Slc4a1 (solute carrier family 4 member 1 (Diego blood group)) - Rat Genome Database
Submit Data |  Help |  Video Tutorials |  News |  Publications |  FTP Download |  REST API |  Citing RGD |  Contact   
Gene: Slc4a1 (solute carrier family 4 member 1 (Diego blood group)) Rattus norvegicus
Analyze
Symbol: Slc4a1
Name: solute carrier family 4 member 1 (Diego blood group)
RGD ID: 3710
Description: Exhibits actin binding activity; enzyme binding activity; and protein C-terminus binding activity. Involved in several processes, including positive regulation of T cell proliferation; response to alkaline pH; and response to carbon dioxide. Localizes to several cellular components, including Z disc; basolateral plasma membrane; and intercalated disc. Biomarker of iron deficiency anemia; metabolic acidosis; and renal tubular acidosis. Human ortholog(s) of this gene implicated in congenital hemolytic anemia; hereditary spherocytosis; hereditary spherocytosis type 4; malaria; and renal tubular acidosis. Orthologous to human SLC4A1 (solute carrier family 4 member 1 (Diego blood group)); INTERACTS WITH 1-naphthyl isothiocyanate; 2,3,7,8-tetrachlorodibenzodioxine; 3,3',4,4',5-pentachlorobiphenyl.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: AE 1; anion exchange protein 1; anion exchanger 1; band 3 anion transport protein; MGC93554; solute carrier family 4 (anion exchanger), member 1; solute carrier family 4 member 1; Solute carrier family 4 member 1 anion exchange protein 1 (kidney band 3); solute carrier family 4, member 1; Solute carrier family 4, member 1, anion exchange protein 1 (kidney band 3)
Orthologs:
Is Marker For: QTLs:   BpQTLcluster1   BpQTLcluster9  
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.01090,296,144 - 90,312,401 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1090,296,141 - 90,312,386 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01090,084,734 - 90,101,181 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41091,454,824 - 91,471,072 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11091,470,679 - 91,479,502 (-)NCBI
Celera1086,018,849 - 86,032,669 (-)NCBICelera
Cytogenetic Map10q32.1NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dimethylhydrazine  (ISO)
1-naphthyl isothiocyanate  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2-butoxyethanol  (ISO)
3,3',4,4',5-pentachlorobiphenyl  (EXP)
3,3',5,5'-tetrabromobisphenol A  (EXP)
4,4'-diisothiocyano-trans-stilbene-2,2'-disulfonic acid  (ISO)
4,4'-dinitrostilbene-2,2'-disulfonic acid  (ISO)
4,4'-sulfonyldiphenol  (ISO)
6-propyl-2-thiouracil  (EXP)
acetamide  (EXP)
aldehydo-D-glucose  (ISO)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
atorvastatin calcium  (EXP)
benzo[a]pyrene  (ISO)
benzo[b]fluoranthene  (ISO)
benzo[e]pyrene  (ISO)
Benzo[ghi]perylene  (ISO)
Benzo[k]fluoranthene  (ISO)
beta-naphthoflavone  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP)
C60 fullerene  (EXP)
cadmium dichloride  (EXP)
carbon nanotube  (ISO)
cholesterol  (EXP)
cisplatin  (ISO)
clofibrate  (ISO)
copper(II) sulfate  (ISO)
D-glucose  (ISO)
D-penicillamine  (EXP)
dexamethasone  (EXP)
dextran sulfate  (ISO)
dibenz[a,h]anthracene  (ISO)
dibutyl phthalate  (ISO)
dichloroacetic acid  (ISO)
diclofenac  (ISO)
dioxygen  (ISO)
dipyridamole  (ISO)
folic acid  (ISO)
furan  (EXP)
furans  (ISO)
gentamycin  (EXP)
glucose  (ISO)
hydrogen peroxide  (EXP)
lead diacetate  (EXP)
metformin  (EXP)
methapyrilene  (ISO)
methotrexate  (EXP)
methoxychlor  (EXP)
methyl isocyanate  (EXP)
monosodium L-glutamate  (EXP)
N-acetyl-L-cysteine  (EXP)
N-ethyl-N-nitrosourea  (ISO)
Niflumic acid  (ISO)
oxaliplatin  (EXP)
paracetamol  (ISO)
perfluorooctane-1-sulfonic acid  (EXP)
phenformin  (EXP)
phenobarbital  (ISO)
pirinixic acid  (ISO)
potassium atom  (ISO)
potassium dichromate  (ISO)
resveratrol  (ISO)
rotenone  (EXP)
silicon dioxide  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (EXP)
sodium atom  (ISO)
sodium hydrogencarbonate  (EXP)
sulfates  (ISO)
tebuconazole  (ISO)
tert-butyl hydroperoxide  (ISO)
testosterone  (EXP)
tetrachloromethane  (EXP)
titanium dioxide  (ISO)
topotecan  (EXP)
triphenyl phosphate  (EXP)
Triptolide  (EXP)
tungsten  (ISO)
valdecoxib  (EXP)
valproic acid  (ISO)
vancomycin  (ISO)


