Slc28a1 (solute carrier family 28 member 1) - Chinchilla Research Resource Database
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Gene: Slc28a1 (solute carrier family 28 member 1) Rattus norvegicus
Analyze
Symbol: Slc28a1
Name: solute carrier family 28 member 1
CRRD ID: 621223
Description: Exhibits pyrimidine- and adenine-specific:sodium symporter activity. Involved in pyrimidine nucleobase transport. Localizes to apical plasma membrane. Orthologous to human SLC28A1 (solute carrier family 28 member 1); PARTICIPATES IN capecitabine pharmacodynamics pathway; capecitabine pharmacokinetics pathway; gemcitabine pharmacodynamics pathway; INTERACTS WITH 5-iodo-2'-deoxyuridine; ammonium chloride; copper atom.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: CNT 1; Cnt1; concentrative nucleoside transporter 1; Na(+)/nucleoside cotransporter 1; sodium-coupled nucleoside transporter 1; sodium/nucleoside cotransporter 1; solute carrier family 28 (concentrative nucleoside transporter), member 1; solute carrier family 28 (sodium-coupled nucleoside transporter), member 1; solute carrier family 28, member 1
Orthologs:
Homo sapiens (human) : SLC28A1 (solute carrier family 28 member 1)  HGNC  Alliance
Mus musculus (house mouse) : Slc28a1 (solute carrier family 28 (sodium-coupled nucleoside transporter), member 1)  MGI  Alliance
Chinchilla lanigera (long-tailed chinchilla) : Slc28a1 (solute carrier family 28 member 1)
Pan paniscus (bonobo/pygmy chimpanzee) : SLC28A1 (solute carrier family 28 member 1)
Canis lupus familiaris (dog) : SLC28A1 (solute carrier family 28 member 1)
Ictidomys tridecemlineatus (thirteen-lined ground squirrel) : Slc28a1 (solute carrier family 28 member 1)
Sus scrofa (pig) : SLC28A1 (solute carrier family 28 member 1)
Chlorocebus sabaeus (African green monkey) : SLC28A1 (solute carrier family 28 member 1)
Heterocephalus glaber (naked mole-rat) : Slc28a1 (solute carrier family 28 member 1)
more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.01142,948,942 - 142,992,410 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1142,950,540 - 142,992,615 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01143,893,827 - 143,937,045 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41137,323,995 - 137,365,983 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11137,402,400 - 137,444,389 (+)NCBI
Celera1127,134,227 - 127,174,932 (+)NCBICelera
Cytogenetic Map1q31NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

References

Additional References at PubMed
PMID:12176019   PMID:16014043   PMID:21998139  


Genomics

Comparative Map Data
Slc28a1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.01142,948,942 - 142,992,410 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1142,950,540 - 142,992,615 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01143,893,827 - 143,937,045 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41137,323,995 - 137,365,983 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11137,402,400 - 137,444,389 (+)NCBI
Celera1127,134,227 - 127,174,932 (+)NCBICelera
Cytogenetic Map1q31NCBI
SLC28A1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1584,884,654 - 84,945,798 (+)EnsemblGRCh38hg38GRCh38
GRCh381584,884,350 - 84,975,649 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371585,427,794 - 85,489,027 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361583,228,917 - 83,290,033 (+)NCBINCBI36hg18NCBI36
Build 341583,228,916 - 83,240,271NCBI
Celera1561,854,219 - 61,915,476 (+)NCBI
Cytogenetic Map15q25.3NCBI
HuRef1561,513,859 - 61,574,856 (+)NCBIHuRef
CHM1_11585,268,880 - 85,360,077 (+)NCBICHM1_1
Slc28a1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39780,763,017 - 80,820,164 (+)NCBI
GRCm38781,113,269 - 81,170,416 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl781,114,799 - 81,170,416 (+)EnsemblGRCm38mm10GRCm38
MGSCv37788,259,685 - 88,315,302 (+)NCBIGRCm37mm9NCBIm37
MGSCv36780,988,312 - 81,043,929 (+)NCBImm8
Celera778,524,102 - 78,579,064 (+)NCBICelera
Cytogenetic Map7D3NCBI
Slc28a1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541614,226,278 - 14,268,350 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495541614,226,411 - 14,267,962 (-)NCBIChiLan1.0ChiLan1.0
SLC28A1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11582,875,337 - 82,936,104 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1582,875,339 - 82,935,762 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01563,551,499 - 63,613,461 (+)NCBIMhudiblu_PPA_v0panPan3
SLC28A1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl354,128,680 - 54,367,400 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1354,128,172 - 54,177,544 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Slc28a1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_00493648316,929,896 - 16,976,560 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SLC28A1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl752,605,289 - 52,652,876 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1752,606,428 - 52,652,928 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
SLC28A1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1 Ensembl293,403,685 - 3,468,626 (-)Ensembl
ChlSab1.1293,387,226 - 3,469,461 (-)NCBI
Slc28a1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462476818,117,729 - 18,204,613 (+)NCBI

