Oma1 (OMA1 zinc metallopeptidase)

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Gene: Oma1 (OMA1 zinc metallopeptidase) Rattus norvegicus

Analyze

Symbol:

Oma1

Name:

OMA1 zinc metallopeptidase

RGD ID:

1304821

Description:

Predicted to have metalloendopeptidase activity. Predicted to be involved in several processes, including mitochondrion organization; proteolysis; and regulation of mitochondrion organization. Predicted to localize to mitochondrial inner membrane. Orthologous to human OMA1 (OMA1 zinc metallopeptidase); INTERACTS WITH (+)-schisandrin B; 6-propyl-2-thiouracil; acetamide.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Also known as:

LOC298282; metalloendopeptidase OMA1, mitochondrial; OMA1 homolog, zinc metallopeptidase; OMA1 homolog, zinc metallopeptidase (S. cerevisiae); overlapping with the m-AAA protease 1 homolog; RGD1304821; similar to RIKEN cDNA 2010001O09; zinc metallopeptidase homolog; zinc metallopeptidase homolog (S. cerevisiae)

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):	OMA1 (OMA1 zinc metallopeptidase)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, PhylomeDB, Treefam
Mus musculus (house mouse):	Oma1 (OMA1 zinc metallopeptidase)	HGNC	Treefam, EggNOG, OrthoMCL, NCBI, OMA, HomoloGene, Inparanoid, Panther, PhylomeDB, OrthoDB, Ensembl
Chinchilla lanigera (long-tailed chinchilla):	Oma1 (OMA1 zinc metallopeptidase)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	OMA1 (OMA1 zinc metallopeptidase)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	OMA1 (OMA1 zinc metallopeptidase)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Oma1 (OMA1 zinc metallopeptidase)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	OMA1 (OMA1 zinc metallopeptidase)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (African green monkey):	OMA1 (OMA1 zinc metallopeptidase)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Oma1 (OMA1 zinc metallopeptidase)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	OMA1 (OMA1 zinc metallopeptidase)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Mus musculus (house mouse):	Oma1 (OMA1 zinc metallopeptidase)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Saccharomyces cerevisiae (baker's yeast):	OMA1	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)
Danio rerio (zebrafish):	oma1	Alliance	DIOPT (Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|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	5	118,083,728 - 118,136,980 (+)	NCBI
Rnor_6.0 Ensembl	5	122,847,645 - 122,900,475 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	5	122,847,624 - 122,900,475 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	5	126,714,757 - 126,767,291 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	5	124,261,197 - 124,314,715 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	5	124,271,169 - 124,319,934 (+)	NCBI
Celera	5	116,654,899 - 116,707,757 (+)	NCBI		Celera
Cytogenetic Map	5	q33	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(+)-schisandrin B (EXP)

1,2-dimethylhydrazine (ISO)

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

4-\{[(5,5,8,8-tetramethyl-5,6,7,8-tetrahydronaphthalen-2-yl)carbonyl]amino\}benzoic acid (ISO)

5-aza-2'-deoxycytidine (ISO)

6-propyl-2-thiouracil (EXP)

acetamide (EXP)

benzo[a]pyrene (ISO)

bisphenol A (EXP)

carbamazepine (ISO)

carbon nanotube (ISO)

cisplatin (ISO)

copper(II) sulfate (ISO)

cyclosporin A (ISO)

dibutyl phthalate (EXP,ISO)

dicrotophos (ISO)

dorsomorphin (ISO)

entinostat (ISO)

ethanol (EXP)

fluoranthene (ISO)

formaldehyde (ISO)

linsidomine (EXP)

methamphetamine (EXP)

methyl methanesulfonate (ISO)

methylmercury chloride (ISO)

paracetamol (ISO)

phenobarbital (ISO)

pirinixic acid (EXP)

quercetin (ISO)

quercitrin (ISO)

SB 431542 (ISO)

sunitinib (ISO)

tetrachloromethane (EXP,ISO)

tris(2-butoxyethyl) phosphate (ISO)

valproic acid (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

cristae formation (ISO)

diet induced thermogenesis (ISO,ISS)

energy homeostasis (ISO,ISS)

glucose metabolic process (ISO,ISS)

HRI-mediated signaling (ISO,ISS)

integrated stress response signaling (ISO,ISS)

lipid metabolic process (ISO,ISS)

mitochondrial protein processing (ISO,ISS)

mitochondrial respiratory chain complex assembly (ISO,ISS)

mitochondrion organization (ISO)

negative regulation of mitochondrial fusion (ISO,ISS)

positive regulation of apoptotic process (ISO,ISS)

positive regulation of cold-induced thermogenesis (ISO,ISS)

protein autoprocessing (ISO,ISS)

protein quality control for misfolded or incompletely synthesized proteins (ISO,ISS)

regulation of cristae formation (ISO,ISS)

zymogen activation (ISO,ISS)

