Slc6a20a (solute carrier family 6 member 20a) - Rat Genome Database

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Gene: Slc6a20a (solute carrier family 6 member 20a) Rattus norvegicus
Analyze
Symbol: Slc6a20a
Name: solute carrier family 6 member 20a
RGD ID: 621651
Description: Enables L-proline transmembrane transporter activity; amino-acid betaine transmembrane transporter activity; and proline:sodium symporter activity. Involved in L-proline import across plasma membrane and amino-acid betaine transport. Predicted to be located in brush border membrane. Predicted to be active in apical plasma membrane. Orthologous to human SLC6A20 (solute carrier family 6 member 20); PARTICIPATES IN amiloride pharmacodynamics pathway; bendroflumethiazide pharmacodynamics pathway; bumetanide pharmacodynamics pathway; INTERACTS WITH 17beta-estradiol; 2,3,7,8-Tetrachlorodibenzofuran; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: rB21a; Slc6a20; sodium- and chloride-dependent transporter XTRP3; sodium/imino-acid transporter 1; solute carrier family 6 (neurotransmitter transporter), member 20; solute carrier family 6 (proline IMINO transporter), member 20; solute carrier family 6 member 20; solute carrier family 6, member 20; transporter rB21A; X transporter protein 3; Xtrp3
RGD Orthologs
Human
Mouse
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr88132,159,768 - 132,200,016 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl8132,158,915 - 132,200,008 (-)EnsemblGRCr8
mRatBN7.28123,282,325 - 123,322,609 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl8123,281,472 - 123,322,573 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx8128,872,218 - 128,912,417 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.08127,071,181 - 127,111,393 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.08124,900,709 - 124,940,903 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.08132,713,013 - 132,753,145 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl8132,665,927 - 132,753,292 (-)Ensemblrn6Rnor6.0
Rnor_5.08131,865,713 - 131,905,845 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.48128,412,080 - 128,452,212 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera8122,390,559 - 122,430,719 (-)NCBICelera
RGSC_v3.18128,431,816 - 128,471,949 (-)NCBI
Cytogenetic Map8q32NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
apical plasma membrane  (IBA,IEA,ISO,ISS)
brush border membrane  (ISO)
membrane  (IEA)
plasma membrane  (IBA,IEA,ISO)

References

References - curated
# Reference Title Reference Citation
1. Na+-dependent and Na+-independent betaine transport across the apical membrane of rat renal epithelium. Cano M, etal., Biochim Biophys Acta. 2015 Oct;1848(10 Pt A):2172-9. doi: 10.1016/j.bbamem.2015.05.020. Epub 2015 May 29.
2. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
3. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
4. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
5. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
6. SMPDB Annotation Import Pipeline Pipeline to import SMPDB annotations from SMPDB into RGD
7. GOA pipeline RGD automated data pipeline
8. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
9. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
10. Molecular cloning of an orphan transporter. A new member of the neurotransmitter transporter family. Smith KE, etal., FEBS Lett 1995 Jan 2;357(1):86-92.
11. Identification of mammalian proline transporter SIT1 (SLC6A20) with characteristics of classical system imino. Takanaga H, etal., J Biol Chem. 2005 Mar 11;280(10):8974-84. Epub 2005 Jan 4.
Additional References at PubMed
PMID:15689184   PMID:16174864   PMID:19029042   PMID:19033659  


