Slco4c1 (solute carrier organic anion transporter family, member 4C1) - Rat Genome Database

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Gene: Slco4c1 (solute carrier organic anion transporter family, member 4C1) Rattus norvegicus
Analyze
Symbol: Slco4c1
Name: solute carrier organic anion transporter family, member 4C1
RGD ID: 1303048
Description: Predicted to enable sodium-independent organic anion transmembrane transporter activity. Involved in organic anion transport. Located in basolateral plasma membrane. Biomarker of kidney failure. Orthologous to human SLCO4C1 (solute carrier organic anion transporter family member 4C1); PARTICIPATES IN multispecific organic anion transporter mediated transport pathway; INTERACTS WITH acrylamide; allopurinol; amphetamine.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: Oatp-H; Oatp-M1; Oatp4c1; Organic anion transporter member 4C1; organic anion transporting polypeptide 4C1; Slc21A20; solute carrier family 21 member 20; solute carrier organic anion transporter family member 4C1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr89104,624,802 - 104,676,462 (-)NCBIGRCr8
mRatBN7.2997,177,497 - 97,229,161 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl997,178,861 - 97,229,715 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx9105,608,724 - 105,660,364 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.09110,736,698 - 110,788,338 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.09109,080,112 - 109,131,752 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.09104,301,935 - 104,350,262 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl9104,299,277 - 104,350,308 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.09103,911,906 - 103,960,233 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4996,042,701 - 96,092,537 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1996,252,180 - 96,302,017 (-)NCBI
Celera994,630,117 - 94,678,252 (-)NCBICelera
Cytogenetic Map9q36NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-demecolcine  (ISO)
1,1-dichloroethene  (ISO)
1,2-dichloroethane  (ISO)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2-palmitoylglycerol  (ISO)
3-iodothyronamine  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
8-Br-cAMP  (ISO)
acrylamide  (EXP)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
allopurinol  (EXP)
amiodarone  (ISO)
amphetamine  (EXP)
aristolochic acid A  (ISO)
atenolol  (ISO)
azathioprine  (ISO)
belinostat  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bisphenol A  (EXP)
butanal  (ISO)
cadmium atom  (ISO)
cadmium dichloride  (ISO)
caffeine  (ISO)
carbon nanotube  (ISO)
chloroprene  (ISO)
cyclosporin A  (ISO)
dexamethasone  (ISO)
Dibutyl phosphate  (ISO)
dicrotophos  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
entinostat  (ISO)
ethyl methanesulfonate  (ISO)
folic acid  (ISO)
formaldehyde  (ISO)
herbicide  (EXP)
hexane  (EXP)
isotretinoin  (ISO)
L-homoarginine  (ISO)
lipopolysaccharide  (ISO)
mercury dibromide  (ISO)
mercury dichloride  (EXP,ISO)
methamphetamine  (ISO)
methylmercury chloride  (ISO)
N(omega),N(omega)-dimethyl-L-arginine  (ISO)
N-methyl-4-phenylpyridinium  (ISO)
nickel atom  (ISO)
nitrofen  (EXP)
ozone  (ISO)
p-chloromercuribenzoic acid  (ISO)
panobinostat  (ISO)
paraquat  (EXP)
perfluorononanoic acid  (EXP,ISO)
perfluorooctane-1-sulfonic acid  (ISO)
phenylmercury acetate  (ISO)
pioglitazone  (ISO)
potassium chromate  (ISO)
quercetin  (ISO)
raloxifene  (ISO)
rifampicin  (ISO)
ritonavir  (ISO)
S-(1,2-dichlorovinyl)-L-cysteine  (ISO)
SB 431542  (ISO)
silicon dioxide  (ISO)
sodium arsenite  (ISO)
sulforaphane  (ISO)
sunitinib  (ISO)
tamoxifen  (ISO)
thalidomide  (ISO)
titanium dioxide  (ISO)
traumatic acid  (EXP,ISO)
trichostatin A  (ISO)
triphenyl phosphate  (ISO)
valproic acid  (ISO)
vincristine  (ISO)
vorinostat  (ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Constitutive expression of various xenobiotic and endobiotic transporter mRNAs in the choroid plexus of rats. Choudhuri S, etal., Drug Metab Dispos 2003 Nov;31(11):1337-45.
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. Isolation and characterization of a digoxin transporter and its rat homologue expressed in the kidney. Mikkaichi T, etal., Proc Natl Acad Sci U S A 2004 Mar 9;101(10):3569-74. Epub 2004 Mar 01.
5. GOA pipeline RGD automated data pipeline
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:19056867   PMID:22768102  


Genomics

Comparative Map Data
Slco4c1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr89104,624,802 - 104,676,462 (-)NCBIGRCr8
mRatBN7.2997,177,497 - 97,229,161 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl997,178,861 - 97,229,715 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx9105,608,724 - 105,660,364 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.09110,736,698 - 110,788,338 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.09109,080,112 - 109,131,752 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.09104,301,935 - 104,350,262 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl9104,299,277 - 104,350,308 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.09103,911,906 - 103,960,233 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4996,042,701 - 96,092,537 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1996,252,180 - 96,302,017 (-)NCBI
Celera994,630,117 - 94,678,252 (-)NCBICelera
Cytogenetic Map9q36NCBI
SLCO4C1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh385102,233,986 - 102,296,284 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl5102,233,986 - 102,296,284 (-)EnsemblGRCh38hg38GRCh38
GRCh375101,569,690 - 101,631,988 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 365101,597,589 - 101,660,152 (-)NCBINCBI36Build 36hg18NCBI36
Build 345101,597,592 - 101,660,152NCBI
Celera597,517,512 - 97,580,066 (-)NCBICelera
Cytogenetic Map5q21.1NCBI
HuRef596,751,342 - 96,813,898 (-)NCBIHuRef
CHM1_15101,002,338 - 101,064,896 (-)NCBICHM1_1
T2T-CHM13v2.05102,742,066 - 102,804,356 (-)NCBIT2T-CHM13v2.0
Slco4c1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39196,744,918 - 96,800,027 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl196,743,995 - 96,799,896 (-)EnsemblGRCm39 Ensembl
GRCm38196,816,270 - 96,872,193 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl196,816,270 - 96,872,171 (-)EnsemblGRCm38mm10GRCm38
MGSCv37198,715,361 - 98,768,748 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36198,648,137 - 98,702,541 (-)NCBIMGSCv36mm8
Celera199,699,173 - 99,753,380 (-)NCBICelera
Cytogenetic Map1DNCBI
cM Map147.76NCBI
Slco4c1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541811,587,014 - 11,646,242 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495541811,587,016 - 11,646,242 (+)NCBIChiLan1.0ChiLan1.0
SLCO4C1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2497,509,920 - 97,572,395 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1595,663,570 - 95,726,041 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0597,580,977 - 97,643,539 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.15103,282,074 - 103,344,543 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl5103,284,947 - 103,344,320 (-)Ensemblpanpan1.1panPan2
SLCO4C1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.138,750,409 - 8,827,555 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl38,751,318 - 8,825,961 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha310,160,219 - 10,236,348 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.038,641,139 - 8,717,339 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl38,640,994 - 8,715,745 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.138,580,749 - 8,656,864 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.038,604,739 - 8,680,893 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.038,758,958 - 8,835,111 (+)NCBIUU_Cfam_GSD_1.0
Slco4c1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024407213163,991,490 - 164,047,023 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365232,176,830 - 2,234,019 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365232,176,899 - 2,231,467 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SLCO4C1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl2107,814,844 - 107,887,383 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.12107,815,058 - 107,887,399 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.22111,912,145 - 111,981,763 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SLCO4C1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1235,691,054 - 5,755,350 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl235,704,129 - 5,755,126 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660368,596,816 - 8,661,158 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Slco4c1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474320,337,978 - 20,395,652 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462474320,335,522 - 20,395,652 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Slco4c1
543 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:89
Count of miRNA genes:65
Interacting mature miRNAs:71
Transcripts:ENSRNOT00000033958
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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1578760Cm53Cardiac mass QTL 533.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)956771635101771635Rat
1582203Gluco19Glucose level QTL 193.30.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)992491589100929786Rat
1300134Bp185Blood pressure QTL 1853.73arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)961381434104821652Rat
1354626Bvd1Brain ventricular dilatation QTL 13.730.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)975712843111552878Rat
4889852Pur26Proteinuria QTL 26150.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)977813894101597663Rat
7794784Mcs31Mammary carcinoma susceptibility QTL 312.98mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)977813894111552878Rat
731164Uae25Urinary albumin excretion QTL 253.50.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)925661188100929786Rat
724515Uae16Urinary albumin excretion QTL 168urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)958163035100929646Rat
731171Glom6Glomerulus QTL 62.80.0003kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)964573531109573531Rat
724547Cm21Cardiac mass QTL 212.7heart mass (VT:0007028)calculated heart weight (CMO:0000073)979271511102910209Rat
61385Edpm9Estrogen-dependent pituitary mass QTL 93.430.05pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)963869687108869687Rat
724544Uae9Urinary albumin excretion QTL 94.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)925268044114175309Rat


