LOC500028 (hypothetical protein LOC500028)

Gene: LOC500028 (hypothetical protein LOC500028) Rattus norvegicus

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Symbol:

LOC500028

Name:

hypothetical protein LOC500028

Description:

Orthologous to human YAE1 (YAE1 maturation factor of ABCE1).

Type:

protein-coding

RefSeq Status:

PREDICTED

Also known as:

uncharacterized protein LOC500028

Orthologs:

No known orthologs.

homologs ...

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	4	35,889,550 - 35,890,224 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	4	35,745,595 - 35,746,269 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	4	34,958,168 - 34,958,842 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
Celera	4	33,400,199 - 33,400,873 (-)	NCBI		Celera
Cytogenetic Map	4	q21	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation (Toggle Annotation Detail/Summary View)

References - curated

Genomics

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
634323	Hc2	Hypercalciuria QTL 2	2.15		urine calcium amount (VT:0002985)	urine calcium excretion rate (CMO:0000763)	4	1	42118977	Rat
619616	Bp79	Blood pressure QTL 79		0.0292	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	4	3043231	79575658	Rat
2303168	Bp330	Blood pressure QTL 330	4.25	0.017	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	4	3043231	145254791	Rat
2302371	Stl22	Serum triglyceride level QTL 22	5.15		blood triglyceride amount (VT:0002644)	serum triglyceride level (CMO:0000360)	4	3044017	55791834	Rat
1358203	Stl19	Serum triglyceride level QTL 19	2.8	0.002	blood triglyceride amount (VT:0002644)	serum triglyceride level (CMO:0000360)	4	3044017	64915903	Rat
631642	Stl2	Serum triglyceride level QTL 2	3.3		blood triglyceride amount (VT:0002644)	serum triglyceride level (CMO:0000360)	4	3047807	55324857	Rat
631209	Bw2	Body weight QTL2	4.2		retroperitoneal fat pad mass (VT:0010430)	retroperitoneal fat pad weight to body weight ratio (CMO:0000635)	4	6467693	43414792	Rat
1300141	Bp178	Blood pressure QTL 178			arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	4	6572939	37703537	Rat
631261	Tcas3	Tongue tumor susceptibility QTL 3	6.88		tongue integrity trait (VT:0010553)	number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)	4	7342404	92484039	Rat
2316958	Gluco58	Glucose level QTL 58	10		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	4	7850904	182171018	Rat
9590304	Scort17	Serum corticosterone level QTL 17	4.96	0.001	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	4	8052189	53052189	Rat
6478724	Anxrr35	Anxiety related response QTL 35		0.00449	defecation behavior trait (VT:0010462)	defecation measurement (CMO:0000997)	4	8052189	53052189	Rat
6478766	Anxrr47	Anxiety related response QTL 47		0.09637	locomotor behavior trait (VT:0001392)	number of entries into a discrete space in an experimental apparatus (CMO:0000960)	4	8052189	53052189	Rat
6478769	Anxrr48	Anxiety related response QTL 48		0.02514	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	4	8052189	53052189	Rat
8552906	Pigfal3	Plasma insulin-like growth factor 1 level QTL 3			blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	4	8052189	53052189	Rat
8694374	Bw155	Body weight QTL 155	3.39	0.001	body lean mass (VT:0010483)	lean tissue morphological measurement (CMO:0002184)	4	8052189	53052189	Rat
2303585	Bw86	Body weight QTL 86	4		body mass (VT:0001259)	body weight (CMO:0000012)	4	12638974	57638974	Rat
7387227	Uae40	Urinary albumin excretion QTL 40	2.9	0.0052	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	4	16149941	61149941	Rat