Cellular Component

integral component of membrane (IEA)

mitochondrial inner membrane (ISO,ISS)

mitochondrial membrane (ISO,ISS)

mitochondrion (ISO)

Molecular Function

lipid binding (IEA)

metal ion binding (IEA)

metalloendopeptidase activity (ISO,ISS)

References

References - curated


1.	MGD data from the GO Consortium
2.	Quirós PM, etal., EMBO J. 2012 May 2;31(9):2117-33. doi: 10.1038/emboj.2012.70. Epub 2012 Mar 20.
3.	RGD automated import pipeline for gene-chemical interactions

Additional References at PubMed

PMID:18614015	PMID:20038677	PMID:20038678	PMID:25605331

Genomics

Comparative Map Data

Oma1
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	5	118,083,728 - 118,136,980 (+)	NCBI
Rnor_6.0 Ensembl	5	122,847,645 - 122,900,475 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	5	122,847,624 - 122,900,475 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	5	126,714,757 - 126,767,291 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	5	124,261,197 - 124,314,715 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	5	124,271,169 - 124,319,934 (+)	NCBI
Celera	5	116,654,899 - 116,707,757 (+)	NCBI		Celera
Cytogenetic Map	5	q33	NCBI

OMA1
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	1	58,415,384 - 58,546,802 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	1	58,480,719 - 58,546,726 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	1	58,946,391 - 59,012,398 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	1	58,718,979 - 58,785,034 (-)	NCBI	NCBI36		hg18	NCBI36
Build 34	1	58,658,412 - 58,724,467	NCBI
Celera	1	57,230,483 - 57,296,551 (-)	NCBI
Cytogenetic Map	1	p32.2-p32.1	NCBI
HuRef	1	57,056,927 - 57,123,029 (-)	NCBI		HuRef
CHM1_1	1	59,060,902 - 59,127,834 (-)	NCBI		CHM1_1

Oma1
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	4	103,169,072 - 103,229,066 (+)	NCBI	GRCm39		mm39
GRCm39 Ensembl	4	103,171,009 - 103,229,065 (+)	Ensembl
GRCm38	4	103,311,875 - 103,371,869 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	4	103,313,812 - 103,371,868 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	4	102,986,451 - 103,039,033 (+)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	4	102,811,778 - 102,864,360 (+)	NCBI			mm8
Celera	4	101,671,650 - 101,724,301 (+)	NCBI		Celera
Cytogenetic Map	4	C6	NCBI

Oma1
(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_004955464	1,305,802 - 1,393,788 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955464	1,305,802 - 1,393,190 (+)	NCBI	ChiLan1.0	ChiLan1.0

OMA1
(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	1	59,253,869 - 59,516,474 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	1	59,448,436 - 59,516,170 (-)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	1	57,549,404 - 57,811,246 (-)	NCBI	Mhudiblu_PPA_v0		panPan3

OMA1
(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	5	51,134,685 - 51,213,673 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
CanFam3.1	5	51,143,437 - 51,213,913 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1

Oma1
(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_004936522	3,232,877 - 3,294,832 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

OMA1
(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	153,882,461 - 153,950,477 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	6	153,882,398 - 153,950,460 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	6	141,476,698 - 141,544,839 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

OMA1
(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	20	74,435,190 - 74,500,220 (+)	NCBI
ChlSab1.1 Ensembl	20	74,442,696 - 74,499,969 (+)	Ensembl

Oma1
(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_004624862	1,745,188 - 1,823,261 (+)	NCBI