Genomics

Comparative Map Data
Slc6a20a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr88132,159,768 - 132,200,016 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl8132,158,915 - 132,200,008 (-)EnsemblGRCr8
mRatBN7.28123,282,325 - 123,322,609 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl8123,281,472 - 123,322,573 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx8128,872,218 - 128,912,417 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.08127,071,181 - 127,111,393 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.08124,900,709 - 124,940,903 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.08132,713,013 - 132,753,145 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl8132,665,927 - 132,753,292 (-)Ensemblrn6Rnor6.0
Rnor_5.08131,865,713 - 131,905,845 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.48128,412,080 - 128,452,212 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera8122,390,559 - 122,430,719 (-)NCBICelera
RGSC_v3.18128,431,816 - 128,471,949 (-)NCBI
Cytogenetic Map8q32NCBI
SLC6A20
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38345,755,449 - 45,796,536 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl345,755,449 - 45,796,591 (-)Ensemblhg38GRCh38
GRCh37345,796,941 - 45,838,028 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36345,771,946 - 45,812,966 (-)NCBIBuild 36Build 36hg18NCBI36
Celera345,734,543 - 45,775,644 (-)NCBICelera
Cytogenetic Map3p21.31NCBI
HuRef345,840,974 - 45,881,992 (-)NCBIHuRef
CHM1_1345,746,576 - 45,787,673 (-)NCBICHM1_1
T2T-CHM13v2.0345,771,093 - 45,812,175 (-)NCBIT2T-CHM13v2.0
Slc6a20b
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm399123,422,888 - 123,461,603 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl9123,419,865 - 123,461,630 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm389123,593,823 - 123,632,538 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl9123,590,800 - 123,632,565 (-)Ensemblmm10GRCm38
MGSCv379123,502,938 - 123,541,683 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv369123,443,524 - 123,481,174 (-)NCBIMGSCv36mm8
Celera9124,048,718 - 124,087,483 (-)NCBICelera
Cytogenetic Map9F4NCBI
cM Map974.19NCBI
SLC6A20
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2245,721,021 - 45,760,714 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1345,725,790 - 45,765,483 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0345,663,830 - 45,703,576 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1346,770,067 - 46,811,158 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl346,770,067 - 46,811,158 (-)EnsemblpanPan2panpan1.1
SLC6A20
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12042,702,368 - 42,725,804 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2042,702,379 - 42,724,658 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha2042,604,583 - 42,642,873 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.02043,172,646 - 43,210,926 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2043,172,634 - 43,210,151 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12042,412,873 - 42,451,212 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02042,820,410 - 42,858,724 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02043,095,423 - 43,133,672 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Slc6a20
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118197,794,009 - 197,842,662 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936695146,421 - 195,121 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_004936695146,571 - 193,428 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SLC6A20
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1328,899,821 - 28,945,187 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.11328,897,831 - 28,945,191 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21332,015,969 - 32,043,611 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SLC6A20
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1227,228,039 - 7,265,441 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl227,228,517 - 7,265,031 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_023666041159,900,571 - 159,938,890 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Slc6a20
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462473075,084,748 - 75,109,112 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_00462473075,081,189 - 75,107,288 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Slc6a20
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v18114,715,324 - 114,751,501 (-)NCBIRrattus_CSIRO_v1

miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:132
Count of miRNA genes:97
Interacting mature miRNAs:114
Transcripts:ENSRNOT00000007467
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.


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2303171Bp331Blood pressure QTL 3315.570.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)8105462581132782436Rat
738011Anxrr9Anxiety related response QTL 96.1exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)8102413464132782436Rat
634332Pia18Pristane induced arthritis QTL 184joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)884192326132782436Rat
1300171Bp184Blood pressure QTL 1843.66arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)879394435132782436Rat

Markers in Region
RH139708  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.28123,284,430 - 123,284,635 (+)MAPPERmRatBN7.2
Rnor_6.08132,715,119 - 132,715,323NCBIRnor6.0
Rnor_5.08131,867,819 - 131,868,023UniSTSRnor5.0
RGSC_v3.48128,414,186 - 128,414,390UniSTSRGSC3.4
Celera8122,392,665 - 122,392,869UniSTS
Cytogenetic Map8q32UniSTS
Slc6a20a  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.28123,299,128 - 123,300,129 (+)MAPPERmRatBN7.2
Rnor_6.08132,729,817 - 132,730,817NCBIRnor6.0
Rnor_5.08131,882,517 - 131,883,517UniSTSRnor5.0
RGSC_v3.48128,428,884 - 128,429,884UniSTSRGSC3.4
Celera8122,407,368 - 122,408,368UniSTS
Cytogenetic Map8q32UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 11 52 146 91 90 59 59 59 6 304 143 11 118 78 89 31 3 3