70222	Eae2	Experimental allergic encephalomyelitis QTL 2	4.3		nervous system integrity trait (VT:0010566)	experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)	4	18222187	37685319	Rat
1354665	Stl10	Serum triglyceride level QTL 10	3.57		blood triglyceride amount (VT:0002644)	serum triglyceride level (CMO:0000360)	4	18222187	43414792	Rat
61412	Pia2	Pristane induced arthritis QTL 2	3.9		joint integrity trait (VT:0010548)	post-insult time to onset of experimental arthritis (CMO:0001450)	4	18222187	61039065	Rat
10755501	Bp390	Blood pressure QTL 390	2.5		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	4	23850384	169318094	Rat
6909122	Insul22	Insulin level QTL 22	4.63		blood insulin amount (VT:0001560)	plasma insulin level (CMO:0000342)	4	23991721	76238799	Rat
6909128	Pancm4	Pancreatic morphology QTL 4	11.35		pancreas mass (VT:0010144)	pancreas wet weight (CMO:0000626)	4	23991721	76238799	Rat
1578655	Bmd11	Bone mineral density QTL 11	11		femur mineral mass (VT:0010011)	total volumetric bone mineral density (CMO:0001728)	4	24631874	69631874	Rat
8655906	Rf60	Renal function QTL 60	3.8		blood creatinine amount (VT:0005328)	creatinine clearance (CMO:0000765)	4	26654749	81874227	Rat
12798520	Anxrr55	Anxiety related response QTL 55	4.45	0.01	locomotor behavior trait (VT:0001392)	number of rearing movements with lid-pushing in an experimental apparatus (CMO:0002715)	4	29549895	112807890	Rat
11530004	Niddm71	Non-insulin dependent diabetes mellitus QTL 71		0.001	blood glucose amount (VT:0000188)	blood glucose level area under curve (AUC) (CMO:0000350)	4	31554484	51311866	Rat
8655949	Rf62	Renal function QTL 62	22		blood urea nitrogen amount (VT:0005265)	plasma urea nitrogen level (CMO:0000586)	4	31825200	43414792	Rat
8552782	Vie1	Viral induced encephalitis QTL 1	26.4		brain integrity trait (VT:0010579)	encephalitis incidence/prevalence measurement (CMO:0002361)	4	31825560	83531021	Rat
8552801	Bw143	Body weight QTL 143	7.3		body mass (VT:0001259)	ratio of change in body weight to total body weight (CMO:0002216)	4	31825560	83531021	Rat
8552809	Vie5	Viral induced encephalitis QTL 5	25.3		brain integrity trait (VT:0010579)	encephalitis incidence/prevalence measurement (CMO:0002361)	4	31825560	83531021	Rat
61415	Eae11	Experimental allergic encephalomyelitis QTL 11	2.9		nervous system integrity trait (VT:0010566)	post-insult time to onset of experimental autoimmune encephalomyelitis (CMO:0001422)	4	33637803	37685319	Rat
2313401	Anxrr27	Anxiety related response QTL 27			aggression-related behavior trait (VT:0015014)	tameness/aggressiveness composite score (CMO:0002136)	4	33637803	61708341	Rat
8655961	Kidm43	Kidney mass QTL 43	18		kidney mass (VT:0002707)	both kidneys wet weight (CMO:0000085)	4	34277932	99067150	Rat
4889511	Gluco61	Glucose level QTL 61	4.7	0.001	blood glucose amount (VT:0000188)	blood glucose level area under curve (AUC) (CMO:0000350)	4	35138860	39073276	Rat
2290374	Gluco32	Glucose level QTL 32	6.27		blood glucose amount (VT:0000188)	blood glucose level area under curve (AUC) (CMO:0000350)	4	35138860	43414792	Rat

Sequence

Nucleotide Sequences

RefSeq Transcripts	NM_001047954	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AABR07059786	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AAHX01028497	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AY383683	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

NM_001047954 ⟹ NP_001041419

RefSeq Status:

PREDICTED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	4	35,889,550 - 35,890,224 (-)	NCBI
Rnor_5.0	4	35,745,595 - 35,746,269 (-)	NCBI
RGSC_v3.4	4	34,958,168 - 34,958,842 (-)	RGD
Celera	4	33,400,199 - 33,400,873 (-)	RGD