Position Markers
RH127467  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01142,992,028 - 142,992,229NCBIRnor6.0
Rnor_5.01143,936,663 - 143,936,864UniSTSRnor5.0
RGSC_v3.41137,366,085 - 137,366,286UniSTSRGSC3.4
Celera1127,175,034 - 127,175,235UniSTS
Cytogenetic Map1q31UniSTS
RH 3.4 Map11081.6UniSTS
44.MMHAP69FRG11.seq  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01142,969,638 - 142,969,797NCBIRnor6.0
Rnor_5.01143,914,273 - 143,914,432UniSTSRnor5.0
RGSC_v3.41137,342,622 - 137,342,781UniSTSRGSC3.4
Celera1127,152,774 - 127,152,933UniSTS
Cytogenetic Map1q31UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
CRRD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
70225Bp58Blood pressure QTL 583.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)134993530173445086Rat
10059597Bp377Blood pressure QTL 3773.420.025arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)135377692217372257Rat
2313402Anxrr24Anxiety related response QTL 24aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)149147799156446783Rat
1578654Bss10Bone structure and strength QTL 104femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)149578577169852184Rat
634314Niddm44Non-insulin dependent diabetes mellitus QTL 44blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)149578693217054291Rat
2298545Neuinf8Neuroinflammation QTL 84.6nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)158354072161711996Rat
1578780Cm52Cardiac mass QTL 523.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)182788437239853971Rat
724529Cm16Cardiac mass QTL 162.7heart mass (VT:0007028)calculated heart weight (CMO:0000073)190804143161321256Rat
724521Uae1Urinary albumin excretion QTL 13.80.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)194201400184846632Rat
1358902Bw47Body weight QTL 471.67body mass (VT:0001259)body weight (CMO:0000012)194201400197187904Rat
1300153Bp171Blood pressure QTL 1713.37arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)194364073153076991Rat
724567Tcas6Tongue tumor susceptibility QTL 66.85tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)195304961156446783Rat
1331793Bp200Blood pressure QTL 2003.71601arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)199983293188289386Rat
1331751Bp199Blood pressure QTL 1993.60022arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)199983293198656062Rat
1331749Hrtrt11Heart rate QTL 112.973heart pumping trait (VT:2000009)heart rate (CMO:0000002)199983293216213510Rat
70209Niddm23Non-insulin dependent diabetes mellitus QTL 232.82blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)199983293216325819Rat
731168Bp154Blood pressure QTL 1543.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1100131562236763528Rat
2293142Bp314Blood pressure QTL 314arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1100354344145354344Rat
8655649Arrd1Age-related retinal degeneration QTL 14.89retinal layer morphology trait (VT:0003727)percentage of study population developing retinopathy during a period of time (CMO:0002453)1106002252202571904Rat
61370Mcs3Mammary carcinoma susceptibility QTL 32.15mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1108057233167517487Rat
1641897Alcrsp1Alcohol response QTL 1response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)1108417193153417193Rat
2317833Alcrsp19Alcohol response QTL 1912.40.001response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)1108417193153417193Rat
1354623Rf46Renal function QTL 463.8blood creatinine amount (VT:0005328)plasma creatinine level (CMO:0000537)1108986301161784422Rat
1354591Cm36Cardiac mass QTL 364.1heart left ventricle mass (VT:0007031)calculated heart weight (CMO:0000073)1108986301219232156Rat
1354615Cm32Cardiac mass QTL 325.2heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)1108986301219232156Rat
1354606Bp246Blood pressure QTL 2463.6arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)1108986301238830534Rat
2303591Gluco41Glucose level QTL 412blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1109634374154634374Rat
9590300Scort16Serum corticosterone level QTL 164.390.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)1110620749155620749Rat
8694370Bw154Body weight QTL 1548.910.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)1110620749155620749Rat
61399Tcat1Tongue tumor resistance QTL 13.3tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 5 mm (CMO:0001879)1111446783156446783Rat
61346Rf2Renal disease susceptibility QTL 23.7urine protein amount (VT:0005160)urine protein level (CMO:0000591)1111446783156446783Rat
631496Bp97Blood pressure QTL 973.08arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1113593576158593576Rat
1300158Bp173Blood pressure QTL 1733.48arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)1122614824201146953Rat
7794788Mcs32Mammary carcinoma susceptibility QTL 322.61mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)1122614824262664716Rat
2313060Bss71Bone structure and strength QTL 712.60.0001long bone metaphysis morphology trait (VT:0000133)tibia midshaft total cross-sectional area (CMO:0001715)1124090312169090312Rat
631199Cm23Cardiac mass QTL 234.60.0004heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)1124603592188289386Rat
7421630Bp362Blood pressure QTL 3620.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1125875758262433692Rat
631205Bp196Blood pressure QTL 19640.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1126240667217054291Rat
2293140Bp313Blood pressure QTL 313arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1129208943174208943Rat
631544Bp84Blood pressure QTL 845.6arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1130779148198585664Rat
1358189Cstrr1Cold stress response QTL 10.0001catecholamine amount (VT:0010543)urine norepinephrine level (CMO:0001629)1130779148199254774Rat
1578770Stresp23Stress response QTL 23kidney sympathetic nerve activity (VT:0004050)stimulated renal sympathetic nerve activity to basal renal sympathetic nerve activity ratio (CMO:0001786)1130779148199254774Rat
1641895Bp298Blood pressure QTL 298arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1130779148199254774Rat
631549Bp89Blood pressure QTL 895.7arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1130779320219238476Rat
631570Bp94Blood pressure QTL 940.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1130917121152871103Rat
1598850Bp297Blood pressure QTL 2972.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1131334152176334152Rat
1598866Bp287Blood pressure QTL 2875.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1131334152176334152Rat
631654Bp107Blood pressure QTL 107arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1133076978178076978Rat
9685799Bp375Blood pressure QTL 375arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1133076978178076978Rat
634348Bp138Blood pressure QTL 138arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1133076978184188922Rat
61442Strs1Sensitivity to stroke QTL 17.4cerebrum integrity trait (VT:0010549)post-insult time to onset of cerebrovascular lesion (CMO:0002343)1133946489178946489Rat
9685802Bp376Blood pressure QTL 376arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1134089429179089429Rat
724562Rends1Renal damage susceptibility QTL 10.05kidney glomerulus integrity trait (VT:0010546)index of glomerular damage (CMO:0001135)1137787261236763528Rat
61341Bp26Blood pressure QTL 26arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1137787261236763528Rat
631202Gluco13Glucose level QTL 130.0001blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1139523928170246858Rat
738006Anxrr14Anxiety related response QTL 1440.00035locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)1141296374186296374Rat
738028Anxrr12Anxiety related response QTL 124.90.00001locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)1141296374186296374Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:57
Count of miRNA genes:50
Interacting mature miRNAs:52
Transcripts:ENSRNOT00000025621
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 12
Low 1 27 1 1 1 11 9 1
Below cutoff 2 16 44 28 17 28 8 10 33 6 29 10 8