Cellular Component

References

References - curated
1. Alloisio N, etal., Blood. 1997 Jul 1;90(1):414-20.
2. Alvarez BV, etal., Am J Physiol Heart Circ Physiol. 2007 Mar;292(3):H1301-12. Epub 2006 Oct 20.
3. Barker RN, etal., Clin Exp Immunol. 2002 Aug;129(2):208-13.
4. Barker RN, etal., Eur J Immunol. 1993 Jul;23(7):1723-6.
5. Barone S, etal., J Am Soc Nephrol. 2004 Aug;15(8):2002-11.
6. Barone S, etal., Nephrol Dial Transplant. 2007 Dec;22(12):3462-70. Epub 2007 Sep 5.
7. Biswas D, etal., Toxicol Appl Pharmacol. 2010 May 1;244(3):315-27. doi: 10.1016/j.taap.2010.01.009. Epub 2010 Jan 28.
8. Biswas D, etal., Toxicol Appl Pharmacol. 2011 Jan 1;250(1):39-53. doi: 10.1016/j.taap.2010.10.002. Epub 2010 Oct 12.
9. Bruce LJ, etal., Nat Genet. 2005 Nov;37(11):1258-63. Epub 2005 Oct 9.
10. Charney AN, etal., Am J Physiol Cell Physiol. 2004 May;286(5):C1062-70. Epub 2003 Dec 24.
11. Fawaz NA, etal., Eur J Haematol. 2012 Apr;88(4):350-5. doi: 10.1111/j.1600-0609.2011.01739.x. Epub 2012 Jan 4.
12. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
13. GOA data from the GO Consortium
14. Hasegawa A, etal., Blood. 2012 Mar 15;119(11):2615-23. doi: 10.1182/blood-2011-09-382473. Epub 2012 Jan 25.
15. Huber S, etal., Am J Physiol. 1999 Dec;277(6 Pt 2):F841-9.
16. Jarolim P, etal., J Clin Invest. 1994 Jan;93(1):121-30.
17. Jarolim P, etal., Proc Natl Acad Sci U S A. 1991 Dec 15;88(24):11022-6.
18. Kay MM, etal., Proc Natl Acad Sci U S A. 1986 Apr;83(8):2463-7.
19. Khositseth S, etal., QJM. 2012 Sep;105(9):861-77. doi: 10.1093/qjmed/hcs139.
20. Kudrycki KE and Shull GE, J Biol Chem 1989 May 15;264(14):8185-92.
21. Li JY, etal., Chin Med J (Engl). 1992 Feb;105(2):116-9.
22. Lima PR, etal., Blood. 1997 Oct 1;90(7):2810-8.
23. Maillet P, etal., Br J Haematol. 1995 Dec;91(4):804-10.
24. MGD data from the GO Consortium
25. Mohebbi N, etal., Am J Physiol Renal Physiol. 2009 Aug;297(2):F499-509. doi: 10.1152/ajprenal.90489.2008. Epub 2009 May 13.
26. Morgan PE, etal., Am J Physiol Cell Physiol. 2007 Aug;293(2):C738-48. Epub 2007 Jul 25.
27. Moura Lima PR, etal., J Cell Biochem. 2003 Aug 15;89(6):1215-21.
28. NCBI rat LocusLink and RefSeq merged data July 26, 2002
29. Obrador G, etal., J Am Soc Nephrol. 1998 May;9(5):746-54.
30. OMIM Disease Annotation Pipeline
31. Pantaleo A, etal., PLoS One. 2011 Jan 5;6(1):e15847. doi: 10.1371/journal.pone.0015847.
32. Petrovic S, etal., Am J Physiol Renal Physiol. 2006 May;290(5):F1194-201. Epub 2005 Dec 13.
33. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
34. RGD automated import pipeline for gene-chemical interactions
35. Seshadri RM, etal., Am J Physiol Renal Physiol. 2006 Feb;290(2):F397-408. Epub 2005 Sep 6.
36. Simon JS, etal., Mamm Genome 1996 May;7(5):380-2.
37. Smythe JS, etal., Blood. 1995 May 15;85(10):2929-36.
38. Sotak M, etal., Am J Physiol Gastrointest Liver Physiol. 2011 Dec;301(6):G1066-74. doi: 10.1152/ajpgi.00256.2011. Epub 2011 Sep 8.
39. Southgate CD, etal., Nat Genet. 1996 Oct;14(2):227-30.
40. Stehberger PA, etal., J Am Soc Nephrol. 2007 May;18(5):1408-18. Epub 2007 Apr 4.
41. Su Y, etal., Am J Physiol Renal Physiol. 2011 Jan;300(1):F157-66. doi: 10.1152/ajprenal.00228.2010. Epub 2010 Oct 27.
42. Villaescusa R, etal., C R Biol. 2013 Mar;336(3):173-6. doi: 10.1016/j.crvi.2012.09.002. Epub 2012 Oct 12.
43. von Kalckreuth V, etal., J Infect Dis. 2006 Oct 1;194(7):949-57. Epub 2006 Aug 30.
44. Xiong Y, etal., Can J Physiol Pharmacol. 2013 Dec;91(12):1127-34. doi: 10.1139/cjpp-2013-0145. Epub 2013 Jul 26.
Additional References at PubMed
PMID:379653   PMID:8456965   PMID:9716609   PMID:12388412   PMID:12477932   PMID:12539048   PMID:14734552   PMID:16077082   PMID:16669616   PMID:17690150   PMID:17715300   PMID:18698006  
PMID:18723693   PMID:19056867   PMID:22452706   PMID:22516433   PMID:23878365   PMID:24121512  


