Krtcap3 (keratinocyte associated protein 3)

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Gene: Krtcap3 (keratinocyte associated protein 3) Rattus norvegicus

Analyze

Symbol:

Krtcap3

Name:

keratinocyte associated protein 3

RGD ID:

1596516

Description:

Predicted to localize to integral component of membrane. Orthologous to human KRTCAP3 (keratinocyte associated protein 3); INTERACTS WITH acrylamide; bisphenol A; fenvalerate.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Also known as:

KCP-3; keratinocyte-associated protein 3; LOC683980; similar to keratinocytes associated protein 3

RGD Orthologs

Human

Mouse

Chinchilla

Bonobo

Dog

Squirrel

Pig

Green Monkey

Naked Mole-Rat

Alliance Genes

More Info

more info ...

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
Rnor_6.0	6	26,485,126 - 26,486,695 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	6	26,485,126 - 26,486,695 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	6	36,304,329 - 36,305,898 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
Celera	6	24,613,034 - 24,614,603 (-)	NCBI		Celera
Cytogenetic Map	6	q14	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

microphthalmia (ISO)

retinitis pigmentosa 71 (ISO)

short-rib thoracic dysplasia 10 with or without polydactyly (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2-dimethylhydrazine (ISO)

17alpha-ethynylestradiol (ISO)

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

3,4-methylenedioxymethamphetamine (ISO)

4,4'-diaminodiphenylmethane (ISO)

4-hydroxyphenyl retinamide (ISO)

acrylamide (EXP)

aflatoxin B1 (ISO)

benzo[a]pyrene (ISO)

bis(2-ethylhexyl) phthalate (ISO)

bisphenol A (EXP)

butanal (ISO)

calcitriol (ISO)

carbamazepine (ISO)

cyclosporin A (ISO)

dichloroacetic acid (ISO)

ethanol (ISO)

fenvalerate (EXP)

folic acid (ISO)

furan (EXP)

pentanal (ISO)

pirinixic acid (ISO)

progesterone (ISO)

tamoxifen (ISO)

tetraphene (ISO)

titanium dioxide (ISO)

valproic acid (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Cellular Component

integral component of membrane (IEA)

Molecular Function

protein binding (ISO)

References

References - curated


1.	RGD automated data pipeline
2.	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
3.	RGD automated import pipeline for gene-chemical interactions

Additional References at PubMed

PMID:12477932	PMID:15489334

Genomics

Comparative Map Data

Krtcap3
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Rnor_6.0	6	26,485,126 - 26,486,695 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	6	26,485,126 - 26,486,695 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	6	36,304,329 - 36,305,898 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
Celera	6	24,613,034 - 24,614,603 (-)	NCBI		Celera
Cytogenetic Map	6	q14	NCBI

KRTCAP3
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	2	27,442,366 - 27,446,481 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	2	27,442,381 - 27,446,481 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	2	27,665,233 - 27,669,348 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	2	27,518,767 - 27,520,668 (+)	NCBI	NCBI36		hg18	NCBI36
Build 34	2	27,576,913 - 27,578,814	NCBI
Celera	2	27,511,407 - 27,515,522 (+)	NCBI
Cytogenetic Map	2	p23.3	NCBI
HuRef	2	27,407,121 - 27,411,236 (+)	NCBI		HuRef
CHM1_1	2	27,595,145 - 27,599,260 (+)	NCBI		CHM1_1

Krtcap3
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	5	31,409,050 - 31,410,541 (+)	NCBI	GRCm39		mm39
GRCm38	5	31,251,670 - 31,253,202 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	5	31,251,691 - 31,253,202 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	5	31,554,079 - 31,555,570 (+)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	5	31,528,297 - 31,529,778 (+)	NCBI			mm8
Celera	5	28,730,858 - 28,732,349 (+)	NCBI		Celera
Cytogenetic Map	5	B1	NCBI

Krtcap3
(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_004955469	9,416,732 - 9,418,523 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955469	9,416,732 - 9,418,523 (+)	NCBI	ChiLan1.0	ChiLan1.0

KRTCAP3
(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	2A	27,534,580 - 27,536,458 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	2A	27,534,571 - 27,536,458 (+)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	2A	27,446,103 - 27,448,063 (+)	NCBI	Mhudiblu_PPA_v0		panPan3

