Tgm5 (transglutaminase 5) - Rat Genome Database

Name: Tgm5
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

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Gene: Tgm5 (transglutaminase 5) Rattus norvegicus

Analyze

Symbol:

Tgm5

Name:

transglutaminase 5

RGD ID:

1593350

Description:

Predicted to have protein-glutamine gamma-glutamyltransferase activity. Predicted to be involved in peptide cross-linking. Human ortholog(s) of this gene implicated in peeling skin syndrome. Orthologous to human TGM5 (transglutaminase 5); INTERACTS WITH bisphenol A; 2,3,7,8-tetrachlorodibenzodioxine (ortholog); 2-hydroxypropanoic acid (ortholog).

Type:

protein-coding

RefSeq Status:

MODEL

Also known as:

glutamine gamma-glutamyltransferase 5; LOC366173; LOC691932; protein-glutamine gamma-glutamyltransferase 5; similar to transglutaminase 7; Tgm7l1; transglutaminase 7-like 1

RGD Orthologs

Human

Mouse

Chinchilla

Bonobo

Dog

Squirrel

Pig

Green Monkey

Naked Mole-Rat

Alliance Genes

More Info

more info ...

More Info

Species	Gene symbol and name	Data Source	Assertion derived from	less info ...
Orthologs ¹				less info ...
Homo sapiens (human):	TGM5 (transglutaminase 5)	HGNC	Ensembl, HomoloGene, NCBI, Panther
Mus musculus (house mouse):	Tgm5 (transglutaminase 5)	HGNC	NCBI, HomoloGene, Panther, Ensembl
Chinchilla lanigera (long-tailed chinchilla):	Tgm5 (transglutaminase 5)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	TGM5 (transglutaminase 5)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	TGM5 (transglutaminase 5)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Tgm5 (transglutaminase 5)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	TGM5 (transglutaminase 5)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (African green monkey):	TGM5 (transglutaminase 5)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Tgm5 (transglutaminase 5)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	TGM5 (transglutaminase 5)	Alliance	DIOPT (HGNC)

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	3	108,008,087 - 108,014,813 (-)	NCBI
Rnor_6.0 Ensembl	3	112,995,568 - 113,023,532 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	3	112,995,469 - 113,033,110 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	3	119,538,113 - 119,567,431 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	3	107,880,960 - 107,905,261 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
Celera	3	106,911,345 - 106,947,086 (-)	NCBI		Celera
Cytogenetic Map	3	q35	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

genetic disease (ISO)

Peeling Skin Syndrome 1 (ISO)

Peeling Skin Syndrome 2 (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

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

2-hydroxypropanoic acid (ISO)

aflatoxin B1 (ISO)

all-trans-retinoic acid (ISO)

arsane (ISO)

arsenic atom (ISO)

benzo[a]pyrene (ISO)

bisphenol A (EXP)

cisplatin (ISO)

clothianidin (ISO)

crocidolite asbestos (ISO)

genistein (ISO)

N-acetyl-beta-D-glucosamine (ISO)

N-acetyl-D-glucosamine (ISO)

paracetamol (ISO)

pirinixic acid (ISO)

rac-lactic acid (ISO)

resveratrol (ISO)

sodium arsenate (ISO)

succimer (ISO)

tamibarotene (ISO)

tris(2-butoxyethyl) phosphate (ISO)

urethane (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

peptide cross-linking (IBA)

protein phosphopantetheinylation (IEA)

Molecular Function

metal ion binding (IEA)

protein binding (ISO)

protein-glutamine gamma-glutamyltransferase activity (IBA)

References

References - curated


1.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2.	RGD automated data pipeline
3.	RGD automated import pipeline for gene-chemical interactions

Genomics

Comparative Map Data

Tgm5
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	3	108,008,087 - 108,014,813 (-)	NCBI
Rnor_6.0 Ensembl	3	112,995,568 - 113,023,532 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	3	112,995,469 - 113,033,110 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	3	119,538,113 - 119,567,431 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	3	107,880,960 - 107,905,261 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
Celera	3	106,911,345 - 106,947,086 (-)	NCBI		Celera
Cytogenetic Map	3	q35	NCBI

TGM5
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	15	43,232,590 - 43,266,928 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	15	43,232,590 - 43,266,928 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	15	43,524,793 - 43,559,055 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
GRCh37	15	43,524,788 - 43,559,126 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	15	41,312,667 - 41,346,347 (-)	NCBI	NCBI36		hg18	NCBI36
Celera	15	20,295,623 - 20,329,891 (-)	NCBI
Cytogenetic Map	15	q15.2	NCBI
HuRef	15	20,373,584 - 20,407,843 (-)	NCBI		HuRef
CHM1_1	15	43,643,581 - 43,677,843 (-)	NCBI		CHM1_1

Tgm5
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	2	120,876,592 - 120,916,322 (-)	NCBI	GRCm39		mm39
GRCm38	2	121,046,111 - 121,085,841 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	2	121,046,111 - 121,085,841 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	2	120,871,847 - 120,911,495 (-)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	2	120,737,552 - 120,777,200 (-)	NCBI			mm8
Celera	2	122,198,147 - 122,237,106 (-)	NCBI		Celera
Cytogenetic Map	2	E5	NCBI

Tgm5
(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_004955416	9,805,033 - 9,842,798 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955416	9,808,903 - 9,842,784 (-)	NCBI	ChiLan1.0	ChiLan1.0

TGM5
(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	15	40,348,487 - 40,382,739 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	15	40,349,085 - 40,382,737 (-)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	15	22,193,639 - 22,227,977 (-)	NCBI	Mhudiblu_PPA_v0		panPan3

TGM5
(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	30	10,097,762 - 10,128,221 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
CanFam3.1	30	10,097,388 - 10,123,139 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1

Tgm5
(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_004936471	6,406,040 - 6,442,026 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

TGM5
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	1	128,191,630 - 128,217,664 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	1	128,191,647 - 128,217,249 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	1	143,048,392 - 143,073,905 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

TGM5
(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	26	39,727,129 - 39,761,648 (+)	NCBI
ChlSab1.1 Ensembl	26	39,734,288 - 39,761,441 (+)	Ensembl

Tgm5
(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_004624804	10,339,841 - 10,391,449 (-)	NCBI

Position Markers

D3Got71

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	3	113,062,915 - 113,063,086	NCBI	Rnor6.0
Rnor_5.0	3	119,602,812 - 119,602,983	UniSTS	Rnor5.0
RGSC_v3.4	3	107,902,299 - 107,902,469	RGD	RGSC3.4
RGSC_v3.4	3	107,902,298 - 107,902,469	UniSTS	RGSC3.4
RGSC_v3.1	3	107,798,727 - 107,798,897	RGD
Celera	3	106,977,390 - 106,977,561	UniSTS
RH 3.4 Map	3	944.4	RGD
RH 3.4 Map	3	944.4	UniSTS
RH 2.0 Map	3	609.5	RGD
Cytogenetic Map	3	q35	UniSTS

D3Got252

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	3	113,061,060 - 113,061,226	NCBI	Rnor6.0
Rnor_5.0	3	119,600,957 - 119,601,123	UniSTS	Rnor5.0
RGSC_v3.4	3	107,900,443 - 107,900,609	UniSTS	RGSC3.4
Celera	3	106,975,535 - 106,975,701	UniSTS
Cytogenetic Map	3	q35	UniSTS

Tgm7

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	3	113,041,827 - 113,042,249	NCBI	Rnor6.0
Rnor_5.0	3	119,581,724 - 119,582,146	UniSTS	Rnor5.0
RGSC_v3.4	3	107,881,210 - 107,881,632	UniSTS	RGSC3.4
Celera	3	106,956,389 - 106,956,811	UniSTS
Cytogenetic Map	3	q35	UniSTS

BF387459

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	3	113,041,655 - 113,041,815	NCBI	Rnor6.0
Rnor_5.0	3	119,581,552 - 119,581,712	UniSTS	Rnor5.0
RGSC_v3.4	3	107,881,038 - 107,881,198	UniSTS	RGSC3.4
Celera	3	106,956,217 - 106,956,377	UniSTS
RH 3.4 Map	3	943.2	UniSTS
Cytogenetic Map	3	q35	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
1358885	Bp251	Blood pressure QTL 251	3.8		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	3	10639528	127023997	Rat
1358888	Bp264	Blood pressure QTL 264	4.43		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	3	10639528	127023997	Rat
737818	Hcar12	Hepatocarcinoma resistance QTL 12	2.6		liver integrity trait (VT:0010547)	volume of individual liver tumorous lesion (CMO:0001078)	3	30114912	123700444	Rat
70216	Cm14	Cardiac mass QTL 14	2.1		heart mass (VT:0007028)	heart wet weight (CMO:0000069)	3	30846101	172879276	Rat
1358362	Srcrt2	Stress Responsive Cort QTL 2	2.78		blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	3	39248391	140271184	Rat
2301970	Bw81	Body weight QTL 81	5.19		body mass (VT:0001259)	body weight (CMO:0000012)	3	43295930	163640485	Rat
2301971	Cm71	Cardiac mass QTL 71	4.63		heart left ventricle mass (VT:0007031)	heart left ventricle weight (CMO:0000776)	3	43295930	163640485	Rat
1581503	Cm58	Cardiac mass QTL 58	2.7	0.05	heart left ventricle mass (VT:0007031)	heart left ventricle weight to body weight ratio (CMO:0000530)	3	45406058	127023997	Rat
1559282	Emca5	Estrogen-induced mammary cancer QTL 5	3.9		mammary gland integrity trait (VT:0010552)	percentage of study population developing mammary tumors during a period of time (CMO:0000948)	3	45406058	177699992	Rat
2292591	Esta4	Estrogen-induced thymic atrophy QTL 4			thymus mass (VT:0004954)	thymus wet weight (CMO:0000855)	3	48561928	155263151	Rat
1358186	Ept2	Estrogen-induced pituitary tumorigenesis QTL 2	8.3		pituitary gland mass (VT:0010496)	pituitary gland wet weight (CMO:0000853)	3	48562146	115249962	Rat
2292613	Ept16	Estrogen-induced pituitary tumorigenesis QTL 16	8.3		pituitary gland mass (VT:0010496)	pituitary gland wet weight (CMO:0000853)	3	48562146	115249962	Rat
631665	Bw8	Body weight QTL 8	5.5		body mass (VT:0001259)	body weight (CMO:0000012)	3	51821836	124513579	Rat
724523	Tsu1	Thymus enlargement suppressive QTL 1	3.84		thymus mass (VT:0004954)	thymus weight to body weight ratio (CMO:0000612)	3	51822008	120917851	Rat
1582218	Bw74	Body weight QTL 74	3.9	0.0021	body mass (VT:0001259)	body weight (CMO:0000012)	3	54630948	119830094	Rat
1582238	Bw68	Body weight QTL 68	3.2	0.0064	body mass (VT:0001259)	body weight (CMO:0000012)	3	54630948	119830094	Rat
1582239	Epfw1	Epididymal fat weight QTL 1	4.5	0.0006	epididymal fat pad mass (VT:0010421)	epididymal fat pad weight to body weight ratio (CMO:0000658)	3	54630948	119830094	Rat
1581568	Rf53	Renal function QTL 53			total urine protein amount (VT:0000032)	urine protein excretion rate to body weight ratio (CMO:0001099)	3	58204463	170534769	Rat
8662816	Vetf4	Vascular elastic tissue fragility QTL 4	4		renal artery integrity trait (VT:0010642)	number of ruptures of the internal elastic lamina of the renal arteries (CMO:0002563)	3	61241033	165369047	Rat
1300111	Rf12	Renal function QTL 12	3.78		renal blood flow trait (VT:2000006)	absolute change in renal blood flow rate (CMO:0001168)	3	62922868	127023997	Rat
1582221	Kidm30	Kidney mass QTL 30	3.5	0.0008	kidney mass (VT:0002707)	both kidneys wet weight (CMO:0000085)	3	66711607	119830094	Rat
1582210	Bw71	Body weight QTL 71	3.3	0.0012	body mass (VT:0001259)	body weight (CMO:0000012)	3	66711607	119830094	Rat
12879848	Bw181	Body weght QTL 181		0.015	body mass (VT:0001259)	body weight (CMO:0000012)	3	72672290	127023997	Rat
2301414	Kidm37	Kidney mass QTL 37		0.001	kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	3	72973445	127023997	Rat
1600376	Arunc5	Aerobic running capacity QTL 5		0.21	exercise endurance trait (VT:0002332)	maximum distance run on treadmill (CMO:0001406)	3	78700444	123700444	Rat
1581546	Pur13	Proteinuria QTL 13	2.93	0.0335	total urine protein amount (VT:0000032)	urine protein excretion rate (CMO:0000759)	3	81136227	154416635	Rat
2302273	Gluco35	Glucose level QTL 35	5.3	0.001	blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	3	83817637	119509260	Rat
7387306	Bw124	Body weight QTL 124	3.2	0.0003	body mass (VT:0001259)	body weight (CMO:0000012)	3	88910015	133910015	Rat
631649	Bp123	Blood pressure QTL 123	3.2		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	3	94788365	139788365	Rat
8694437	Bw167	Body weight QTL 167	22.46	0.001	retroperitoneal fat pad mass (VT:0010430)	retroperitoneal fat pad weight to body weight ratio (CMO:0000635)	3	97009185	142009185	Rat
631841	Niddm39	Non-insulin dependent diabetes mellitus QTL 39	3.36		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	3	99465522	168732722	Rat
1582219	Bw63	Body weight QTL 63	3.8	0.001	body mass (VT:0001259)	body weight (CMO:0000012)	3	100730984	119830094	Rat
724532	Cm17	Cardiac mass QTL 17	2		heart mass (VT:0007028)	calculated heart weight (CMO:0000073)	3	101058963	146058963	Rat
2293087	Iddm27	Insulin dependent diabetes mellitus QTL 27	2.68		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	3	102152812	155263151	Rat
1354611	Despr2	Despair related QTL 2	3.03	0.0028	locomotor behavior trait (VT:0001392)	amount of time spent in voluntary immobility (CMO:0001043)	3	102466149	147466149	Rat
2312659	Slep7	Serum leptin concentration QTL 7		0.001	blood leptin amount (VT:0005667)	serum leptin level (CMO:0000780)	3	103141814	176418101	Rat
2312670	Bw94	Body weight QTL 94		0.01	inguinal fat pad mass (VT:0010424)	inguinal fat pad weight to body weight ratio (CMO:0001253)	3	103141814	176418101	Rat
2312673	Scl63	Serum cholesterol level QTL 63		0.001	blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	3	103141814	176418101	Rat
2302373	Gluco39	Glucose level QTL 39	5.01		blood glucose amount (VT:0000188)	blood glucose level area under curve (AUC) (CMO:0000350)	3	103141944	170934860	Rat
1582216	Bw65	Body weight QTL 65	6.3		body mass (VT:0001259)	body weight (CMO:0000012)	3	106900427	119830094	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	100
Count of miRNA genes:	76
Interacting mature miRNAs:	81
Transcripts:	ENSRNOT00000056190, ENSRNOT00000056195
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
Low	1		1	1		1			12		14	8
Below cutoff	3	31	38	22	11	22	6	7	74	41	47	14	6

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	XM_039106079	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC094543	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473949	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000118	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	KM669282	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000084921 ⟹ ENSRNOP00000071692

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	3	112,995,568 - 113,023,532 (-)	Ensembl

RefSeq Acc Id:

XM_008762205 ⟹ XP_008760427

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	3	112,995,469 - 113,033,110 (-)	NCBI

Sequence:

show sequence

CTTGGCATGGAAGGGGAAGCAGCCACTCCGGGATCAGTTTCCTGAAGCTTCAATCCATCCAGCA
GTCTGGGGGAGCAGTCCAGGAGCCAGAAGCAGCCACTATGGCCCAAGGGCTAGAGGTGGCCCTC
ACAGACCTCCAGAGCTCCCGGAACAATGTTCGGCACCACACGGAAGAGATCAGTTTTGACCGTC
TTGTTGTCCGCCGGGGTCAGGCCTTCTGCATCACCCTGTACTTTAAGAATCGGGGCTTCCAGCC
AGGCATGGACAGTATCATGTTTGTGGCTGAGACTGGTGAGGAACTGCCCACAGGNNNNCGTGCA
GTGTTTAGCCTCACAGGCAGTGGTGGCTCAAGCCCCTGGATTGCTTCCCTGGAAGCCAACAGGG
CCAACTCCCTGGAAGTCAGCCTCTGTGCCCCTCCCATGGCGGCCGTGGGTCGATACCTCCTGAA
AGTTCGGATTGACTCCTACCAGGGTTCCGTCACTGCCTACCAGCTGGGGGAGTTCATCCTGCTC
TTCAATCCCTGGTGCCCAGCGGATACAGTGTACTTGGAGAGTGAGCCCCAGAGGCAGGAGTATG
TTGTGAACGATTATGGCTTCATCTACCAAGGGAGCAAGAGTTGGATCCGCCCGTGCCCCTGGAA
CTATGGGCAGTTTGAAGAGAACATCATAGACATCTGCTTGGAGCTGCTAGAGAAAAGCCTGAAC
TTCCAGGTTGACCCATCCACAGATTGTGCCCTGCGGGGAAGCCCCGTCTACATCAGCAGAGTTG
TGTGTGCCATGATAAACAGCAATGATGACAGCGGAGTGCTCAATGGCAACTGGAGTGAGAATTA
TATGGACGGTGCCAACCCCGCAGAGTGGACTGGCAGTGTAGCCATCCTAAAGCAGTGGCATGCC
ACGGGCTGCCAACCCGTGCGCTATGGGCAGTGCTGGGTTTTTGCTGCTGTCATGTGCACAGTGA
TGAGGTGCCTGGGGATTCCCACCCGCGTGATCACCAACTTTGACTCTGGTCATGACACCGATGG
TAACCTGATCATTGATGAGTATTATGACAACACAGGCAGAATTTTGGAGAATATGAAGAAGGAT
ACTGTCTGGAATTTCCATGTGTGGAATGAATGCTGGATGGCGCGCAAGGACCTCCCTCCTGGAT
ATGGAGGCTGGCAAGTGCTTGATGCTACACCCCAGGAAACCAGCAATGGTCTCTACTGCTGTGG
CCCTGCTTCTGTCAAAGCCATCAAAGAGGGAGAAGTCGATCTGAACTATGATACACGCTTTGCA
TTTTCTATGGTGAATGCTGACTGCATGTCCTGGCTAGTCTATGGAGGGAAGGAGCAGAAACTTC
ACCAGGACACAGCCACTGTTGGGAATTTTATCAGCACCAAGAGCATCCAGAGTGATGAGCGTGA
TGATGTCACTGAGAACTACAAGTATGAAGAAGGTTCCCTTCAAGAGAGACAGGTGTTTCTAAAA
GCTCTGCAGAAGCTACAGGCTGGAAGGTCTCAAGGGCCTCACCAAGCAAACTCAAATCCCTTCA
GCTCCATGCCACCACGGCAGGACAGTGCCAGAAGCCCCACTACACCTTCCCTTCGACCCAGTGA
TGTCCTCCAGGTCTCTCTGAAGTTTGAGCTGCTGGACTCACCCAAAATGGGCCAAGATATAAAC
TTTGTCCTGTTGGCTGTCAACATGTCACCTCAGTTCAAGGATCTCAAACTCAACTTGAGTGCCC
AGTCTCTGTTGCACGATGGCAGCCCCCTGGCCCCGTTTTGGCAGGACACGGCATTCATCACACT
GTTCCCTAAAGAAGAAAAGACCTACCCTTGCAAAATCCTCTACTCACAGTACAGCCAGTACCTG
TCGACAGACAAGCTAATTCGCATCAGTGCCCTGGGTGAAGAGAAGAGCAGTCCTGAGAAAATCC
TGGTGAACAAGATCATCACCTTGACTTTCCCAGGCATCATGATTAACGTTCTAGGAGCTGCCTT
TGTGAATCAGCCACTCACTGTCCAGGTGGTCTTTTCAAACCCACTCTCAGAGCCGGTTGAGGAC
TGCGTGCTGACCTTGGAAGGAAGTGGTCTCTTTAGGAAGCAGCAGAGAGTTCTCATTGGAGTCC
TCAAACCGCATAACAAAGCCAGCATCACTCTAAAGACTGTCCCTTTCAAGAGTGGCCAAAGACA
GATCCAAGCTAACCTGAGAAGCAATAGGTTTAAAGACATCAAGGGCTACAAGAATGTGTACGTA
GACATTGGCTTATAAACTCTGAGACAGAGGCTGGAGAATTAGCTCAGCGGTTGAGCGTATGTGT
TGCTTCTGCAAAGGACTTGGGTTCAACTTCCCACAACGCACTTGGGGGCCCCCAATCATCTGTA
ACCCCAGTTTCCGGGGATCAATCCGACCAGCACACATGATACACATCCATGCATGCAGGGGAAA
AAAAGATTTTCATACACATAAAGTGAAAATAAATAAATCTAAATTTTTTAAAAATTTTATTTAA
ATTTATTTTTTAATTTAAACTTATTTAAAATAAACTCTGGGATATACCG

hide sequence

RefSeq Acc Id:

XM_008775489 ⟹ XP_008773711

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Celera	3	106,911,345 - 106,947,086 (-)	NCBI

Sequence:

show sequence

CCCACCTCCAGTGTCTCTCGGAACCTTGGCATGGAAGGGGAAGCAGCCACTCCGGGATCAGTTT
CCTGAAGCTTCAATCCATCCAGCAGTCTGGGGGAGCAGTCCAGGAGCCAGAAGCAGCCACTATG
GCCCAAGGGCTAGAGGTGGCCCTCACAGACCTCCAGAGCTCCCGGAACAATGTTCGGCACCACA
CGGAAGAGATCAGTTTTGACCGTCTTGTTGTCCGCCGGGGTCAGGCCTTCTGCATCACCCTGTA
CTTTAAGAATCGGGGCTTCCAGCCAGGCATGGACAGTATCATGTTTGTGGCTGAGACTGGACCC
TTGCCGGACCTGGCCAAAGGGACTCGTGCAGTGTTTAGCCTCACAGGCAGTGGTGGCTCAAGCC
CCTGGATTGCTTCCCTGGAAGCCAACAGGGCCAACTCCCTGGAAGTCAGCCTCTGTGCCCCTCC
CATGGCGGCCGTGGGTCGATACCTCCTGAAAGTTCGGATTGACTCCTACCAGGGTTCCATCACT
GCCTACCAGCTGGGGGAGTTCATCCTGCTCTTCAATCCCTGGTGCCCAGCGGATACAGTGTACT
TGGAGAGTGAGCCCCAGAGGCAGGAGTATGTTGTGAACGATTATGGCTTCATCTACCAAGGGAG
CAAGAGTTGGATCCGCCCGTGCCCCTGGAACTATGGGCAGTTTGAAGAGAACATCATAGACATC
TGCTTGGAGCTGCTAGAGAAAAGCCTGAACTTCCAGGTTGACCCATCCACAGATTGTGCCCTGC
GGGGAAGCCCCGTCTACATCAGCAGAGTTGTGTGTGCCATGATAAACAGCAATGATGACAGCGG
AGTGCTCAATGGCAACTGGAGTGAGAATTATATGGACGGTGCCAACCCCGCAGAGTGGACTGGC
AGTGTAGCCATCCTAAAGCAGTGGCATGCCACGGGCTGCCAACCCGTGCGCTATGGGCAGTGCT
GGGTTTTTGCTGCTGTCATGTGCACAGTGATGAGGTGCCTGGGGATTCCCACCCGCGTGATCAC
CAACTTTGACTCTGGTCATGACACCGATGGTAACCTGATCATTGATGAGTATTATGACAACACA
GGCAGAATTTTGGAGAATATGAAGAAGGATACTGTCTGGAATTTCCATGTGTGGAATGAATGCT
GGATGGCGCGCAAGGACCTCCCTCCTGGATATGGAGGCTGGCAAGTGCTTGATGCTACACCCCA
GGAAACCAGCAATGGTCTCTACTGCTGTGGCCCTGCTTCTGTCAAAGCCATCAAAGAGGGAGAA
GTCGATCTGAACTATGATACACGCTTTGCATTTTCTATGGTGAATGCTGACTGCATGTCCTGGC
TAGTCTATGGAGGGAAGGAGCAGAAACTTCACCAGGACACAGCCACTGTTGGGAATTTTATCAG
CACCAAGAGCATCCAGAGTGATGAGCGTGATGATGTCACTGAGAACTACAAGTATGAAGAAGGT
TCCCTTCAAGAGAGACAGGTGTTTCTAAAAGCTCTGCAGAAGCTACAGGCTGGAAGGTCTCAAG
GGCCTCACCAAGCAAACTCAAATCCCTTCAGCTCCATGCCACCACGGCAGGACAGTGCCAGAAG
CCCCACTACACCTTCCCTTCGACCCAGTGATGTCCTCCAGGTCTCTCTGAAGTTTGAGCTGCTG
GACTCACCCAAAATGGGCCAAGATATAAACTTTGTCCTGTTGGCTGTCAACATGTCACCTCAGT
TCAAGGATCTCAAACTCAACTTGAGTGCCCAGTCTCTGTTGCACGATGGCAGCCCCCTGGCCCC
GTTTTGGCAGGACACGGCATTCATCACACTGTTCCCTAAAGAAGAAAAGACCTACCCTTGCAAA
ATCCTCTACTCACAGTACAGCCAGTACCTGTCGACAGACAAGCTAATTCGCATCAGTGCCCTGG
GTGAAGAGAAGAGCAGTCCTGAGAAAATCCTGGTGAACAAGATCATCACCTTGACTTTCCCAGG
CATCATGATTAACGTTCTAGGAGCTGCCTTTGTGAATCAGCCACTCACTGTCCAGGTGGTCTTT
TCAAACCCACTCTCAGAGCCGGTTGAGGACTGCGTGCTGACCTTGGAAGGAAGTGGTCTCTTTA
GGAAGCAGCAGAGAGTTCTCATTGGAGTCCTCAAACCGCATAACAAAGCCAGCATCACTCTAAA
GACTGTCCCTTTCAAGAGTGGCCAAAGACAGATCCAAGCTAACCTGAGAAGCAATAGGTTTAAA
GACATCAAGGGCTACAAGAATGTGTACGTAGACATTGGCTTATAAACTCTGAGACAGAGGCTGG
AGAATTAGCTCAGCGGTTGAGCGTATGTGTTGCTTCTGCAAAGGACTTGGGTTCAACTTCCCAC
AACGCACTTGGGGGCCCCCAATCATCTGTAACCCCAGTTTCCGGGGATCAATCCGACCAGCACA
CATGATACACATCCATGCATGCAGGGGAAAAAAAGATTTTCATACACATAAAGTGAAAATAAAT
AAATCTAAATTTTTTAAAAATTTTATTTAAATTTATTTTTTAATTTAAACTTATTTAAAATAAA
CTCTGGGATATACCG

hide sequence

RefSeq Acc Id:

XM_039106079 ⟹ XP_038962007

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	3	108,008,087 - 108,014,813 (-)	NCBI

Protein Sequences


Protein RefSeqs	XP_038962007	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AJD87525	(Get FASTA)	NCBI Sequence Viewer
	EDL79971	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

XP_008773711 ⟸ XM_008775489

- Peptide Label:

isoform X2

- Sequence:

show sequence

MAQGLEVALTDLQSSRNNVRHHTEEISFDRLVVRRGQAFCITLYFKNRGFQPGMDSIMFVAETG
PLPDLAKGTRAVFSLTGSGGSSPWIASLEANRANSLEVSLCAPPMAAVGRYLLKVRIDSYQGSI
TAYQLGEFILLFNPWCPADTVYLESEPQRQEYVVNDYGFIYQGSKSWIRPCPWNYGQFEENIID
ICLELLEKSLNFQVDPSTDCALRGSPVYISRVVCAMINSNDDSGVLNGNWSENYMDGANPAEWT
GSVAILKQWHATGCQPVRYGQCWVFAAVMCTVMRCLGIPTRVITNFDSGHDTDGNLIIDEYYDN
TGRILENMKKDTVWNFHVWNECWMARKDLPPGYGGWQVLDATPQETSNGLYCCGPASVKAIKEG
EVDLNYDTRFAFSMVNADCMSWLVYGGKEQKLHQDTATVGNFISTKSIQSDERDDVTENYKYEE
GSLQERQVFLKALQKLQAGRSQGPHQANSNPFSSMPPRQDSARSPTTPSLRPSDVLQVSLKFEL
LDSPKMGQDINFVLLAVNMSPQFKDLKLNLSAQSLLHDGSPLAPFWQDTAFITLFPKEEKTYPC
KILYSQYSQYLSTDKLIRISALGEEKSSPEKILVNKIITLTFPGIMINVLGAAFVNQPLTVQVV
FSNPLSEPVEDCVLTLEGSGLFRKQQRVLIGVLKPHNKASITLKTVPFKSGQRQIQANLRSNRF
KDIKGYKNVYVDIGL

hide sequence

RefSeq Acc Id:

XP_008760427 ⟸ XM_008762205

- Peptide Label:

isoform X1

- Sequence:

show sequence

MAQGLEVALTDLQSSRNNVRHHTEEISFDRLVVRRGQAFCITLYFKNRGFQPGMDSIMFVAETG
EELPTGXRAVFSLTGSGGSSPWIASLEANRANSLEVSLCAPPMAAVGRYLLKVRIDSYQGSVTA
YQLGEFILLFNPWCPADTVYLESEPQRQEYVVNDYGFIYQGSKSWIRPCPWNYGQFEENIIDIC
LELLEKSLNFQVDPSTDCALRGSPVYISRVVCAMINSNDDSGVLNGNWSENYMDGANPAEWTGS
VAILKQWHATGCQPVRYGQCWVFAAVMCTVMRCLGIPTRVITNFDSGHDTDGNLIIDEYYDNTG
RILENMKKDTVWNFHVWNECWMARKDLPPGYGGWQVLDATPQETSNGLYCCGPASVKAIKEGEV
DLNYDTRFAFSMVNADCMSWLVYGGKEQKLHQDTATVGNFISTKSIQSDERDDVTENYKYEEGS
LQERQVFLKALQKLQAGRSQGPHQANSNPFSSMPPRQDSARSPTTPSLRPSDVLQVSLKFELLD
SPKMGQDINFVLLAVNMSPQFKDLKLNLSAQSLLHDGSPLAPFWQDTAFITLFPKEEKTYPCKI
LYSQYSQYLSTDKLIRISALGEEKSSPEKILVNKIITLTFPGIMINVLGAAFVNQPLTVQVVFS
NPLSEPVEDCVLTLEGSGLFRKQQRVLIGVLKPHNKASITLKTVPFKSGQRQIQANLRSNRFKD
IKGYKNVYVDIGL

