Slc38a5 (solute carrier family 38, member 5) - Rat Genome Database

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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 ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X14,213,727 - 14,222,498 (-)NCBI
Rnor_6.0 EnsemblX14,963,921 - 14,972,675 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0X14,963,919 - 14,972,675 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0X15,748,231 - 15,756,314 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X26,244,421 - 26,253,596 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1X26,297,889 - 26,307,057 (-)NCBI
CeleraX14,299,226 - 14,307,991 (-)NCBICelera
Cytogenetic MapXq12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


References

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 AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X14,213,727 - 14,222,498 (-)NCBI
Rnor_6.0 EnsemblX14,963,921 - 14,972,675 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0X14,963,919 - 14,972,675 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0X15,748,231 - 15,756,314 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X26,244,421 - 26,253,596 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1X26,297,889 - 26,307,057 (-)NCBI
CeleraX14,299,226 - 14,307,991 (-)NCBICelera
Cytogenetic MapXq12NCBI
SLC38A5
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 EnsemblX48,458,537 - 48,470,260 (-)EnsemblGRCh38hg38GRCh38
GRCh38X48,458,544 - 48,470,260 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37X48,316,927 - 48,328,648 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36X48,201,871 - 48,213,509 (-)NCBINCBI36hg18NCBI36
Build 34X48,073,181 - 48,084,819NCBI
CeleraX53,337,091 - 53,348,808 (+)NCBI
Cytogenetic MapXp11.23NCBI
HuRefX45,981,068 - 45,992,834 (-)NCBIHuRef
CHM1_1X48,348,162 - 48,359,900 (-)NCBICHM1_1
Slc38a5
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X8,137,620 - 8,146,418 (+)NCBIGRCm39mm39
GRCm39 EnsemblX8,137,372 - 8,146,418 (+)Ensembl
GRCm38X8,271,381 - 8,280,179 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX8,271,133 - 8,280,179 (+)EnsemblGRCm38mm10GRCm38
MGSCv37X7,848,518 - 7,857,305 (+)NCBIGRCm37mm9NCBIm37
MGSCv36X7,428,353 - 7,437,133 (+)NCBImm8
CeleraX3,190,181 - 3,198,970 (-)NCBICelera
Cytogenetic MapXA1.1NCBI
Slc38a5
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495554316,089 - 24,668 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495554315,968 - 24,644 (-)NCBIChiLan1.0ChiLan1.0
SLC38A5
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1X48,621,018 - 48,632,682 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX48,621,018 - 48,632,682 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0X40,756,423 - 40,768,327 (-)NCBIMhudiblu_PPA_v0panPan3
SLC38A5
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X41,709,441 - 41,718,702 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX41,709,467 - 41,717,080 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX16,085,681 - 16,094,898 (-)NCBI
ROS_Cfam_1.0X41,845,558 - 41,854,816 (-)NCBI
UMICH_Zoey_3.1X41,832,556 - 41,841,772 (-)NCBI
UNSW_CanFamBas_1.0X41,820,836 - 41,830,050 (-)NCBI
UU_Cfam_GSD_1.0X41,914,395 - 41,923,619 (-)NCBI
Slc38a5
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X34,178,875 - 34,200,906 (-)NCBI
SpeTri2.0NW_004936721419,286 - 441,224 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SLC38A5
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX42,585,013 - 42,605,511 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X42,590,608 - 42,601,537 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X47,547,735 - 47,558,567 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SLC38A5
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X45,588,992 - 45,598,771 (-)NCBI
Vero_WHO_p1.0NW_02366607611,040,195 - 11,052,121 (-)NCBI
Slc38a5
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624893275,906 - 284,883 (-)NCBI


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
731181Uae27Urinary albumin excretion QTL 272.70.0059urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)X144092703Rat
634325Bw13Body weight QTL 130body mass (VT:0001259)body weight (CMO:0000012)X166245321592783Rat
70165Bp64Blood pressure QTL 645.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)X166260933443848Rat
631204Gluco15Glucose level QTL 150.001blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)X183816624331837Rat
1298071Edpm12Estrogen-dependent pituitary mass QTL 123.2pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)X428214049282140Rat
631666Iddm5Insulin dependent diabetes mellitus QTL 5blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)X595407850954078Rat

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

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000038068   ⟹   ENSRNOP00000038781
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX14,963,921 - 14,972,389 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000079664   ⟹   ENSRNOP00000073818
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX14,963,921 - 14,972,675 (-)Ensembl
RefSeq Acc Id: NM_138854   ⟹   NP_620209
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X14,213,727 - 14,222,498 (-)NCBI
Rnor_6.0X14,963,919 - 14,972,675 (-)NCBI
Rnor_5.0X15,748,231 - 15,756,314 (-)NCBI
RGSC_v3.4X26,244,421 - 26,253,596 (-)RGD
CeleraX14,299,226 - 14,307,991 (-)RGD
Sequence:
RefSeq Acc Id: XM_008773068   ⟹   XP_008771290
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X14,213,727 - 14,222,291 (-)NCBI
Rnor_6.0X14,963,919 - 14,972,382 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039099443   ⟹   XP_038955371
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X14,213,727 - 14,222,277 (-)NCBI
RefSeq Acc Id: XM_039099444   ⟹   XP_038955372
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X14,213,727 - 14,222,260 (-)NCBI
RefSeq Acc Id: XM_039099445   ⟹   XP_038955373
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X14,213,727 - 14,222,273 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_620209   ⟸   NM_138854
- Sequence:
RefSeq Acc Id: XP_008771290   ⟸   XM_008773068
- Peptide Label: isoform X1
- 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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
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
BBDP/Wor (RGD)
Visual CSV TAB Printer
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)
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
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
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
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
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
MHS/Gib (RGD)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
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
SBH/Ygl (MCW)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
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
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

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