Calr4 (calreticulin 4) - Rat Genome Database

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Pathways
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Gene: Calr4 (calreticulin 4) Rattus norvegicus
Analyze
No known orthologs.
Symbol: Calr4
Name: calreticulin 4
RGD ID: 1591090
Description: Predicted to enable calcium ion binding activity. Predicted to be involved in ERAD pathway and protein folding. Predicted to be located in endoplasmic reticulum lumen. Predicted to be active in endoplasmic reticulum membrane.
Type: protein-coding
RefSeq Status: MODEL
Previously known as: calreticulin; LOC689537; rCG50286-like; similar to Calreticulin precursor (CRP55) (Calregulin) (HACBP) (ERp60) (grp60)
RGD Orthologs
Alliance Genes
More Info homologs ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr85129,216,293 - 129,251,077 (+)NCBIGRCr8
mRatBN7.25123,986,870 - 124,022,436 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl5123,987,474 - 124,022,417 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.05128,865,339 - 128,900,135 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5128,865,389 - 128,899,792 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.05132,710,283 - 132,739,574 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45130,580,191 - 130,615,801 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera5122,716,917 - 122,751,933 (+)NCBICelera
Cytogenetic Map5q34NCBI
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. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Variants

.
Variants in Calr4
266 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:132
Count of miRNA genes:99
Interacting mature miRNAs:107
Transcripts:ENSRNOT00000057216, ENSRNOT00000068697
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
70212Niddm25Non-insulin dependent diabetes mellitus QTL 253.54blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)51131345958Rat
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)52138965166875058Rat
2290448Scl54Serum cholesterol level QTL 542.93blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)531663789131345958Rat
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
1331801Rf33Renal function QTL 334.149kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)543726656129132602Rat
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
70189Mcs5Mammary carcinoma susceptibility QTL 510.51mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)555805606132207589Rat
1358895Bp254Blood pressure QTL 2543.60.0003arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)558829236128034027Rat
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
2306971Anxrr21Anxiety related response QTL 219.47fear/anxiety-related behavior trait (VT:1000241)number of entries into a discrete space in an experimental apparatus (CMO:0000960)566174080124160948Rat
1354598Srn6Serum renin concentration QTL 63.8blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)569540295151018848Rat
1298070Scl18Serum cholesterol level QTL 183.7blood LDL cholesterol amount (VT:0000181)calculated plasma low density lipoprotein cholesterol level (CMO:0001245)579584860124584860Rat
1598846Bp293Blood pressure QTL 2933.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)579584860124584860Rat
1598859Cm66Cardiac mass QTL 662heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)579584860124584860Rat
1302790Scl20Serum cholesterol level QTL 206.40.0001blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)582394392166664054Rat
1298086Bp156Blood pressure QTL 156arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)584132602129132602Rat
7411601Foco12Food consumption QTL 1219.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)587468046132468046Rat
7411564Bw135Body weight QTL 1350.001body mass (VT:0001259)body weight gain (CMO:0000420)587468046132468046Rat
7411582Foco3Food consumption QTL 37.50.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)587468046132468046Rat
6903316Bw113Body weight QTL 11320.0103body mass (VT:0001259)body weight (CMO:0000012)587765973132765973Rat
1358889Bp261Blood pressure QTL 2612.86arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)590067849128034027Rat
1358909Kidm25Kidney mass QTL 251.87kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)590067849128034027Rat
631527Tls1T-lymphoma susceptibility QTL 100.001thymus integrity trait (VT:0010555)post-insult time to onset of T-cell lymphoma (CMO:0001907)590450144135450144Rat
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
2317753Glom24Glomerulus QTL 243.1kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)597570330136479578Rat
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
7794739Bp372Blood pressure QTL 3720.0058arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5117913688125222967Rat
1582230Bw78Body weight QTL 783.20.0016epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)5119085612128034027Rat
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

Markers in Region
AU022466  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.25124,022,072 - 124,022,276 (+)MAPPERmRatBN7.2
Rnor_6.05128,899,772 - 128,899,975NCBIRnor6.0
Rnor_5.05132,739,211 - 132,739,414UniSTSRnor5.0
RGSC_v3.45130,615,438 - 130,615,641UniSTSRGSC3.4
Celera5122,751,570 - 122,751,773UniSTS
Cytogenetic Map5q35UniSTS
RH141816  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.25123,999,787 - 123,999,972 (+)MAPPERmRatBN7.2
Rnor_6.05128,877,490 - 128,877,674NCBIRnor6.0
Rnor_5.05132,716,929 - 132,717,113UniSTSRnor5.0
RGSC_v3.45130,593,153 - 130,593,337UniSTSRGSC3.4
Celera5122,729,282 - 122,729,466UniSTS
RH 3.4 Map5812.1UniSTS
Cytogenetic Map5q35UniSTS


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 1
Low 1 1 15 8 59 10 25 9
Below cutoff 1 36 14 13 11 13 7 10 13 11 12 2 7

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000057216   ⟹   ENSRNOP00000054042
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl5123,991,485 - 124,022,417 (+)Ensembl
Rnor_6.0 Ensembl5128,881,062 - 128,899,792 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000068697   ⟹   ENSRNOP00000063135
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl5123,987,474 - 124,022,417 (+)Ensembl
Rnor_6.0 Ensembl5128,865,389 - 128,899,792 (+)Ensembl
RefSeq Acc Id: XM_039111170   ⟹   XP_038967098
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85129,221,708 - 129,251,077 (+)NCBI
mRatBN7.25123,993,049 - 124,022,436 (+)NCBI
RefSeq Acc Id: XM_039111171   ⟹   XP_038967099
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85129,221,341 - 129,251,077 (+)NCBI
mRatBN7.25123,992,686 - 124,022,436 (+)NCBI
RefSeq Acc Id: XM_039111172   ⟹   XP_038967100
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85129,221,706 - 129,251,077 (+)NCBI
mRatBN7.25123,993,048 - 124,022,436 (+)NCBI
RefSeq Acc Id: XM_039111174   ⟹   XP_038967102
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85129,216,293 - 129,251,077 (+)NCBI
mRatBN7.25123,986,870 - 124,022,436 (+)NCBI
RefSeq Acc Id: XM_063288592   ⟹   XP_063144662
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85129,228,679 - 129,251,077 (+)NCBI
RefSeq Acc Id: XM_063288593   ⟹   XP_063144663
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85129,221,695 - 129,251,077 (+)NCBI
Reference Protein Sequences
RefSeq Acc Id: ENSRNOP00000054042   ⟸   ENSRNOT00000057216
RefSeq Acc Id: ENSRNOP00000063135   ⟸   ENSRNOT00000068697
RefSeq Acc Id: XP_038967102   ⟸   XM_039111174
- Peptide Label: isoform X6
- UniProtKB: A6JYX7 (UniProtKB/TrEMBL),   D3ZYM6 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038967099   ⟸   XM_039111171
- Peptide Label: isoform X2
- UniProtKB: F1M5A1 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038967100   ⟸   XM_039111172
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038967098   ⟸   XM_039111170
- Peptide Label: isoform X1
- UniProtKB: F1M5A1 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063144663   ⟸   XM_063288593
- Peptide Label: isoform X5
RefSeq Acc Id: XP_063144662   ⟸   XM_063288592
- Peptide Label: isoform X4

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZYM6-F1-model_v2 AlphaFold D3ZYM6 1-439 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1591090 AgrOrtholog
BioCyc Gene G2FUF-40360 BioCyc
Ensembl Genes ENSRNOG00000037710 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000057216.4 UniProtKB/TrEMBL
  ENSRNOT00000068697.5 UniProtKB/TrEMBL
Gene3D-CATH 2.10.250.10 UniProtKB/TrEMBL
  2.60.120.200 UniProtKB/TrEMBL
InterPro Calret/calnex UniProtKB/TrEMBL
  Calret/calnex_CS UniProtKB/TrEMBL
  Calreticulin UniProtKB/TrEMBL
  Calreticulin/calnexin_P_dom UniProtKB/TrEMBL
  ConA-like_subgrp UniProtKB/TrEMBL
NCBI Gene 689537 ENTREZGENE
PANTHER Calret/calnex UniProtKB/TrEMBL
  CALRETICULIN UniProtKB/TrEMBL
Pfam Calreticulin UniProtKB/TrEMBL
PhenoGen Calr4 PhenoGen
PIRSF Calreticulin UniProtKB/TrEMBL
PRINTS CALRETICULIN UniProtKB/TrEMBL
PROSITE CALRETICULIN_1 UniProtKB/TrEMBL
  CALRETICULIN_2 UniProtKB/TrEMBL
  CALRETICULIN_REPEAT UniProtKB/TrEMBL
RatGTEx ENSRNOG00000037710 RatGTEx
Superfamily-SCOP ConA_like_lec_gl UniProtKB/TrEMBL
  SSF63887 UniProtKB/TrEMBL
UniProt A6JYX7 ENTREZGENE, UniProtKB/TrEMBL
  A6JYX8_RAT UniProtKB/TrEMBL
  D3ZYM6 ENTREZGENE, UniProtKB/TrEMBL
  F1M5A1 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-05-24 Calr4  calreticulin 4  LOC100364128  rCG50286-like  Data merged from RGD:2321630 1643240 APPROVED
2010-05-06 LOC100364128  rCG50286-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2008-03-06 Calr4  calreticulin 4  LOC689537  similar to Calreticulin precursor (CRP55) (Calregulin) (HACBP) (ERp60) (grp60)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-01-09 LOC689537  similar to Calreticulin precursor (CRP55) (Calregulin) (HACBP) (ERp60) (grp60)  LOC683830  similar to Calreticulin precursor (CRP55) (Calregulin) (HACBP) (ERp60) (grp60)  Data merged from RGD:1597849 1643240 APPROVED
2006-11-20 LOC689537  similar to Calreticulin precursor (CRP55) (Calregulin) (HACBP) (ERp60) (grp60)      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-20 LOC683830  similar to Calreticulin precursor (CRP55) (Calregulin) (HACBP) (ERp60) (grp60)      Symbol and Name status set to provisional 70820 PROVISIONAL