KRTCAP3
(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	17	21,387,781 - 21,389,383 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
CanFam3.1	17	21,387,682 - 21,389,385 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1

Krtcap3
(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_004936493	5,145,237 - 5,146,904 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

KRTCAP3
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	3	111,718,806 - 111,720,186 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	3	111,718,581 - 111,720,245 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	3	118,753,140 - 118,754,315 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

KRTCAP3
(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	14	80,171,335 - 80,173,295 (-)	NCBI
ChlSab1.1 Ensembl	14	80,167,492 - 80,174,059 (-)	Ensembl

Krtcap3
(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_004624738	9,508,571 - 9,510,376 (+)	NCBI

Position Markers

RH92034

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	6	26,484,730 - 26,484,992	NCBI	Rnor6.0
Rnor_5.0	6	36,303,933 - 36,304,195	UniSTS	Rnor5.0
Celera	6	24,612,638 - 24,612,900	UniSTS

RH131827

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	6	26,485,159 - 26,485,443	NCBI	Rnor6.0
Rnor_5.0	6	36,304,362 - 36,304,646	UniSTS	Rnor5.0
Celera	6	24,613,067 - 24,613,351	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
738023	Alc17	Alcohol consumption QTL 17	3.1	0.003	consumption behavior trait (VT:0002069)	ethanol drink intake rate to body weight ratio (CMO:0001616)	6	1	35623029	Rat
1354616	Despr12	Despair related QTL 12		0.0012	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	6	1	35623029	Rat
1549905	Stresp10	Stress response QTL 10	6.83	0.0066	stress-related behavior trait (VT:0010451)	number of approaches toward negative stimulus before onset of defensive burying response (CMO:0001960)	6	1	35623029	Rat
2300176	Bmd51	Bone mineral density QTL 51	11.7	0.0001	femur mineral mass (VT:0010011)	bone mineral density (CMO:0001226)	6	1	35623029	Rat
2300190	Bmd52	Bone mineral density QTL 52	11.2	0.0001	femur mineral mass (VT:0010011)	volumetric bone mineral density (CMO:0001553)	6	1	35623029	Rat
1331743	Uae28	Urinary albumin excretion QTL 28	4.5		urine albumin amount (VT:0002871)	urine albumin level (CMO:0000130)	6	1	41917988	Rat
9589048	Scfw3	Subcutaneous fat weight QTL 3	4.57	0.001	subcutaneous adipose mass (VT:1000472)	abdominal subcutaneous fat pad weight (CMO:0002069)	6	1	42388212	Rat
9589129	Insul24	Insulin level QTL 24	19.06	0.001	blood insulin amount (VT:0001560)	plasma insulin level (CMO:0000342)	6	1	42388212	Rat
7411603	Foco13	Food consumption QTL 13	5.5	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	6	1	42388212	Rat
7411542	Bw127	Body weight QTL 127	5.5	0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	6	1	42388212	Rat
8552962	Pigfal16	Plasma insulin-like growth factor 1 level QTL 16	9.4		blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	6	1	42388212	Rat
2293709	Bss23	Bone structure and strength QTL 23	5.18	0.0001	femur morphology trait (VT:0000559)	femur cross-sectional area (CMO:0001661)	6	1	43665660	Rat
2293650	Bss31	Bone structure and strength QTL 31	5.05	0.0001	femur strength trait (VT:0010010)	femur midshaft polar moment of inertia (CMO:0001669)	6	1	43665660	Rat