Genomics

Comparative Map Data
Slc4a1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.01090,296,144 - 90,312,401 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1090,296,141 - 90,312,386 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01090,084,734 - 90,101,181 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41091,454,824 - 91,471,072 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11091,470,679 - 91,479,502 (-)NCBI
Celera1086,018,849 - 86,032,669 (-)NCBICelera
Cytogenetic Map10q32.1NCBI
SLC4A1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1744,248,390 - 44,268,141 (-)EnsemblGRCh38hg38GRCh38
GRCh381744,248,390 - 44,268,161 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371742,325,758 - 42,351,654 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361739,682,566 - 39,700,993 (-)NCBINCBI36hg18NCBI36
Build 341739,682,565 - 39,700,993NCBI
Celera1739,034,465 - 39,054,210 (-)NCBI
Cytogenetic Map17q21.31NCBI
HuRef1738,089,106 - 38,108,850 (-)NCBIHuRef
CHM1_11742,561,259 - 42,581,020 (-)NCBICHM1_1
Slc4a1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3911102,239,646 - 102,256,107 (-)NCBI
GRCm3811102,348,820 - 102,365,281 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl11102,348,824 - 102,366,203 (-)EnsemblGRCm38mm10GRCm38
MGSCv3711102,210,134 - 102,226,595 (-)NCBIGRCm37mm9NCBIm37
MGSCv3611102,164,917 - 102,181,205 (-)NCBImm8
Celera11114,058,195 - 114,074,658 (-)NCBICelera
Cytogenetic Map11DNCBI
cM Map1166.29NCBI
Slc4a1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495545117,315,024 - 17,328,103 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495545117,318,600 - 17,330,943 (-)NCBIChiLan1.0ChiLan1.0
SLC4A1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11713,302,796 - 13,317,312 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1713,302,796 - 13,317,312 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01713,131,851 - 13,150,872 (+)NCBI
SLC4A1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl919,146,480 - 19,157,915 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1919,142,884 - 19,159,449 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Slc4a1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_004936541718,577 - 727,420 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SLC4A1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1218,957,805 - 18,974,216 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11218,957,813 - 18,975,266 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21219,180,392 - 19,196,592 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SLC4A1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1 Ensembl1662,131,709 - 62,146,182 (+)Ensembl
ChlSab1.11662,126,370 - 62,146,192 (+)NCBI
Slc4a1
(Heterocephalus glaber - naked mole-rat)
No map positions available.

