Clvs2 (clavesin 2) - Rat Genome Database

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Gene: Clvs2 (clavesin 2) Rattus norvegicus
Analyze
Symbol: Clvs2
Name: clavesin 2
RGD ID: 1306801
Description: Predicted to enable phosphatidylinositol-3,5-bisphosphate binding activity. Involved in lysosome organization. Located in clathrin-coated vesicle and trans-Golgi network. Orthologous to human CLVS2 (clavesin 2); INTERACTS WITH 17alpha-ethynylestradiol; bisphenol A; dimethylarsinic acid.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: clavesin-2; LOC361459; retinaldehyde binding protein 1-like 2; retinaldehyde-binding protein 1-like 2; Retinaldehyde-binding protein 1-like protein 2; RGD1306801; Rlbp1l2; similar to hypothetical protein MGC34646
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8125,553,981 - 25,661,806 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl125,554,375 - 25,580,830 (+)EnsemblGRCr8
mRatBN7.2123,735,660 - 23,842,685 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl123,735,272 - 23,842,692 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx123,507,180 - 23,534,942 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0129,506,888 - 29,534,672 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0123,704,238 - 23,732,022 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0125,173,089 - 25,217,625 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl125,173,242 - 25,296,927 (+)Ensemblrn6Rnor6.0
Rnor_5.0126,631,832 - 26,677,841 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4124,279,841 - 24,309,821 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera122,443,160 - 22,472,626 (+)NCBICelera
RGSC_v3.1124,282,808 - 24,393,034 (+)NCBI
Cytogenetic Map1p12NCBI
JBrowse:




Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
lysosome organization  (IBA,IEA,IMP)

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. The clavesin family, neuron-specific lipid- and clathrin-binding Sec14 proteins regulating lysosomal morphology. Katoh Y, etal., J Biol Chem. 2009 Oct 2;284(40):27646-54. doi: 10.1074/jbc.M109.034884. Epub 2009 Aug 3.
3. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
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

