Slc38a5 (solute carrier family 38, member 5)

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Gene: Slc38a5 (solute carrier family 38, member 5) Rattus norvegicus

Analyze

Symbol:

Slc38a5

Name:

solute carrier family 38, member 5

RGD ID:

620702

Description:

Enables L-amino acid transmembrane transporter activity. Involved in amino acid transport. Predicted to be integral component of membrane. Predicted to be integral component of plasma membrane. Orthologous to human SLC38A5 (solute carrier family 38 member 5); INTERACTS WITH 17beta-estradiol; 17beta-estradiol 3-benzoate; 2,3,7,8-tetrachlorodibenzodioxine.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Also known as:

AF276870; amino acid transporter system N2; SN2; sodium-coupled neutral amino acid transporter 5; solute carrier family 38 member 5; system N transporter 2

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):	SLC38A5 (solute carrier family 38 member 5)	HGNC	Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, Panther, PhylomeDB
Mus musculus (house mouse):	Slc38a5 (solute carrier family 38, member 5)	HGNC	NCBI, OMA, HomoloGene, Inparanoid, Panther, PhylomeDB, Ensembl
Chinchilla lanigera (long-tailed chinchilla):	Slc38a5 (solute carrier family 38 member 5)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	SLC38A5 (solute carrier family 38 member 5)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	SLC38A5 (solute carrier family 38 member 5)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Slc38a5 (solute carrier family 38 member 5)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	SLC38A5 (solute carrier family 38 member 5)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	SLC38A5 (solute carrier family 38 member 5)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Slc38a5 (solute carrier family 38 member 5)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	SLC38A5 (solute carrier family 38 member 5)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Mus musculus (house mouse):	Slc38a5 (solute carrier family 38, member 5)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Danio rerio (zebrafish):	slc38a5b (solute carrier family 38 member 5b)	Alliance	DIOPT (OMA\|OrthoFinder\|PANTHER\|PhylomeDB\|TreeFam)
Danio rerio (zebrafish):	slc38a5a (solute carrier family 38 member 5a)	Alliance	DIOPT (OrthoFinder\|PANTHER\|TreeFam)
Saccharomyces cerevisiae (baker's yeast):	AVT7	Alliance	DIOPT (Ensembl Compara\|OMA\|PANTHER)
Caenorhabditis elegans (roundworm):	Y51F10.4	Alliance	DIOPT (InParanoid\|OMA\|PANTHER)
Saccharomyces cerevisiae (baker's yeast):	AVT5	Alliance	DIOPT (Ensembl Compara\|OMA\|PANTHER)
Saccharomyces cerevisiae (baker's yeast):	AVT6	Alliance	DIOPT (Ensembl Compara\|OMA\|PANTHER)
Drosophila melanogaster (fruit fly):	mah	Alliance	DIOPT (Ensembl Compara\|OMA)

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	X	14,213,727 - 14,222,498 (-)	NCBI
Rnor_6.0 Ensembl	X	14,963,921 - 14,972,675 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	X	14,963,919 - 14,972,675 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	X	15,748,231 - 15,756,314 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	X	26,244,421 - 26,253,596 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	X	26,297,889 - 26,307,057 (-)	NCBI
Celera	X	14,299,226 - 14,307,991 (-)	NCBI		Celera
Cytogenetic Map	X	q12	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

autistic disorder (ISO)

Endotoxemia (IEP)

Malformations of Cortical Development, Group II (ISO)

syndromic X-linked intellectual disability Lubs type (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

17beta-estradiol (EXP,ISO)

17beta-estradiol 3-benzoate (EXP)

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

2,3,7,8-Tetrachlorodibenzofuran (EXP)

3,7-dihydropurine-6-thione (EXP)

3-isobutyl-1-methyl-7H-xanthine (ISO)

4,4'-sulfonyldiphenol (ISO)

4-hydroxyphenyl retinamide (ISO)

