Slc4a4 (solute carrier family 4 member 4) - Rat Genome Database

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Gene: Slc4a4 (solute carrier family 4 member 4) Rattus norvegicus
Analyze
Symbol: Slc4a4
Name: solute carrier family 4 member 4
RGD ID: 68936
Description: Enables sodium:bicarbonate symporter activity. Involved in metanephric proximal tubule development. Located in membrane. Used to study nephrogenic diabetes insipidus. Biomarker of hypertension. Human ortholog(s) of this gene implicated in renal tubular acidosis. Orthologous to human SLC4A4 (solute carrier family 4 member 4); PARTICIPATES IN bile acid transport pathway; INTERACTS WITH 1-naphthyl isothiocyanate; 17beta-estradiol; 17beta-estradiol 3-benzoate.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: electrogenic sodium bicarbonate cotransporter 1; HHNMC; HNBC1; KNBC; LOC108352724; na(+)/HCO3(-) cotransporter; Na+HCO3- cotransporter 4; NBC-like protein; NBC1; NBC2; Nbc4; PNBC; SLC4A5; sodium bicarbonate cotransporter; solute carrier family 4 (anion exchanger), member 4; solute carrier family 4 sodium bicarbonate cotransporter member 4; solute carrier family 4, member 4; solute carrier family 4, sodium bicarbonate cotransporter, member 4; uncharacterized LOC108352724
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
GRCr81419,125,394 - 19,577,379 (-)NCBIGRCr8
mRatBN7.21418,841,289 - 19,293,297 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1418,845,159 - 19,272,883 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1418,835,659 - 19,168,521 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01420,154,535 - 20,487,378 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01418,866,264 - 19,200,389 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01420,476,258 - 20,817,042 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1420,479,323 - 20,920,286 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01420,382,241 - 20,803,426 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41420,381,545 - 20,739,216 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11420,381,544 - 20,739,216 (-)NCBI
Celera1418,198,665 - 18,528,992 (-)NCBICelera
Cytogenetic Map14p22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(1->4)-beta-D-glucan  (ISO)
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (ISO)
1-naphthyl isothiocyanate  (EXP)
17beta-estradiol  (EXP,ISO)
17beta-estradiol 3-benzoate  (EXP)
17beta-hydroxy-5alpha-androstan-3-one  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
2,4,6-trinitrobenzenesulfonic acid  (ISO)
2,4-dinitrotoluene  (EXP)
2-amino-2-deoxy-D-glucopyranose  (EXP)
3,4-methylenedioxymethamphetamine  (EXP,ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4,4'-diaminodiphenylmethane  (EXP,ISO)
4,4'-diisothiocyano-trans-stilbene-2,2'-disulfonic acid  (EXP)
4-amino-2,6-dinitrotoluene  (EXP)
4-hydroxyphenyl retinamide  (ISO)
6-propyl-2-thiouracil  (EXP)
acetamide  (EXP)
acrylamide  (EXP)
aflatoxin B1  (ISO)
aflatoxin M1  (ISO)
aldehydo-D-glucosamine  (EXP)
all-trans-retinoic acid  (ISO)
allethrin  (EXP)
amiodarone  (ISO)
amitrole  (EXP)
ammonium chloride  (EXP)
amphetamine  (EXP)
aristolochic acid A  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
atrazine  (EXP)
benzo[a]pyrene  (ISO)
beta-D-glucosamine  (EXP)
bicalutamide  (ISO)
bisphenol A  (EXP,ISO)
bromobenzene  (EXP)
butanal  (ISO)
cadmium dichloride  (EXP)
cefaloridine  (EXP)
CGP 52608  (ISO)
chloroprene  (ISO)
ciprofibrate  (ISO)
cocaine  (EXP)
Cuprizon  (EXP)
cyclosporin A  (ISO)
cyhalothrin  (EXP)
cypermethrin  (EXP)
dexamethasone  (ISO)
diclofenac  (ISO)
dioxygen  (ISO)
doxorubicin  (ISO)
elemental selenium  (ISO)
endosulfan  (EXP)
ethanol  (ISO)
