C8a (complement C8 alpha chain) - Rat Genome Database

Name: C8a
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

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Gene: C8a (complement C8 alpha chain) Rattus norvegicus

Analyze

Symbol:

C8a

Name:

complement C8 alpha chain

RGD ID:

1308355

Description:

Exhibits complement binding activity. Predicted to be involved in complement activation. Localizes to extracellular space. Biomarker of myocardial infarction. Human ortholog(s) of this gene implicated in type I complement component 8 deficiency. Orthologous to human C8A (complement C8 alpha chain); PARTICIPATES IN coagulation cascade pathway; complement system pathway; Entamoebiasis pathway; INTERACTS WITH (+)-schisandrin B; 2,4-dinitrotoluene; 2,6-dinitrotoluene.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Also known as:

complement component 8 alpha subunit; complement component 8, alpha polypeptide; complement component C8 alpha chain; LOC298288

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):	C8A (complement C8 alpha chain)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, Panther, Treefam
Mus musculus (house mouse):	C8a (complement component 8, alpha polypeptide)	HGNC	Treefam, EggNOG, NCBI, OMA, HomoloGene, Inparanoid, Panther, OrthoDB, Ensembl
Chinchilla lanigera (long-tailed chinchilla):	C8a (complement C8 alpha chain)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	C8A (complement C8 alpha chain)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	C8A (complement C8 alpha chain)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	C8a (complement C8 alpha chain)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	C8A (complement C8 alpha chain)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (African green monkey):	C8A (complement C8 alpha chain)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	C8a (complement C8 alpha chain)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Other homologs ²
Homo sapiens (human):	C7 (complement C7)	HGNC	OrthoDB
Homo sapiens (human):	C9 (complement C9)	HGNC	OrthoDB
Homo sapiens (human):	C8B (complement C8 beta chain)	HGNC	OrthoDB
Homo sapiens (human):	C6 (complement C6)	HGNC	OrthoDB
Alliance orthologs ³
Homo sapiens (human):	C8A (complement C8 alpha chain)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|TreeFam)
Mus musculus (house mouse):	C8a (complement component 8, alpha polypeptide)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|TreeFam)
Danio rerio (zebrafish):	c8a (complement component 8, alpha polypeptide)	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	119,583,168 - 119,637,675 (-)	NCBI
Rnor_6.0 Ensembl	5	124,348,461 - 124,403,195 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	5	124,348,536 - 124,403,117 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	5	128,207,204 - 128,261,785 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	5	125,776,549 - 125,831,049 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	5	125,783,597 - 125,836,315 (-)	NCBI
Celera	5	118,140,155 - 118,194,619 (-)	NCBI		Celera
Cytogenetic Map	5	q34	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

meningitis (ISO)

myocardial infarction (IEP)

Neisseriaceae Infections (ISO)

primary immunodeficiency disease (ISO)

type I complement component 8 deficiency (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(+)-schisandrin B (EXP)

1,1-dichloroethene (ISO)

1,2-dichloroethane (ISO)

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

2,4-dinitrotoluene (EXP)

2,6-dinitrotoluene (EXP)

3,3',4,4'-tetrachlorobiphenyl (ISO)

4,4'-diaminodiphenylmethane (ISO)

acetamide (EXP)

aflatoxin B1 (ISO)

benzo[a]pyrene (ISO)

Benzo[k]fluoranthene (ISO)

bisphenol A (EXP,ISO)

buta-1,3-diene (ISO)

cadmium dichloride (EXP)

carbon nanotube (ISO)

cobalt dichloride (EXP)

copper(II) sulfate (ISO)

cyclosporin A (ISO)

decabromodiphenyl ether (EXP)

dichloroacetic acid (ISO)

dicrotophos (ISO)

disodium selenite (ISO)

endosulfan (EXP)

flutamide (EXP)

genistein (ISO)

methotrexate (ISO)

mono(2-ethylhexyl) phthalate (ISO)

N-Nitrosopyrrolidine (ISO)

nefazodone (EXP)

nickel atom (ISO)

nimesulide (EXP)