6-propyl-2-thiouracil (EXP)

acrolein (ISO)

aflatoxin B1 (ISO)

alpha-pinene (ISO)

ammonium chloride (EXP)

arsenite(3-) (ISO)

benzo[a]pyrene (ISO)

bisphenol A (EXP,ISO)

carbon nanotube (ISO)

chloroprene (ISO)

choline (ISO)

cisplatin (ISO)

dexamethasone (ISO)

dibutyl phthalate (ISO)

dichloroacetic acid (ISO)

dioxygen (ISO)

dorsomorphin (ISO)

entinostat (ISO)

ethanol (EXP)

ethyl methanesulfonate (ISO)

flavonoids (EXP)

folic acid (ISO)

formaldehyde (ISO)

gentamycin (EXP)

indometacin (ISO)

ketamine (EXP)

L-methionine (ISO)

mercaptopurine (EXP)

methamphetamine (EXP)

methyl methanesulfonate (ISO)

nickel sulfate (ISO)

oxaliplatin (EXP)

ozone (ISO)

paracetamol (ISO)

pioglitazone (ISO)

purine-6-thiol (EXP)

quercetin (ISO)

SB 431542 (ISO)

SCH 23390 (EXP)

silicon dioxide (EXP)

sodium arsenite (ISO)

tamoxifen (ISO)

testosterone (EXP)

titanium dioxide (ISO)

toluene (EXP)

topotecan (EXP)

tris(2-butoxyethyl) phosphate (ISO)

valproic acid (EXP)

XL147 (ISO)

zidovudine (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

amino acid transmembrane transport (IBA)

asparagine transmembrane transport (IEA,ISO)

asparagine transport (IEA)

glutamine transport (IBA,IDA,IEA,ISO)

glycine transport (IBA,IDA,IEA,ISO)

L-alanine transmembrane transport (IEA,ISO)

L-histidine transmembrane transport (IBA,IDA,IEA,ISO)

L-serine transport (IDA)

neutral amino acid transport (IDA)

serine transport (IBA,IEA,ISO)

Cellular Component

integral component of membrane (IEA)

integral component of plasma membrane (IBA)

Molecular Function

alanine transmembrane transporter activity (IEA,ISO)

amino acid transmembrane transporter activity (IBA,IDA)

glycine transmembrane transporter activity (IBA,IDA,IEA,ISO)

L-asparagine transmembrane transporter activity (IEA,ISO)

L-glutamine transmembrane transporter activity (IBA,IDA,IEA,ISO)

L-histidine transmembrane transporter activity (IDA,IEA,ISO)

L-serine transmembrane transporter activity (IDA)

neutral amino acid transmembrane transporter activity (IDA)

serine transmembrane transporter activity (IEA,ISO)

References

References - curated


1.	Baird FE, etal., J Physiol. 2004 Sep 1;559(Pt 2):367-81. doi: 10.1113/jphysiol.2003.060293. Epub 2004 Jun 24.
2.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
3.	Nakanishi T, etal., Am J Physiol Cell Physiol 2001 Dec;281(6):C1757-68.
4.	NCBI rat LocusLink and RefSeq merged data July 26, 2002
5.	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
6.	RGD automated import pipeline for gene-chemical interactions
7.	Wang W, etal., J Surg Res. 2011 Apr;166(2):290-7. doi: 10.1016/j.jss.2009.08.027. Epub 2009 Sep 23.

Additional References at PubMed

PMID:11243884	PMID:12477932	PMID:15390093	PMID:16629640	PMID:22821889	PMID:24333324

Genomics

Comparative Map Data

Slc38a5
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	X	14,213,727 - 14,222,498 (-)	NCBI
Rnor_6.0 Ensembl	X	14,963,921 - 14,972,675 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	X	14,963,919 - 14,972,675 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	X	15,748,231 - 15,756,314 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	X	26,244,421 - 26,253,596 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	X	26,297,889 - 26,307,057 (-)	NCBI
Celera	X	14,299,226 - 14,307,991 (-)	NCBI		Celera
Cytogenetic Map	X	q12	NCBI