Position Markers
D10Wox20  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01090,296,897 - 90,297,007NCBIRnor6.0
Rnor_5.01090,085,487 - 90,085,597UniSTSRnor5.0
RGSC_v3.41091,455,572 - 91,455,683RGDRGSC3.4
RGSC_v3.41091,455,573 - 91,455,683UniSTSRGSC3.4
RGSC_v3.11091,469,942 - 91,470,053RGD
Celera1086,019,596 - 86,019,706UniSTS
Cytogenetic Map10q32UniSTS
RH 3.4 Map10880.59RGD
RH 3.4 Map10880.59UniSTS
RH 2.0 Map101017.0RGD
D10Arb13  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01090,296,864 - 90,297,132NCBIRnor6.0
Rnor_5.01090,085,454 - 90,085,722UniSTSRnor5.0
RGSC_v3.41091,455,539 - 91,455,808RGDRGSC3.4
RGSC_v3.41091,455,540 - 91,455,808UniSTSRGSC3.4
RGSC_v3.11091,469,909 - 91,470,178RGD
Celera1086,019,563 - 86,019,831UniSTS
Cytogenetic Map10q32UniSTS
FHH x ACI Map1071.36UniSTS
FHH x ACI Map1071.36RGD


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61427Cia16Collagen induced arthritis QTL 163.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10642907599492409Rat
2303118Mamtr7Mammary tumor resistance QTL 70.003mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)109841807108540162Rat
2301967Cm73Cardiac mass QTL 734.55heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)101482789492423564Rat
631268Cia21Collagen induced arthritis QTL 213.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1014827894107857673Rat
2316949Gluco60Glucose level QTL 603.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1014827894110992275Rat
1554317Bmd4Bone mineral density QTL 49.40.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)1020170031102897474Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)12152390690312401Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)12152390690312401Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)12152390690312401Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)12152390690312401Rat
70198BpQTLcluster9Blood pressure QTL cluster 92.94arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)102152390690312401Rat
724556Pur2Proteinuria QTL 25.5urine protein amount (VT:0005160)urine protein level (CMO:0000591)102290149793886300Rat
1331791Cm31Cardiac mass QTL 313.84606heart mass (VT:0007028)heart wet weight (CMO:0000069)1023861015112626471Rat
631267Cia20Collagen induced arthritis QTL 203.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1024483076107857673Rat
61325Aia5Adjuvant induced arthritis QTL 50.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1024483076107857673Rat
61354Pia10Pristane induced arthritis QTL 100.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1024483076107857673Rat
1298069Bp168Blood pressure QTL 1685.5blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)1027237530101482600Rat
631542Bp82Blood pressure QTL 826.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1027237530102427718Rat
631552Vetf2Vascular elastic tissue fragility QTL 24.50.0002aorta elastic tissue integrity trait (VT:0010556)artery internal elastic lamina non-tumorous lesion count (CMO:0001913)103618592995845311Rat
1576308Schws1Schwannoma susceptibility QTL 10.0041nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)1041260363106105607Rat
631269Cia22Collagen induced arthritis QTL 228.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1041260363107857673Rat
631270Cia23Collagen induced arthritis QTL 233.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1041260363107857673Rat
1298078Stresp5Stress response QTL 52.990.00025blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)1043289657108540162Rat
2300218Hpcl2Hepatic cholesterol level QTL 2liver cholesterol amount (VT:0010498)liver cholesterol level (CMO:0001597)104659302198939209Rat
9589030Epfw9Epididymal fat weight QTL 919.240.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)104684834691848346Rat
7411614Foco18Food consumption QTL 180.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)104684834691848346Rat
