Calb1 (calbindin 1) - Rat Genome Database

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Gene: Calb1 (calbindin 1) Rattus norvegicus
Analyze
Symbol: Calb1
Name: calbindin 1
RGD ID: 69340
Description: Enables calcium ion binding activity. Involved in several processes, including cochlea development; regulation of presynaptic cytosolic calcium ion concentration; and response to auditory stimulus. Located in several cellular components, including cuticular plate; dendritic spine; and stereocilium. Is active in calyx of Held; postsynaptic cytosol; and presynaptic cytosol. Biomarker of alcohol use disorder and bilirubin metabolic disorder. Orthologous to human CALB1 (calbindin 1); PARTICIPATES IN calcium/calcium-mediated signaling pathway; INTERACTS WITH (S)-nicotine; 3H-1,2-dithiole-3-thione; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: CaBP28K; calbindin; calbindin 1 28 kD; calbindin 1, (28kD); calbindin 1, 28 kD; calbindin D28; cerebellar Ca-binding protein spot 35 protein; cerebellar Ca-binding protein, spot 35 protein; D-28K; MGC93326; spot 35 protein; vitamin D-dependent calcium-binding protein, avian-type
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8534,172,612 - 34,199,555 (+)NCBIGRCr8
mRatBN7.2529,375,624 - 29,402,532 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl529,375,642 - 29,402,431 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx531,531,877 - 31,556,210 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0533,124,545 - 33,148,878 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0533,084,720 - 33,109,051 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0529,538,380 - 29,562,774 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl529,538,380 - 29,562,773 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0534,217,930 - 34,242,324 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4530,455,665 - 30,480,122 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1530,455,683 - 30,480,116 (+)NCBI
Celera528,581,243 - 28,605,619 (+)NCBICelera
Cytogenetic Map5q13NCBI
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
(1->4)-beta-D-glucan  (ISO)
(S)-nicotine  (EXP)
1,1-dichloroethene  (ISO)
1,2-dichloroethane  (ISO)
17alpha-ethynylestradiol  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',5,5'-tetrachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
3H-1,2-dithiole-3-thione  (EXP)
6-propyl-2-thiouracil  (EXP)
acrylamide  (ISO)
adefovir  (EXP)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
aristolochic acid A  (EXP)
arsenite(3-)  (ISO)
bacitracin  (EXP)
belinostat  (ISO)
benzo[a]pyrene  (ISO)
bisphenol A  (EXP,ISO)
Brodifacoum  (EXP)
buta-1,3-diene  (ISO)
cadmium dichloride  (EXP)
cadmium sulfate  (ISO)
calcitriol  (EXP,ISO)
calcium atom  (EXP)
calcium(0)  (EXP)
captopril  (ISO)
cefaloridine  (EXP)
CGP 52608  (ISO)
cisplatin  (EXP,ISO)
copper(II) chloride  (ISO)
copper(II) sulfate  (ISO)
cycloheximide  (ISO)
cyclosporin A  (EXP)
cytarabine  (EXP)
DDE  (ISO)
dexamethasone  (EXP)
diethanolamine  (ISO)
diethylstilbestrol  (ISO)
dioxygen  (ISO)
dorsomorphin  (ISO)
entinostat  (ISO)
ethanol  (EXP,ISO)
furosemide  (ISO)
genistein  (ISO)
gentamycin  (EXP,ISO)
glycidol  (EXP)
ivermectin  (ISO)
kainic acid  (ISO)
ketoconazole  (ISO)
lead diacetate  (EXP)
Mecamylamine  (EXP)
menadione  (ISO)
mercury dibromide  (ISO)
methimazole  (EXP)
morphine  (ISO)
nicotine  (EXP)
ochratoxin A  (EXP)
ouabain  (EXP)
p-chloromercuribenzoic acid  (ISO)
paracetamol  (ISO)
PCB138  (EXP,ISO)
perfluorooctane-1-sulfonic acid  (ISO)
phenylmercury acetate  (ISO)
picrotoxin  (EXP)
progesterone  (ISO)
quercetin  (ISO)
rotenone  (EXP)
SB 431542  (ISO)
simvastatin  (ISO)
sodium arsenite  (ISO)
sodium fluoride  (EXP)
tacrolimus hydrate  (EXP)
testosterone  (ISO)
thalidomide  (ISO)
titanium dioxide  (ISO)
trichostatin A  (ISO)
triphenyl phosphate  (ISO)
uranium atom  (EXP)
valproic acid  (ISO)
vancomycin  (EXP,ISO)
vandetanib  (ISO)
vinclozolin  (EXP)
vorinostat  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Tracking the expression of excitatory and inhibitory neurotransmission-related proteins and neuroplasticity markers after noise induced hearing loss. Browne CJ, etal., PLoS One. 2012;7(3):e33272. doi: 10.1371/journal.pone.0033272. Epub 2012 Mar 12.
2. Overexpression of calbindin D(28k) in dentate gyrus granule cells alters mossy fiber presynaptic function and impairs hippocampal-dependent memory. Dumas TC, etal., Hippocampus 2004;14(6):701-9.
3. Developmental expression of the Ca2+-binding proteins calretinin and parvalbumin at the calyx of Held of rats and mice. Felmy F and Schneggenburger R, Eur J Neurosci. 2004 Sep;20(6):1473-82. doi: 10.1111/j.1460-9568.2004.03604.x.