Genomics

Comparative Map Data
Clvs2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8125,553,981 - 25,661,806 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl125,554,375 - 25,580,830 (+)EnsemblGRCr8
mRatBN7.2123,735,660 - 23,842,685 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl123,735,272 - 23,842,692 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx123,507,180 - 23,534,942 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0129,506,888 - 29,534,672 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0123,704,238 - 23,732,022 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0125,173,089 - 25,217,625 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl125,173,242 - 25,296,927 (+)Ensemblrn6Rnor6.0
Rnor_5.0126,631,832 - 26,677,841 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4124,279,841 - 24,309,821 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera122,443,160 - 22,472,626 (+)NCBICelera
RGSC_v3.1124,282,808 - 24,393,034 (+)NCBI
Cytogenetic Map1p12NCBI
CLVS2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh386122,996,235 - 123,072,925 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl6122,996,131 - 123,072,925 (+)Ensemblhg38GRCh38
GRCh376123,317,380 - 123,394,070 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 366123,359,281 - 123,426,762 (+)NCBIBuild 36Build 36hg18NCBI36
Celera6124,062,048 - 124,129,515 (+)NCBICelera
Cytogenetic Map6q22.31NCBI
HuRef6120,894,951 - 120,962,427 (+)NCBIHuRef
CHM1_16123,581,348 - 123,648,817 (+)NCBICHM1_1
T2T-CHM13v2.06124,184,248 - 124,261,165 (+)NCBIT2T-CHM13v2.0
Clvs2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391033,388,282 - 33,500,680 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1033,388,282 - 33,500,765 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm381033,512,286 - 33,624,684 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1033,512,286 - 33,624,769 (-)Ensemblmm10GRCm38
MGSCv371033,232,140 - 33,344,406 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361033,201,750 - 33,314,016 (-)NCBIMGSCv36mm8
Celera1034,420,461 - 34,534,817 (-)NCBICelera
Cytogenetic Map10A4- B1NCBI
cM Map1018.62NCBI
Clvs2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554364,758,743 - 4,823,383 (+)Ensembl
ChiLan1.0NW_0049554364,758,749 - 4,823,383 (+)NCBIChiLan1.0ChiLan1.0
CLVS2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v25142,991,128 - 143,072,736 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan16140,892,499 - 140,974,473 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v06120,784,849 - 120,858,655 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.16124,907,667 - 124,985,026 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl6124,907,667 - 124,975,839 (+)EnsemblpanPan2panpan1.1
CLVS2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1162,217,473 - 62,286,853 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl162,217,837 - 62,282,449 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha163,025,578 - 63,096,929 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0162,420,539 - 62,491,590 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl162,422,598 - 62,496,418 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1162,354,446 - 62,425,787 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0162,142,463 - 62,213,279 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0162,791,442 - 62,862,485 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Clvs2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404946113,139,246 - 113,212,531 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936802872,577 - 936,649 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_004936802872,224 - 936,660 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CLVS2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl139,682,689 - 39,752,486 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1139,680,741 - 39,755,398 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2143,889,759 - 43,979,654 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CLVS2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11350,743,405 - 50,816,387 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1350,749,014 - 50,815,951 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366604023,041,383 - 23,113,693 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Clvs2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247988,219,329 - 8,302,061 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046247988,219,972 - 8,302,159 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Clvs2
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v12207,792,031 - 207,887,217 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Clvs2
770 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:108
Count of miRNA genes:99
Interacting mature miRNAs:103
Transcripts:ENSRNOT00000016518
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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2313090Bmd69Bone mineral density QTL 694.40.0001tibia mineral mass (VT:1000283)compact volumetric bone mineral density (CMO:0001730)1529322934184556Rat
631688Hcas2Hepatocarcinoma susceptibility QTL 230.0001liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)1774611852746118Rat
4889451Eae29Experimental allergic encephalomyelitis QTL 295.51nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)1774612152746121Rat
70179Xhs2X-ray hypersensitivity QTL 23.2intestine integrity trait (VT:0010554)post-insult time to onset of moribundity (CMO:0001896)1143965634Rat
1354647Despr8Despair related QTL 80.0000341locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)1126564886Rat
1558642Prcr2Prostate cancer resistance QTL 24.3prostate integrity trait (VT:0010571)area of ventral prostate occupied by tumorous lesions to total ventral prostate area ratio (CMO:0000899)11037949255379492Rat
7421626Bp360Blood pressure QTL 3600.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1694102251941022Rat
2313070Bss52Bone structure and strength QTL 524.40.0001body length (VT:0001256)body length (CMO:0000013)1529322934184556Rat
1357401Bw43Body weight QTL 433.75body mass (VT:0001259)body weight (CMO:0000012)1690935351909353Rat
631494Bp95Blood pressure QTL 95400.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)11731537851816258Rat
1600360Mcs16Mammary carcinoma susceptibility QTL 162.4mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1126564886Rat
5684998Bss101Bone structure and strength QTL 1013.6tibia strength trait (VT:1000284)tibia ultimate force (CMO:0001734)1690935351909353Rat
5684999Bss102Bone structure and strength QTL 1025.57e-07tibia strength trait (VT:1000284)tibia stiffness (CMO:0001735)1690935351909353Rat
2302038Pia31Pristane induced arthritis QTL 315.50.001blood autoantibody amount (VT:0003725)serum immunoglobulin M-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002111)11282049457820494Rat
2317755Glom22Glomerulus QTL 223.8urine protein amount (VT:0005160)urine protein level (CMO:0000591)1134184556Rat
634353Rends2Renal damage susceptibility QTL 20.05kidney blood vessel morphology trait (VT:0000530)organ lesion measurement (CMO:0000677)12065642065656420Rat
1300170Rf6Renal function QTL 63.14renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)1128483164Rat
1578756Iddm22Insulin dependent diabetes mellitus QTL 222.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)12050832665508326Rat
631508Sald1Serum aldosterone level QTL 13.7blood aldosterone amount (VT:0005346)serum aldosterone level (CMO:0000487)11168446456684464Rat
2313053Bss51Bone structure and strength QTL 513.80.0001tibia length (VT:0004357)tibia length (CMO:0000450)1529322934184556Rat

Markers in Region
BE107559  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2123,837,592 - 23,837,767 (+)MAPPERmRatBN7.2
Rnor_6.0125,291,879 - 25,292,053NCBIRnor6.0
Rnor_5.0126,752,095 - 26,752,269UniSTSRnor5.0
RGSC_v3.4124,385,060 - 24,385,234UniSTSRGSC3.4
Celera122,547,109 - 22,547,283UniSTS
RH 3.4 Map1234.0UniSTS
Cytogenetic Map1p11UniSTS
AU040424  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2123,797,485 - 23,797,605 (+)MAPPERmRatBN7.2
Rnor_6.0125,252,120 - 25,252,239NCBIRnor6.0
Rnor_5.0126,712,336 - 26,712,455UniSTSRnor5.0
RGSC_v3.4124,344,243 - 24,344,362UniSTSRGSC3.4
Celera122,507,113 - 22,507,232UniSTS
Cytogenetic Map1p11UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
9 5 27 123 31 26 10 19 10 3 118 64 3 103 30 69 16 8 8