fenvalerate  (EXP)
flavonoids  (EXP)
flutamide  (EXP)
folic acid  (ISO)
FR900359  (ISO)
fulvestrant  (ISO)
gamma-hexachlorocyclohexane  (EXP)
geneticin  (ISO)
gentamycin  (EXP)
leflunomide  (EXP)
methimazole  (EXP)
monosodium L-glutamate  (EXP)
Muraglitazar  (EXP)
N-nitrosodiethylamine  (ISO)
N-nitrosodimethylamine  (EXP)
N-nitrosomorpholine  (EXP)
N-Nitrosopyrrolidine  (ISO)
nickel sulfate  (ISO)
nitroglycerin  (EXP)
O-methyleugenol  (ISO)
paracetamol  (EXP,ISO)
pentachlorophenol  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (EXP)
phenformin  (EXP)
phenobarbital  (EXP,ISO)
pirinixic acid  (EXP,ISO)
pregnenolone 16alpha-carbonitrile  (EXP,ISO)
pyrethrins  (EXP)
rotenone  (EXP)
selenium atom  (ISO)
silicon dioxide  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
sodium atom  (ISO)
sodium hydrogencarbonate  (EXP,ISO)
sulfadimethoxine  (EXP)
temozolomide  (ISO)
Tesaglitazar  (EXP)
testosterone  (EXP)
tetrachloromethane  (EXP,ISO)
trichostatin A  (ISO)
triclosan  (ISO)
triptonide  (ISO)
tunicamycin  (ISO)
valproic acid  (EXP,ISO)
venlafaxine hydrochloride  (EXP)
vinclozolin  (EXP)
vitamin E  (ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
basolateral plasma membrane  (IBA,IEA,ISO,ISS,TAS)
cell surface  (IEA,ISO)
lateral plasma membrane  (IEA)
membrane  (IDA,ISO)
plasma membrane  (IBA,ISO)

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. An electrogenic Na(+)-HCO(-)(3) cotransporter (NBC) with a novel COOH-terminus, cloned from rat brain. Bevensee MO, etal., Am J Physiol Cell Physiol. 2000 Jun;278(6):C1200-11. doi: 10.1152/ajpcell.2000.278.6.C1200.
2. Cloning, renal distribution, and regulation of the rat Na+-HCO3- cotransporter. Burnham CE, etal., Am J Physiol 1998 Jun;274(6 Pt 2):F1119-26.
3. Role of glycosylation in the renal electrogenic Na+-HCO3- cotransporter (NBCe1). Choi I, etal., Am J Physiol Renal Physiol. 2003 Jun;284(6):F1199-206. doi: 10.1152/ajprenal.00131.2002. Epub 2003 Feb 25.
4. Cloning and characterization of a human electrogenic Na+-HCO-3 cotransporter isoform (hhNBC). Choi I, etal., Am J Physiol. 1999 Mar;276(3):C576-84. doi: 10.1152/ajpcell.1999.276.3.C576.
5. Molecular and functional characterization of the electroneutral Na/HCO3 cotransporter NBCn1 in rat hippocampal neurons. Cooper DS, etal., J Biol Chem. 2005 May 6;280(18):17823-30. Epub 2005 Feb 17.
6. 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.
7. The electrogenic sodium bicarbonate cotransporter: developmental expression in rat brain and possible role in acid vulnerability. Giffard RG, etal., J Neurosci 2000 Feb 1;20(3):1001-8.
8. Mutations in SLC4A4 cause permanent isolated proximal renal tubular acidosis with ocular abnormalities. Igarashi T, etal., Nat Genet 1999 Nov;23(3):264-6.
9. Functional up-regulation of basolateral Na+-dependent HCO3- transporter NBCn1 in medullary thick ascending limb of K+-depleted rats. Jakobsen JK, etal., Pflugers Arch. 2004 Sep;448(6):571-8. Epub 2004 Aug 13.
10. Altered expression of renal acid-base transporters in rats with lithium-induced NDI. Kim YH, etal., Am J Physiol Renal Physiol. 2003 Dec;285(6):F1244-57. Epub 2003 Aug 26.
11. Expression of Na+/HCO3- co-transporter proteins (NBCs) in rat and human skeletal muscle. Kristensen JM, etal., Acta Physiol Scand. 2004 Sep;182(1):69-76.
12. Chronic metabolic acidosis upregulates rat kidney Na-HCO cotransporters NBCn1 and NBC3 but not NBC1. Kwon TH, etal., Am J Physiol Renal Physiol 2002 Feb;282(2):F341-51.
13. Identification of key genes and pathways associated with cholangiocarcinoma development based on weighted gene correlation network analysis. Liu J, etal., PeerJ. 2019 Oct 31;7:e7968. doi: 10.7717/peerj.7968. eCollection 2019.
14. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
15. Renogenic characterization and in vitro differentiation of rat amniotic fluid stem cells into renal proximal tubular- and juxtaglomerular-like cells. Minocha E, etal., In Vitro Cell Dev Biol Anim. 2019 Feb;55(2):138-147. doi: 10.1007/s11626-018-00315-2. Epub 2019 Jan 15.
16. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
17. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
18. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
19. NBCn1 is a basolateral Na+-HCO3- cotransporter in rat kidney inner medullary collecting ducts. Praetorius J, etal., Am J Physiol Renal Physiol. 2004 May;286(5):F903-12. Epub 2004 Jan 13.
20. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
21. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
22. Cloning and functional expression of rNBC, an electrogenic Na(+)-HCO3- cotransporter from rat kidney. Romero MF, etal., Am J Physiol 1998 Feb;274(2 Pt 2):F425-32.
23. Increased expression of the sodium transporter BSC-1 in spontaneously hypertensive rats. Sonalker PA, etal., J Pharmacol Exp Ther. 2004 Dec;311(3):1052-61. Epub 2004 Aug 30.
24. Tentative Sequence Identification Numbers Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
25. Cloning and immunolocalization of a rat pancreatic Na(+) bicarbonate cotransporter. Thevenod F, etal., Biochem Biophys Res Commun 1999 Oct 14;264(1):291-8.
26. Expression of the Na+-HCO-3 cotransporter NBC4 in rat kidney and characterization of a novel NBC4 variant. Xu J, etal., Am J Physiol Renal Physiol 2003 Jan;284(1):F41-50.
Additional References at PubMed
PMID:9651366   PMID:11703600   PMID:12907161   PMID:14733916   PMID:15273250   PMID:15781297   PMID:16575514   PMID:16636648   PMID:16769890   PMID:16807546   PMID:17038436   PMID:17182531  
PMID:17416604   PMID:17609257   PMID:17661077   PMID:17855492   PMID:17909850   PMID:18067590   PMID:18177483   PMID:18508879   PMID:18582537   PMID:18815229   PMID:19033647   PMID:19056867  
PMID:19381888   PMID:19710533   PMID:20798035   PMID:21700703   PMID:21976511   PMID:22538240   PMID:22871113   PMID:22966160   PMID:23205667   PMID:23376485   PMID:23450392   PMID:23690961  
PMID:24253522   PMID:24453308   PMID:24721237   PMID:25755028   PMID:25866180   PMID:26497404   PMID:27249584   PMID:27717805   PMID:27920473   PMID:28719339   PMID:29476059   PMID:29500354  
PMID:30526387   PMID:30615862   PMID:32357304   PMID:34231059  


Genomics

Comparative Map Data
Slc4a4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81419,125,394 - 19,577,379 (-)NCBIGRCr8
mRatBN7.21418,841,289 - 19,293,297 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1418,845,159 - 19,272,883 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1418,835,659 - 19,168,521 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01420,154,535 - 20,487,378 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01418,866,264 - 19,200,389 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01420,476,258 - 20,817,042 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1420,479,323 - 20,920,286 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01420,382,241 - 20,803,426 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41420,381,545 - 20,739,216 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11420,381,544 - 20,739,216 (-)NCBI
Celera1418,198,665 - 18,528,992 (-)NCBICelera
Cytogenetic Map14p22NCBI
SLC4A4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38471,062,660 - 71,572,083 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl471,062,667 - 71,572,087 (+)EnsemblGRCh38hg38GRCh38
GRCh37472,052,482 - 72,437,800 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36472,271,867 - 72,656,663 (+)NCBINCBI36Build 36hg18NCBI36
Build 34472,569,851 - 72,802,834NCBI
Celera469,409,858 - 69,794,385 (+)NCBICelera
Cytogenetic Map4q13.3NCBI
HuRef467,858,038 - 68,243,033 (+)NCBIHuRef
CHM1_1472,088,838 - 72,473,646 (+)NCBICHM1_1
T2T-CHM13v2.0474,404,936 - 74,914,352 (+)NCBIT2T-CHM13v2.0
Slc4a4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39588,941,717 - 89,387,515 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl589,034,345 - 89,387,512 (+)EnsemblGRCm39 Ensembl
GRCm38588,793,858 - 89,239,656 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl588,886,486 - 89,239,653 (+)EnsemblGRCm38mm10GRCm38
GRCm38.p6 Ensembl588,886,818 - 89,239,653 (+)EnsemblGRCm38mm10GRCm38
MGSCv37589,316,285 - 89,668,681 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36590,009,308 - 90,310,099 (+)NCBIMGSCv36mm8
Celera587,083,219 - 87,378,244 (+)NCBICelera
Cytogenetic Map5E1NCBI