Sequence:

show sequence

ATGGCTCGGGCAATGTCTTGGTTTCGAGCGACTCCCGAGATCCCCAGCCCTGGAGAGCAGGACG
TGTTTGATGAGGAAGCAGACGAATCTCTGTTAGTGCAGCGGGAATGGCAGGATCACATGAGGAA
ACGAGTCCAAGAAGGTTACAGAGATGGGATAGATGCTGGCAAAGCAGTAACCCTTCAACAGGGC
TTCAATCAAGGCTATAAAGAGGGTGCCGATGTCATTTTAAACTACGGACTACTCAGGGGAACAT
TGAGCGCTTTGCTTTCCTGGTGTCACCTTCATGGTAATAGTTCAACGCTGATTGGCAAGATAAA
TAACCTTCTGAATGCAGTTGGCCAGTGTGAAGAGTGTGTGATCAAACATCTGAAATCAGTTACG
TCACCGCCACGCATTACAGATTTATTGGACTCCATTGAGGATCTGGACCTTTGTCATGTAGTCC
CGCCTGAGAAAGCTGTTGAAGCAAGAGGTGACACTAGTGCTGACATTAGCACAGATGCTGACAG
GAGTCCGAATGGGATGGATTGTTCACATCCAGAATGTTGCAGAACACAAGAGCATGCGCATTTG
GAAAAACCAAGCCTCACTTGGATTCTGGAACAGACATCCAACTTGGTGAAACAGCTGGGAATAT
CAGTAGACATATTACAGCACCTGAGACAACTGTAA

hide sequence

Protein Sequences

Strain Variation

Strain Sequence Variants (Rnor 5.0)

ACI/EurMcwi (KNAW)

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Secondary Analysis:	GATK
Description:	Provided by Hermsen at al

ACI/EurMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.5.9-r16 and GATK v1.3-14
Description:	Medical College of Wisconsin (Dr. Howard Jacob)

ACI/N (KNAW)

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Secondary Analysis:	GATK
Description:	Provided by Hermsen at al

BBDP/WorN (KNAW)

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Secondary Analysis:	GATK
Description:	Provided by Hermsen at al

BDIX.Cg-Tal/NemOda (KyushuU)

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Sequenced By:	Kyushu University (Dr. Mikita Suyama) Kyoto University (Dr. Takashi Kuramoto)
Platform:	Illumina NextSeq 500
Secondary Analysis:	BWA (v0.7.4), SAMtools (v.0.1.12a), Picard tools (v.1.87), GATK (v.2.5.2)
Breeder:	NBRP-Rat/Kyoto University
Description:	Target capture sequencing of exons and conserved non-coding sequences. Provided by: Dr. Mikita Suyama (Kyushu University) and Dr. Takashi Kuramoto (Kyoto University)
Publications:	Yoshihara M, etal., Genom Data. 2016 Nov 14;10:155-157. eCollection 2016 Dec.

BDIX/NemOda (KyushuU)

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Sequenced By:	Kyushu University (Dr. Mikita Suyama) Kyoto University (Dr. Takashi Kuramoto)
Platform:	Illumina NextSeq 500
Secondary Analysis:	BWA (v0.7.4), SAMtools (v.0.1.12a), Picard tools (v.1.87), GATK (v.2.5.2)
Breeder:	NBRP-Rat/Kyoto University
Description:	Target capture sequencing of exons and conserved non-coding sequences. Provided by: Dr. Mikita Suyama (Kyushu University) and Dr. Takashi Kuramoto (Kyoto University)
Publications:	Yoshihara M, etal., Genom Data. 2016 Nov 14;10:155-157. eCollection 2016 Dec.