8694173Bw149Body weight QTL 1494.380.001body mass (VT:0001259)body weight gain (CMO:0000420)104684834691848346Rat
631547Bp87Blood pressure QTL 874.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)105063833795638337Rat
1549846Scl47Serum cholesterol level QTL 473.6blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)105310471898104718Rat
61387Bp1Blood pressure QTL 15.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1053621375112626471Rat
61387Bp1Blood pressure QTL 15.1arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)1053621375112626471Rat
631530Tls3T-lymphoma susceptibility QTL 300.0001thymus integrity trait (VT:0010555)percentage of study population developing T-cell lymphomas during a period of time (CMO:0001911)105362581598939209Rat
631535Cm51Cardiac mass QTL 513heart mass (VT:0007028)calculated heart weight (CMO:0000073)105363748594807701Rat
1359017Hrtrt21Heart rate QTL 212.4heart pumping trait (VT:2000009)heart rate (CMO:0000002)1055224855100224855Rat
70171Cari1Carrageenan-induced inflammation QTL 14.90.0005hypodermis integrity trait (VT:0010550)inflammatory exudate volume (CMO:0001429)1055678976112626471Rat
70164Bw21Body weight QTL 214.360.00005body mass (VT:0001259)body weight (CMO:0000012)1055679084102427604Rat
1354608Cm33Cardiac mass QTL 332.8heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)1056698730101698730Rat
1549831Bss6Bone structure and strength QTL 64lumbar vertebra strength trait (VT:0010574)vertebra ultimate force (CMO:0001678)1060450007105450007Rat
2312662Slep8Serum leptin concentration QTL 80.05blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)1060875260105875260Rat
2312668Scl65Serum cholesterol level QTL 650.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1060875260105875260Rat
2312672Insul15Insulin level QTL 150.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1060875260105875260Rat
2293698Bss43Bone structure and strength QTL 435.330.0001lumbar vertebra size trait (VT:0010518)lumbar vertebra cross-sectional area (CMO:0001689)1062096293107096293Rat
2306970Anxrr22Anxiety related response QTL 225.95fear/anxiety-related behavior trait (VT:1000241)number of periods of voluntary immobility (CMO:0001045)1064648175101691360Rat
1558643Cm44Cardiac mass QTL 444.80.0000368heart mass (VT:0007028)heart wet weight (CMO:0000069)1064648175102149713Rat
6893336Cm75Cardiac mass QTL 750.10.87heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)1064648175102149713Rat
61449Ciaa2CIA Autoantibody QTL 27.1blood autoantibody amount (VT:0003725)calculated serum anti-type 2 collagen antibody titer (CMO:0001279)1065590122110590122Rat
2313103Bss80Bone structure and strength QTL 8020.0001tibia strength trait (VT:1000284)tibia midshaft endosteal cross-sectional area (CMO:0001716)1065992275110992275Rat
2313105Bss79Bone structure and strength QTL 791.80.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)1065992275110992275Rat
7387312Bw125Body weight QTL 12530.0047retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight (CMO:0000356)1067880046112626471Rat
1581559Eae18Experimental allergic encephalomyelitis QTL 180.00002nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)1067988218110992091Rat
1357344Bp249Blood pressure QTL 2490.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1069123603101482600Rat
2317029Aia19Adjuvant induced arthritis QTL 192.98joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)1069385595112626471Rat
2317039Aia6Adjuvant induced arthritis QTL 64.31joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)1069385595112626471Rat
10450498Bp384Blood pressure QTL 3840.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1070166960112626471Rat
1642980Bp300Blood pressure QTL 300arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1070800069112626471Rat
61396Bp9Blood pressure QTL 94.80.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1071692298112626471Rat
