Slc49a4 (solute carrier family 49 member 4) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: Slc49a4 (solute carrier family 49 member 4) Rattus norvegicus
Analyze
Symbol: Slc49a4
Name: solute carrier family 49 member 4
RGD ID: 1310939
Description: Predicted to be located in lysosomal membrane. Predicted to be active in intracellular membrane-bounded organelle. Human ortholog(s) of this gene implicated in renal cell carcinoma. Orthologous to human SLC49A4 (solute carrier family 49 member 4); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,6-dinitrotoluene; 3-chloropropane-1,2-diol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: Dirc2; disrupted in renal carcinoma 2; disrupted in renal carcinoma 2 (human); disrupted in renal carcinoma 2 homolog; disrupted in renal carcinoma 2 homolog (human); disrupted in renal carcinoma protein 2 homolog; LOC303902
RGD Orthologs
Human
Mouse
Chinchilla
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
mRatBN7.21164,995,629 - 65,068,929 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1164,995,679 - 65,068,926 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1173,817,633 - 73,890,823 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01166,479,898 - 66,553,087 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01165,511,155 - 65,584,329 (+)NCBIRnor_WKY
Rnor_6.01168,198,709 - 68,272,766 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1168,198,709 - 68,272,758 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01171,288,001 - 71,359,978 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41166,829,715 - 66,910,201 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11166,887,303 - 66,967,787 (+)NCBI
Celera1164,458,017 - 64,531,072 (+)NCBICelera
Cytogenetic Map11q22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Disruption of a novel MFS transporter gene, DIRC2, by a familial renal cell carcinoma-associated t(2;3)(q35;q21). Bodmer D, etal., Hum Mol Genet. 2002 Mar 15;11(6):641-9.
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. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
4. GOA pipeline RGD automated data pipeline
5. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
7. Comprehensive gene review and curation RGD comprehensive gene curation
Additional References at PubMed
PMID:12477932   PMID:15489334  


Genomics

Comparative Map Data
Slc49a4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21164,995,629 - 65,068,929 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1164,995,679 - 65,068,926 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1173,817,633 - 73,890,823 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01166,479,898 - 66,553,087 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01165,511,155 - 65,584,329 (+)NCBIRnor_WKY
Rnor_6.01168,198,709 - 68,272,766 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1168,198,709 - 68,272,758 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01171,288,001 - 71,359,978 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41166,829,715 - 66,910,201 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11166,887,303 - 66,967,787 (+)NCBI
Celera1164,458,017 - 64,531,072 (+)NCBICelera
Cytogenetic Map11q22NCBI
SLC49A4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh383122,795,069 - 122,881,139 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl3122,795,069 - 122,881,139 (+)EnsemblGRCh38hg38GRCh38
GRCh373122,513,916 - 122,599,986 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 363123,996,597 - 124,081,451 (+)NCBINCBI36Build 36hg18NCBI36
Build 343123,996,596 - 124,081,451NCBI
Celera3120,923,989 - 121,010,083 (+)NCBICelera
Cytogenetic Map3q21.1NCBI
HuRef3119,887,284 - 119,973,384 (+)NCBIHuRef
CHM1_13122,477,575 - 122,563,652 (+)NCBICHM1_1
T2T-CHM13v2.03125,514,258 - 125,600,338 (+)NCBIT2T-CHM13v2.0
Slc49a4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391635,514,432 - 35,589,740 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1635,514,432 - 35,589,726 (-)EnsemblGRCm39 Ensembl
GRCm381635,694,062 - 35,769,370 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1635,694,062 - 35,769,356 (-)EnsemblGRCm38mm10GRCm38
MGSCv371635,694,989 - 35,769,442 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361635,614,650 - 35,689,103 (-)NCBIMGSCv36mm8
Celera1636,163,922 - 36,243,077 (-)NCBICelera
Cytogenetic Map16B3NCBI
Slc49a4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542722,005,161 - 22,080,336 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495542722,005,161 - 22,093,700 (+)NCBIChiLan1.0ChiLan1.0
SLC49A4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.13126,786,344 - 126,872,936 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl3126,782,782 - 126,872,936 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v03119,883,252 - 119,968,881 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
SLC49A4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13325,869,848 - 25,945,328 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3325,870,052 - 25,940,745 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3325,893,905 - 25,975,658 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.03326,103,324 - 26,185,129 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl3326,103,246 - 26,180,820 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.13325,900,745 - 25,982,376 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.03325,943,611 - 26,014,683 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.03326,502,697 - 26,584,500 (+)NCBIUU_Cfam_GSD_1.0
Slc49a4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405602128,388,779 - 128,483,453 (-)NCBIHiC_Itri_2
SpeTri2.0NW_00493735839,940 - 86,612 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SLC49A4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl13137,641,425 - 137,739,098 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.113137,633,471 - 137,739,114 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.213147,189,008 - 147,238,913 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SLC49A4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12257,998,168 - 58,080,900 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2257,998,708 - 58,081,270 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666041108,268,994 - 108,353,144 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Slc49a4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046249121,102,279 - 1,212,569 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046249121,102,252 - 1,212,569 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Slc49a4
415 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:501
Count of miRNA genes:252
Interacting mature miRNAs:319
Transcripts:ENSRNOT00000003048
Prediction methods:Microtar, 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
1300147Bp187Blood pressure QTL 1873.67arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)11169446234Rat
1558659Tescar1Testicular tumor resistance QTL 13.9testis integrity trait (VT:0010572)percentage of study population developing testis tumors during a period of time (CMO:0001261)11104193166113562Rat
724554Iddm17Insulin dependent diabetes mellitus QTL 170.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)111897620886241447Rat
10058952Gmadr6Adrenal mass QTL 62.290.0072adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)112295940367959403Rat
8694376Bw156Body weight QTL 1562.250.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)112328045668280456Rat
9590313Scort20Serum corticosterone level QTL 206.510.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)112328045668280456Rat
9589032Epfw10Epididymal fat weight QTL 109.290.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)112328045668280456Rat
8694424Bw162Body weight QTL 1623.80.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)112328045668280456Rat
724563Uae10Urinary albumin excretion QTL 106urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)112767241082846715Rat
1300110Stl7Serum triglyceride level QTL 74.64blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)112952841882566702Rat
2298551Neuinf10Neuroinflammation QTL 103.7nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)113123913478851519Rat
70180BpQTLcluster10Blood pressure QTL cluster 103.19arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)113491804179918041Rat
1300135Rf19Renal function QTL 193.38blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)114094618882566702Rat
2312566Glom20Glomerulus QTL 203.60.001kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)114428575982566702Rat
1581565Pur10Proteinuria QTL 100.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)114480331882846466Rat
1581572Uae35Urinary albumin excretion QTL 350.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)114480331882846466Rat
4889859Pur28Proteinuria QTL 2819.50.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)114545932375190161Rat
724561Plsm4Polydactyly-luxate syndrome (PLS) morphotypes QTL 40.0003forelimb integrity trait (VT:0010562)front foot phalanges count (CMO:0001947)115445753486241447Rat
4889521Gluco62Glucose level QTL 622.820.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)115513672982993457Rat
7411658Foco27Food consumption QTL 2716.20.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)115635142486241447Rat
631506Bp104Blood pressure QTL 1042.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)115980279482566545Rat
70208Niddm22Non-insulin dependent diabetes mellitus QTL 223.61blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)115980279482566553Rat
10058954Gmadr7Adrenal mass QTL 72.490.0049adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)116034659086241447Rat