SLC38A5
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	X	48,458,537 - 48,470,260 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	X	48,458,544 - 48,470,260 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	X	48,316,927 - 48,328,648 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	X	48,201,871 - 48,213,509 (-)	NCBI	NCBI36		hg18	NCBI36
Build 34	X	48,073,181 - 48,084,819	NCBI
Celera	X	53,337,091 - 53,348,808 (+)	NCBI
Cytogenetic Map	X	p11.23	NCBI
HuRef	X	45,981,068 - 45,992,834 (-)	NCBI		HuRef
CHM1_1	X	48,348,162 - 48,359,900 (-)	NCBI		CHM1_1

Slc38a5
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	X	8,137,620 - 8,146,418 (+)	NCBI	GRCm39		mm39
GRCm39 Ensembl	X	8,137,372 - 8,146,418 (+)	Ensembl
GRCm38	X	8,271,381 - 8,280,179 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	X	8,271,133 - 8,280,179 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	X	7,848,518 - 7,857,305 (+)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	X	7,428,353 - 7,437,133 (+)	NCBI			mm8
Celera	X	3,190,181 - 3,198,970 (-)	NCBI		Celera
Cytogenetic Map	X	A1.1	NCBI

Slc38a5
(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_004955543	16,089 - 24,668 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955543	15,968 - 24,644 (-)	NCBI	ChiLan1.0	ChiLan1.0

SLC38A5
(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	X	48,621,018 - 48,632,682 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	X	48,621,018 - 48,632,682 (-)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	X	40,756,423 - 40,768,327 (-)	NCBI	Mhudiblu_PPA_v0		panPan3

SLC38A5
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	X	41,709,441 - 41,718,702 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	X	41,709,467 - 41,717,080 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	X	16,085,681 - 16,094,898 (-)	NCBI
ROS_Cfam_1.0	X	41,845,558 - 41,854,816 (-)	NCBI
UMICH_Zoey_3.1	X	41,832,556 - 41,841,772 (-)	NCBI
UNSW_CanFamBas_1.0	X	41,820,836 - 41,830,050 (-)	NCBI
UU_Cfam_GSD_1.0	X	41,914,395 - 41,923,619 (-)	NCBI

Slc38a5
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	X	34,178,875 - 34,200,906 (-)	NCBI
SpeTri2.0	NW_004936721	419,286 - 441,224 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

SLC38A5
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	X	42,585,013 - 42,605,511 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	X	42,590,608 - 42,601,537 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	X	47,547,735 - 47,558,567 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

SLC38A5
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	X	45,588,992 - 45,598,771 (-)	NCBI
Vero_WHO_p1.0	NW_023666076	11,040,195 - 11,052,121 (-)	NCBI

Slc38a5
(Heterocephalus glaber - naked mole-rat)

Naked Mole-rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Naked Mole-rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla 1.0	NW_004624893	275,906 - 284,883 (-)	NCBI

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
731181	Uae27	Urinary albumin excretion QTL 27	2.7	0.0059	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	X	1	44092703	Rat
634325	Bw13	Body weight QTL 13	0		body mass (VT:0001259)	body weight (CMO:0000012)	X	1662453	21592783	Rat
70165	Bp64	Blood pressure QTL 64	5.2		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	X	1662609	33443848	Rat
631204	Gluco15	Glucose level QTL 15		0.001	blood glucose amount (VT:0000188)	blood glucose level area under curve (AUC) (CMO:0000350)	X	1838166	24331837	Rat
1298071	Edpm12	Estrogen-dependent pituitary mass QTL 12	3.2		pituitary gland mass (VT:0010496)	pituitary gland wet weight (CMO:0000853)	X	4282140	49282140	Rat
631666	Iddm5	Insulin dependent diabetes mellitus QTL 5			blood glucose amount (VT:0000188)	plasma glucose level (CMO:0000042)	X	5954078	50954078	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	63
Count of miRNA genes:	49
Interacting mature miRNAs:	55
Transcripts:	ENSRNOT00000038068
Prediction methods:	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		2	20	20	10	20			49		5	9
Low	2	34	8	7	2	7			25	21	29	2
Below cutoff	1	7	19	9	5	9	6	9		11	7		6