2293656	Bss28	Bone structure and strength QTL 28	6.79	0.0001	femur morphology trait (VT:0000559)	femur midshaft cortical cross-sectional area (CMO:0001663)	6	1	43665660	Rat
7411584	Foco4	Food consumption QTL 4	4.3	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	6	1	44015370	Rat
738024	Sach5	Saccharine consumption QTL 5	3.9	0.00039	consumption behavior trait (VT:0002069)	saccharin intake volume to total fluid intake volume ratio (CMO:0001601)	6	1	44570292	Rat
2301972	Bp325	Blood pressure QTL 325	4.8		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	6	1	75623393	Rat
1359023	Bp272	Blood pressure QTL 272	2.5		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	6	1120393	28706721	Rat
2292589	Emca10	Estrogen-induced mammary cancer QTL 10		0.048	mammary gland integrity trait (VT:0010552)	post-insult time to mammary tumor formation (CMO:0000345)	6	1120393	46120393	Rat
1354664	Slep2	Serum leptin concentration QTL 2	4.49		blood leptin amount (VT:0005667)	serum leptin level (CMO:0000780)	6	1120393	75023446	Rat
1576309	Emca7	Estrogen-induced mammary cancer QTL 7	4		mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	6	2537030	111715717	Rat
1578665	Bss16	Bone structure and strength QTL 16	4.4		femur morphology trait (VT:0000559)	bone trabecular cross-sectional area (CMO:0002311)	6	6161722	76002731	Rat
1578668	Bmd14	Bone mineral density QTL 14	3.8		femur mineral mass (VT:0010011)	total volumetric bone mineral density (CMO:0001728)	6	6161722	76002731	Rat
4145119	Mcs25	Mammary carcinoma susceptibility QTL 25		0.0001	mammary gland integrity trait (VT:0010552)	ratio of deaths to total study population during a period of time (CMO:0001023)	6	7009971	115379601	Rat
634322	Bw12	Body weight QTL 12	0		body mass (VT:0001259)	body weight (CMO:0000012)	7	10173862	55173862	Rat
1300128	Rf16	Renal function QTL 16	3.89		renal blood flow trait (VT:2000006)	absolute change in renal blood flow rate (CMO:0001168)	6	13122958	34367603	Rat
1300164	Rf15	Renal function QTL 15	3.12		renal blood flow trait (VT:2000006)	absolute change in renal blood flow rate (CMO:0001168)	6	13122958	57516539	Rat
10401812	Kidm54	Kidney mass QTL 54			kidney mass (VT:0002707)	both kidneys wet weight (CMO:0000085)	6	16810107	61810107	Rat
10401800	Kidm49	Kidney mass QTL 49			kidney mass (VT:0002707)	both kidneys wet weight (CMO:0000085)	6	16810107	61810107	Rat
8552910	Pigfal5	Plasma insulin-like growth factor 1 level QTL 5	4.3		blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	6	19417887	64417887	Rat
1641898	Colcr4	Colorectal carcinoma resistance QTL4	3.71	0.0007	intestine integrity trait (VT:0010554)	well differentiated malignant colorectal tumor surface area measurement (CMO:0002077)	6	21515302	65784818	Rat
2293839	Kiddil2	Kidney dilation QTL 2	4.8		kidney pelvis morphology trait (VT:0004194)	hydronephrosis severity score (CMO:0001208)	6	22042854	84763421	Rat
2293841	Kiddil4	Kidney dilation QTL 4	4.4		kidney pelvis morphology trait (VT:0004194)	hydronephrosis severity score (CMO:0001208)	6	22042854	84763421	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	46
Count of miRNA genes:	43
Interacting mature miRNAs:	46
Transcripts:	ENSRNOT00000073236
Prediction methods:	Miranda, Rnahybrid
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									6	18	11
Low		16	54	38	19	38	3	3	47	29	23		3
Below cutoff		26	3	3		3	5	8	25				5