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000025621   ⟹   ENSRNOP00000025621
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1142,950,540 - 142,991,926 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000077441   ⟹   ENSRNOP00000070095
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1142,951,094 - 142,992,615 (+)Ensembl
RefSeq Acc Id: NM_053863   ⟹   NP_446315
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01142,950,540 - 142,991,926 (+)NCBI
Rnor_5.01143,893,827 - 143,937,045 (+)NCBI
RGSC_v3.41137,323,995 - 137,365,983 (+)RGD
Celera1127,134,227 - 127,174,932 (+)RGD
Sequence:
RefSeq Acc Id: XM_006229422   ⟹   XP_006229484
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01142,948,943 - 142,992,410 (+)NCBI
Rnor_5.01143,893,827 - 143,937,045 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006229423   ⟹   XP_006229485
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01142,948,942 - 142,992,410 (+)NCBI
Rnor_5.01143,893,827 - 143,937,045 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_446315 (Get FASTA)   NCBI Sequence Viewer  
  XP_006229484 (Get FASTA)   NCBI Sequence Viewer  
  XP_006229485 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAB03626 (Get FASTA)   NCBI Sequence Viewer  
  EDM08676 (Get FASTA)   NCBI Sequence Viewer  
  Q62674 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_446315   ⟸   NM_053863
- UniProtKB: Q62674 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006229485   ⟸   XM_006229423
- Peptide Label: isoform X1
- UniProtKB: F1LNH7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006229484   ⟸   XM_006229422
- Peptide Label: isoform X1
- UniProtKB: F1LNH7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000070095   ⟸   ENSRNOT00000077441
RefSeq Acc Id: ENSRNOP00000025621   ⟸   ENSRNOT00000025621
Protein Domains
Gate   Nucleos_tra2_C   Nucleos_tra2_N