2300172Bmd57Bone mineral density QTL 579.80.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)1073008136112626471Rat
2293646Bss25Bone structure and strength QTL 2510.960.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)1073008136112626471Rat
2293663Bss33Bone structure and strength QTL 339.340.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)1073008136112626471Rat
6893366Bw106Body weight QTL 1060.30.47body mass (VT:0001259)body weight (CMO:0000012)1073467158112626471Rat
2306793Ean5Experimental allergic neuritis QTL 54.7nervous system integrity trait (VT:0010566)IFNG-secreting splenocyte count (CMO:0002122)107504539197308358Rat
70193Mcs7Mammary carcinoma susceptibility QTL 72.38mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1075544754112626471Rat
2298548Neuinf7Neuroinflammation QTL 73.4nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)1075544754112626471Rat
1358188Ept9Estrogen-induced pituitary tumorigenesis QTL 93.9pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)107598380599492217Rat
2292617Ept18Estrogen-induced pituitary tumorigenesis QTL 183.9pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)107598380599492217Rat
1579919Bp281Blood pressure QTL 2810.01arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)107705574198282519Rat
10450495Bp383Blood pressure QTL 3830.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)107897027998282519Rat
2292438Bp311Blood pressure QTL 311arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1078970279112626471Rat
1302404Cia27Collagen induced arthritis QTL 272.60.0045joint integrity trait (VT:0010548)experimental arthritis severity measurement (CMO:0001459)1079927661112626471Rat
4889492Pancm2Pancreatic morphology QTL 23.2pancreatic beta cell morphology trait (VT:0005217)ratio of insulin-positive cell area to total area of splenic region of pancreas (CMO:0001814)1080239190112626471Rat
1300107Rf18Renal function QTL 183.41urine output (VT:0003620)timed urine volume (CMO:0000260)1081515116101758478Rat
1358915Stresp7Stress response QTL 73.52blood norepinephrine amount (VT:0005663)plasma norepinephrine level (CMO:0001010)108164977590297007Rat
631555Bp134Blood pressure QTL 1340.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)108338982894488181Rat
6893357Bw102Body weight QTL 1020.50.36body mass (VT:0001259)body weight (CMO:0000012)1083389828104994768Rat
2303589Bw87Body weight QTL 872body mass (VT:0001259)body weight (CMO:0000012)1085079943112626471Rat
4889948Bss91Bone structure and strength QTL 914tibia area (VT:1000281)tibia midshaft total cross-sectional area (CMO:0001715)108551382295638337Rat
2317754Glom25Glomerulus QTL 253.5urine protein amount (VT:0005160)urine protein level (CMO:0000591)1086566908112626471Rat
2301398Kidm38Kidney mass QTL 380.002kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)108696256399303173Rat
12880055Am11Aortic mass QTL 110.004aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)108696256399303173Rat
2306792Ean4Experimental allergic neuritis QTL 44nervous system integrity trait (VT:0010566)IFNG-secreting splenocyte count (CMO:0002122)108697786197308569Rat
1600367Mcs15Mammary carcinoma susceptibility QTL 154.5mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1088544136107545372Rat
631538Oia5Oil induced arthritis QTL 5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1090041957112626471Rat
2313856Bp342Blood pressure QTL 3424.40.0001life span trait (VT:0005372)age at time of death (CMO:0001193)109029689799492409Rat
61363Oia3Oil induced arthritis QTL 30.001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1090296897112626471Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:253
Count of miRNA genes:172
Interacting mature miRNAs:192
Transcripts:ENSRNOT00000028445
Prediction methods:Microtar, Miranda, Rnahybrid
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.


