), CDR, LEW/NCrlBR (RGD), LEW/Crl (RGD), WN/N (MCW)

Assembly: RGSC_v3.4

Chromosome	Start Pos	End Pos	Reference Nucleotide	Variant Nucleotide	Variant Type	Strain
4	56003638	56003639	C	T	snv	WN/N (KNAW), HCR/1Mco (UMich), COP/CrCrl (MCW & UW)

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1311336	AgrOrtholog
Ensembl Genes	ENSRNOG00000005468	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000059579	ENTREZGENE, UniProtKB/TrEMBL
	ENSRNOP00000069435	ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000064007	UniProtKB/TrEMBL
	ENSRNOT00000077079	ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH	3.30.70.330	UniProtKB/TrEMBL
InterPro	Nucleotide-bd_a/b_plait_sf	UniProtKB/TrEMBL
	RBD_domain_sf	UniProtKB/TrEMBL
	RRM_RNP1	UniProtKB/TrEMBL
KEGG Report	rno:312182	UniProtKB/TrEMBL
NCBI Gene	312182	ENTREZGENE
Pfam	RRM_1	UniProtKB/TrEMBL
PhenoGen	Rbm28	PhenoGen
PROSITE	RRM	UniProtKB/TrEMBL
SMART	RRM	UniProtKB/TrEMBL
Superfamily-SCOP	SSF54928	UniProtKB/TrEMBL
UniProt	A0A0G2JVD0	ENTREZGENE, UniProtKB/TrEMBL
	D4A5K7	ENTREZGENE, UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2008-04-30	Rbm28	RNA binding motif protein 28	Rbm28_predicted	RNA binding motif protein 28 (predicted)	'predicted' is removed	2292626	APPROVED
2005-01-12	Rbm28_predicted	RNA binding motif protein 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)

Imported Disease Annotations - ClinVar

Imported Disease Annotations - OMIM

RGD Manual Annotations

Imported Annotations - KEGG (archival)