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
nervous system
renal system
reproductive system
respiratory system
9 7 9 101 65 72 41 25 41 6 144 42 89 45 49 31

Sequence


Ensembl Acc Id: ENSRNOT00000033958   ⟹   ENSRNOP00000037089
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl997,178,861 - 97,229,715 (-)Ensembl
Rnor_6.0 Ensembl9104,299,277 - 104,350,308 (-)Ensembl
RefSeq Acc Id: NM_001002024   ⟹   NP_001002024
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr89104,624,802 - 104,676,462 (-)NCBI
mRatBN7.2997,177,497 - 97,229,161 (-)NCBI
Rnor_6.09104,301,935 - 104,350,262 (-)NCBI
Rnor_5.09103,911,906 - 103,960,233 (-)NCBI
RGSC_v3.4996,042,701 - 96,092,537 (-)RGD
Celera994,630,117 - 94,678,252 (-)RGD
Sequence:
RefSeq Acc Id: XM_063267565   ⟹   XP_063123635
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr89104,640,521 - 104,676,436 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001002024 (Get FASTA)   NCBI Sequence Viewer  
  XP_063123635 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAQ04697 (Get FASTA)   NCBI Sequence Viewer  
  EDL91884 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000037089
  ENSRNOP00000037089.4
GenBank Protein Q71MB6 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_001002024   ⟸   NM_001002024
- UniProtKB: Q71MB6 (UniProtKB/Swiss-Prot),   F1LRH8 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000037089   ⟸   ENSRNOT00000033958
RefSeq Acc Id: XP_063123635   ⟸   XM_063267565
- Peptide Label: isoform X1
Protein Domains
Kazal-like   Major facilitator superfamily (MFS) profile

Transcriptome

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

Promoters
RGD ID:13696888
Promoter ID:EPDNEW_R7412
Type:multiple initiation site
Name:Slco4c1_1
Description:solute carrier organic anion transporter family, member 4C1
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_6.09104,350,285 - 104,350,345EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1303048 AgrOrtholog
BioCyc Gene G2FUF-26595 BioCyc
Ensembl Genes ENSRNOG00000022711 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000033958 ENTREZGENE
  ENSRNOT00000033958.5 UniProtKB/TrEMBL
Gene3D-CATH 1.20.1250.20 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Kazal_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Kazal_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MFS_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MFS_trans_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  OATP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:432363 UniProtKB/Swiss-Prot
NCBI Gene 432363 ENTREZGENE
PANTHER PTHR11388 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SOLUTE CARRIER ORGANIC ANION TRANSPORTER FAMILY MEMBER 4C1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Kazal_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  OATP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Slco4c1 PhenoGen
PROSITE KAZAL_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MFS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000022711 RatGTEx
Superfamily-SCOP SSF100895 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF103473 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A6JR53_RAT UniProtKB/TrEMBL
  F1LRH8 ENTREZGENE, UniProtKB/TrEMBL
  Q71MB6 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2005-11-17 Slco4c1  solute carrier organic anion transporter family, member 4C1      Symbol and Name status set to approved 1299863 APPROVED
2005-02-14 Slco4c1  solute carrier organic anion transporter family, member 4C1      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_drugs involved in the transport of digoxin, a commonly prescribed drug for treatment of heart failure, into urine in the kidney 1303977