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_138854	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_008773068	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039099443	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039099444	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039099445	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AF276870	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC128725	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH474078	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000351	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000038068 ⟹ ENSRNOP00000038781

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	X	14,963,921 - 14,972,389 (-)	Ensembl

RefSeq Acc Id:

ENSRNOT00000079664 ⟹ ENSRNOP00000073818

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	X	14,963,921 - 14,972,675 (-)	Ensembl

RefSeq Acc Id:

NM_138854 ⟹ NP_620209

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	X	14,213,727 - 14,222,498 (-)	NCBI
Rnor_6.0	X	14,963,919 - 14,972,675 (-)	NCBI
Rnor_5.0	X	15,748,231 - 15,756,314 (-)	NCBI
RGSC_v3.4	X	26,244,421 - 26,253,596 (-)	RGD
Celera	X	14,299,226 - 14,307,991 (-)	RGD

Sequence:

show sequence

CCCACGCGTCCGCACCTAGTTGCACTCGCATACTGGTCAGTTCTGTCCCAGGAAGAGGGACGCT
TCAATTTGCTTCGGTCTCTGCTGAAGAAAGTCAGAACCGGAATAAAAGCGGATGGAAATGCAGG
AACCAAAGATGAACGGAACCCTCTCTACGGGTGCTGCTGCGGGCTACAGACAGGAACGCGAAGG
CTTCCTGCCCACCACCCATGGCCCTGCTCCAGGGAGGAAACCTGTCCAATTCTTGGATTTCGAG
GGGAAGACATCATTCGGAATGTCAGTGTTCAACCTTAGCAATGCCATCATGGGGAGTGGCATCC
TGGGGCTCGCCTACGCCATGGCCCACACTGGAGTCATCTTCTTCTTGGCCCTCTTGCTGTGCAT
TGCCCTCCTGTCTTCTTACTCTATCCACCTCCTGCTGACCTGCGCCAGTGTTGTAGGAATCCGC
GCCTATGAGCAGCTGGGACAGAGGGCATTTGGACCTGCCGGGAAAGTAGTGGTGGCCATTATCA
TCTGTCTGCACAATGTTGGCGCTATGTCCAGTTACCTGTTCATCATCAAATCTGAACTGCCCCT
GGTTATTGGCACCTTCCTGCACATGGACCCTGAGGGGGACTGGTTCTTGAAGGGAAACCTCCTC
ATCATCCTGGTTAGCTTGTTAATCATCTTGCCTCTGGCTCTCATGAAACATCTGGGCTACTTGG
GGTATACAAGCAGCCTCTCTCTGACCTGCATGCTGTTTTTCCTTATTTCAGTCATCTATAAGAA
GTTCCAGCTTGGCTGTGTTGTGAGCCACAATGACACAGTAGTGGAGAGTGAACCAGCTCCCTTG
CAGGCGTTTAATAGCAGCTGTGAGGCCAAGCTCTTCACAGTTGACTCACAGATGTCTTACACAG
TGCCTATTATGGCTTTTGCCTTTGTCTGCCACCCTGAGGTGCTGCCCATTTACACGGAACTTTG
CTGCCCTACTCAGCGCAGGATGCAAGCTGTGGCCAACATGTCCATCGGGGCTATGTTCATCATG
TACGGACTCACAGCTACCTTTGGATACCTTACCTTCTACAGCACTGTGAAGGCAGAGATGCTGG
AGATGTACACCCAGGAGGACCTGCTTATTCTTTGTGTGCGCCTGGCCGTACTGCTTGCAGTAAC
CCTCACTGTGCCTGTTGTCCTTTTCCCTATCCGCCGAGCCCTCCAGCAGCTGCTCTTCCCAAGT
AAGGCCTTCAGCTGGCCACGACATGTGGCAATTGCCCTGATTCTGCTTAATTTGGTCAATATCC
TTGTCATTTGTGTGCCAACCATCCGGGATATCTTTGGGTTTATTGGCTCCACTTCAGCCCCTAG
CCTCATCTTCATCCTTCCCAGTGTCTTCTACCTCCGCATTGTACCTGCTGACATGGAACCCTTG
TTTTCCTGGCCCAAGATCCAGGCCCTGTGTTTTGGCGTCCTGGGAGTCCTCTTCATGGCCATCA
GTCTGGGCTTTATGTTTGCTAATTGGGCTACAGGCCAGAGCCGTATGTCTGGCCATTGAGCTGG
CCTGTCCTGCCTCACTCAGTCCCTGTGCTCACATGTGTGTATATTAGGGAATCCAAGTCACTTT
CCTGAGTCCCTTCTGCCTGGGACATGGAGGTGGCTGGTCTCTAGTAACACTGCTGTGGGAAATG
GGGACAGTCGAGGAGGCATAGTAAGTAGTCCATTTCCTTTTCCCCAGAGCTGCCTCACTGCCGA
CCCCATGAGAGGAGGAAGGGAGGCCAGCTCCTTAGAAGAGTTCTTACCCAACATAGTTCTCACT
TCCTAGATGAAGCTGTTAGGCTTACCCTGGCGCTAAAAGGGAAGAATAAAGATGCTGAATGGCA
AAAAAAAAAAAAAAAGAAAAAAAAAAAAAAAAAAA

