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 (Ensembl: Slc6a20)
Name: solute carrier family 6 member 20a (Ensembl:solute carrier family 6 member 20)
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 apical plasma membrane and brush border membrane. Predicted to be active in plasma membrane. Human ortholog(s) of this gene implicated in iminoglycinuria. 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
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.28123,282,325 - 123,322,609 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl8123,281,472 - 123,322,573 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx8128,872,218 - 128,912,417 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.08127,071,181 - 127,111,393 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.08124,900,709 - 124,940,903 (-)NCBIRnor_WKY
Rnor_6.08132,713,013 - 132,753,145 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl8132,665,927 - 132,753,292 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.08131,865,713 - 131,905,845 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.48128,412,080 - 128,452,212 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.18128,431,816 - 128,471,949 (-)NCBI
Celera8122,390,559 - 122,430,719 (-)NCBICelera
Cytogenetic Map8q32NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

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
mRatBN7.28123,282,325 - 123,322,609 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl8123,281,472 - 123,322,573 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx8128,872,218 - 128,912,417 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.08127,071,181 - 127,111,393 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.08124,900,709 - 124,940,903 (-)NCBIRnor_WKY
Rnor_6.08132,713,013 - 132,753,145 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl8132,665,927 - 132,753,292 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.08131,865,713 - 131,905,845 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.48128,412,080 - 128,452,212 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.18128,431,816 - 128,471,949 (-)NCBI
Celera8122,390,559 - 122,430,719 (-)NCBICelera
Cytogenetic Map8q32NCBI
SLC6A20
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38345,755,449 - 45,796,536 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl345,755,449 - 45,796,574 (-)EnsemblGRCh38hg38GRCh38
GRCh37345,796,941 - 45,838,028 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36345,771,946 - 45,812,966 (-)NCBINCBI36Build 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 Ensembl
GRCm389123,593,823 - 123,632,538 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl9123,590,800 - 123,632,565 (-)EnsemblGRCm38mm10GRCm38
MGSCv379123,502,938 - 123,541,683 (-)NCBIGRCm37MGSCv37mm9NCBIm37
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
PanPan1.1346,770,067 - 46,811,158 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl346,770,067 - 46,811,158 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0345,663,830 - 45,703,576 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
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 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2042,604,583 - 42,642,873 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02043,172,646 - 43,210,926 (+)NCBIROS_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_1.0
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
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 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
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 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
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_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462473075,081,189 - 75,107,288 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Slc6a20a
149 total Variants
miRNA Target Status

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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1554321Bmd3Bone mineral density QTL 37.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)840952565123900184Rat
738011Anxrr9Anxiety related response QTL 96.1exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)893535351123900184Rat
1358893Bp263Blood pressure QTL 2635.01arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)893965141123900184Rat
1358903Bp252Blood pressure QTL 25270.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)893965141123900184Rat
738014Anxrr15Anxiety related response QTL 153.60.005locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)895718998123900184Rat
2300182Bmd56Bone mineral density QTL 565.4femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)895718998123900184Rat

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
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 1 1 29 23 1
Low 2 1 45 30 18 30 3 3 33 8 14 10 3
Below cutoff 30 12 11 11 5 7 12 4 24 5

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000007467   ⟹   ENSRNOP00000007467
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl8123,281,472 - 123,322,573 (-)Ensembl
Rnor_6.0 Ensembl8132,713,013 - 132,753,145 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000008172   ⟹   ENSRNOP00000008172
RefSeq Status:
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
RefSeq Acc Id: ENSRNOT00000108032   ⟹   ENSRNOP00000093413
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl8123,234,714 - 123,278,680 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000113514   ⟹   ENSRNOP00000094119
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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
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
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.28123,290,720 - 123,322,609 (-)NCBI
RefSeq Acc Id: XR_005487736
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.28123,287,104 - 123,322,599 (-)NCBI
RefSeq Acc Id: XR_005487737
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.28123,282,376 - 123,322,605 (-)NCBI
Protein Sequences
Protein RefSeqs NP_579830 (Get FASTA)   NCBI Sequence Viewer  
  XP_038936581 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAB32806 (Get FASTA)   NCBI Sequence Viewer  
  Q64093 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_579830   ⟸   NM_133296
- UniProtKB: G3V6Q4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000008172   ⟸   ENSRNOT00000008172
RefSeq Acc Id: ENSRNOP00000007467   ⟸   ENSRNOT00000007467
RefSeq Acc Id: XP_038936581   ⟸   XM_039080653
- Peptide Label: isoform X1
RefSeq Acc Id: ENSRNOP00000094119   ⟸   ENSRNOT00000113514
RefSeq Acc Id: ENSRNOP00000093413   ⟸   ENSRNOT00000108032

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, UniProtKB/TrEMBL
  ENSRNOG00000068642 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000007467 ENTREZGENE
  ENSRNOP00000007467.4 UniProtKB/TrEMBL
  ENSRNOP00000008172.7 UniProtKB/TrEMBL
  ENSRNOP00000094119.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000007467 ENTREZGENE
  ENSRNOT00000007467.7 UniProtKB/TrEMBL
  ENSRNOT00000008172.8 UniProtKB/TrEMBL
  ENSRNOT00000113514.1 UniProtKB/TrEMBL
InterPro Na/ntran_symport UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Neutral_aa_SLC6 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SNS_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:113918 UniProtKB/Swiss-Prot
NCBI Gene 113918 ENTREZGENE
PANTHER PTHR11616 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam SNF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Slc6a20a PhenoGen
PRINTS NANEUSMPORT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ORPHTRNSPORT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE NA_NEUROTRAN_SYMP_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NA_NEUROTRAN_SYMP_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NA_NEUROTRAN_SYMP_3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF161070 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A8I6ALF7_RAT UniProtKB/TrEMBL
  F1LZT7_RAT 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