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 12 12 1 12
Medium 24 12 12 10 12 27 35 19 5
Low 2 19 33 17 8 17 5 5 44 15 6 5
Below cutoff 1 3 6 3 7 3

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000028445   ⟹   ENSRNOP00000028445
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1090,296,141 - 90,312,386 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000092102   ⟹   ENSRNOP00000074568
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1090,296,151 - 90,307,658 (-)Ensembl
RefSeq Acc Id: NM_012651   ⟹   NP_036783
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01090,296,148 - 90,312,396 (-)NCBI
Rnor_5.01090,084,734 - 90,101,181 (-)NCBI
RGSC_v3.41091,454,824 - 91,471,072 (-)RGD
Celera1086,018,849 - 86,032,669 (-)RGD
Sequence:
RefSeq Acc Id: XM_008767946   ⟹   XP_008766168
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01090,296,144 - 90,312,401 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_036783   ⟸   NM_012651
- UniProtKB: P23562 (UniProtKB/Swiss-Prot),   F8WFT7 (UniProtKB/TrEMBL),   Q5U329 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008766168   ⟸   XM_008767946
- Peptide Label: isoform X1
- UniProtKB: P23562 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000074568   ⟸   ENSRNOT00000092102
RefSeq Acc Id: ENSRNOP00000028445   ⟸   ENSRNOT00000028445
Protein Domains
Band_3_cyto   HCO3_cotransp

Transcriptome

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

Promoters
RGD ID:13697789
Promoter ID:EPDNEW_R8308
Type:single initiation site
Name:Slc4a1_2
Description:solute carrier family 4 member 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R8309  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01090,307,676 - 90,307,736EPDNEW
RGD ID:13697785
Promoter ID:EPDNEW_R8309
Type:multiple initiation site
Name:Slc4a1_1
Description:solute carrier family 4 member 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R8308  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01090,312,336 - 90,312,396EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
10 90087257 90087258 G A snv Crl:SD (UDEL)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3710 AgrOrtholog
Ensembl Genes ENSRNOG00000020951 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000028445 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000074568 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000028445 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000092102 UniProtKB/TrEMBL
Gene3D-CATH 3.40.930.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7126960 IMAGE-MGC_LOAD
InterPro Anion_exchange UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Anion_exchange_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Anion_exchange_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Band3_cytoplasmic_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HCO3_transpt_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HCO3_transpt_euk UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTrfase/Anion_transptr UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:24779 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGC_CLONE MGC:93554 IMAGE-MGC_LOAD
NCBI Gene 24779 ENTREZGENE
PANTHER PTHR11453 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Band_3_cyto UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HCO3_cotransp UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Slc4a1 PhenoGen
PRINTS ANIONEXCHNGR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ANIONEXHNGR1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HCO3TRNSPORT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE ANION_EXCHANGER_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ANION_EXCHANGER_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF55804 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGRFAMs TIGR00834 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniGene Rn.32202 ENTREZGENE
UniProt B3AT_RAT UniProtKB/Swiss-Prot
  F8WFT7 ENTREZGENE, UniProtKB/TrEMBL
  P23562 ENTREZGENE
  Q5U329 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2019-04-02 Slc4a1  solute carrier family 4 member 1 (Diego blood group)  Slc4a1  solute carrier family 4 member 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2017-01-17 Slc4a1  solute carrier family 4 member 1  Slc4a1  solute carrier family 4 (anion exchanger), member 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-02-15 Slc4a1  solute carrier family 4 (anion exchanger), member 1  Slc4a1  solute carrier family 4, member 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2003-04-09 Slc4a1  solute carrier family 4, member 1    Solute carrier family 4, member 1, anion exchange protein 1 (kidney band 3)  Name updated 629478 APPROVED
2002-06-10 Slc4a1  Solute carrier family 4, member 1, anion exchange protein 1 (kidney band 3)      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_mapping segregates on chr 10 within the Bp1 QTL region which has a major effect on systolic and diastolic blood pressure 1342444
gene_protein 848 amino acids 729968
 



Contact Us |  About Us |  License CC BY 4.0 |  Legal Disclaimer |  © Medical College of Wisconsin
NHLBI Logo

RGD is funded by grant HL64541 from the National Heart, Lung, and Blood Institute on behalf of the NIH.