Position Markers

RH134945

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	5	122,900,239 - 122,900,446	NCBI	Rnor6.0
Rnor_5.0	5	126,767,055 - 126,767,262	UniSTS	Rnor5.0
RGSC_v3.4	5	124,314,479 - 124,314,686	UniSTS	RGSC3.4
Celera	5	116,707,521 - 116,707,728	UniSTS
Cytogenetic Map	5	q34	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
70212	Niddm25	Non-insulin dependent diabetes mellitus QTL 25	3.54		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	5	1	136640934	Rat
2290448	Scl54	Serum cholesterol level QTL 54	2.93		blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	5	31926122	136640934	Rat
1641912	Alcrsp18	Alcohol response QTL 18			response to alcohol trait (VT:0010489)	duration of loss of righting reflex (CMO:0002289)	5	35788756	147487820	Rat
1549845	Scl44	Serum cholesterol level QTL 44	6		blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	5	40777918	154732375	Rat
1331801	Rf33	Renal function QTL 33	4.149		kidney blood vessel physiology trait (VT:0100012)	absolute change in renal vascular resistance (CMO:0001900)	5	44404276	134502294	Rat
1578766	Tcas11	Tongue tumor susceptibility QTL 11	4.12		tongue integrity trait (VT:0010553)	number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)	5	47745646	167946134	Rat
1576312	Emca8	Estrogen-induced mammary cancer QTL 8	4.1		mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	5	51418671	147487820	Rat
70189	Mcs5	Mammary carcinoma susceptibility QTL 5	10.51		mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	5	56991667	137729065	Rat
1358895	Bp254	Blood pressure QTL 254	3.6	0.0003	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	5	60072951	133313852	Rat
61426	Scl2	Serum cholesterol level QTL 2	7.3	0.001	blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	5	61086525	149030144	Rat
61393	Bp7	Blood pressure QTL 7	4.5	0.0001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	5	61612600	168109659	Rat
2306971	Anxrr21	Anxiety related response QTL 21	9.47		fear/anxiety-related behavior trait (VT:1000241)	number of entries into a discrete space in an experimental apparatus (CMO:0000960)	5	65696672	129038896	Rat
1354598	Srn6	Serum renin concentration QTL 6	3.8		blood renin amount (VT:0003349)	plasma renin activity level (CMO:0000116)	5	71552569	157225114	Rat
1298070	Scl18	Serum cholesterol level QTL 18	3.7		blood LDL cholesterol amount (VT:0000181)	calculated plasma low density lipoprotein cholesterol level (CMO:0001245)	5	83424556	128424556	Rat
1598846	Bp293	Blood pressure QTL 293	3.9		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	5	83424556	128424556	Rat
1598859	Cm66	Cardiac mass QTL 66	2		heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	5	83424556	128424556	Rat
1302790	Scl20	Serum cholesterol level QTL 20	6.4	0.0001	blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	5	84963058	173504662	Rat
1298086	Bp156	Blood pressure QTL 156			arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	5	89502294	134502294	Rat
7411582	Foco3	Food consumption QTL 3	7.5	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	5	91585539	136585539	Rat
7411601	Foco12	Food consumption QTL 12	19.7	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	5	91585539	136585539	Rat
7411564	Bw135	Body weight QTL 135		0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	5	91585539	136585539	Rat
6903316	Bw113	Body weight QTL 113	2	0.0103	body mass (VT:0001259)	body weight (CMO:0000012)	5	91884213	136884213	Rat
1358889	Bp261	Blood pressure QTL 261	2.86		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	5	93037304	133313852	Rat
1358909	Kidm25	Kidney mass QTL 25	1.87		kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	5	93037304	133313852	Rat
631527	Tls1	T-lymphoma susceptibility QTL 1	0	0.001	thymus integrity trait (VT:0010555)	post-insult time to onset of T-cell lymphoma (CMO:0001907)	5	93273130	138273130	Rat
61452	Ciaa5	CIA Autoantibody QTL 5	3.5		blood autoantibody amount (VT:0003725)	calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)	5	97921932	149030144	Rat
1331796	Thshl2	Thyroid stimulating hormone level QTL 2	2.3		blood thyroid-stimulating hormone amount (VT:0005119)	serum thyroid stimulating hormone level (CMO:0001248)	5	100723739	153577831	Rat
2317753	Glom24	Glomerulus QTL 24	3.1		kidney glomerulus integrity trait (VT:0010546)	kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)	5	101265591	141912026	Rat
1582212	Livw2	Liver weight QTL 2	3.5	0.0004	liver mass (VT:0003402)	liver weight as percentage of body weight (CMO:0000141)	5	102498468	123852688	Rat
1358187	Emca1	Estrogen-induced mammary cancer QTL 1	4.4		mammary gland integrity trait (VT:0010552)	post-insult time to mammary tumor formation (CMO:0000345)	5	102945579	154732228	Rat
1578673	Bmd13	Bone mineral density QTL 13	4.9		femur mineral mass (VT:0010011)	trabecular volumetric bone mineral density (CMO:0001729)	5	107119214	152119214	Rat
2317056	Wbc3	White blood cell count QTL 3	2.51	0.01	leukocyte quantity (VT:0000217)	white blood cell count (CMO:0000027)	5	111278451	156278451	Rat
1549838	Bss4	Bone structure and strength QTL 4	9.2		femur strength trait (VT:0010010)	femur midshaft polar moment of inertia (CMO:0001669)	5	112279412	157279412	Rat
7207481	Bss106	Bone structure and strength QTL 106	7.9		femur strength trait (VT:0010010)	femur ultimate force (CMO:0001675)	5	112279412	157279412	Rat
7207486	Bss109	Bone structure and strength QTL 109			femur strength trait (VT:0010010)	femur total energy absorbed before break (CMO:0001677)	5	112279412	157279412	Rat
7207488	Bss110	Bone structure and strength QTL 1	8.4		femur strength trait (VT:0010010)	femur stiffness (CMO:0001674)	5	112279412	157279412	Rat
7207491	Bss112	Bone structure and strength QTL 112	7		femur morphology trait (VT:0000559)	femur midshaft cortical cross-sectional area (CMO:0001663)	5	112279412	157279412	Rat
1298089	Scl14	Serum cholesterol level QTL 14	5.8	0.0004	blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	5	114140832	159140832	Rat
1598847	Cm62	Cardiac mass QTL 62	3.4		heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	5	114140832	159140832	Rat
8552960	Pigfal15	Plasma insulin-like growth factor 1 level QTL 15			blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	5	116767924	161767924	Rat
8694198	Abfw3	Abdominal fat weight QTL 3	16.13	0.001	visceral adipose mass (VT:0010063)	abdominal fat pad weight to body weight ratio (CMO:0000095)	5	116767924	161767924	Rat
8694389	Bw160	Body weight QTL 160	6.17	0.001	body lean mass (VT:0010483)	lean tissue morphological measurement (CMO:0002184)	5	116767924	161767924	Rat
8694441	Bw169	Body weight QTL 169	17.61	0.001	retroperitoneal fat pad mass (VT:0010430)	retroperitoneal fat pad weight to body weight ratio (CMO:0000635)	5	116767924	161767924	Rat
7794739	Bp372	Blood pressure QTL 372		0.0058	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	5	122679716	130167412	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	93
Count of miRNA genes:	75
Interacting mature miRNAs:	81
Transcripts:	ENSRNOT00000009516
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	3	13	29	22	17	22	7	10	6	29	17	2	7
Low		30	28	19	2	19	1	1	68	6	22	9	1
Below cutoff											2