hide sequence

RefSeq Acc Id:

XM_008773068 ⟹ XP_008771290

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	X	14,213,727 - 14,222,291 (-)	NCBI
Rnor_6.0	X	14,963,919 - 14,972,382 (-)	NCBI

Sequence:

show sequence

CTATTTCCGCACTTAAATGGCCATTTCAGGCGCTGTGGGGATGGAAATGCAGGAACCAAAGATG
AACGGAACCCTCTCTACGGGTGCTGCTGCGGGCTACAGACAGGAACGCGAAGGCTTCCTGCCCA
CCACCCATGGCCCTGCTCCAGGGAGGAAACCTGTCCAATTCTTGGATTTCGAGGGGAAGACATC
ATTCGGAATGTCAGTGTTCAACCTTAGCAATGCCATCATGGGGAGTGGCATCCTGGGGCTCGCC
TACGCCATGGCCCACACTGGAGTCATCTTCTTCTTGGCCCTCTTGCTGTGCATTGCCCTCCTGT
CTTCTTACTCTATCCACCTCCTGCTGACCTGCGCCAGTGTTGTAGGAATCCGCGCCTATGAGCA
GCTGGGACAGAGGGCATTTGGACCTGCCGGGAAAGTAGTGGTGGCCATTATCATCTGTCTGCAC
AATGTTGGCGCTATGTCCAGTTACCTGTTCATCATCAAATCTGAACTGCCCCTGGTTATTGGCA
CCTTCCTGCACATGGACCCTGAGGGGGACTGGTTCTTGAAGGGAAACCTCCTCATCATCCTGGT
TAGCTTGTTAATCATCTTGCCTCTGGCTCTCATGAAACATCTGGGCTACTTGGGGTATACAAGC
AGCCTCTCTCTGACCTGCATGCTGTTTTTCCTTATTTCAGTCATCTATAAGAAGTTCCAGCTTG
GCTGTGTTGTGAGCCACAATGACACAGTAGTGGAGAGTGAACCAGCTCCCTTGCAGGCGTTTAA
TAGCAGCTGTGAGGCCAAGCTCTTCACAGTTGACTCACAGATGTCTTACACAGTGCCTATTATG
GCTTTTGCCTTTGTCTGCCACCCTGAGGTGCTGCCCATTTACACGGAACTTTGCTGCCCTACTC
AGCGCAGGATGCAAGCTGTGGCCAACATGTCCATCGGGGCTATGTTCATCATGTACGGACTCAC
AGCTACCTTTGGATACCTTACCTTCTACAGCACTGTGAAGGCAGAGATGCTGGAGATGTACACC
CAGGAGGACCTGCTTATTCTTTGTGTGCGCCTGGCCGTACTGCTTGCAGTAACCCTCACTGTGC
CTGTTGTCCTTTTCCCTATCCGCCGAGCCCTCCAGCAGCTGCTCTTCCCAAGTAAGGCCTTCAG
CTGGCCACGACATGTGGCCATTGCCCTGATCCTGCTTATTTTGGTCAATATCCTTGTCATTTGT
GTGCCAACCATCCGGGATATCTTTGGGTTTATTGGCTCCACTTCAGCCCCTAGCCTCATCTTCA
TCCTTCCCAGTGTCTTCTACCTCCGCATTGTACCTGCTGACATGGAACCCTTGTTTTCCTGGCC
CAAGATCCAGGCCCTGTGTTTTGGCGTCCTGGGAGTCCTCTTCATGGCCATCAGTCTGGGCTTT
ATGTTTGCTAATTGGGCTACAGGCCAGAGCCGTATGTCTGGCCATTGAGCTGGCCTGTCCTGCC
TCACTCAGTCCCTGTGCTCACATGTGTGTATATTAGGGAATCCAAGTCACTTTCCTGAGTCCCT
TCTGCCTGGGACATGGAGGTGGCTGGTCTCTAGTAACACTGCTGTGGGAAATGGGGACAGTCGA
GGAGGCATAGTAAGTAGTCCATTTCCTTTTCCCCAGAGCTGCCTCACTGCCGACCCCATGAGAG
GAGGAAGGGAGGCCAGCTCCTTAGAAGGGTTCTTACCCAACATAGTTCTCACTTCCTAGATGAA
GCTGTTAGGCTTACCCTGGCGCTAAAAGGGAAGAATAAAGATGCTGAATGGCAA