BN-Lx/Cub (KNAW)

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Secondary Analysis:	GATK
Description:	Provided by Hermsen at al

BN-Lx/CubPrin (KNAW)

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Secondary Analysis:	GATK
Description:	Provided by Hermsen at al

BN/SsN (KNAW)

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Secondary Analysis:	GATK
Description:	Provided by Hermsen at al

BN/SsNSlc (KyushuU)

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Sequenced By:	Kyushu University (Dr. Mikita Suyama) Kyoto University (Dr. Takashi Kuramoto)
Platform:	Illumina NextSeq 500
Secondary Analysis:	BWA (v0.7.4), SAMtools (v.0.1.12a), Picard tools (v.1.87), GATK (v.2.5.2)
Breeder:	NBRP-Rat/Kyoto University
Description:	Target capture sequencing of exons and conserved non-coding sequences. Provided by: Dr. Mikita Suyama (Kyushu University) and Dr. Takashi Kuramoto (Kyoto University)
Publications:	Yoshihara M, etal., Genom Data. 2016 Nov 14;10:155-157. eCollection 2016 Dec.

BUF/MNa (KyushuU)

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Sequenced By:	Kyushu University (Dr. Mikita Suyama) Kyoto University (Dr. Takashi Kuramoto)
Platform:	Illumina NextSeq 500
Secondary Analysis:	BWA (v0.7.4), SAMtools (v.0.1.12a), Picard tools (v.1.87), GATK (v.2.5.2)
Breeder:	NBRP-Rat/Kyoto University
Description:	Target capture sequencing of exons and conserved non-coding sequences. Provided by: Dr. Mikita Suyama (Kyushu University) and Dr. Takashi Kuramoto (Kyoto University)
Publications:	Yoshihara M, etal., Genom Data. 2016 Nov 14;10:155-157. eCollection 2016 Dec.

BUF/N (KNAW)

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Secondary Analysis:	GATK
Description:	Provided by Hermsen at al

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 v0.5.9-r16 and GATK v2.3-5
Breeder:	Charles River Laboratories
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)

Crl:SD (UDEL)

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Secondary Analysis:	GATK (HaplotypeCaller v.3.1-1, VariantAnnotator v.3.1-1, SnpEff v.3.6)
Description:	Provided by Barthold at al

DA/BklArbNsi (KNAW)

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Secondary Analysis:	GATK
Description:	Provided by Hermsen at al

DOB/Oda (KyushuU)

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Sequenced By:	Kyushu University (Dr. Mikita Suyama) Kyoto University (Dr. Takashi Kuramoto)
Platform:	Illumina NextSeq 500
Secondary Analysis:	BWA (v0.7.4), SAMtools (v.0.1.12a), Picard tools (v.1.87), GATK (v.2.5.2)
Breeder:	NBRP-Rat/Kyoto University
Description:	Target capture sequencing of exons and conserved non-coding sequences. Provided by: Dr. Mikita Suyama (Kyushu University) and Dr. Takashi Kuramoto (Kyoto University)
Publications:	Yoshihara M, etal., Genom Data. 2016 Nov 14;10:155-157. eCollection 2016 Dec.

F344/DuCrlCrlj (KyushuU)

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Sequenced By:	Kyushu University (Dr. Mikita Suyama) Kyoto University (Dr. Takashi Kuramoto)
Platform:	Illumina NextSeq 500
Secondary Analysis:	BWA (v0.7.4), SAMtools (v.0.1.12a), Picard tools (v.1.87), GATK (v.2.5.2)
Breeder:	NBRP-Rat/Kyoto University
Description:	Target capture sequencing of exons and conserved non-coding sequences. Provided by: Dr. Mikita Suyama (Kyushu University) and Dr. Takashi Kuramoto (Kyoto University)
Publications:	Yoshihara M, etal., Genom Data. 2016 Nov 14;10:155-157. eCollection 2016 Dec.

F344/Jcl (KyushuU)

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Sequenced By:	Kyushu University (Dr. Mikita Suyama) Kyoto University (Dr. Takashi Kuramoto)
Platform:	Illumina NextSeq 500
Secondary Analysis:	BWA (v0.7.4), SAMtools (v.0.1.12a), Picard tools (v.1.87), GATK (v.2.5.2)
Breeder:	NBRP-Rat/Kyoto University
Description:	Target capture sequencing of exons and conserved non-coding sequences. Provided by: Dr. Mikita Suyama (Kyushu University) and Dr. Takashi Kuramoto (Kyoto University)
Publications:	Yoshihara M, etal., Genom Data. 2016 Nov 14;10:155-157. eCollection 2016 Dec.