4. 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.
5. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
6. The concentrations of calcium buffering proteins in mammalian cochlear hair cells. Hackney CM, etal., J Neurosci. 2005 Aug 24;25(34):7867-75.
7. Structural characterization of the conformational change in calbindin-D28k upon calcium binding using differential surface modification analyzed by mass spectrometry. Hobbs CA, etal., Biochemistry. 2009 Sep 15;48(36):8603-14. doi: 10.1021/bi900350q.
8. Rat brain calbindin D28: six domain structure and extensive amino acid homology with chicken calbindin D28. Hunziker W and Schrickel S, Mol Endocrinol 1988 May;2(5):465-73.
9. Ankyrin-G coordinates assembly of the spectrin-based membrane skeleton, voltage-gated sodium channels, and L1 CAMs at Purkinje neuron initial segments. Jenkins SM and Bennett V, J Cell Biol. 2001 Nov 26;155(5):739-46. Epub 2001 Nov 26.
10. Light microscopic study of GluR1 and calbindin expression in interneurons of neocortical microgyral malformations. Kharazia VN, etal., Neuroscience 2003;120(1):207-18.
11. Cloning and analysis of calbindin-D28K cDNA and its expression in the central nervous system. Lomri N, etal., Gene 1989 Aug 1;80(1):87-98.
12. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
13. Synaptic connections of distinct interneuronal subpopulations in the rat basolateral amygdalar nucleus. Muller JF, etal., J Comp Neurol 2003 Feb 10;456(3):217-36.
14. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
15. Ultrastructural localization of calbindin-D28k and GABA in the matrix compartment of the rat caudate-putamen nuclei. Pickel VM and Heras A, Neuroscience. 1996 Mar;71(1):167-78.
16. GOA pipeline RGD automated data pipeline
17. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
18. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
19. Calbindin D28k targets myo-inositol monophosphatase in spines and dendrites of cerebellar Purkinje neurons. Schmidt H, etal., Proc Natl Acad Sci U S A. 2005 Apr 19;102(16):5850-5. doi: 10.1073/pnas.0407855102. Epub 2005 Apr 4.
20. Cytosolic Ca2+ buffers. Schwaller B, Cold Spring Harb Perspect Biol. 2010 Nov;2(11):a004051. doi: 10.1101/cshperspect.a004051. Epub 2010 Oct 13.
21. Immunohistochemical localization of calcium-binding proteins in the brainstem vestibular nuclei of the jaundiced Gunn rat. Shaia WT, etal., Hear Res 2002 Nov;173(1-2):82-90.
22. Alcohol-induced cognitive deficits are associated with decreased circulating levels of the neurotrophin BDNF in humans and rats. Silva-Peña D, etal., Addict Biol. 2019 Sep;24(5):1019-1033. doi: 10.1111/adb.12668. Epub 2018 Sep 12.
23. Changes in calcium-binding protein expression in the auditory brainstem nuclei of the jaundiced Gunn rat. Spencer RF, etal., Hear Res 2002 Sep;171(1-2):129-141.
24. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
25. Disrupted placental vitamin D metabolism and calcium signaling in gestational diabetes and pre-eclampsia patients. Varshney S, etal., Endocrine. 2023 Apr;80(1):191-200. doi: 10.1007/s12020-022-03272-9. Epub 2022 Dec 8.
26. Composition of isolated synaptic boutons reveals the amounts of vesicle trafficking proteins. Wilhelm BG, etal., Science. 2014 May 30;344(6187):1023-8. doi: 10.1126/science.1252884.
27. Nucleotide sequence of cDNA to mRNA for a cerebellar Ca-binding protein, spot 35 protein. Yamakuni T, etal., Nucleic Acids Res 1986 Aug 26;14(16):6768.
Additional References at PubMed
PMID:1988053   PMID:3031218   PMID:3049577   PMID:9037080   PMID:10741426   PMID:10828532   PMID:10973246   PMID:10989258   PMID:11955516   PMID:12115678   PMID:12115694   PMID:12205031  
PMID:12691666   PMID:12716955   PMID:12834886   PMID:15143625   PMID:15464957   PMID:15479642   PMID:15489334   PMID:15579147   PMID:15659591   PMID:15922086   PMID:16278289   PMID:16530828  
PMID:16600497   PMID:16814779   PMID:16928804   PMID:16977577   PMID:17561837   PMID:17825480   PMID:17850982   PMID:17880944   PMID:18359862   PMID:18394865   PMID:18497889   PMID:18618131  
PMID:18703048   PMID:18769561   PMID:18846343   PMID:19056867   PMID:19194547   PMID:19857553   PMID:19936227   PMID:20040500   PMID:20531390   PMID:21835217   PMID:22037839   PMID:22221733  
PMID:22226503   PMID:22544312   PMID:22796338   PMID:23199000   PMID:23253375   PMID:23376485   PMID:23628656   PMID:24378673   PMID:24466353   PMID:25828920   PMID:26671463   PMID:26975894  
PMID:30289411   PMID:32357304   PMID:33040447  