cM Map544.1NCBI
Slc4a4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554471,599,929 - 1,900,791 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554471,599,986 - 1,900,791 (-)NCBIChiLan1.0ChiLan1.0
SLC4A4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2358,518,761 - 58,902,521 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1458,714,895 - 59,097,574 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0452,659,221 - 52,994,053 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1459,002,200 - 59,337,558 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl459,002,200 - 59,385,608 (-)Ensemblpanpan1.1panPan2
SLC4A4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11360,375,215 - 60,670,664 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1360,328,136 - 60,666,728 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1360,062,119 - 60,404,847 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01361,134,685 - 61,478,360 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1361,054,824 - 61,475,687 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11360,748,991 - 61,092,136 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01360,240,742 - 60,583,813 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01361,388,701 - 61,732,082 (+)NCBIUU_Cfam_GSD_1.0
Slc4a4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440528514,940,952 - 15,261,596 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365983,391,575 - 3,713,635 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365983,391,587 - 3,713,629 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SLC4A4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl867,706,874 - 68,177,212 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1867,768,955 - 68,177,213 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2871,840,687 - 72,050,150 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SLC4A4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1719,581,399 - 20,043,334 (+)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660842,813,860 - 3,204,408 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Slc4a4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248902,523,327 - 2,919,148 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248902,523,368 - 2,940,081 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Slc4a4
2769 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:251
Count of miRNA genes:164
Interacting mature miRNAs:182
Transcripts:ENSRNOT00000004391, ENSRNOT00000033806
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
2300159Bmd61Bone mineral density QTL 615.30.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)14126541967Rat
2300183Bmd60Bone mineral density QTL 605.70.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)14126541967Rat
619619Rf4Renal disease susceptibility QTL 44.10.002urine total protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)14132754612Rat
634352Apr6Acute phase response QTL 63.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)14141131407Rat
1300114Srn2Serum renin concentration QTL 23.27blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)14381307421217635Rat
70195Mcs8Mammary carcinoma susceptibility QTL 84.28mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)14381307424531477Rat
1331740Bw26Body weight QTL 263.028body mass (VT:0001259)body weight (CMO:0000012)14381307430767156Rat
1581500Renag1Renal agenesis QTL 1kidney development trait (VT:0000527)percentage of study population developing unilateral renal agenesis during a period of time (CMO:0000940)14817066868298175Rat
1358296Ael3Aortic elastin QTL 33.70.00051aorta elastin amount (VT:0003905)aortic elastin14826709053267090Rat
2302045Pia39Pristane induced arthritis QTL 394.90.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G2a level (CMO:0002116)14826709053267090Rat
731183Pia20Pristane induced arthritis QTL 203.55joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)14908897839057237Rat
2302277Gluco38Glucose level QTL 385.8blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)141103062228035204Rat
631839Niddm37Non-insulin dependent diabetes mellitus QTL 373.37blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)141103062295876975Rat
631212Bw5Body weight QTL55.43retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)141103081230320092Rat
1300140Srn3Serum renin concentration QTL 33.19blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)141487516830883947Rat
631528Scl11Serum cholesterol level QTL 114.9blood cholesterol amount (VT:0000180)blood total cholesterol level (CMO:0000051)141757341219726296Rat