F344/NCrl (KNAW)

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Secondary Analysis:	GATK
Description:	Provided by Hermsen at al

F344/NHsd (KNAW)

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Secondary Analysis:	GATK
Description:	Provided by Hermsen at al

F344/NRrrc (Illumina) (KNAW)

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Platform:	Illumina
Secondary Analysis:	GATK
Description:	Provided by Hermsen at al

F344/NRrrc (SOLiD) (KNAW)

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Platform:	SOLID
Secondary Analysis:	GATK
Description:	Provided by Hermsen at al

F344/NSlc (KyushuU)

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Sequenced By:	Kyushu University (Dr. Mikita Suyama) Kyoto University (Dr. Takashi Kuramoto)
Platform:	Illumina NextSeq 500
Secondary Analysis:	BWA (v0.7.4), SAMtools (v.0.1.12a), Picard tools (v.1.87), GATK (v.2.5.2)
Breeder:	NBRP-Rat/Kyoto University
Description:	Target capture sequencing of exons and conserved non-coding sequences. Provided by: Dr. Mikita Suyama (Kyushu University) and Dr. Takashi Kuramoto (Kyoto University)
Publications:	Yoshihara M, etal., Genom Data. 2016 Nov 14;10:155-157. eCollection 2016 Dec.

F344/Stm (KyushuU)

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Sequenced By:	Kyushu University (Dr. Mikita Suyama) Kyoto University (Dr. Takashi Kuramoto)
Platform:	Illumina NextSeq 500
Secondary Analysis:	BWA (v0.7.4), SAMtools (v.0.1.12a), Picard tools (v.1.87), GATK (v.2.5.2)
Breeder:	NBRP-Rat/Kyoto University
Description:	Target capture sequencing of exons and conserved non-coding sequences. Provided by: Dr. Mikita Suyama (Kyushu University) and Dr. Takashi Kuramoto (Kyoto University)
Publications:	Yoshihara M, etal., Genom Data. 2016 Nov 14;10:155-157. eCollection 2016 Dec.

FHH/EurMcwi (KNAW)

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Secondary Analysis:	GATK
Description:	Provided by Hermsen at al

FHH/EurMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.5.9-r16 and GATK v1.3-14
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

FHL/EurMcwi (KNAW)

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Secondary Analysis:	GATK
Description:	Provided by Hermsen at al

FHL/EurMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.5.9-r16 and GATK v1.3-14
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

GH/OmrMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.5.9-r16 and GATK v2.3-5
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

GK/Ox (KNAW)

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Secondary Analysis:	GATK
Description:	Provided by Hermsen at al

HTX/Kyo (KyushuU)

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Sequenced By:	Kyushu University (Dr. Mikita Suyama) Kyoto University (Dr. Takashi Kuramoto)
Platform:	Illumina NextSeq 500
Secondary Analysis:	BWA (v0.7.4), SAMtools (v.0.1.12a), Picard tools (v.1.87), GATK (v.2.5.2)
Breeder:	NBRP-Rat/Kyoto University
Description:	Target capture sequencing of exons and conserved non-coding sequences. Provided by: Dr. Mikita Suyama (Kyushu University) and Dr. Takashi Kuramoto (Kyoto University)
Publications:	Yoshihara M, etal., Genom Data. 2016 Nov 14;10:155-157. eCollection 2016 Dec.

HWY/Slc (KyushuU)

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Sequenced By:	Kyushu University (Dr. Mikita Suyama) Kyoto University (Dr. Takashi Kuramoto)
Platform:	Illumina NextSeq 500
Secondary Analysis:	BWA (v0.7.4), SAMtools (v.0.1.12a), Picard tools (v.1.87), GATK (v.2.5.2)
Breeder:	NBRP-Rat/Kyoto University
Description:	Target capture sequencing of exons and conserved non-coding sequences. Provided by: Dr. Mikita Suyama (Kyushu University) and Dr. Takashi Kuramoto (Kyoto University)
Publications:	Yoshihara M, etal., Genom Data. 2016 Nov 14;10:155-157. eCollection 2016 Dec.