O-methyleugenol (ISO)

paracetamol (ISO)

perfluorononanoic acid (ISO)

perfluorooctane-1-sulfonic acid (ISO)

perfluorooctanoic acid (ISO)

phenobarbital (ISO)

pirinixic acid (ISO)

potassium dichromate (ISO)

quercetin (ISO)

sodium arsenite (ISO)

tamoxifen (ISO)

tetrachloromethane (EXP)

tolcapone (EXP)

tris(2-butoxyethyl) phosphate (ISO)

troglitazone (ISO)

urethane (ISO)

valproic acid (ISO)

vancomycin (ISO)

zinc atom (ISO)

zinc(0) (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

complement activation (ISO)

complement activation, classical pathway (IEA)

cytolysis (IEA)

innate immune response (IEA)

Cellular Component

extracellular region (IDA)

extracellular space (IDA)

membrane attack complex (ISO)

Molecular Function

complement binding (IPI)

protein binding (ISO)

protein-containing complex binding (IPI)

Molecular Pathway Annotations Click to see Annotation Detail View

coagulation cascade pathway (IEA)

complement system pathway (IEA)

Entamoebiasis pathway (IEA)

prion disease pathway (IEA)

systemic lupus erythematosus pathway (IEA)

References

References - curated


1.	GOA data from the GO Consortium
2.	Lehto T, etal., Immunology. 1997 Jan;90(1):121-8.
3.	Ng SC and Sodetz JM, J Immunol. 1987 Nov 1;139(9):3021-7.
4.	OMIM Disease Annotation Pipeline
5.	Pipeline to import KEGG annotations from KEGG into RGD
6.	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
7.	RGD automated import pipeline for gene-chemical interactions
8.	Sawant-Mane S, etal., J Neuroimmunol. 1996 Sep;69(1-2):63-71.
9.	Vakeva A, etal., Am J Pathol. 1994 Jun;144(6):1357-68.
10.	Xiong ZQ, etal., J Neurosci. 2003 Feb 1;23(3):955-60.

Additional References at PubMed

PMID:12413696	PMID:18178252	PMID:22516433	PMID:22832194	PMID:23533145

Genomics

Comparative Map Data

C8a
(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	119,583,168 - 119,637,675 (-)	NCBI
Rnor_6.0 Ensembl	5	124,348,461 - 124,403,195 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	5	124,348,536 - 124,403,117 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	5	128,207,204 - 128,261,785 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	5	125,776,549 - 125,831,049 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	5	125,783,597 - 125,836,315 (-)	NCBI
Celera	5	118,140,155 - 118,194,619 (-)	NCBI		Celera
Cytogenetic Map	5	q34	NCBI

C8A
(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	56,854,806 - 56,918,221 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh38.p13 Ensembl	1	56,854,797 - 56,918,223 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	1	56,854,796 - 56,918,223 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	1	57,320,470 - 57,383,896 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	1	57,093,065 - 57,156,482 (+)	NCBI	NCBI36		hg18	NCBI36
Build 34	1	57,032,499 - 57,095,915	NCBI
Celera	1	55,604,960 - 55,668,425 (+)	NCBI
Cytogenetic Map	1	p32.2	NCBI
HuRef	1	55,432,491 - 55,495,955 (+)	NCBI		HuRef
CHM1_1	1	57,435,807 - 57,499,133 (+)	NCBI		CHM1_1

C8a
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	4	104,672,876 - 104,733,684 (-)	NCBI	GRCm39		mm39
GRCm39 Ensembl	4	104,672,876 - 104,733,595 (-)	Ensembl
GRCm38	4	104,815,679 - 104,876,487 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	4	104,815,679 - 104,876,398 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	4	104,488,284 - 104,549,003 (-)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	4	104,313,615 - 104,374,314 (-)	NCBI			mm8
Celera	4	103,167,290 - 103,227,258 (-)	NCBI		Celera
Cytogenetic Map	4	C6	NCBI

C8a
(Chinchilla lanigera - long-tailed chinchilla)

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0	NW_004955464	2,806,859 - 2,874,444 (-)	NCBI	ChiLan1.0	ChiLan1.0