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001106669	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	CH473998	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000162	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000009516 ⟹ ENSRNOP00000009515

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	5	122,847,645 - 122,900,475 (+)	Ensembl

RefSeq Acc Id:

NM_001106669 ⟹ NP_001100139

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	5	118,083,728 - 118,136,980 (+)	NCBI
Rnor_6.0	5	122,847,645 - 122,900,475 (+)	NCBI
Rnor_5.0	5	126,714,757 - 126,767,291 (+)	NCBI
RGSC_v3.4	5	124,261,197 - 124,314,715 (+)	RGD
Celera	5	116,654,899 - 116,707,757 (+)	RGD

Sequence:

show sequence

GCCTGCGCGGAGCCAGCAGCTGGATCCGGCTCCGGCTGCGGCTCGAGTGCGCGCTCACGATAAC
CAAGCAGAGGTAAGATGAACTTCCTTTATGGACTGCAGTCTGCCACAAGAAATCAGTTTCTCTC
TGGAGTGAATACGCTGGCCCGCAGGAGAACGTGGACCCCACCAGCAGGCTGTCCACTGGCATCG
AGGCTCCCAGCAGTAAATGCAAACTGGGGACTTAGCACAGTCAGTCACTGTTATTCAGTGATCT
TACTGCCCAGAAACCTTCATTTCTGTAGGACTCTCAAGAACAAAAGATCAAGATGCCTCTCAAG
TGCCCAAAGCAAGGAAATGGGGGTGCTCACCTACAATTGGACGGTTTGGGGTGATGCCTCATGT
TCTCCGAACTATGCCGCCATAAGAGAGGTCCGGAGTTTCCACACATCTGCGCCACGTCAGGCCG
CTCCAGTCCCTCTCTTGATGCTCATTCTGAAACCAGTGCAAAAGCTCCTTGCTATCATTGTGGG
CAGGGGCATAAGGAAATGGTGGCAAGCACTTCCCCCTGACAAGAAGGCGCTATTTAAAGACAGC
GTGAAGAGGAACAAGTGGAGGCTGCTCCTTGGTCTGAGTGCCTTTGGACTGCTGTTTGTGGTGT
TTTATTTCACTCACCTGGAAGTGAGCCCTGTCACTGGAAGGAGCAAACTACTGTTAGTGGGGAA
AGAACACTTCAGACTCCTGTCAGACCTGGAATATGAAGTGTGGATGGAAGAGTTTAAAAATGAT
CTGCTGCCTGAGGAAGACCCCCGGTACCTGACTGTCAAGAAGGTGGTTTATCATCTAACACAGT
GCAATCAAGATGTCCCAGGGGTCTCTGAGATCAACTGGGTGGTTCACGTGGTCCATTCGCCCAA
GGTCAATGCCTTCGTGCTTCCAAACGGACAAGTGTTTGTTTTCACTGGGCTTTTGAATAGCGTG
ACCGATATGCACCAGCTTTCCTTCCTCCTGGGCCATGAGATCGCGCATGCGGTCCTGGGGCATG
CCGCAGAAAAGGCTAGCTTGGTTCATTTACTGGATTTCCTTGGCATGATTTTTCTCACAATGAT
TTGGGCCATTTGTCCAAGAGACAGCTTGGCAGTTCTGGGCCAGTGGATACAGTCAAAGTTGCAG
GAGTATATGTTTGATAGACCATACAGTAGAACATTGGAGGCCGAAGCTGACAAAATTGGACTAC
AGCTGGCTGCAAAGGCATGTGTGGACGTAAGAGCTAGTTCAGTGTTTTGGCAGCAGATGGAGTT
CTCAGAGAGCCTTCATGGCTACCCCAAGTTGCCAGAGTGGCTATCAACACATCCTTCTCACGGG
AACCGAGCTGAGTACTTGGACAGACTCATACCACAGGCTCTCAAACTTCGGGAGGTCTGTAATT
GCCCACCACTCTCTGGACCAGACCCTCGGTTACTGTTCAGACTTACTGTGAAACATTTACTTGA
AGACTCCGAGAAAGAGGACCTAAACATCACTGTCAAAAAGCAGAAACCGGATGCTCTGCCCATT
CAGAAGCAGGAGCAGATACCACTGACATACGCACTTGGGAAAAGAACTGCAGGTTGAACTGAAC
CGAATGAATCTTGGGTTCCGTGAGGAGCACAGTGAGCCTTTTCATTCTTATGCAACTCTCAAAA
ACGATGTTTTCAAGGAAAAAAATGGATGTTCAAAGATCAAATCATGTATATTACAGATAATATC
CGGATTTTTCTAGATTTTTATCTTTCATGAAATATTGATGTGTTTTAATCTACTTTAAAATACT
GCCAACGAGGACAATGTCACAGAATAAATCGATGTTACGCATTTCAC

hide sequence

RefSeq Acc Id:

XM_006238475 ⟹ XP_006238537

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	5	122,847,750 - 122,900,472 (+)	NCBI
Rnor_5.0	5	126,714,757 - 126,767,291 (+)	NCBI

Sequence:

show sequence

GGGGAGCGGGGCCGGGGGGTTCGGGGACTGCGGTGGGCATGGACCGTGCCGAGTCAGAGTGAAC
GGCCCGGTGGGTGGGCTTTCTATAACCAAGCAGAGGTAAGATGAACTTCCTTTATGGACTGCAG
TCTGCCACAAGAAATCAGTTTCTCTCTGGAGTGAATACGCTGGCCCGCAGGAGAACGTGGACCC
CACCAGCAGGCTGTCCACTGGCATCGAGGCTCCCAGCAGTAAATGCAAACTGGGGACTTAGCAC
AGTCAGTCACTGTTATTCAGTGATCTTACTGCCCAGAAACCTTCATTTCTGTAGGACTCTCAAG
AACAAAAGATCAAGATGCCTCTCAAGTGCCCAAAGCAAGGAAATGGGGGTGCTCACCTACAATT
GGACGGTTTGGGGTGATGCCTCATGTTCTCCGAACTATGCCGCCATAAGAGAGGTCCGGAGTTT
CCACACATCTGCGCCACGTCAGGCCGCTCCAGTCCCTCTCTTGATGCTCATTCTGAAACCAGTG
CAAAAGCTCCTTGCTATCATTGTGGGCAGGGGCATAAGGAAATGGTGGCAAGCACTTCCCCCTG
ACAAGAAGGCGCTATTTAAAGACAGCGTGAAGAGGAACAAGTGGAGGCTGCTCCTTGGTCTGAG
TGCCTTTGGACTGCTGTTTGTGGTGTTTTATTTCACTCACCTGGAAGTGAGCCCTGTCACTGGA
AGGAGCAAACTACTGTTAGTGGGGAAAGAACACTTCAGACTCCTGTCAGACCTGGAATATGAAG
TGTGGATGGAAGAGTTTAAAAATGATCTGCTGCCTGAGGAAGACCCCCGGTACCTGACTGTCAA
GAAGGTGGTTTATCATCTAACACAGTGCAATCAAGATGTCCCAGGGGTCTCTGAGATCAACTGG
GTGGTTCACGTGGTCCATTCGCCCAAGGTCAATGCCTTCGTGCTTCCAAACGGACAAGTGTTTG
TTTTCACTGGGCTTTTGAATAGCGTGACCGATATGCACCAGCTTTCCTTCCTCCTGGGCCATGA
GATCGCGCATGCGGTCCTGGGGCATGCCGCAGAAAAGGCTAGCTTGGTTCATTTACTGGATTTC
CTTGGCATGATTTTTCTCACAATGATTTGGGCCATTTGTCCAAGAGACAGCTTGGCAGTTCTGG
GCCAGTGGATACAGTCAAAGTTGCAGGAGTATATGTTTGATAGACCATACAGTAGAACATTGGA
GGCCGAAGCTGACAAAATTGGACTACAGCTGGCTGCAAAGGCATGTGTGGACGTAAGAGCTAGT
TCAGTGTTTTGGCAGCAGATGGAGTTCTCAGAGAGCCTTCATGGCTACCCCAAGTTGCCAGAGT
GGCTATCAACACATCCTTCTCACGGGAACCGAGCTGAGTACTTGGACAGACTCATACCACAGGC
TCTCAAACTTCGGGAGGTCTGTAATTGCCCACCACTCTCTGGACCAGACCCTCGGTTACTGTTC
AGACTTACTGTGAAACATTTACTTGAAGACTCCGAGAAAGAGGACCTAAACATCACTGTCAAAA
AGCAGAAACCGGATGCTCTGCCCATTCAGAAGCAGGAGCAGATACCACTGACATACGCACTTGG
GAAAAGAACTGCAGGTTGAACTGAACCGAATGAATCTTGGGTTCCGTGAGGAGCACAGTGAGCC
TTTTCATTCTTATGCAACTCTCAAAAACGATGTTTTCAAGGAAAAAAATGGATGTTCAAAGATC
AAATCATGTATATTACAGATAATATCCGGATTTTTCTAGATTTTTATCTTTCATGAAATATTGA
TGTGTTTTAATCTACTTTAAAATACTGCCAACGAGGACAATGTCACAGAATAAATCGATGTTAC
GCATTT

hide sequence

RefSeq Acc Id:

XM_006238476 ⟹ XP_006238538

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	5	122,847,624 - 122,900,472 (+)	NCBI
Rnor_5.0	5	126,714,757 - 126,767,291 (+)	NCBI

Sequence:

show sequence

CGGGGCTTGGAAAAGACGTGCGCCTGCGCGGAGCCAGCAGCTGGATCCGGCTCCGGCTGCGGCT
CGAGTGCGCGCTCACGATAACCAAGCAGAGGTAAGATGAACTTCCTTTATGGACTGCAGTCTGC
CACAAGAAATCAGTTTCTCTCTGGAGTGAATACGCTGGCCCGCAGGAGAACGTGGACCCCACCA
GCAGGCTGTCCACTGGCATCGAGGCTCCCAGCAGTAAATGCAAACTGGGGACTTAGCACAGTCA
GTCACTGTTATTCAGTGATCTTACTGCCCAGAAACCTTCATTTCTGTAGGACTCTCAAGAACAA
AAGATCAAGATGCCTCTCAAGTGCCCAAAGCAAGGAAATGGGGGTGCTCACCTACAATTGGACG
GTTTGGGGTGATGCCTCATGTTCTCCGAACTATGCCGCCATAAGAGAGGTCCGGAGTTTCCACA
CATCTGCGCCACGTCAGGCCGCTCCAGTCCCTCTCTTGATGCTCATTCTGAAACCAGTGCAAAA
GCTCCTTGCTATCATTGTGGGCAGGGGCATAAGGAAATGGTGGCAAGCACTTCCCCCTGACAAG
AAGGCGCTATTTAAAGACAGCGTGAAGAGGAACAAGTGGAGGCTGCTCCTTGGTCTGAGTGCCT
TTGGACTGCTGTTTGTGGTGTTTTATTTCACTCACCTGGAAGTGAGCCCTGTCACTGGAAGGAG
CAAACTACTGTTAGTGGGGAAAGAACACTTCAGACTCCTGTCAGACCTGGAATATGAAGTGTGG
ATGGAAGAGTTTAAAAATGATCTGCTGCCTGAGGAAGACCCCCGGTACCTGACTGTCAAGAAGG
TGGTTTATCATCTAACACAGTGCAATCAAGATGTCCCAGGGGTCTCTGAGATCAACTGGGTGGT
TCACGTGGTCCATTCGCCCAAGGTCAATGCCTTCGTGCTTCCAAACGGACAAGTGTTTGTTTTC
ACTGGGCTTTTGAATAGCGTGACCGATATGCACCAGCTTTCCTTCCTCCTGGGCCATGAGATCG
CGCATGCGGTCCTGGGGCATGCCGCAGAAAAGGCTAGCTTGGTTCATTTACTGGATTTCCTTGG
CATGATTTTTCTCACAATGATTTGGGCCATTTGTCCAAGAGACAGCTTGGCAGTTCTGGGCCAG
TGGATACAGTCAAAGTTGCAGGAGTATATGTTTGATAGACCATACAGTAGAACATTGGAGGCCG
AAGCTGACAAAATTGGACTACAGCTGGCTGCAAAGGCTCTCAAACTTCGGGAGGTCTGTAATTG
CCCACCACTCTCTGGACCAGACCCTCGGTTACTGTTCAGACTTACTGTGAAACATTTACTTGAA
GACTCCGAGAAAGAGGACCTAAACATCACTGTCAAAAAGCAGAAACCGGATGCTCTGCCCATTC
AGAAGCAGGAGCAGATACCACTGACATACGCACTTGGGAAAAGAACTGCAGGTTGAACTGAACC
GAATGAATCTTGGGTTCCGTGAGGAGCACAGTGAGCCTTTTCATTCTTATGCAACTCTCAAAAA
CGATGTTTTCAAGGAAAAAAATGGATGTTCAAAGATCAAATCATGTATATTACAGATAATATCC
GGATTTTTCTAGATTTTTATCTTTCATGAAATATTGATGTGTTTTAATCTACTTTAAAATACTG
CCAACGAGGACAATGTCACAGAATAAATCGATGTTACGCATTT

