Hpca (hippocalcin) - Rat Genome Database

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Gene: Hpca (hippocalcin) Rattus norvegicus
Analyze
Symbol: Hpca
Name: hippocalcin
RGD ID: 620060
Description: Enables calcium ion binding activity and kinase binding activity. Involved in several processes, including activation of phospholipase D activity; cellular response to electrical stimulus; and negative regulation of guanylate cyclase activity. Located in several cellular components, including dendrite; neuronal cell body membrane; and perikaryon. Is extrinsic component of membrane. Is active in glutamatergic synapse and postsynapse. Human ortholog(s) of this gene implicated in torsion dystonia 2. Orthologous to human HPCA (hippocalcin); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran; ammonium chloride.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: calcium-binding protein; MGC105450; neuron-specific calcium-binding protein hippocalcin; P23K
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.25141,455,616 - 141,466,252 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl5141,455,613 - 141,463,841 (-)Ensembl
Rnor_6.05147,295,124 - 147,305,757 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5147,294,820 - 147,303,346 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.05151,029,882 - 151,040,514 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45148,267,898 - 148,276,223 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.15148,277,936 - 148,286,262 (-)NCBI
Celera5139,935,623 - 139,943,977 (-)NCBICelera
Cytogenetic Map5q36NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Hippocalcin in rat retina. Comparison with calbindin-D28k, calretinin and neurocalcin. Bastianelli E, etal., Exp Eye Res. 1995 Mar;60(3):257-66.
2. Brain region-specific changes in the expression of calcium sensor proteins after repeated applications of ketamine to rats. Bernstein HG, etal., Neurosci Lett. 2003 Mar 20;339(2):95-8.
3. Expression profiling shows differential molecular pathways and provides potential new diagnostic biomarkers for colorectal serrated adenocarcinoma. Conesa-Zamora P, etal., Int J Cancer. 2013 Jan 15;132(2):297-307. doi: 10.1002/ijc.27674. Epub 2012 Jun 28.
4. Decoding glutamate receptor activation by the Ca2+ sensor protein hippocalcin in rat hippocampal neurons. Dovgan AV, etal., Eur J Neurosci. 2010 Aug;32(3):347-58. doi: 10.1111/j.1460-9568.2010.07303.x.
5. Analysis of the interacting partners of the neuronal calcium-binding proteins L-CaBP1, hippocalcin, NCS-1 and neurocalcin delta. Haynes LP, etal., Proteomics. 2006 Mar;6(6):1822-32.
6. Role of hippocalcin in Ca2+ -induced activation of phospholipase D. Hyun JK, etal., Mol Cells. 2000 Dec 31;10(6):669-77.
7. Muscarinic receptors induce LTD of NMDAR EPSCs via a mechanism involving hippocalcin, AP2 and PSD-95. Jo J, etal., Nat Neurosci. 2010 Oct;13(10):1216-24. doi: 10.1038/nn.2636. Epub 2010 Sep 19.
8. Molecular cloning of hippocalcin, a novel calcium-binding protein of the recoverin family exclusively expressed in hippocampus. Kobayashi M, etal., Biochem Biophys Res Commun 1992 Nov 30;189(1):511-7.
9. Hippocalcin mediates calcium-dependent translocation of brain-type creatine kinase (BB-CK) in hippocampal neurons. Kobayashi M, etal., Biochem Biophys Res Commun. 2012 Dec 14;429(3-4):142-7. doi: 10.1016/j.bbrc.2012.10.125. Epub 2012 Nov 6.
10. Myristoylation of hippocalcin is linked to its calcium-dependent membrane association properties. Kobayashi M, etal., J Biol Chem. 1993 Sep 5;268(25):18898-904.
11. Hippocalcin in the olfactory epithelium: a mediator of second messenger signaling. Mammen A, etal., Biochem Biophys Res Commun. 2004 Oct 1;322(4):1131-9.
12. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
13. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
14. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
15. GOA pipeline RGD automated data pipeline
16. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
17. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
18. Gene expression profiles following exposure to a developmental neurotoxicant, Aroclor 1254: pathway analysis for possible mode(s) of action. Royland JE and Kodavanti PR, Toxicol Appl Pharmacol. 2008 Sep 1;231(2):179-96. Epub 2008 May 6.
19. Diminished hippocalcin expression in Huntington's disease brain does not account for increased striatal neuron vulnerability as assessed in primary neurons. Rudinskiy N, etal., J Neurochem. 2009 Oct;111(2):460-72. doi: 10.1111/j.1471-4159.2009.06344.x. Epub 2009 Aug 17.
20. Expression of hippocalcin in the developing rat brain. Saitoh S, etal., Brain Res Dev Brain Res. 1994 Jul 15;80(1-2):199-208.
21. Distribution of hippocalcin mRNA and immunoreactivity in rat brain. Saitoh S, etal., Neurosci Lett. 1993 Jul 9;157(1):107-10.
22. Hippocalcin expression in the brain of the Snell dwarf mutant mouse. Sugisaki T, etal., Brain Res. 1994 Nov 28;665(1):101-6.
23. Molecular cloning of human hippocalcin cDNA and chromosomal mapping of its gene. Takamatsu K, etal., Biochem Biophys Res Commun 1994 Apr 15;200(1):606-11.
24. Isolation and characterization of recoverin-like Ca(2+)-binding protein from rat brain. Takamatsu K, etal., Biochem Biophys Res Commun. 1992 Feb 28;183(1):245-51.
Additional References at PubMed
PMID:8240319   PMID:8938744   PMID:11964161   PMID:12477932   PMID:12657681   PMID:15489334   PMID:16102532   PMID:16294323   PMID:21795542   PMID:21873635   PMID:22639951   PMID:28398555  
PMID:29061397   PMID:31301343  