C8A
(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	57,847,726 - 57,912,392 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	1	57,847,726 - 57,912,392 (+)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	1	56,137,596 - 56,201,975 (+)	NCBI	Mhudiblu_PPA_v0		panPan3

C8A
(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	52,584,934 - 52,653,794 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
CanFam3.1	5	52,584,707 - 52,649,612 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1

C8a
(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	4,686,306 - 4,745,175 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

C8A
(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	155,464,852 - 155,530,472 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	6	155,464,855 - 155,530,473 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	6	143,217,805 - 143,266,588 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

C8A
(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	76,045,027 - 76,111,402 (-)	NCBI
ChlSab1.1 Ensembl	20	76,043,594 - 76,110,710 (-)	Ensembl

C8a
(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	3,234,826 - 3,288,574 (-)	NCBI

Position Markers

D5Rhm4

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	5	124,357,602 - 124,357,746	NCBI	Rnor6.0
Rnor_5.0	5	128,216,270 - 128,216,414	UniSTS	Rnor5.0
RGSC_v3.4	5	125,785,615 - 125,785,759	UniSTS	RGSC3.4
Celera	5	118,149,222 - 118,149,370	UniSTS
Cytogenetic Map	5	q34	UniSTS

RH130236

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	5	124,348,581 - 124,348,760	NCBI	Rnor6.0
Rnor_5.0	5	128,207,249 - 128,207,428	UniSTS	Rnor5.0
RGSC_v3.4	5	125,776,594 - 125,776,773	UniSTS	RGSC3.4
Celera	5	118,140,200 - 118,140,379	UniSTS
RH 3.4 Map	5	717.8	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
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
1582230	Bw78	Body weight QTL 78	3.2	0.0016	epididymal fat pad mass (VT:0010421)	epididymal fat pad weight to body weight ratio (CMO:0000658)	5	123852489	133313852	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	901
Count of miRNA genes:	307
Interacting mature miRNAs:	409
Transcripts:	ENSRNOT00000067850
Prediction methods:	Microtar, Miranda, 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

	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		41	41		41					1
Low	1	6		4		2	2	2	2	6	4	2
Below cutoff	11	10		13		6	6	15	17	24	4	6

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001106670	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039109541	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	CH473998	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ211202	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ211244	(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:

ENSRNOT00000067850 ⟹ ENSRNOP00000063871

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	5	124,348,461 - 124,403,195 (-)	Ensembl

RefSeq Acc Id:

NM_001106670 ⟹ NP_001100140

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	5	119,583,174 - 119,637,675 (-)	NCBI
Rnor_6.0	5	124,348,536 - 124,403,117 (-)	NCBI
Rnor_5.0	5	128,207,204 - 128,261,785 (-)	NCBI
RGSC_v3.4	5	125,776,549 - 125,831,049 (-)	RGD
Celera	5	118,140,155 - 118,194,619 (-)	RGD

Sequence:

show sequence

TTCTTTTCCATAGATGCTAAGTGGTGACTTCTGGATGAGATGTTTACAGTTGCTTTCTTTGGTT
TGTCTCTGATGGCATGGCACTCCGGGGTAACTGCACAAGAGAAGGTGAACCAGCGGGTCACCCG
AGCTGTGACCCCAGGAGCGGTTGCCTGTCAGTTGAGTGACTGGTCAGAATGGACAGATTGTTTT
CCATGTCAGAACGAAAAGTACCGATACCGGAGCCTCTTGCAGCCAAGCAAGTTTGGAGGAACCA
TCTGCAGTGGTGATATATGGGATAAGGCCAACTGTGACAGCCCCACACCTTGTCTAAGGCAAGC
ACAGTGTGGACAGGATTTCCAGTGTAGAGAGACAGGTCGCTGCCTGAAACGCCACCTGGTATGC
AATGGAGATCAGGACTGCCTTGATGGCTCTGATGAGGATAACTGTGATGATGCCAGGGTCATTG
AAGATGATTGCCGTCAGTATGAACCAATCCCAGGATCAGAAAGGGCAGCCTTGGGGTACAATAT
CCTGACTCAAGAAGAAGGCCAGAGTGTGTATGATGCTAAGTATTATGGAGGCCAGTGTGAAACT
GTGTACAATGGAGACTGGAGAAGGCTGCAGTACGACCCCACCTGTGAGCGCCTCTACTATGGGG
AGGATGAGAAATACTTCCGGAAGCCCTACAACTTCCTTAAGTACCACTTTGAAGCCCTGGCGGA
TACTTTAATCTCTTCAGAGTTTTATGATGATGCAAATGACCTTTTTTCTAAGATACAGAGGGAC
AAATCCCAGTCAAATAGTGTAACATTTGGCATAAGCCCAGCAAAAAGTCCTATCACACTAGACG
CGTCCGTATCCTGGTCCGATGAATCTTCCTTCATGAAGGAGTTAAGCAAGTATAATGAGAAGAA
ATATAGCTTCATGAGAGTGTCCACGAAGGTACAGACGGCACATTTTAAGATGAGGAGGCACAAT
ATTGTGCTGGATGAAGGGATGATGGAGTCACTGATGGAGCTCCCAGAGCAGTTTAACTACGGCA
TGTACTCCAAGTTCATCAATGACTATGGCACCCACTACATCACCTCTGGAACCATGGGTGGCAT
TTACGAATATGTTCTGGTGCTTGACAAAGAGAAAATGAGAATTCATGGCATTACTGTGGAAGAT
GTCAAAAAATGCATCGGAGGTGGCGTTGGCCTGCAGTTTGGAGAGAAAATAATTGGTGAAGGAG
ATTTATCAGGAGAGTCTTGTGTCATGACTGGAGATGGCAACCAGGACAAAAGGAAGAAGGACTT
GGCAGTGGAGGACATCATTTCTCGGGTACAAGGTGGAAGTTCTCGCTGGAGCACTGGCTTGGCA
CACAACAGCAGTGCTATTACATACCGGTCTTGGGGGAGATCATTAAAGTATAACCCTGTTGTTA
TCGATTTTGAGATGCAGCCCATCTATCAGCTACTGCAGCACACAAACCTGGGGCCTCTGGAGAC
TAAACGTCGGAACCTGCGCAGGGCTTTGGACCAGTACCTGATGGAATTTAATGCCTGCCGCTGT
GGGCCCTGCTTCAACAATGGGGTACCCATACTCGAGGGCACCAGCTGCTCGTGTCAATGTAGCA
TGGGCCGGCAGGGCCCTGCCTGTGAGAGCATGGTATTGGAAGCGATGGAGGGAGCCAAAGCTGA
TGGTCGTTGGAGCTGCTGGAGTTCCTGGTCAGAGTGTAGAGGAGGGTCCCGGGAGAGGAGGAGA
CAGTGCAACAATCCAGCACCCCAGAATGGAGGTGCCCCATGCCTAGGGAAGAGCCTGCAGACCC
AGGCCTGCTGAGTAGCTCTGGAGGCAGACTTGGAAGGAAGCTGTAGATGCTGCTGCCTGTCCTG
GCTGCTGGTTAGGACTGATTGCTGCTCTGAGTAAATGCAAACCCACGAAGGCTGTTCCCTTCAC
ACACTCATTTTTTTTTCTAGTACCAACCTCATAATCTTTAGCCTCTACCAATAACCTGGCTCTA
GGTTGCCTCCTTGTCCCAGAGGGTCGCTACCCTTTACATCTCAGAACCACCTCCCTATCTTATT
CCATTCAGGATGCTCAATAATAAACTGGGTGTGGTTTAGACACATCAGAAATAATTCCTCACAA
TTCTGGAGGCATAAACTGCAAGATGAAGGTTCCAGCAGGTCTAGGGTCTGGAGAGGCTGTGTTC
TATTTTATATATGTCCTTTCATTGGGTTATTACATGGCAGAGGGGTAGCAAGTCTCTAGGTCCT
CTTTAGTAAGGACACCAGTCCTACTCATGAGAATGTTGCCTTTATGACTTCATCATCTCCCGAA
GTCCAGCCTCCTCTTTTGACACTGGGTGTAGGTCTTCCATGTGGAGAACTTAGAGAGACCTCAA
CATTCAGACCCCAGAATATCTTTTGTTACTCTCTCTCAGTAAGCAATCATATTTGAAGGCATCA
TATTTGAAGGCAGAAACTGGGCCAGTTTTATTCAGCATAGCGTCTTTAGATGCGAAGGCTATGC
ATTGCAGACTGTAGGGGATCTCATCAGCAATGGTTGCTGGACAAGCAGACAGATCAAGAGTCAG
TTCATGGGTGAGGTCTGTACTGGTCAGTCTTGCAGAGCTGTGGGTGGACTTGGAAGGGTCAATC
AGTAAAGATCAACATCCATTCTCTGATCTTCTCAAGAAGAGCCAGTCACAGCAGCCAGCCTAGT
GTTCCTACATACTCTAAACCATGTGCATGTTCAGCATTGACTTAATTGGGGTTTCTCCTGCCAT
GAGAAAACATCATGAGTAAAAGCAACTGGGGCAAAAAGGGTTAACTTCAGCTTGCATGCCCCAC
TCGCAGTCTATCATGAAAAGAAGTCAGAGCAGGAACTCAAGTCAGGAACCTGGTGGCAGGAACT
GAAGCAGAGATCATAGAGGGGTGCTGCTTACTGACTTCCTCCTCATAATTTTCTCTGCCTGTTA
GGTATGGCAACACCCAGAGTGAACTGGGCCCTCCCACATTAATCAGTAATTTTTAAAAAACAGT
TCACTACAGACTTGCTCAGAGGCCAGTCTAGTGGGCTCCCTCTACCCCTAACTGAAGTTCCCTC
TTCCAAAATGTGTCAAGTTGATGAAAAACTAGATAAATCAACAACCCAGGCTTACCCTTGGCTT
CTCTTTGAAGTTGGTAGACTTTGTAGATATGAAGCCTTCAGAAACAGAGGGCAACTGTATAAAT
GAAAAAGAGGAGGATCTTGGGCTACTGGGAATAAATTATTGACATCAACATATGTAGCATCCAA
GTGATTGCTGAGGGAGAACAAGTCAAGAGAGTGCAGTCTTCACATGTTATATATACATCAGGGG
CAGCAAGTGCAGGGTCTATCTGATCTGGATGGACTTTTAACAGATCAGCAGGGAGGAGACTTTT
GAAGAGGAAATCCATCTTGATACAAAGCCAGATGGTGAGACAGAACATGGGGACCGGGAACTCG
CAGGTGAATGTGTTGGACATTGGGGACTGGGAAAAACAGTAACAAAGTCAGGGTGTGTAAGACC
CACCTCAGTGCCTGCCACATGGCAAATCATTACCATCATTGTTGTTATTTCCATTGTGAAAACG
TGGTTCAGAATTTTATCTAAATAAACTTGGCTCTTCTAGCTG

hide sequence

RefSeq Acc Id:

XM_039109541 ⟹ XP_038965469

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	5	119,583,168 - 119,633,829 (-)	NCBI

Protein Sequences


Protein RefSeqs	NP_001100140	(Get FASTA)	NCBI Sequence Viewer
	XP_038965469	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	EDL97880	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:	NP_001100140 ⟸ NM_001106670
- Peptide Label:	precursor
- UniProtKB:	D3ZWD6 (UniProtKB/TrEMBL)
- Sequence:	show sequence MFTVAFFGLSLMAWHSGVTAQEKVNQRVTRAVTPGAVACQLSDWSEWTDCFPCQNEKYRYRSLL QPSKFGGTICSGDIWDKANCDSPTPCLRQAQCGQDFQCRETGRCLKRHLVCNGDQDCLDGSDED NCDDARVIEDDCRQYEPIPGSERAALGYNILTQEEGQSVYDAKYYGGQCETVYNGDWRRLQYDP TCERLYYGEDEKYFRKPYNFLKYHFEALADTLISSEFYDDANDLFSKIQRDKSQSNSVTFGISP AKSPITLDASVSWSDESSFMKELSKYNEKKYSFMRVSTKVQTAHFKMRRHNIVLDEGMMESLME LPEQFNYGMYSKFINDYGTHYITSGTMGGIYEYVLVLDKEKMRIHGITVEDVKKCIGGGVGLQF GEKIIGEGDLSGESCVMTGDGNQDKRKKDLAVEDIISRVQGGSSRWSTGLAHNSSAITYRSWGR SLKYNPVVIDFEMQPIYQLLQHTNLGPLETKRRNLRRALDQYLMEFNACRCGPCFNNGVPILEG TSCSCQCSMGRQGPACESMVLEAMEGAKADGRWSCWSSWSECRGGSRERRRQCNNPAPQNGGAP CLGKSLQTQAC hide sequence