Genomics

Comparative Map Data
Calb1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8534,172,612 - 34,199,555 (+)NCBIGRCr8
mRatBN7.2529,375,624 - 29,402,532 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl529,375,642 - 29,402,431 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx531,531,877 - 31,556,210 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0533,124,545 - 33,148,878 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0533,084,720 - 33,109,051 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0529,538,380 - 29,562,774 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl529,538,380 - 29,562,773 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0534,217,930 - 34,242,324 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4530,455,665 - 30,480,122 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1530,455,683 - 30,480,116 (+)NCBI
Celera528,581,243 - 28,605,619 (+)NCBICelera
Cytogenetic Map5q13NCBI
CALB1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38890,058,608 - 90,082,879 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl890,058,608 - 90,095,475 (-)EnsemblGRCh38hg38GRCh38
GRCh37891,070,836 - 91,095,107 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36891,140,014 - 91,164,283 (-)NCBINCBI36Build 36hg18NCBI36
Build 34891,140,013 - 91,164,283NCBI
Celera887,265,760 - 87,290,030 (-)NCBICelera
Cytogenetic Map8q21.3ENTREZGENE
HuRef886,281,630 - 86,305,899 (-)NCBIHuRef
CHM1_1891,111,762 - 91,136,036 (-)NCBICHM1_1
T2T-CHM13v2.0891,182,279 - 91,206,531 (-)NCBIT2T-CHM13v2.0
Calb1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39415,881,264 - 15,906,709 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl415,881,264 - 15,908,064 (+)EnsemblGRCm39 Ensembl
GRCm38415,881,264 - 15,906,709 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl415,881,264 - 15,908,064 (+)EnsemblGRCm38mm10GRCm38
MGSCv37415,808,411 - 15,833,856 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36415,808,411 - 15,833,795 (+)NCBIMGSCv36mm8
Celera415,684,341 - 15,710,097 (+)NCBICelera
Cytogenetic Map4A2NCBI
cM Map46.66NCBI
Calb1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554176,942,900 - 6,969,502 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554176,944,300 - 6,969,341 (-)NCBIChiLan1.0ChiLan1.0
CALB1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v27107,454,698 - 107,478,231 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1882,994,347 - 83,017,871 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0886,747,702 - 86,771,995 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1888,699,532 - 88,723,814 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl888,699,532 - 88,723,814 (-)Ensemblpanpan1.1panPan2
CALB1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12935,551,836 - 35,572,985 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2935,552,436 - 35,572,925 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2935,704,729 - 35,725,872 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02935,749,189 - 35,770,350 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2935,748,436 - 35,770,338 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12935,736,414 - 35,757,553 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02935,754,732 - 35,775,854 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02936,190,515 - 36,211,601 (-)NCBIUU_Cfam_GSD_1.0