Genomics

Comparative Map Data
Hpca
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.25141,455,616 - 141,466,252 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl5141,455,613 - 141,463,841 (-)Ensembl
Rnor_6.05147,295,124 - 147,305,757 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5147,294,820 - 147,303,346 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.05151,029,882 - 151,040,514 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45148,267,898 - 148,276,223 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.15148,277,936 - 148,286,262 (-)NCBI
Celera5139,935,623 - 139,943,977 (-)NCBICelera
Cytogenetic Map5q36NCBI
HPCA
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38132,885,996 - 32,894,646 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl132,885,994 - 32,898,441 (+)EnsemblGRCh38hg38GRCh38
GRCh37133,352,092 - 33,360,247 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36133,124,685 - 33,132,834 (+)NCBINCBI36hg18NCBI36
Build 34133,021,190 - 33,029,339NCBI
Celera131,620,733 - 31,628,882 (+)NCBI
Cytogenetic Map1p35.1NCBI
HuRef131,467,222 - 31,475,369 (+)NCBIHuRef
CHM1_1133,467,533 - 33,475,680 (+)NCBICHM1_1
T2T-CHM13v2.0132,746,286 - 32,754,441 (+)NCBI
Hpca
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm394129,005,363 - 129,019,712 (-)NCBIGRCm39mm39
GRCm39 Ensembl4129,005,363 - 129,015,829 (-)Ensembl
GRCm384129,111,570 - 129,125,919 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl4129,111,570 - 129,122,036 (-)EnsemblGRCm38mm10GRCm38
MGSCv374128,788,819 - 128,798,984 (-)NCBIGRCm37mm9NCBIm37
MGSCv364128,613,879 - 128,621,062 (-)NCBImm8
Celera4127,451,599 - 127,461,862 (-)NCBICelera
Cytogenetic Map4D2.2NCBI
Hpca
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495545211,140,373 - 11,154,261 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495545211,142,282 - 11,150,798 (+)NCBIChiLan1.0ChiLan1.0
HPCA
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1133,362,921 - 33,371,524 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl133,363,673 - 33,371,524 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0132,176,465 - 32,185,133 (+)NCBIMhudiblu_PPA_v0panPan3
HPCA
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1268,464,631 - 68,473,661 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl268,465,280 - 68,473,310 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha265,045,221 - 65,053,618 (-)NCBI
ROS_Cfam_1.0269,030,436 - 69,038,834 (-)NCBI
ROS_Cfam_1.0 Ensembl269,029,808 - 69,039,028 (-)Ensembl
UMICH_Zoey_3.1265,841,971 - 65,850,366 (-)NCBI
UNSW_CanFamBas_1.0266,864,436 - 66,872,823 (-)NCBI
UU_Cfam_GSD_1.0267,856,319 - 67,864,715 (-)NCBI
Hpca
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440505849,961,196 - 49,969,278 (+)NCBI
SpeTri2.0NW_00493647415,786,171 - 15,794,830 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
HPCA
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl689,186,670 - 89,200,441 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1689,187,544 - 89,197,049 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2683,214,827 - 83,224,104 (+)NCBISscrofa10.2Sscrofa10.2susScr3
HPCA
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12099,974,952 - 99,983,194 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl2099,975,742 - 99,980,728 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366603316,708,814 - 16,717,377 (+)NCBIVero_WHO_p1.0
Hpca