Sequence


Ensembl Acc Id: ENSRNOT00000007467   ⟹   ENSRNOP00000007467
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl8132,158,915 - 132,200,008 (-)Ensembl
mRatBN7.2 Ensembl8123,281,472 - 123,322,573 (-)Ensembl
Rnor_6.0 Ensembl8132,713,013 - 132,753,145 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000008172   ⟹   ENSRNOP00000008172
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl8123,234,714 - 123,266,606 (-)Ensembl
Rnor_6.0 Ensembl8132,665,927 - 132,753,292 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000108032   ⟹   ENSRNOP00000093413
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl8123,234,714 - 123,278,680 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000113514   ⟹   ENSRNOP00000094119
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl8132,158,915 - 132,200,008 (-)Ensembl
mRatBN7.2 Ensembl8123,281,472 - 123,322,573 (-)Ensembl
RefSeq Acc Id: NM_133296   ⟹   NP_579830
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88132,159,768 - 132,199,900 (-)NCBI
mRatBN7.28123,282,325 - 123,322,465 (-)NCBI
Rnor_6.08132,713,013 - 132,753,145 (-)NCBI
Rnor_5.08131,865,713 - 131,905,845 (-)NCBI
RGSC_v3.48128,412,080 - 128,452,212 (-)RGD
Celera8122,390,559 - 122,430,719 (-)RGD
Sequence:
RefSeq Acc Id: XM_039080653   ⟹   XP_038936581
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88132,167,934 - 132,200,016 (-)NCBI
mRatBN7.28123,290,720 - 123,322,609 (-)NCBI
RefSeq Acc Id: XM_063264725   ⟹   XP_063120795
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88132,169,953 - 132,200,012 (-)NCBI
RefSeq Acc Id: XM_063264726   ⟹   XP_063120796
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88132,167,934 - 132,200,012 (-)NCBI
RefSeq Acc Id: XM_063264728   ⟹   XP_063120798
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88132,164,534 - 132,200,014 (-)NCBI
RefSeq Acc Id: XM_063264729   ⟹   XP_063120799
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88132,169,953 - 132,200,016 (-)NCBI
RefSeq Acc Id: NP_579830   ⟸   NM_133296
- UniProtKB: Q64093 (UniProtKB/Swiss-Prot),   G3V6Q4 (UniProtKB/TrEMBL),   A6I4C2 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000008172   ⟸   ENSRNOT00000008172
Ensembl Acc Id: ENSRNOP00000007467   ⟸   ENSRNOT00000007467
RefSeq Acc Id: XP_038936581   ⟸   XM_039080653
- Peptide Label: isoform X3
Ensembl Acc Id: ENSRNOP00000094119   ⟸   ENSRNOT00000113514
Ensembl Acc Id: ENSRNOP00000093413   ⟸   ENSRNOT00000108032
RefSeq Acc Id: XP_063120798   ⟸   XM_063264728
- Peptide Label: isoform X3
RefSeq Acc Id: XP_063120796   ⟸   XM_063264726
- Peptide Label: isoform X2
RefSeq Acc Id: XP_063120799   ⟸   XM_063264729
- Peptide Label: isoform X3
RefSeq Acc Id: XP_063120795   ⟸   XM_063264725
- Peptide Label: isoform X1

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q64093-F1-model_v2 AlphaFold Q64093 1-616 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:621651 AgrOrtholog
BioCyc Gene G2FUF-28610 BioCyc
Ensembl Genes ENSRNOG00000006010 Ensembl
  ENSRNOG00000068642 Ensembl, ENTREZGENE
Ensembl Transcript ENSRNOT00000007467 ENTREZGENE
InterPro Na/ntran_symport UniProtKB/Swiss-Prot
  Neutral_aa_SLC6 UniProtKB/Swiss-Prot
  SNS_sf UniProtKB/Swiss-Prot
KEGG Report rno:113918 UniProtKB/Swiss-Prot
NCBI Gene 113918 ENTREZGENE
PANTHER PTHR11616 UniProtKB/Swiss-Prot
  SODIUM- AND CHLORIDE-DEPENDENT TRANSPORTER XTRP3 UniProtKB/Swiss-Prot
Pfam SNF UniProtKB/Swiss-Prot
PhenoGen Slc6a20a PhenoGen
PRINTS NANEUSMPORT UniProtKB/Swiss-Prot
  ORPHTRNSPORT UniProtKB/Swiss-Prot
PROSITE NA_NEUROTRAN_SYMP_1 UniProtKB/Swiss-Prot
  NA_NEUROTRAN_SYMP_2 UniProtKB/Swiss-Prot
  NA_NEUROTRAN_SYMP_3 UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000006010 RatGTEx
  ENSRNOG00000068642 RatGTEx
Superfamily-SCOP SSF161070 UniProtKB/Swiss-Prot
UniProt A0A8I6ALF7_RAT UniProtKB/TrEMBL
  A6I4C2 ENTREZGENE, UniProtKB/TrEMBL
  G3V6Q4 ENTREZGENE, UniProtKB/TrEMBL
  Q64093 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2022-03-03 Slc6a20a  solute carrier family 6 member 20a  Slc6a20  solute carrier family 6 member 20  Name and Symbol changed 629549 APPROVED
2016-03-09 Slc6a20  solute carrier family 6 member 20  Slc6a20  solute carrier family 6 (proline IMINO transporter), member 20  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2009-10-22 Slc6a20  solute carrier family 6 (proline IMINO transporter), member 20  Slc6a20  solute carrier family 6 (neurotransmitter transporter), member 20  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-02-25 Slc6a20  solute carrier family 6 (neurotransmitter transporter), member 20  Xtrp3  X transporter protein 3  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-08-07 Xtrp3        Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_expression mRNA is expressed in brain leptomeninges 634536