IS-Tlk/Kyo (KyushuU)

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Sequenced By:	Kyushu University (Dr. Mikita Suyama) Kyoto University (Dr. Takashi Kuramoto)
Platform:	Illumina NextSeq 500
Secondary Analysis:	BWA (v0.7.4), SAMtools (v.0.1.12a), Picard tools (v.1.87), GATK (v.2.5.2)
Breeder:	NBRP-Rat/Kyoto University
Description:	Target capture sequencing of exons and conserved non-coding sequences. Provided by: Dr. Mikita Suyama (Kyushu University) and Dr. Takashi Kuramoto (Kyoto University)
Publications:	Yoshihara M, etal., Genom Data. 2016 Nov 14;10:155-157. eCollection 2016 Dec.

IS/Kyo (KyushuU)

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Sequenced By:	Kyushu University (Dr. Mikita Suyama) Kyoto University (Dr. Takashi Kuramoto)
Platform:	Illumina NextSeq 500
Secondary Analysis:	BWA (v0.7.4), SAMtools (v.0.1.12a), Picard tools (v.1.87), GATK (v.2.5.2)
Breeder:	NBRP-Rat/Kyoto University
Description:	Target capture sequencing of exons and conserved non-coding sequences. Provided by: Dr. Mikita Suyama (Kyushu University) and Dr. Takashi Kuramoto (Kyoto University)
Publications:	Yoshihara M, etal., Genom Data. 2016 Nov 14;10:155-157. eCollection 2016 Dec.

KFRS3B/Kyo (KyushuU)

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Sequenced By:	Kyushu University (Dr. Mikita Suyama) Kyoto University (Dr. Takashi Kuramoto)
Platform:	Illumina NextSeq 500
Secondary Analysis:	BWA (v0.7.4), SAMtools (v.0.1.12a), Picard tools (v.1.87), GATK (v.2.5.2)
Breeder:	NBRP-Rat/Kyoto University
Description:	Target capture sequencing of exons and conserved non-coding sequences. Provided by: Dr. Mikita Suyama (Kyushu University) and Dr. Takashi Kuramoto (Kyoto University)
Publications:	Yoshihara M, etal., Genom Data. 2016 Nov 14;10:155-157. eCollection 2016 Dec.

LE/OrlBarth (UDEL)

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Secondary Analysis:	GATK (HaplotypeCaller v.3.1-1, VariantAnnotator v.3.1-1, SnpEff v.3.6)
Description:	Provided by Barthold at al

LE/Stm (Illumina) (KNAW)

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Secondary Analysis:	GATK
Description:	Provided by Hermsen at al

LE/Stm (KyushuU)

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Sequenced By:	Kyushu University (Dr. Mikita Suyama) Kyoto University (Dr. Takashi Kuramoto)
Platform:	Illumina NextSeq 500
Secondary Analysis:	BWA (v0.7.4), SAMtools (v.0.1.12a), Picard tools (v.1.87), GATK (v.2.5.2)
Breeder:	NBRP-Rat/Kyoto University
Description:	Target capture sequencing of exons and conserved non-coding sequences. Provided by: Dr. Mikita Suyama (Kyushu University) and Dr. Takashi Kuramoto (Kyoto University)
Publications:	Yoshihara M, etal., Genom Data. 2016 Nov 14;10:155-157. eCollection 2016 Dec.

LE/Stm (SOLiD) (KNAW)

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Secondary Analysis:	GATK
Description:	Provided by Hermsen at al

LEC/Tj (KyushuU)

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Sequenced By:	Kyushu University (Dr. Mikita Suyama) Kyoto University (Dr. Takashi Kuramoto)
Platform:	Illumina NextSeq 500
Secondary Analysis:	BWA (v0.7.4), SAMtools (v.0.1.12a), Picard tools (v.1.87), GATK (v.2.5.2)
Breeder:	NBRP-Rat/Kyoto University
Description:	Target capture sequencing of exons and conserved non-coding sequences. Provided by: Dr. Mikita Suyama (Kyushu University) and Dr. Takashi Kuramoto (Kyoto University)
Publications:	Yoshihara M, etal., Genom Data. 2016 Nov 14;10:155-157. eCollection 2016 Dec.