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462476415,990,729 - 15,999,615 (+)EnsemblHetGla_female_1.0hetGla2
HetGla 1.0NW_00462476415,990,910 - 15,999,617 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
D5Wox35  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.25141,455,734 - 141,455,935 (+)MAPPERmRatBN7.2
Rnor_6.05147,295,243 - 147,295,443NCBIRnor6.0
Rnor_5.05151,030,004 - 151,030,204UniSTSRnor5.0
RGSC_v3.45148,267,965 - 148,268,165UniSTSRGSC3.4
Celera5139,935,690 - 139,935,890UniSTS
Cytogenetic Map5q36UniSTS
PMC126259P4  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.25141,456,496 - 141,456,779 (+)MAPPERmRatBN7.2
Rnor_6.05147,296,005 - 147,296,287NCBIRnor6.0
Rnor_5.05151,030,766 - 151,031,048UniSTSRnor5.0
RGSC_v3.45148,268,727 - 148,269,009UniSTSRGSC3.4
Cytogenetic Map5q36UniSTS
PMC126259P5  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.25141,456,496 - 141,456,756 (+)MAPPERmRatBN7.2
Rnor_6.05147,296,005 - 147,296,264NCBIRnor6.0
Rnor_5.05151,030,766 - 151,031,025UniSTSRnor5.0
RGSC_v3.45148,268,727 - 148,268,986UniSTSRGSC3.4
Cytogenetic Map5q36UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)52138965166875058Rat
1641912Alcrsp18Alcohol response QTL 18response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)535189153141643988Rat
1549845Scl44Serum cholesterol level QTL 446blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)540128307148607290Rat
1578766Tcas11Tongue tumor susceptibility QTL 114.12tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)546711509161317411Rat
1576312Emca8Estrogen-induced mammary cancer QTL 84.1mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)550328551141643988Rat
61426Scl2Serum cholesterol level QTL 27.30.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)559793399143070159Rat
61393Bp7Blood pressure QTL 74.50.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)560293434161481680Rat
1354598Srn6Serum renin concentration QTL 63.8blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)569540295151018848Rat
1302790Scl20Serum cholesterol level QTL 206.40.0001blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)582394392166664054Rat
61452Ciaa5CIA Autoantibody QTL 53.5blood autoantibody amount (VT:0003725)calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)594858972143070159Rat
1331796Thshl2Thyroid stimulating hormone level QTL 22.3blood thyroid-stimulating hormone amount (VT:0005119)serum thyroid stimulating hormone level (CMO:0001248)597059760147465714Rat
1358187Emca1Estrogen-induced mammary cancer QTL 14.4mammary gland integrity trait (VT:0010552)post-insult time to mammary tumor formation (CMO:0000345)599216724148607142Rat
1578673Bmd13Bone mineral density QTL 134.9femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)5103689353148689353Rat
2317056Wbc3White blood cell count QTL 32.510.01leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)5105999803150999803Rat
7207488Bss110Bone structure and strength QTL 18.4femur strength trait (VT:0010010)femur stiffness (CMO:0001674)5106906205151906205Rat
7207491Bss112Bone structure and strength QTL 1127femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)5106906205151906205Rat
7207481Bss106Bone structure and strength QTL 1067.9femur strength trait (VT:0010010)femur ultimate force (CMO:0001675)5106906205151906205Rat
7207486Bss109Bone structure and strength QTL 109femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)5106906205151906205Rat