71117Niddm17Non-insulin dependent diabetes mellitus QTL 172.35blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)141759376142336881Rat
631262Tcas4Tongue tumor susceptibility QTL 47.29tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)141762256142337007Rat
2313397Coatc1Coat color QTL1coat/hair pigmentation trait (VT:0010463)coat/hair color measurement (CMO:0001808)141854133263541332Rat
61420Pia6Pristane induced arthritis QTL 64.9joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)141863134542337007Rat

Markers in Region
AW527043  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21419,023,981 - 19,024,073 (+)MAPPERmRatBN7.2
Rnor_6.01420,659,920 - 20,660,011NCBIRnor6.0
Rnor_5.01420,565,848 - 20,565,939UniSTSRnor5.0
RGSC_v3.41420,577,858 - 20,577,949UniSTSRGSC3.4
Celera1418,376,511 - 18,376,602UniSTS
RH 3.4 Map14290.8UniSTS
Cytogenetic Map14p22UniSTS
AI176955  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21418,844,743 - 18,844,878 (+)MAPPERmRatBN7.2
Rnor_6.01420,479,713 - 20,479,847NCBIRnor6.0
Rnor_5.01420,385,696 - 20,385,830UniSTSRnor5.0
RGSC_v3.41420,381,130 - 20,381,264UniSTSRGSC3.4
Celera1418,198,250 - 18,198,384UniSTS
RH 3.4 Map14259.89UniSTS
Cytogenetic Map14p22UniSTS
G46840  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21419,061,870 - 19,062,080 (+)MAPPERmRatBN7.2
Rnor_6.01420,697,593 - 20,697,802NCBIRnor6.0
Rnor_5.01420,603,915 - 20,604,124UniSTSRnor5.0
RGSC_v3.41420,615,670 - 20,615,879UniSTSRGSC3.4
Celera1418,414,130 - 18,414,339UniSTS
Cytogenetic Map14p22UniSTS


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 2 14 23 16 4 16 50 29 16 8
Low 1 29 34 25 15 25 8 10 24 6 25 3 8
Below cutoff 1

Sequence


RefSeq Acc Id: ENSRNOT00000004391   ⟹   ENSRNOP00000004391
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1418,845,159 - 19,137,725 (-)Ensembl
Rnor_6.0 Ensembl1420,479,323 - 20,920,286 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000033806   ⟹   ENSRNOP00000035006
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1418,845,159 - 19,184,184 (-)Ensembl
Rnor_6.0 Ensembl1420,480,128 - 20,816,588 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000095074   ⟹   ENSRNOP00000089282
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1418,845,159 - 19,272,883 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000101333   ⟹   ENSRNOP00000092374
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1418,845,159 - 19,272,883 (-)Ensembl
RefSeq Acc Id: NM_053424   ⟹   NP_445876
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81419,129,264 - 19,468,282 (-)NCBI
mRatBN7.21418,845,159 - 19,184,184 (-)NCBI
Rnor_6.01420,480,128 - 20,816,588 (-)NCBI
Rnor_5.01420,382,241 - 20,803,426 (-)NCBI
RGSC_v3.41420,381,545 - 20,739,216 (-)RGD
Celera1418,198,665 - 18,528,992 (-)RGD
Sequence:
RefSeq Acc Id: XM_006250791   ⟹   XP_006250853
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81419,125,394 - 19,468,368 (-)NCBI
mRatBN7.21418,841,289 - 19,184,265 (-)NCBI
Rnor_6.01420,476,258 - 20,817,042 (-)NCBI
Rnor_5.01420,382,241 - 20,803,426 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039092507   ⟹   XP_038948435
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81419,125,394 - 19,422,026 (-)NCBI
mRatBN7.21418,841,289 - 19,137,916 (-)NCBI
RefSeq Acc Id: XM_039092508   ⟹   XP_038948436
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81419,129,440 - 19,422,028 (-)NCBI
mRatBN7.21418,841,289 - 19,137,918 (-)NCBI
RefSeq Acc Id: XM_039092509   ⟹   XP_038948437
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81419,125,394 - 19,577,379 (-)NCBI
mRatBN7.21418,841,289 - 19,293,297 (-)NCBI
RefSeq Acc Id: XM_039092511   ⟹   XP_038948439
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81419,125,394 - 19,459,108 (-)NCBI
mRatBN7.21418,841,289 - 19,175,001 (-)NCBI
RefSeq Acc Id: NP_445876   ⟸   NM_053424
- UniProtKB: Q9JJ32 (UniProtKB/Swiss-Prot),   O54815 (UniProtKB/Swiss-Prot),   O35422 (UniProtKB/Swiss-Prot),   Q9QXH6 (UniProtKB/Swiss-Prot),   Q9JI66 (UniProtKB/Swiss-Prot),   A6KKH6 (UniProtKB/TrEMBL),   A0A8I6ABC3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006250853   ⟸   XM_006250791
- Peptide Label: isoform X4
- UniProtKB: A6KKH5 (UniProtKB/TrEMBL),   A0A0H2UHB7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000035006   ⟸   ENSRNOT00000033806
RefSeq Acc Id: ENSRNOP00000004391   ⟸   ENSRNOT00000004391
RefSeq Acc Id: XP_038948437   ⟸   XM_039092509
- Peptide Label: isoform X3
- UniProtKB: A0A8I6AFE1 (UniProtKB/TrEMBL),   A0A0H2UHB7 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038948439   ⟸   XM_039092511
- Peptide Label: isoform X4
- UniProtKB: A6KKH5 (UniProtKB/TrEMBL),   A0A0H2UHB7 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038948436   ⟸   XM_039092508
- Peptide Label: isoform X2
- UniProtKB: A0A8I6ABC3 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038948435   ⟸   XM_039092507
- Peptide Label: isoform X1
- UniProtKB: A0A0H2UHB7 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSRNOP00000092374   ⟸   ENSRNOT00000101333
RefSeq Acc Id: ENSRNOP00000089282   ⟸   ENSRNOT00000095074
Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q9JI66-F1-model_v2 AlphaFold Q9JI66 1-1079 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:68936 AgrOrtholog
BioCyc Gene G2FUF-16169 BioCyc
Ensembl Genes ENSRNOG00000003134 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000004391.4 UniProtKB/TrEMBL
  ENSRNOT00000033806 ENTREZGENE
  ENSRNOT00000033806.3 UniProtKB/TrEMBL
  ENSRNOT00000095074.1 UniProtKB/TrEMBL
  ENSRNOT00000101333.1 UniProtKB/TrEMBL
Gene3D-CATH Helical hairpin bin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Band3_cytoplasmic_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HCO3_transpt_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HCO3_transpt_euk UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Na/HCO3_transpt UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTrfase/Anion_transptr UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:84484 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 84484 ENTREZGENE
PANTHER ELECTROGENIC SODIUM BICARBONATE COTRANSPORTER 1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR11453 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Band_3_cyto UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HCO3_cotransp UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Slc4a4 PhenoGen
PRINTS HCO3TRNSPORT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NAHCO3TRSPRT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000003134 RatGTEx
Superfamily-SCOP SSF55804 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR TC229872
UniProt A0A0H2UHB7 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6ABC3 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6AFE1 ENTREZGENE, UniProtKB/TrEMBL
  A0A8L2QHQ0_RAT UniProtKB/TrEMBL
  A6KKH5 ENTREZGENE, UniProtKB/TrEMBL
  A6KKH6 ENTREZGENE, UniProtKB/TrEMBL
  A6KKH7_RAT UniProtKB/TrEMBL
  A6KKH8_RAT UniProtKB/TrEMBL
  O35422 ENTREZGENE
  O54815 ENTREZGENE
  Q9JI66 ENTREZGENE
  Q9JJ32 ENTREZGENE
  Q9QXH6 ENTREZGENE
  S4A4_RAT UniProtKB/Swiss-Prot
UniProt Secondary O35422 UniProtKB/Swiss-Prot
  O54815 UniProtKB/Swiss-Prot
  Q9JJ32 UniProtKB/Swiss-Prot
  Q9QXH6 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Slc4a4  solute carrier family 4 member 4  LOC108352724  uncharacterized LOC108352724  Data merged from RGD:11469569 737654 PROVISIONAL
2016-08-02 LOC108352724  uncharacterized LOC108352724      Symbol and Name status set to provisional 70820 PROVISIONAL
2016-03-09 Slc4a4  solute carrier family 4 member 4  Slc4a4  solute carrier family 4, sodium bicarbonate cotransporter, member 4  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2011-01-19 Slc4a4  solute carrier family 4, sodium bicarbonate cotransporter, member 4  Slc4a4  solute carrier family 4 (anion exchanger), member 4  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-02-18 Slc4a4  solute carrier family 4 (anion exchanger), member 4  Slc4a4  solute carrier family 4, member 4  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-06-10 Slc4a4  solute carrier family 4, member 4      Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_expression expression not affected in chronic metabolic acidosis 70580
gene_expression expressed in spinal chord,cerebellum, cortex, olfactory bulb, and subcortical structures 1299161
gene_expression widely expressed in organs like brain,liver, cornea,heart and lung; higher levels found in outer medulla and cortex of kidneys than inner medulla; predominant distribution in the thick ascending limb of Henles loop in renal medulla and cortex 628547
gene_function sodium bicarbonate cotransporter 61795
gene_process mediates the coupled movement of sodium and bicarbonate ions across the plasma membrane 61795
gene_process plays a role in the transport of HCO(-)(3) by pancreatic acinar and duct cells 68865
gene_process may be involved in cellular HCO3- uptake in Henles loop in kidneys 628547
gene_process important role in Na+ dependent HCO3- flux in renal basolateral membranes 628547
gene_protein predicted 1035 amino acid, 116 kDa protein 61795
gene_transcript 8kb mRNA 61795
gene_transcript human homolog has 6 (a-f) splice variants 628547