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001109674	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AABR07063281	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AAHX01042319	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC100633	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473947	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000073236 ⟹ ENSRNOP00000063910

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	6	26,485,126 - 26,486,695 (-)	Ensembl

RefSeq Acc Id:

NM_001109674 ⟹ NP_001103144

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	6	26,485,126 - 26,486,695 (-)	NCBI
Rnor_5.0	6	36,304,329 - 36,305,898 (-)	NCBI
Celera	6	24,613,034 - 24,614,603 (-)	RGD

Sequence:

show sequence

CCTACGGCAGCGCGGAAGCCGGCCTTCGGGTCGGGTCGGGTCGGGTCGGATCGGATCGGGTCGG
GTCCGGGCGAAGCCAGTTCCCGGTAGAGCAGCCTGGCGGAGGGGGCAGAGCGGCCACGATGAGG
TGCTGCCGCGTCTGCGCCTTCGATGCCGCCCGAGGGCCCCGGCGGCTGATGCGCGTGGGACTTG
CGCTGATCCTGGTGGGCCACGTGAATCTCCTAGTGGGAGCTGTGCTGCATGGTACTGTCCTGCG
GCACGTGGCCAACCCCCGTGGCGCGGTCACTCCTGAGTACACCACAGCCAATGTCATTTCTGTG
GGTTCGGGACTACTGAGCGTTACCGTGGGACTTGTGGCCCTTTTGGCATCCAGGAACCTTCTTC
TCCCACGACTGCACTGGGCCCTGCTGACGCTGGCCTTGGTGAACCTGCTCTTGTCTGCTGCCTG
CTCCATGGGCCTCCTCCTGGCTGTGTCGCTCACTATTGCCAATGGTGGCCGCCGTCTTATTGCT
GACTGCCATCCAGGACTGATGGATCATTCCATACCACTGGACCAGGGGCCTGGACACACTGACT
GCCCCTTTGATCCCACAAGAATTTATGATACAGCCTTGGCTCTCTGGATCCCTTCTCTGTTCAT
GTCTGCAGCTGAAGCTGTTCTCTCTGGTTACTGTTGTGTGGCTGCACTCACGCTACGGGGAATT
GGGCCCTTCAGGAAGGAAGGGTTGCAGGGACAGCTGGAGGAACTGACAGAGCTTGAACCTCTTG
AGTGTAAAAGGCAGGAGAATATACAGCTGCTCCACCACCACCAGGATTTCCAGGCCTTACAGAA
AACCTGGGTTTAGGACAGGAGGTGCTCGGCTGAGGCGCATACCACAGGTGTTTTCTACTACGCA
CGCCATGGGGCCCCAACCCTAGGGCGCTATAAATAATTGTAATAAAAGAACTTGGTTTTTGTCT
TCG

hide sequence

Protein Sequences


Protein RefSeqs	NP_001103144	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAI00634	(Get FASTA)	NCBI Sequence Viewer
	EDM02918	(Get FASTA)	NCBI Sequence Viewer
	Q497B3	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_001103144 ⟸ NM_001109674

- UniProtKB:

Q497B3 (UniProtKB/Swiss-Prot)

- Sequence:

show sequence

MRCCRVCAFDAARGPRRLMRVGLALILVGHVNLLVGAVLHGTVLRHVANPRGAVTPEYTTANVI
SVGSGLLSVTVGLVALLASRNLLLPRLHWALLTLALVNLLLSAACSMGLLLAVSLTIANGGRRL
IADCHPGLMDHSIPLDQGPGHTDCPFDPTRIYDTALALWIPSLFMSAAEAVLSGYCCVAALTLR
GIGPFRKEGLQGQLEELTELEPLECKRQENIQLLHHHQDFQALQKTWV

hide sequence

RefSeq Acc Id:

ENSRNOP00000063910 ⟸ ENSRNOT00000073236

Transcriptome

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

Promoters

RGD ID:

13694437

Promoter ID:

EPDNEW_R4962

Type:

multiple initiation site

Name:

Krtcap3_1

Description:

keratinocyte associated protein 3

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	6	26,486,702 - 26,486,762	EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)

ACI/EurMcwi (MCW)

Visual

CSV

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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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CSV

TAB

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

ACI/N (MCW)

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CSV

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

BBDP/Wor (RGD)

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CSV

TAB

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

BN/SsN (MCW)

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CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1596516	AgrOrtholog
Ensembl Genes	ENSRNOG00000047941	Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein	ENSRNOP00000063910	ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript	ENSRNOT00000073236	ENTREZGENE, UniProtKB/Swiss-Prot
IMAGE_CLONE	IMAGE:5622000	IMAGE-MGC_LOAD
InterPro	Beta-casein-like	UniProtKB/Swiss-Prot
KEGG Report	rno:683980	UniProtKB/Swiss-Prot
MGC_CLONE	MGC:124654	IMAGE-MGC_LOAD
NCBI Gene	683980	ENTREZGENE
PANTHER	PTHR31258	UniProtKB/Swiss-Prot
Pfam	BCLP	UniProtKB/Swiss-Prot
PhenoGen	Krtcap3	PhenoGen
UniGene	Rn.202673	ENTREZGENE
UniProt	KCP3_RAT	UniProtKB/Swiss-Prot, ENTREZGENE

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2010-12-09	Krtcap3	keratinocyte associated protein 3	LOC683980	similar to keratinocytes associated protein 3	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2006-11-20	LOC683980	similar to keratinocytes associated protein 3			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)

Imported Disease Annotations - ClinVar