1549838Bss4Bone structure and strength QTL 49.2femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)5106906205151906205Rat
1298089Scl14Serum cholesterol level QTL 145.80.0004blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)5108845856153845856Rat
1598847Cm62Cardiac mass QTL 623.4heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)5108845856153845856Rat
8657050Bw146Body weight QTL 14619.840.001body mass (VT:0001259)body weight gain (CMO:0000420)5108938288153938288Rat
8694441Bw169Body weight QTL 16917.610.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)5111416838156416838Rat
8694198Abfw3Abdominal fat weight QTL 316.130.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)5111416838156416838Rat
8694389Bw160Body weight QTL 1606.170.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)5111416838156416838Rat
8552960Pigfal15Plasma insulin-like growth factor 1 level QTL 15blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)5111416838156416838Rat
1581510Cm54Cardiac mass QTL 543.40.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)5120740824143608494Rat
2293642Bss37Bone structure and strength QTL 374.640.0001femur strength trait (VT:0010010)femur ultimate force (CMO:0001675)5120740824151018848Rat
1641920Colcs1Colorectal carcinoma susceptibility QTL 12.990.0055intestine integrity trait (VT:0010554)benign colorectal tumor surface area measurement (CMO:0001799)5121846814166846814Rat
10053720Scort26Serum corticosterone level QTL 262.060.0147blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)5124965598166875058Rat
724525Bp147Blood pressure QTL 1474.30.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5126424772166875058Rat
1598819Bp292Blood pressure QTL 2924.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5127798274166875058Rat
1598861Cm64Cardiac mass QTL 642.9heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)5127798274166875058Rat
8552908Pigfal4Plasma insulin-like growth factor 1 level QTL 46.6blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)5128506074166875058Rat
8694169Bw148Body weight QTL 14850.001body mass (VT:0001259)body weight gain (CMO:0000420)5128506074166875058Rat
634349Bp139Blood pressure QTL 1390.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5128924607166875058Rat
1331803Rf32Renal function QTL 322.798kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)5129132428143070159Rat
70156Niddm30Non-insulin dependent diabetes mellitus QTL 303.98blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)5129132447151006154Rat
738018Anxrr4Anxiety related response QTL 45.1exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)5130130159166875058Rat
7794791Mcs33Mammary carcinoma susceptibility QTL 331.93mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)5131345754166875058Rat
631505Bp103Blood pressure QTL 1033.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5132717196165560427Rat
631562Apr2Acute phase response QTL 23.7blood murinoglobulin 1 amount (VT:0010597)plasma murinoglobulin 1 level (CMO:0001931)5135927956166875058Rat
61444Strs2Sensitivity to stroke QTL 24.7cerebrum integrity trait (VT:0010549)post-insult time to onset of cerebrovascular lesion (CMO:0002343)5135929696166875058Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:126
Count of miRNA genes:92
Interacting mature miRNAs:110
Transcripts:ENSRNOT00000009153
Prediction methods: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.