Sequence


Ensembl Acc Id: ENSRNOT00000016518   ⟹   ENSRNOP00000016518
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl125,554,375 - 25,580,830 (+)Ensembl
mRatBN7.2 Ensembl123,735,272 - 23,761,713 (+)Ensembl
Rnor_6.0 Ensembl125,173,242 - 25,296,137 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000092830   ⟹   ENSRNOP00000075964
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl123,735,272 - 23,842,692 (+)Ensembl
Rnor_6.0 Ensembl125,174,456 - 25,296,927 (+)Ensembl
RefSeq Acc Id: NM_001410322   ⟹   NP_001397251
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8125,554,777 - 25,661,806 (+)NCBI
mRatBN7.2123,735,660 - 23,842,685 (+)NCBI
RefSeq Acc Id: XM_063266042   ⟹   XP_063122112
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8125,553,981 - 25,661,806 (+)NCBI
RefSeq Acc Id: XM_063266043   ⟹   XP_063122113
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8125,553,981 - 25,661,806 (+)NCBI
RefSeq Acc Id: XM_063266047   ⟹   XP_063122117
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8125,553,993 - 25,661,806 (+)NCBI
Ensembl Acc Id: ENSRNOP00000075964   ⟸   ENSRNOT00000092830
Ensembl Acc Id: ENSRNOP00000016518   ⟸   ENSRNOT00000016518
RefSeq Acc Id: NP_001397251   ⟸   NM_001410322
- UniProtKB: A6JUQ6 (UniProtKB/Swiss-Prot)
RefSeq Acc Id: XP_063122112   ⟸   XM_063266042
- Peptide Label: isoform X1
- UniProtKB: A6JUQ6 (UniProtKB/Swiss-Prot)
RefSeq Acc Id: XP_063122113   ⟸   XM_063266043
- Peptide Label: isoform X1
- UniProtKB: A6JUQ6 (UniProtKB/Swiss-Prot)
RefSeq Acc Id: XP_063122117   ⟸   XM_063266047
- Peptide Label: isoform X2
- UniProtKB: A6JUQ8 (UniProtKB/TrEMBL)
Protein Domains
CRAL-TRIO   CRAL/TRIO N-terminal

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A6JUQ6-F1-model_v2 AlphaFold A6JUQ6 1-327 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:1306801 AgrOrtholog
BioCyc Gene G2FUF-62004 BioCyc
Ensembl Genes ENSRNOG00000012122 Ensembl, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000092830.2 UniProtKB/Swiss-Prot
Gene3D-CATH 3.40.525.10 UniProtKB/Swiss-Prot
  Alpha-tocopherol transfer UniProtKB/Swiss-Prot
  N-terminal domain of phosphatidylinositol transfer protein sec14p UniProtKB/Swiss-Prot
InterPro CRAL-TRIO_dom UniProtKB/Swiss-Prot
  CRAL-TRIO_dom_sf UniProtKB/Swiss-Prot
  CRAL/TRIO_N_dom UniProtKB/Swiss-Prot
  CRAL/TRIO_N_dom_sf UniProtKB/Swiss-Prot
NCBI Gene 361459 ENTREZGENE
PANTHER ALPHA-TOCOPHEROL TRANSFER PROTEIN-RELATED UniProtKB/Swiss-Prot
  PTHR10174:SF73 UniProtKB/Swiss-Prot
Pfam CRAL_TRIO UniProtKB/Swiss-Prot
  CRAL_TRIO_N UniProtKB/Swiss-Prot
PhenoGen Clvs2 PhenoGen
PRINTS CRETINALDHBP UniProtKB/Swiss-Prot
PROSITE CRAL_TRIO UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000012122 RatGTEx
SMART CRAL_TRIO_N UniProtKB/Swiss-Prot
  SEC14 UniProtKB/Swiss-Prot
Superfamily-SCOP SSF46938 UniProtKB/Swiss-Prot
  SSF52087 UniProtKB/Swiss-Prot
UniProt A0A8L2Q821_RAT UniProtKB/TrEMBL
  A6JUQ6 ENTREZGENE
  A6JUQ8 ENTREZGENE, UniProtKB/TrEMBL
  CLVS2_RAT UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2011-08-01 Clvs2  clavesin 2  Rlbp1l2  retinaldehyde binding protein 1-like 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-07 Rlbp1l2  retinaldehyde binding protein 1-like 2  RGD1306801_predicted  similar to hypothetical protein MGC34646 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-20 RGD1306801_predicted  similar to hypothetical protein MGC34646 (predicted)  LOC361459_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC361459_predicted  similar to hypothetical protein MGC34646 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL