Calr3 (calreticulin 3) - Rat Genome Database

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Gene: Calr3 (calreticulin 3) Rattus norvegicus
Analyze
Symbol: Calr3
Name: calreticulin 3
RGD ID: 1309243
Description: Predicted to enable protein folding chaperone. Predicted to be involved in ERAD pathway and protein folding. Predicted to be located in endoplasmic reticulum lumen and nuclear envelope. Predicted to be active in endoplasmic reticulum membrane. Orthologous to human CALR3 (calreticulin 3); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,4,6-trinitrotoluene; 2,4-dinitrotoluene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: calreticulin-3; LOC364529
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
GRCr81617,430,105 - 17,456,777 (+)NCBIGRCr8
mRatBN7.21617,396,064 - 17,423,166 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1617,396,247 - 17,423,015 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1617,464,589 - 17,488,241 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01618,595,761 - 18,620,537 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01617,517,509 - 17,541,163 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01619,097,391 - 19,124,062 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1619,097,391 - 19,124,062 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01618,960,142 - 18,985,150 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41617,814,237 - 17,842,744 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11617,814,234 - 17,842,742 (+)NCBI
Celera1617,615,842 - 17,640,280 (+)NCBICelera
Cytogenetic Map16p14NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. 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.
2. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
3. GOA pipeline RGD automated data pipeline
4. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932   PMID:21590275   PMID:22357757  


Genomics

Comparative Map Data
Calr3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81617,430,105 - 17,456,777 (+)NCBIGRCr8
mRatBN7.21617,396,064 - 17,423,166 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1617,396,247 - 17,423,015 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1617,464,589 - 17,488,241 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01618,595,761 - 18,620,537 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01617,517,509 - 17,541,163 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01619,097,391 - 19,124,062 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1619,097,391 - 19,124,062 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01618,960,142 - 18,985,150 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41617,814,237 - 17,842,744 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11617,814,234 - 17,842,742 (+)NCBI
Celera1617,615,842 - 17,640,280 (+)NCBICelera
Cytogenetic Map16p14NCBI
CALR3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381916,479,061 - 16,496,167 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1916,479,061 - 16,496,167 (-)EnsemblGRCh38hg38GRCh38
GRCh371916,589,872 - 16,606,978 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361916,450,887 - 16,468,003 (-)NCBINCBI36Build 36hg18NCBI36
Build 341916,450,887 - 16,468,003NCBI
Celera1916,491,740 - 16,508,840 (-)NCBICelera
Cytogenetic Map19p13.11NCBI
HuRef1916,158,784 - 16,175,504 (-)NCBIHuRef
CHM1_11916,589,388 - 16,606,484 (-)NCBICHM1_1
T2T-CHM13v2.01916,613,878 - 16,630,953 (-)NCBIT2T-CHM13v2.0
Calr3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39873,178,020 - 73,197,638 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl873,178,020 - 73,197,714 (-)EnsemblGRCm39 Ensembl
GRCm38872,424,176 - 72,443,819 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl872,424,176 - 72,443,870 (-)EnsemblGRCm38mm10GRCm38
MGSCv37874,948,082 - 74,967,677 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36875,353,172 - 75,372,767 (-)NCBIMGSCv36mm8
Celera876,763,438 - 76,782,291 (-)NCBICelera
Cytogenetic Map8B3.3NCBI
cM Map835.08NCBI
Calr3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555241,245,708 - 1,256,478 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555241,245,607 - 1,256,528 (+)NCBIChiLan1.0ChiLan1.0
CALR3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22021,350,144 - 21,368,984 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11920,356,194 - 20,375,040 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01915,969,684 - 15,986,858 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11916,948,431 - 16,965,232 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1916,948,499 - 16,965,161 (-)Ensemblpanpan1.1panPan2
CALR3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12046,039,115 - 46,060,834 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2046,039,115 - 46,060,814 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2045,953,092 - 45,974,897 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02046,526,579 - 46,548,627 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2046,526,668 - 46,548,607 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12045,761,738 - 45,783,531 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02046,172,531 - 46,194,491 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02046,448,080 - 46,470,106 (+)NCBIUU_Cfam_GSD_1.0
Calr3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118204,571,185 - 204,591,064 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365964,120,295 - 4,140,432 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365964,120,292 - 4,140,432 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CALR3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl261,105,303 - 61,134,961 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1261,105,307 - 61,136,060 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2260,738,182 - 60,767,157 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CALR3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1614,987,761 - 15,007,145 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl614,987,230 - 15,006,857 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660744,464,855 - 4,484,155 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Calr3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624908949,783 - 961,667 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_004624908949,709 - 962,114 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Calr3
290 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:79
Count of miRNA genes:68
Interacting mature miRNAs:71
Transcripts:ENSRNOT00000018018
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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1600369Hcas8Hepatocarcinoma susceptibility QTL 8liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)16122477621Rat
631830Alc7Alcohol consumption QTL 72.9consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)16126727669Rat
634355Rends4Renal damage susceptibility QTL 40.05kidney blood vessel morphology trait (VT:0000530)organ lesion measurement (CMO:0000677)16126727669Rat
1582235Insul8Insulin level QTL 83.30.0063blood insulin amount (VT:0001560)calculated serum insulin level (CMO:0000359)16126727669Rat
9590151Scort8Serum corticosterone level QTL 88.450.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)16130836262Rat
2302380Slep6Serum leptin concentration QTL 63.36blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)16132139025Rat
2307172Activ4Activity QTL 43.710.00023locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)16133418960Rat
1354584Despr6Despair related QTL 63.10.0067locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)16139533930Rat
2303566Bw90Body weight QTL 902body mass (VT:0001259)body weight (CMO:0000012)16139533930Rat
631561Hcuc2Hepatic copper content QTL 22.8liver copper amount (VT:0003065)liver total copper weight (CMO:0001507)16139533949Rat
6903319Bw114Body weight QTL 1142.70.0037body mass (VT:0001259)body weight (CMO:0000012)16143534949Rat
7411664Foco30Food consumption QTL 30110.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)16144588133Rat
1354625Despr7Despair related QTL 73.160.016locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)16144977551Rat
1600378Arunc4Aerobic running capacity QTL 40.03exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)1638024580345693Rat
2293343Glom16Glomerulus QTL 167.4kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)1683223646053497Rat
2312660Bw95Body weight QTL 950.05inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)1683223659492508Rat
2312663Slep9Serum leptin concentration QTL 90.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)1683223659492508Rat
2312666Insul16Insulin level QTL 160.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1683223659492508Rat
2312669Stl23Serum triglyceride level QTL 230.01blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)1683223659492508Rat
1300133Rf24Renal function QTL 243.64blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)16338015021361552Rat
2306902Bp339Blood pressure QTL 3390.01arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)16338015043025077Rat
70183BpQTLcluster13Blood pressure QTL cluster 133.654arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)16422760943025077Rat
70183BpQTLcluster13Blood pressure QTL cluster 133.654arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)16422760943025077Rat
70183BpQTLcluster13Blood pressure QTL cluster 133.654arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)16422760943025077Rat
737819Hcas4Hepatocarcinoma susceptibility QTL 44.43liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)16422760946975965Rat
61405Niddm6Non-insulin dependent diabetes mellitus QTL 63.660.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)16422760948972724Rat
61338Bp23Blood pressure QTL 234.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)16422760949227609Rat
737826Alc11Alcohol consumption QTL 113.2consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)16422760960252231Rat
61372Bp40Blood pressure QTL 402.2blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)16422773017696785Rat
631517Scl9Serum cholesterol level QTL 93.3blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)161572643321034895Rat


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 4 10
Low 3 43 57 41 19 41 8 11 70 35 31 11 8
Below cutoff

Sequence


RefSeq Acc Id: ENSRNOT00000018018   ⟹   ENSRNOP00000018018
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1617,396,247 - 17,423,015 (+)Ensembl
Rnor_6.0 Ensembl1619,097,391 - 19,124,062 (+)Ensembl
RefSeq Acc Id: NM_001012212   ⟹   NP_001012212
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81617,430,105 - 17,456,775 (+)NCBI
mRatBN7.21617,396,064 - 17,422,739 (+)NCBI
Rnor_6.01619,097,391 - 19,124,062 (+)NCBI
Rnor_5.01618,960,142 - 18,985,150 (+)NCBI
RGSC_v3.41617,814,237 - 17,842,744 (+)RGD
Celera1617,615,842 - 17,640,280 (+)RGD
Sequence:
RefSeq Acc Id: XM_039094712   ⟹   XP_038950640
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81617,430,244 - 17,456,777 (+)NCBI
mRatBN7.21617,396,156 - 17,423,166 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001012212 (Get FASTA)   NCBI Sequence Viewer  
  XP_038950640 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH79049 (Get FASTA)   NCBI Sequence Viewer  
  EDL90842 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000018018
  ENSRNOP00000018018.4
RefSeq Acc Id: NP_001012212   ⟸   NM_001012212
- Peptide Label: precursor
- UniProtKB: Q6AYG8 (UniProtKB/TrEMBL),   F7EM31 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000018018   ⟸   ENSRNOT00000018018
RefSeq Acc Id: XP_038950640   ⟸   XM_039094712
- Peptide Label: isoform X1

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q6AYG8-F1-model_v2 AlphaFold Q6AYG8 1-379 view protein structure

Transcriptome

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

Promoters
RGD ID:13699985
Promoter ID:EPDNEW_R10506
Type:initiation region
Name:Calr3_1
Description:calreticulin 3
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_6.01619,097,485 - 19,097,545EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1309243 AgrOrtholog
BioCyc Gene G2FUF-11883 BioCyc
Ensembl Genes ENSRNOG00000013260 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000018018 ENTREZGENE
  ENSRNOT00000018018.6 UniProtKB/TrEMBL
Gene3D-CATH 2.60.120.200 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7115321 IMAGE-MGC_LOAD
InterPro Calret/calnex UniProtKB/TrEMBL
  Calret/calnex_CS UniProtKB/TrEMBL
  Calreticulin UniProtKB/TrEMBL
  Calreticulin/calnexin_P UniProtKB/TrEMBL
  ConA-like_subgrp UniProtKB/TrEMBL
KEGG Report rno:364529 UniProtKB/TrEMBL
MGC_CLONE MGC:93986 IMAGE-MGC_LOAD
NCBI Gene 364529 ENTREZGENE
PANTHER Calret/calnex UniProtKB/TrEMBL
  CALRETICULIN-3 UniProtKB/TrEMBL
Pfam Calreticulin UniProtKB/TrEMBL
PhenoGen Calr3 PhenoGen
PIRSF Calreticulin UniProtKB/TrEMBL
PRINTS CALRETICULIN UniProtKB/TrEMBL
PROSITE CALRETICULIN_1 UniProtKB/TrEMBL
  CALRETICULIN_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000013260 RatGTEx
Superfamily-SCOP Calret_calnex_P UniProtKB/TrEMBL
  ConA_like_lec_gl UniProtKB/TrEMBL
UniProt F7EM31 ENTREZGENE, UniProtKB/TrEMBL
  Q6AYG8 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2005-12-06 Calr3  calreticulin 3  Calr3_predicted  calreticulin 3 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Calr3_predicted  calreticulin 3 (predicted)      Symbol and Name status set to approved 70820 APPROVED