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 64
Low 3 2 2 2 10 8 24
Below cutoff 11 16 14 2 14 4 4 13 12 3 4

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000009153   ⟹   ENSRNOP00000009153
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl5141,455,613 - 141,463,841 (-)Ensembl
Rnor_6.0 Ensembl5147,294,820 - 147,303,346 (-)Ensembl
RefSeq Acc Id: NM_017122   ⟹   NP_058818
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25141,455,668 - 141,463,993 (-)NCBI
Rnor_6.05147,295,176 - 147,303,501 (-)NCBI
Rnor_5.05151,029,882 - 151,040,514 (-)NCBI
RGSC_v3.45148,267,898 - 148,276,223 (-)RGD
Celera5139,935,623 - 139,943,977 (-)RGD
Sequence:
RefSeq Acc Id: XM_006238920   ⟹   XP_006238982
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25141,455,616 - 141,466,252 (-)NCBI
Rnor_6.05147,295,124 - 147,305,757 (-)NCBI
Rnor_5.05151,029,882 - 151,040,514 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006238921   ⟹   XP_006238983
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25141,455,616 - 141,466,047 (-)NCBI
Rnor_6.05147,295,124 - 147,305,488 (-)NCBI
Rnor_5.05151,029,882 - 151,040,514 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_058818   ⟸   NM_017122
- UniProtKB: P84076 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006238982   ⟸   XM_006238920
- Peptide Label: isoform X1
- UniProtKB: P84076 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006238983   ⟸   XM_006238921
- Peptide Label: isoform X1
- UniProtKB: P84076 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000009153   ⟸   ENSRNOT00000009153
Protein Domains
EF-hand

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P84076-F1-model_v2 AlphaFold P84076 1-193 view protein structure

Transcriptome

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

Promoters
RGD ID:13694055
Promoter ID:EPDNEW_R4580
Type:single initiation site
Name:Hpca_1
Description:hippocalcin
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_6.05147,303,382 - 147,303,442EPDNEW

Strain Variation

Strain Sequence Variants (MRatBN7.2)
ACI/EurMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BUF/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
DA/OlaHsd (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE16/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/FarMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB10/IpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF10A/StmMcwi (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrcAek (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrcAek (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrcAek (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/NRrrcMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MWF/Hsd (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHR/OlalpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WAG/RijCrl (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620060 AgrOrtholog
BioCyc Gene G2FUF-39820 BioCyc
Ensembl Genes ENSRNOG00000006979 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000009153 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000009153 ENTREZGENE, UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7319524 IMAGE-MGC_LOAD
InterPro EF-hand-dom_pair UniProtKB/Swiss-Prot
  EF_Hand_1_Ca_BS UniProtKB/Swiss-Prot
  EF_hand_dom UniProtKB/Swiss-Prot
  Recoverin UniProtKB/Swiss-Prot
KEGG Report rno:29177 UniProtKB/Swiss-Prot
MGC_CLONE MGC:105450 IMAGE-MGC_LOAD
NCBI Gene 29177 ENTREZGENE
PANTHER PTHR23055 UniProtKB/Swiss-Prot
Pfam EF-hand_7 UniProtKB/Swiss-Prot
  EF-hand_8 UniProtKB/Swiss-Prot
PhenoGen Hpca PhenoGen
PROSITE EF_HAND_1 UniProtKB/Swiss-Prot
  EF_HAND_2 UniProtKB/Swiss-Prot
SMART EFh UniProtKB/Swiss-Prot
Superfamily-SCOP SSF47473 UniProtKB/Swiss-Prot
UniProt HPCA_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary P32076 UniProtKB/Swiss-Prot
  P41211 UniProtKB/Swiss-Prot
  P70510 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2004-02-26 Hpca  hippocalcin      Symbol and Name status set to approved 625702 APPROVED
2002-08-07 Hpca        Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_domains contains three EF-hand calcium-binding domains 727521
gene_protein 195 amino acids; 22.6 kDa 727521