Calb1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440530343,910,718 - 43,934,361 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365443,858,344 - 3,882,106 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365443,858,344 - 3,881,985 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CALB1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl446,701,045 - 46,725,197 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1446,701,276 - 46,723,548 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2451,177,484 - 51,199,916 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CALB1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1885,135,956 - 85,160,806 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl885,137,528 - 85,160,855 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366603955,715,695 - 55,740,540 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Calb1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247441,929,988 - 1,963,464 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247441,930,085 - 1,960,950 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Calb1
154 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:390
Count of miRNA genes:220
Interacting mature miRNAs:261
Transcripts:ENSRNOT00000010845
Prediction methods:Microtar, Miranda, 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
1331756Rf34Renal function QTL 344.16275kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)5190450412Rat
70212Niddm25Non-insulin dependent diabetes mellitus QTL 253.54blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)51131345958Rat
1331771Rf35Renal function QTL 354.36965kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)572947086724018Rat
2312562Pur18Proteinuria QTL 182.60.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)5213896532656739Rat
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)52138965166875058Rat
8662454Vetf3Vascular elastic tissue fragility QTL 327.4artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)5228222669540447Rat
1300117Hrtrt8Heart rate QTL 83.49heart pumping trait (VT:2000009)heart rate (CMO:0000002)5384401847869213Rat
61462Niddm10Non-insulin dependent diabetes mellitus QTL 103.90.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)5511215947171491Rat
2293666Bmd38Bone mineral density QTL 384.4femur size trait (VT:1000369)femoral neck cortical cross-sectional area (CMO:0001702)5894822853948228Rat
7394712Emca13Estrogen-induced mammary cancer QTL 13mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)5982326699753708Rat
1641903Alcrsp3Alcohol response QTL 3response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)51268928557689285Rat
634305Mamtr1Mammary tumor resistance QTL 10.0001mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)512789751113558310Rat
1600358Mamtr5Mammary tumor resistance QTL 5mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)51887394763873947Rat
1358353Srcrtb2Stress Responsive Cort Basal QTL 23.480.003blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)51887394774251464Rat
8552954Pigfal14Plasma insulin-like growth factor 1 level QTL 149blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)52122674466226744Rat
1549901Neudeg2Neurodegradation QTL 240nervous system integrity trait (VT:0010566)mononuclear cell count (CMO:0002119)52483871044045280Rat
1578767Stresp17Stress response QTL 174.30.01blood aldosterone amount (VT:0005346)plasma aldosterone level (CMO:0000551)52795544072955440Rat
1578776Stresp18Stress response QTL 182.9thymus mass (VT:0004954)thymus wet weight (CMO:0000855)52795544072955440Rat
6903292Stl28Serum triglyceride level QTL 282.60.0073blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)52851548973515489Rat
6903306Scl35Serum cholesterol QTL 352.60.0073blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)52851548973515489Rat

Markers in Region
D26352  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2529,399,246 - 29,399,387 (+)MAPPERmRatBN7.2
Rnor_6.0529,561,968 - 29,562,108NCBIRnor6.0
Rnor_5.0534,241,518 - 34,241,658UniSTSRnor5.0
RGSC_v3.4530,479,316 - 30,479,456UniSTSRGSC3.4
Celera528,604,813 - 28,604,953UniSTS
Cytogenetic Map5q13UniSTS


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 2
Medium 64 27 1
Low 3 8 24 8 17 8 8 9 10 6 22 8 8
Below cutoff 13 21 21 2 21 1 15 3