hide sequence

RefSeq Acc Id:

ENSRNOP00000071692 ⟸ ENSRNOT00000084921

RefSeq Acc Id:

XP_038962007 ⟸ XM_039106079

Protein Domains

TGc Transglut_N

Transcriptome

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

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_6.0

Chromosome	Start Pos	End Pos	Reference Nucleotide	Variant Nucleotide	Variant Type	Strain
3	113000951	113000952	C	T	snv	FHH/EurMcwi (MCW), FHH/EurMcwi (RGD), FHL/EurMcwi (RGD), FHL/EurMcwi (MCW)

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1593350	AgrOrtholog
Ensembl Genes	ENSRNOG00000058755	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000071692	UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000084921	UniProtKB/TrEMBL
Gene3D-CATH	2.60.40.10	UniProtKB/TrEMBL
	3.90.260.10	UniProtKB/TrEMBL
InterPro	Gln_gamma-glutamylTfrase_euk	UniProtKB/TrEMBL
	Ig-like_fold	UniProtKB/TrEMBL
	Ig_E-set	UniProtKB/TrEMBL
	Papain_like_cys_pep_sf	UniProtKB/TrEMBL
	Transglutaminase-like	UniProtKB/TrEMBL
	Transglutaminase-like_sf	UniProtKB/TrEMBL
	Transglutaminase_C	UniProtKB/TrEMBL
	Transglutaminase_C_sf	UniProtKB/TrEMBL
	Transglutaminase_CS	UniProtKB/TrEMBL
	Transglutaminase_N	UniProtKB/TrEMBL
NCBI Gene	691932	ENTREZGENE
Pfam	Transglut_C	UniProtKB/TrEMBL
	Transglut_core	UniProtKB/TrEMBL
	Transglut_N	UniProtKB/TrEMBL
PhenoGen	Tgm5	PhenoGen
PIRSF	TGM_EBP42	UniProtKB/TrEMBL
PROSITE	TRANSGLUTAMINASES	UniProtKB/TrEMBL
SMART	TGc	UniProtKB/TrEMBL
Superfamily-SCOP	Ig_E-set	UniProtKB/TrEMBL
	SSF54001	UniProtKB/TrEMBL
	Transglut_C	UniProtKB/TrEMBL
UniProt	A0A0B5ACW7_RAT	UniProtKB/TrEMBL
	A0A0B5AGM1_RAT	UniProtKB/TrEMBL
	A0A0G2K142_RAT	UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2017-06-27	Tgm5	transglutaminase 5	Tgm7l1	transglutaminase 7-like 1	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2015-06-26	Tgm7l1	transglutaminase 7-like 1	Tgm7	transglutaminase 7	Name and Symbol changed	629549	APPROVED
2010-05-21	LOC691932	similar to transglutaminase 7	Tgm7	transglutaminase 7	Data Merged	737654	APPROVED
2010-05-21	Tgm7	transglutaminase 7	LOC691932	similar to transglutaminase 7	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2008-04-30	Tgm7	transglutaminase 7	Tgm7_predicted	transglutaminase 7 (predicted)	'predicted' is removed	2292626	APPROVED
2008-01-09	LOC691932	similar to transglutaminase 7	LOC688031	similar to transglutaminase 7	Data Merged	1643240	APPROVED
2006-11-20	LOC691932	similar to transglutaminase 7			Symbol and Name status set to provisional	70820	PROVISIONAL
2006-11-20	LOC688031	similar to transglutaminase 7			Symbol and Name status set to provisional	70820	PROVISIONAL
2005-01-12	Tgm7_predicted	transglutaminase 7 (predicted)			Symbol and Name status set to approved	70820	APPROVED

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

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

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

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

Imported Disease Annotations - ClinVar

Imported Disease Annotations - OMIM