hide sequence

RefSeq Acc Id:

XM_039099443 ⟹ XP_038955371

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	X	14,213,727 - 14,222,277 (-)	NCBI

RefSeq Acc Id:

XM_039099444 ⟹ XP_038955372

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	X	14,213,727 - 14,222,260 (-)	NCBI

RefSeq Acc Id:

XM_039099445 ⟹ XP_038955373

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	X	14,213,727 - 14,222,273 (-)	NCBI

Protein Sequences


Protein RefSeqs	NP_620209	(Get FASTA)	NCBI Sequence Viewer
	XP_008771290	(Get FASTA)	NCBI Sequence Viewer
	XP_038955371	(Get FASTA)	NCBI Sequence Viewer
	XP_038955372	(Get FASTA)	NCBI Sequence Viewer
	XP_038955373	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	A2VCW5	(Get FASTA)	NCBI Sequence Viewer
	AAI28726	(Get FASTA)	NCBI Sequence Viewer
	AAK69075	(Get FASTA)	NCBI Sequence Viewer
	EDL83782	(Get FASTA)	NCBI Sequence Viewer
	EDL83783	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_620209 ⟸ NM_138854

- Sequence:

show sequence

MEMQEPKMNGTLSTGAAAGYRQEREGFLPTTHGPAPGRKPVQFLDFEGKTSFGMSVFNLSNAIM
GSGILGLAYAMAHTGVIFFLALLLCIALLSSYSIHLLLTCASVVGIRAYEQLGQRAFGPAGKVV
VAIIICLHNVGAMSSYLFIIKSELPLVIGTFLHMDPEGDWFLKGNLLIILVSLLIILPLALMKH
LGYLGYTSSLSLTCMLFFLISVIYKKFQLGCVVSHNDTVVESEPAPLQAFNSSCEAKLFTVDSQ
MSYTVPIMAFAFVCHPEVLPIYTELCCPTQRRMQAVANMSIGAMFIMYGLTATFGYLTFYSTVK
AEMLEMYTQEDLLILCVRLAVLLAVTLTVPVVLFPIRRALQQLLFPSKAFSWPRHVAIALILLN
LVNILVICVPTIRDIFGFIGSTSAPSLIFILPSVFYLRIVPADMEPLFSWPKIQALCFGVLGVL
FMAISLGFMFANWATGQSRMSGH

hide sequence

RefSeq Acc Id:

XP_008771290 ⟸ XM_008773068

- Peptide Label:

isoform X1

- Sequence:

show sequence

MAISGAVGMEMQEPKMNGTLSTGAAAGYRQEREGFLPTTHGPAPGRKPVQFLDFEGKTSFGMSV
FNLSNAIMGSGILGLAYAMAHTGVIFFLALLLCIALLSSYSIHLLLTCASVVGIRAYEQLGQRA
FGPAGKVVVAIIICLHNVGAMSSYLFIIKSELPLVIGTFLHMDPEGDWFLKGNLLIILVSLLII
LPLALMKHLGYLGYTSSLSLTCMLFFLISVIYKKFQLGCVVSHNDTVVESEPAPLQAFNSSCEA
KLFTVDSQMSYTVPIMAFAFVCHPEVLPIYTELCCPTQRRMQAVANMSIGAMFIMYGLTATFGY
LTFYSTVKAEMLEMYTQEDLLILCVRLAVLLAVTLTVPVVLFPIRRALQQLLFPSKAFSWPRHV
AIALILLILVNILVICVPTIRDIFGFIGSTSAPSLIFILPSVFYLRIVPADMEPLFSWPKIQAL
CFGVLGVLFMAISLGFMFANWATGQSRMSGH

hide sequence

RefSeq Acc Id:

ENSRNOP00000073818 ⟸ ENSRNOT00000079664

RefSeq Acc Id:

ENSRNOP00000038781 ⟸ ENSRNOT00000038068

RefSeq Acc Id:	XP_038955371 ⟸ XM_039099443
- Peptide Label:	isoform X2

RefSeq Acc Id:	XP_038955373 ⟸ XM_039099445
- Peptide Label:	isoform X3

RefSeq Acc Id:	XP_038955372 ⟸ XM_039099444
- Peptide Label:	isoform X3

Protein Domains

Aa_trans

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

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:620702	AgrOrtholog
Ensembl Genes	ENSRNOG00000027767	Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000038781	UniProtKB/TrEMBL
	ENSRNOP00000073818	ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript	ENSRNOT00000038068	UniProtKB/TrEMBL
	ENSRNOT00000079664	ENTREZGENE, UniProtKB/Swiss-Prot
IMAGE_CLONE	IMAGE:8362014	IMAGE-MGC_LOAD
InterPro	AA_transpt_TM	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report	rno:192208	UniProtKB/Swiss-Prot
MGC_CLONE	MGC:156591	IMAGE-MGC_LOAD
NCBI Gene	192208	ENTREZGENE
Pfam	Aa_trans	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen	Slc38a5	PhenoGen
UniProt	A0A0H2UHW1_RAT	UniProtKB/TrEMBL
	A2VCW5	ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary	Q91XR7	UniProtKB/Swiss-Prot

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2005-01-20	Slc38a5	solute carrier family 38, member 5	AF276870	amino acid transporter system N2	Symbol and Name updated	1299863	APPROVED
2002-08-07	AF276870	amino acid transporter system N2			Symbol and Name status set to provisional	70820	PROVISIONAL

RGD Curation Notes

Note Type	Note	Reference
gene_expression	abundant in the liver, also expressed in brain, lung, stomach, kidney, testis, and spleen	628449
gene_homology	amino acid sequence identity between rat and human is 86%	628449
gene_process	mediates H+ movement across the membrane, and Na+-dependent transport of neutral amino into cells, leading to intracellular alkalization	628449
gene_protein	contains 471 amino acids	628449
gene_regulation	transport mechanism involves the influx of Na+ and amino acids coupled to the efflux of H+ and is electrogenic, Li+ tolerant, and pH sensitive	628449
gene_transcript	cDNA is 1,891 bp in length	628449

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)

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Imported Disease Annotations - ClinVar