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 3 43 42 35 11 35 8 11 74 35 34 11 8
Low 15 6 8 6 7
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000003048   ⟹   ENSRNOP00000003048
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1164,995,679 - 65,068,926 (+)Ensembl
Rnor_6.0 Ensembl1168,198,709 - 68,272,758 (+)Ensembl
RefSeq Acc Id: NM_001012017   ⟹   NP_001012017
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21164,995,679 - 65,068,929 (+)NCBI
Rnor_6.01168,198,709 - 68,272,766 (+)NCBI
Rnor_5.01171,288,001 - 71,359,978 (+)NCBI
RGSC_v3.41166,829,715 - 66,910,201 (+)RGD
Celera1164,458,017 - 64,531,072 (+)RGD
Sequence:
RefSeq Acc Id: XM_039088342   ⟹   XP_038944270
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21164,995,629 - 65,068,929 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001012017 (Get FASTA)   NCBI Sequence Viewer  
  XP_038944270 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH81960 (Get FASTA)   NCBI Sequence Viewer  
  Q66H95 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001012017   ⟸   NM_001012017
- UniProtKB: Q66H95 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000003048   ⟸   ENSRNOT00000003048
RefSeq Acc Id: XP_038944270   ⟸   XM_039088342
- Peptide Label: isoform X1

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q66H95-F1-model_v2 AlphaFold Q66H95 1-478 view protein structure

Transcriptome

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

Promoters
RGD ID:13698189
Promoter ID:EPDNEW_R8714
Type:initiation region
Name:Dirc2_1
Description:disrupted in renal carcinoma 2
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_6.01168,198,847 - 68,198,907EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1310939 AgrOrtholog
BioCyc Gene G2FUF-21200 BioCyc
Ensembl Genes ENSRNOG00000002240 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000003048 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000003048 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 1.20.1250.20 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7124589 IMAGE-MGC_LOAD
InterPro MFS_trans_sf UniProtKB/Swiss-Prot
KEGG Report rno:303902 UniProtKB/Swiss-Prot
MGC_CLONE MGC:94084 IMAGE-MGC_LOAD
NCBI Gene 303902 ENTREZGENE
PhenoGen Slc49a4 PhenoGen
Superfamily-SCOP SSF103473 UniProtKB/Swiss-Prot
UniProt DIRC2_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2018-11-09 Slc49a4  solute carrier family 49 member 4  Dirc2  disrupted in renal carcinoma 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-01-10 Dirc2  disrupted in renal carcinoma 2  Dirc2  disrupted in renal carcinoma 2 (human)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-05-08 Dirc2  disrupted in renal carcinoma 2 (human)  Dirc2  disrupted in renal carcinoma 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-04 Dirc2  disrupted in renal carcinoma 2  Dirc2  disrupted in renal carcinoma 2 homolog (human)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-30 Dirc2  disrupted in renal carcinoma 2 homolog (human)    disrupted in renal carcinoma 2  Name updated 1299863 APPROVED
2005-12-06 Dirc2  disrupted in renal carcinoma 2  Dirc2_predicted  disrupted in renal carcinoma 2 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Dirc2_predicted  disrupted in renal carcinoma 2 (predicted)      Symbol and Name status set to approved 70820 APPROVED