LEW/Crl (KNAW)

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Secondary Analysis:	GATK
Description:	Provided by Hermsen at al

LEW/NCrl (KNAW)

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Secondary Analysis:	GATK
Description:	Provided by Hermsen at al

LH/MavRrrc (KNAW)

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Secondary Analysis:	GATK
Description:	Provided by Hermsen at al

LL/MavRrrc (KNAW)

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Secondary Analysis:	GATK
Description:	Provided by Hermsen at al

LN/MavRrrc (KNAW)

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Secondary Analysis:	GATK
Description:	Provided by Hermsen at al

M520/N (KNAW)

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Secondary Analysis:	GATK
Description:	Provided by Hermsen at al

MHS/Gib (KNAW)

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Secondary Analysis:	GATK
Description:	Provided by Hermsen at al

MNS/Gib (KNAW)

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Secondary Analysis:	GATK
Description:	Provided by Hermsen at al

MR/N (KNAW)

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Secondary Analysis:	GATK
Description:	Provided by Hermsen at al

NIG-III/Hok (KyushuU)

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Sequenced By:	Kyushu University (Dr. Mikita Suyama) Kyoto University (Dr. Takashi Kuramoto)
Platform:	Illumina NextSeq 500
Secondary Analysis:	BWA (v0.7.4), SAMtools (v.0.1.12a), Picard tools (v.1.87), GATK (v.2.5.2)
Breeder:	NBRP-Rat/Kyoto University
Description:	Target capture sequencing of exons and conserved non-coding sequences. Provided by: Dr. Mikita Suyama (Kyushu University) and Dr. Takashi Kuramoto (Kyoto University)
Publications:	Yoshihara M, etal., Genom Data. 2016 Nov 14;10:155-157. eCollection 2016 Dec.

RCS/Kyo (KyushuU)

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Sequenced By:	Kyushu University (Dr. Mikita Suyama) Kyoto University (Dr. Takashi Kuramoto)
Platform:	Illumina NextSeq 500
Secondary Analysis:	BWA (v0.7.4), SAMtools (v.0.1.12a), Picard tools (v.1.87), GATK (v.2.5.2)
Breeder:	NBRP-Rat/Kyoto University
Description:	Target capture sequencing of exons and conserved non-coding sequences. Provided by: Dr. Mikita Suyama (Kyushu University) and Dr. Takashi Kuramoto (Kyoto University)
Publications:	Yoshihara M, etal., Genom Data. 2016 Nov 14;10:155-157. eCollection 2016 Dec.

SBH/Ygl (KNAW)

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Secondary Analysis:	GATK
Description:	Provided by Hermsen at al

SBH/Ygl (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA-0.5.8c, GATK-v1.0.6001, samtools, Picard
Breeder:	Medical College of Wisconsin
Description:	SBH/Ygl sequenced by MCW

SBN/Ygl (KNAW)

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Secondary Analysis:	GATK
Description:	Provided by Hermsen at al

SBN/Ygl (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA-0.5.8c, GATK-v1.0.6001, samtools, Picard
Breeder:	Medical College of Wisconsin
Description:	SBN/Ygl sequenced by MCW

SDLEF7/Barth (UDEL)

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Secondary Analysis:	GATK (HaplotypeCaller v.3.1-1, VariantAnnotator v.3.1-1, SnpEff v.3.6)
Description:	Provided by Barthold at al

SHR/NCrlPrin (KNAW)

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Secondary Analysis:	GATK
Description:	Provided by Hermsen at al

SHR/NHsd (KNAW)

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Secondary Analysis:	GATK
Description:	Provided by Hermsen at al

SHR/OlaIpcv (KNAW)

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Secondary Analysis:	GATK
Description:	Provided by Hermsen at al

SHR/OlaIpcvPrin (KNAW)