hide sequence

Protein Sequences


Protein RefSeqs	NP_001100139	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	D3ZS74	(Get FASTA)	NCBI Sequence Viewer
	EDL97870	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_001100139 ⟸ NM_001106669

- UniProtKB:

D3ZS74 (UniProtKB/Swiss-Prot)

- Sequence:

show sequence

MNFLYGLQSATRNQFLSGVNTLARRRTWTPPAGCPLASRLPAVNANWGLSTVSHCYSVILLPRN
LHFCRTLKNKRSRCLSSAQSKEMGVLTYNWTVWGDASCSPNYAAIREVRSFHTSAPRQAAPVPL
LMLILKPVQKLLAIIVGRGIRKWWQALPPDKKALFKDSVKRNKWRLLLGLSAFGLLFVVFYFTH
LEVSPVTGRSKLLLVGKEHFRLLSDLEYEVWMEEFKNDLLPEEDPRYLTVKKVVYHLTQCNQDV
PGVSEINWVVHVVHSPKVNAFVLPNGQVFVFTGLLNSVTDMHQLSFLLGHEIAHAVLGHAAEKA
SLVHLLDFLGMIFLTMIWAICPRDSLAVLGQWIQSKLQEYMFDRPYSRTLEAEADKIGLQLAAK
ACVDVRASSVFWQQMEFSESLHGYPKLPEWLSTHPSHGNRAEYLDRLIPQALKLREVCNCPPLS
GPDPRLLFRLTVKHLLEDSEKEDLNITVKKQKPDALPIQKQEQIPLTYALGKRTAG

hide sequence

RefSeq Acc Id:

XP_006238538 ⟸ XM_006238476

- Peptide Label:

isoform X2

- Sequence:

show sequence

MNFLYGLQSATRNQFLSGVNTLARRRTWTPPAGCPLASRLPAVNANWGLSTVSHCYSVILLPRN
LHFCRTLKNKRSRCLSSAQSKEMGVLTYNWTVWGDASCSPNYAAIREVRSFHTSAPRQAAPVPL
LMLILKPVQKLLAIIVGRGIRKWWQALPPDKKALFKDSVKRNKWRLLLGLSAFGLLFVVFYFTH
LEVSPVTGRSKLLLVGKEHFRLLSDLEYEVWMEEFKNDLLPEEDPRYLTVKKVVYHLTQCNQDV
PGVSEINWVVHVVHSPKVNAFVLPNGQVFVFTGLLNSVTDMHQLSFLLGHEIAHAVLGHAAEKA
SLVHLLDFLGMIFLTMIWAICPRDSLAVLGQWIQSKLQEYMFDRPYSRTLEAEADKIGLQLAAK
ALKLREVCNCPPLSGPDPRLLFRLTVKHLLEDSEKEDLNITVKKQKPDALPIQKQEQIPLTYAL
GKRTAG

hide sequence

RefSeq Acc Id:

XP_006238537 ⟸ XM_006238475

- Peptide Label:

isoform X1

- Sequence:

show sequence

MNFLYGLQSATRNQFLSGVNTLARRRTWTPPAGCPLASRLPAVNANWGLSTVSHCYSVILLPRN
LHFCRTLKNKRSRCLSSAQSKEMGVLTYNWTVWGDASCSPNYAAIREVRSFHTSAPRQAAPVPL
LMLILKPVQKLLAIIVGRGIRKWWQALPPDKKALFKDSVKRNKWRLLLGLSAFGLLFVVFYFTH
LEVSPVTGRSKLLLVGKEHFRLLSDLEYEVWMEEFKNDLLPEEDPRYLTVKKVVYHLTQCNQDV
PGVSEINWVVHVVHSPKVNAFVLPNGQVFVFTGLLNSVTDMHQLSFLLGHEIAHAVLGHAAEKA
SLVHLLDFLGMIFLTMIWAICPRDSLAVLGQWIQSKLQEYMFDRPYSRTLEAEADKIGLQLAAK
ACVDVRASSVFWQQMEFSESLHGYPKLPEWLSTHPSHGNRAEYLDRLIPQALKLREVCNCPPLS
GPDPRLLFRLTVKHLLEDSEKEDLNITVKKQKPDALPIQKQEQIPLTYALGKRTAG

hide sequence

RefSeq Acc Id:

ENSRNOP00000009515 ⟸ ENSRNOT00000009516

Transcriptome

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

Promoters

RGD ID:

13693868

Promoter ID:

EPDNEW_R4393

Type:

single initiation site

Name:

Oma1_1

Description:

OMA1 zinc metallopeptidase

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	5	122,847,666 - 122,847,726	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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CSV

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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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CSV

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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: Rnor_5.0

Chromosome	Start Pos	End Pos	Reference Nucleotide	Variant Nucleotide	Variant Type	Strain
5	126719520	126719521	G	A	snv	LE/Stm (Illumina) (KNAW), LEC/Tj (KyushuU), LE/Stm (KyushuU), LE/Stm (SOLiD) (KNAW)

Assembly: Rnor_6.0

Chromosome	Start Pos	End Pos	Reference Nucleotide	Variant Nucleotide	Variant Type	Strain
5	122852408	122852409	G	A	snv	LE/Stm (RGD)

Assembly: RGSC_v3.4

Chromosome	Start Pos	End Pos	Reference Nucleotide	Variant Nucleotide	Variant Type	Strain
5	124265959	124265960	G	A	snv	LE/Stm (ICL), LE/Stm (KNAW)

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1304821	AgrOrtholog
Ensembl Genes	ENSRNOG00000007214	Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein	ENSRNOP00000009515	ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript	ENSRNOT00000009516	ENTREZGENE, UniProtKB/Swiss-Prot
InterPro	Peptidase_M48	UniProtKB/Swiss-Prot
KEGG Report	rno:298282	UniProtKB/Swiss-Prot
NCBI Gene	298282	ENTREZGENE
Pfam	Peptidase_M48	UniProtKB/Swiss-Prot
PhenoGen	Oma1	PhenoGen
UniProt	D3ZS74	ENTREZGENE, UniProtKB/Swiss-Prot

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2013-11-19	Oma1	OMA1 zinc metallopeptidase	Oma1	zinc metallopeptidase homolog (S. cerevisiae)	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2012-10-05	Oma1	zinc metallopeptidase homolog (S. cerevisiae)	Oma1	OMA1 homolog, zinc metallopeptidase (S. cerevisiae)	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2008-04-30	Oma1	OMA1 homolog, zinc metallopeptidase (S. cerevisiae)	Oma1_predicted	OMA1 homolog, zinc metallopeptidase (S. cerevisiae) (predicted)	'predicted' is removed	2292626	APPROVED
2006-03-30	Oma1_predicted	OMA1 homolog, zinc metallopeptidase (S. cerevisiae) (predicted)	RGD1304821_predicted	similar to RIKEN cDNA 2010001O09 (predicted)	Symbol and Name updated	1299863	APPROVED
2005-01-20	RGD1304821_predicted	similar to RIKEN cDNA 2010001O09 (predicted)	LOC298282_predicted		Symbol and Name status set to approved	1331353	APPROVED
2005-01-12	LOC298282_predicted	similar to RIKEN cDNA 2010001O09 (predicted)			Symbol and Name status set to provisional	70820	PROVISIONAL

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)