Sequence


RefSeq Acc Id: ENSRNOT00000010845   ⟹   ENSRNOP00000010845
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl529,375,643 - 29,400,051 (+)Ensembl
Rnor_6.0 Ensembl529,538,380 - 29,562,773 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000106067   ⟹   ENSRNOP00000088742
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl529,375,642 - 29,400,052 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000119300   ⟹   ENSRNOP00000085057
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl529,375,642 - 29,402,431 (+)Ensembl
RefSeq Acc Id: NM_031984   ⟹   NP_114190
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8534,172,682 - 34,197,076 (+)NCBI
mRatBN7.2529,375,659 - 29,400,053 (+)NCBI
Rnor_6.0529,538,380 - 29,562,774 (+)NCBI
Rnor_5.0534,217,930 - 34,242,324 (+)NCBI
RGSC_v3.4530,455,665 - 30,480,122 (+)RGD
Celera528,581,243 - 28,605,619 (+)RGD
Sequence:
RefSeq Acc Id: XM_039110854   ⟹   XP_038966782
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8534,172,612 - 34,199,555 (+)NCBI
mRatBN7.2529,375,624 - 29,402,532 (+)NCBI
RefSeq Acc Id: NP_114190   ⟸   NM_031984
- UniProtKB: P07171 (UniProtKB/Swiss-Prot),   A6IIA7 (UniProtKB/TrEMBL),   A0A8I6AA30 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000010845   ⟸   ENSRNOT00000010845
RefSeq Acc Id: XP_038966782   ⟸   XM_039110854
- Peptide Label: isoform X1
- UniProtKB: A0A8I6GCE9 (UniProtKB/TrEMBL),   A0A8I6AA30 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSRNOP00000085057   ⟸   ENSRNOT00000119300
RefSeq Acc Id: ENSRNOP00000088742   ⟸   ENSRNOT00000106067
Protein Domains
EF-hand

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P07171-F1-model_v2 AlphaFold P07171 1-261 view protein structure

Transcriptome

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

Promoters
RGD ID:13693578
Promoter ID:EPDNEW_R4103
Type:single initiation site
Name:Calb1_1
Description:calbindin 1
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_6.0529,538,362 - 29,538,422EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:69340 AgrOrtholog
BioCyc Gene G2FUF-41866 BioCyc
Ensembl Genes ENSRNOG00000007456 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ENSRNOG00055000342 UniProtKB/Swiss-Prot
  ENSRNOG00060001115 UniProtKB/Swiss-Prot
  ENSRNOG00065015764 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000010845 ENTREZGENE
  ENSRNOT00000010845.5 UniProtKB/Swiss-Prot
  ENSRNOT00000106067.1 UniProtKB/TrEMBL
  ENSRNOT00000119300.1 UniProtKB/TrEMBL
  ENSRNOT00055000605 UniProtKB/Swiss-Prot
  ENSRNOT00060001539 UniProtKB/Swiss-Prot
  ENSRNOT00065026200 UniProtKB/Swiss-Prot
Gene3D-CATH EF-hand UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7110962 IMAGE-MGC_LOAD
InterPro Calbindin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EF-hand-dom_pair UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EF_Hand_1_Ca_BS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EF_hand_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:83839 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGC_CLONE MGC:93326 IMAGE-MGC_LOAD
NCBI Gene 83839 ENTREZGENE
PANTHER CALBINDIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR19972:SF14 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam EF-hand_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EF-hand_7 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Calb1 PhenoGen
PROSITE EF_HAND_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EF_HAND_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000007456 RatGTEx
  ENSRNOG00055000342 RatGTEx
  ENSRNOG00060001115 RatGTEx
  ENSRNOG00065015764 RatGTEx
SMART EFh UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF47473 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A8I6AA30 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6GCE9 ENTREZGENE, UniProtKB/TrEMBL
  A6IIA7 ENTREZGENE, UniProtKB/TrEMBL
  CALB1_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-06-10 Calb1  calbindin 1      Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_expression expressed in the cerebellum, hippocampus, retina, and kidney 68751
gene_product member of the EF-hand family of calcium binding proteins 68751