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Secondary Analysis:	GATK
Description:	Provided by Hermsen at al

SHRSP/Gcrc (KNAW)

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Secondary Analysis:	GATK
Description:	Provided by Hermsen at al

SR/JrHsd (KNAW)

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Secondary Analysis:	GATK
Description:	Provided by Hermsen at al

SR/JrHsd (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.5.9-r16 and GATK v1.3-14
Breeder:	Harlan Laboratories
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

SS/Jr (KNAW)

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Secondary Analysis:	GATK
Description:	Provided by Hermsen at al

SS/JrHsdMcwi (KNAW)

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Secondary Analysis:	GATK
Description:	Provided by Hermsen at al

SS/JrHsdMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.5.9-r16 and GATK v1.3-14
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

WAG/Rij (KNAW)

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Secondary Analysis:	GATK
Description:	Provided by Hermsen at al

WKY/Gcrc (KNAW)

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Secondary Analysis:	GATK
Description:	Provided by Hermsen at al

WKY/N (KNAW)

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Secondary Analysis:	GATK
Description:	Provided by Hermsen at al

WKY/NCrl (KNAW)

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Secondary Analysis:	GATK
Description:	Provided by Hermsen at al

WKY/NHsd (KNAW)

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Secondary Analysis:	GATK
Description:	Provided by Hermsen at al

WN/N (KNAW)

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Secondary Analysis:	GATK
Description:	Provided by Hermsen at al

ZF (KyushuU)

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Sequenced By:	Kyushu University (Dr. Mikita Suyama) Kyoto University (Dr. Takashi Kuramoto)
Platform:	Illumina NextSeq 500
Secondary Analysis:	BWA (v0.7.4), SAMtools (v.0.1.12a), Picard tools (v.1.87), GATK (v.2.5.2)
Breeder:	NBRP-Rat/Kyoto University
Description:	Target capture sequencing of exons and conserved non-coding sequences. Provided by: Dr. Mikita Suyama (Kyushu University) and Dr. Takashi Kuramoto (Kyoto University)
Publications:	Yoshihara M, etal., Genom Data. 2016 Nov 14;10:155-157. eCollection 2016 Dec.

ZFDM (KyushuU)

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Sequenced By:	Kyushu University (Dr. Mikita Suyama) Kyoto University (Dr. Takashi Kuramoto)
Platform:	Illumina NextSeq 500
Secondary Analysis:	BWA (v0.7.4), SAMtools (v.0.1.12a), Picard tools (v.1.87), GATK (v.2.5.2)
Breeder:	NBRP-Rat/Kyoto University
Description:	Target capture sequencing of exons and conserved non-coding sequences. Provided by: Dr. Mikita Suyama (Kyushu University) and Dr. Takashi Kuramoto (Kyoto University)
Publications:	Yoshihara M, etal., Genom Data. 2016 Nov 14;10:155-157. eCollection 2016 Dec.

Additional Information

External Database Links

Nomenclature History

More on LOC500028
	Alliance Gene
	NCBI Gene
	Ensembl Gene
	JBrowse: rn5 rn6
	NCBI Genome Data Viewer

RGD Object Information
RGD ID:	1560448
Created:	2006-02-09
Species:	Rattus norvegicus
Last Modified:	2019-04-12
Status:	ACTIVE

RGD is funded by grant HL64541 from the National Heart, Lung, and Blood Institute on behalf of the NIH.

Functional Annotation unavailable	Annotation Distribution unavailable	Genomic Variants unavailble for Mouse Genomic Variants unavailable
Functional Annotation	Annotation Distribution	Genomic Variants

Protein-Protein Interactions unavailable	Genome Viewer unavailable	Damaging Variants unavailble for Mouse Damaging Variants unavailable
Protein-Protein Interactions	Genome Viewer	Damaging Variants

Annotation Comparison unavailable	OLGA unavailable
Annotation Comparison	OLGA	Excel (Download)

Gene Enrichment unavailable	Ortholog Finder unavailable
Gene Enrichment	Ortholog Finder