Transcriptome

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

Promoters
RGD ID:13690153
Promoter ID:EPDNEW_R677
Type:single initiation site
Name:Slc28a1_1
Description:solute carrier family 28 member 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01142,950,491 - 142,950,551EPDNEW

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)
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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

Database Acc Id Source(s)
AGR Gene RGD:621223 AgrOrtholog
Ensembl Genes ENSRNOG00000018940 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000025621 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000070095 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000025621 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000077441 UniProtKB/TrEMBL
InterPro C_nuclsd_transpt UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  C_nuclsd_transpt_met_bac UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CNT1/CNT2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CNT_C_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CNT_N_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Gate_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:116642 UniProtKB/Swiss-Prot
NCBI Gene 116642 ENTREZGENE
PANTHER PTHR10590 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR10590:SF16 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Gate UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Nucleos_tra2_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Nucleos_tra2_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB SLC28A1 RGD
PhenoGen Slc28a1 PhenoGen
TIGRFAMs nupC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniGene Rn.10517 ENTREZGENE
UniProt F1LNH7 ENTREZGENE, UniProtKB/TrEMBL
  Q62674 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-24 Slc28a1  solute carrier family 28 member 1  Slc28a1  solute carrier family 28 (concentrative nucleoside transporter), member 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-08-02 Slc28a1  solute carrier family 28 (concentrative nucleoside transporter), member 1  Slc28a1  solute carrier family 28 (sodium-coupled nucleoside transporter), member 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-09-10 Slc28a1  solute carrier family 28 (sodium-coupled nucleoside transporter), member 1      Symbol and Name status set to approved 1299863 APPROVED
2002-08-07 Slc28a1  solute carrier family 28 (sodium-coupled nucleoside transporter), member 1      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_process may be involved in the intestinal absorption and renal transport of pyrimidine nucleoside analogs 730006