RefSeq Acc Id:

ENSRNOP00000063871 ⟸ ENSRNOT00000067850

RefSeq Acc Id:	XP_038965469 ⟸ XM_039109541
- Peptide Label:	isoform X1

Protein Domains

MACPF

Transcriptome

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

Promoters

RGD ID:

13693871

Promoter ID:

EPDNEW_R4396

Type:

initiation region

Name:

C8a_1

Description:

complement C8 alpha chain

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	124,403,157 - 124,403,217	EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)

ACI/EurMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

ACI/EurMcwi (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

ACI/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

BBDP/Wor (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

BN/SsN (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Buf/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

COP/CrCrl (MCW & UW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob) University of Wisconsin (Dr. James Shull)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Charles River Laboratories
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)

F344/NCrl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

F344/NRrrc (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

FHH/EurMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

FHH/EurMcwi (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

FHL/EurMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

FHL/EurMcwi (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

GH/OmrMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

GK/Ox (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LE/Stm (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LEW/Crl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LEW/NCrlBR (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LH/MavRrrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LL/MavRrrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LN/MavRrrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

M520/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

MHS/Gib (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

MNS/Gib (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

MR/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

SBH/Ygl (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	SBH/Ygl sequenced by MCW

SBH/Ygl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SBN/Ygl (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	SBN/Ygl sequenced by MCW

SBN/Ygl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SHR/NHsd (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SHRSP/Gcrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SR/JrHsd (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Harlan Laboratories
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

SR/JrHsd (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SS/Jr (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SS/JrHsdMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

SS/JrHsdMcwi (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WAG/Rij (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WKY/Gcrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WKY/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

WKY/NCrl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WKY/NHsd (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WN/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Damaging Variants

Assembly: Rnor_5.0

Chromosome	Start Pos	End Pos	Reference Nucleotide	Variant Nucleotide	Variant Type	Strain
5	128209127	128209128	C	T	snv	COP/CrCrl (MCW & UW), KFRS3B/Kyo (KyushuU), FHL/EurMcwi (MCW), LL/MavRrrc (KNAW), LN/MavRrrc (KNAW), MR/N (KNAW), SHR/NCrlPrin (KNAW), SHR/NHsd (KNAW), SHR/OlaIpcv (KNAW), SHR/OlaIpcvPrin (KNAW), SHRSP/Gcrc (KNAW), F344/NRrrc (Illumina) (KNAW), WKY/Gcrc (KNAW), WKY/N (KNAW), WKY/NCrl (KNAW), WKY/NHsd (KNAW), BUF/N (KNAW), F344/NRrrc (SOLiD) (KNAW), F344/NCrl (KNAW), F344/NHsd (KNAW), FHH/EurMcwi (KNAW), FHL/EurMcwi (KNAW), GK/Ox (KNAW), M520/N (KNAW), F344/NSlc (KyushuU), F344/Stm (KyushuU), HWY/Slc (KyushuU), F344/Jcl (KyushuU), FHH/EurMcwi (MCW)

Assembly: Rnor_6.0

Chromosome	Start Pos	End Pos	Reference Nucleotide	Variant Nucleotide	Variant Type	Strain
5	124350459	124350460	C	T	snv	COP/CrCrl (MCW & UW), WKY/Gcrc (RGD), FHL/EurMcwi (MCW), CDR, F344/NRrrc (MCW), M520/N (MCW), MR/N (MCW), WKY/N (MCW), FHL/EurMcwi (RGD), F344/NCrl (RGD), FHH/EurMcwi (RGD), GK/Ox (RGD), LN/MavRrrc (RGD), LL/MavRrrc (RGD), SHR/NHsd (RGD), SHRSP/Gcrc (RGD), WKY/NCrl (RGD), FHH/EurMcwi (MCW)

Assembly: RGSC_v3.4

Chromosome	Start Pos	End Pos	Reference Nucleotide	Variant Nucleotide	Variant Type	Strain
5	125778472	125778473	C	T	snv	SHR/OlaIpcv (ICL), F344/NHsd (ICAHN), SHRSP/Gcrc (MDC), F344/NRrrc (KNAW), M520/N (KNAW), MR/N (KNAW), WKY/N (KNAW), SHR/OlaIpcv (KNAW), FHH/EurMcwi (MCW), FHL/EurMcwi (MCW), COP/CrCrl (MCW & UW), F344/NCrl (ICL), FHH/EurMcwi (ICL), FHL/EurMcwi (ICL), GK/Ox (ICL), LL/MavRrrc (ICL), LN/MavRrrc (ICL), SHR/OlaIpcv (ICL), SHR/NHsd (ICL), SHRSP/Gcrc (ICL), WKY/Gcrc (ICL), WKY/NHsd (ICL), WKY/NCrl (ICL), HCR/1Mco (UMich), LCR/1Mco (UMich), HCR/2Mco (UMich), LCR/2Mco (UMich), FHH/EurMcwi (MDC)

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1308355	AgrOrtholog
Ensembl Genes	ENSRNOG00000007697	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000063871	ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000067850	ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH	2.20.100.10	UniProtKB/TrEMBL
	4.10.400.10	UniProtKB/TrEMBL
InterPro	Complement_C8_alpha	UniProtKB/TrEMBL
	LDL_receptor-like_sf	UniProtKB/TrEMBL
	LDLR_class-A_CS	UniProtKB/TrEMBL
	LDrepeatLR_classA_rpt	UniProtKB/TrEMBL
	MAC_perforin	UniProtKB/TrEMBL
	MACPF	UniProtKB/TrEMBL
	MACPF_CS	UniProtKB/TrEMBL
	Thrombospondin_1_rpt	UniProtKB/TrEMBL
	TSP1_rpt_sf	UniProtKB/TrEMBL
KEGG Report	rno:298288	UniProtKB/TrEMBL
NCBI Gene	298288	ENTREZGENE
PANTHER	PTHR45742:SF1	UniProtKB/TrEMBL
Pfam	Ldl_recept_a	UniProtKB/TrEMBL
	MACPF	UniProtKB/TrEMBL
	TSP_1	UniProtKB/TrEMBL
PhenoGen	C8a	PhenoGen
PRINTS	COMPLEMENTC9	UniProtKB/TrEMBL
PROSITE	LDLRA_1	UniProtKB/TrEMBL
	LDLRA_2	UniProtKB/TrEMBL
	MACPF_1	UniProtKB/TrEMBL
	MACPF_2	UniProtKB/TrEMBL
	TSP1	UniProtKB/TrEMBL
SMART	LDLa	UniProtKB/TrEMBL
	MACPF	UniProtKB/TrEMBL
	TSP1	UniProtKB/TrEMBL
Superfamily-SCOP	LDL_rcpt_classA_cys-rich	UniProtKB/TrEMBL
	TSP1	UniProtKB/TrEMBL
UniProt	D3ZWD6	ENTREZGENE, UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2016-08-18	C8a	complement C8 alpha chain	C8a	complement component 8 alpha subunit	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2016-03-08	C8a	complement component 8 alpha subunit	C8a	complement component 8, alpha polypeptide	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2008-04-30	C8a	complement component 8, alpha polypeptide	C8a_predicted	complement component 8, alpha polypeptide (predicted)	'predicted' is removed	2292626	APPROVED
2005-01-12	C8a_predicted	complement component 8, alpha polypeptide (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 - CTD

Imported Disease Annotations - OMIM

Imported Annotations - KEGG (archival)