Ccin (calicin) - Rat Genome Database

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Gene: Ccin (calicin) Rattus norvegicus
Analyze
Symbol: Ccin
Name: calicin
RGD ID: 1359369
Description: Predicted to enable ubiquitin-like ligase-substrate adaptor activity. Predicted to be involved in proteasome-mediated ubiquitin-dependent protein catabolic process and spermatogenesis. Predicted to be located in cytoskeletal calyx. Predicted to be part of Cul3-RING ubiquitin ligase complex. Predicted to be active in cytoplasm. Human ortholog(s) of this gene implicated in spermatogenic failure 91. Orthologous to human CCIN (calicin); INTERACTS WITH bisphenol A; cadmium dichloride; gentamycin.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: MGC94933
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
GRCr8563,002,427 - 63,004,314 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl563,000,138 - 63,010,123 (+)EnsemblGRCr8
mRatBN7.2558,206,676 - 58,208,563 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl558,206,633 - 58,208,951 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx560,188,596 - 60,190,483 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0562,007,409 - 62,009,296 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0561,976,733 - 61,978,620 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0559,452,348 - 59,454,235 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl559,452,348 - 59,454,233 (+)Ensemblrn6Rnor6.0
Rnor_5.0563,974,871 - 63,976,758 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4560,445,684 - 60,447,571 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera556,785,152 - 56,787,039 (+)NCBICelera
RGSC_v3.1560,445,862 - 60,447,748 (+)NCBI
Cytogenetic Map5q22NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
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. GOA pipeline RGD automated data pipeline
3. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
5. 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.
Additional References at PubMed
PMID:21630459  


Genomics

Comparative Map Data
Ccin
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8563,002,427 - 63,004,314 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl563,000,138 - 63,010,123 (+)EnsemblGRCr8
mRatBN7.2558,206,676 - 58,208,563 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl558,206,633 - 58,208,951 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx560,188,596 - 60,190,483 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0562,007,409 - 62,009,296 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0561,976,733 - 61,978,620 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0559,452,348 - 59,454,235 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl559,452,348 - 59,454,233 (+)Ensemblrn6Rnor6.0
Rnor_5.0563,974,871 - 63,976,758 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4560,445,684 - 60,447,571 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera556,785,152 - 56,787,039 (+)NCBICelera
RGSC_v3.1560,445,862 - 60,447,748 (+)NCBI
Cytogenetic Map5q22NCBI
CCIN
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38936,169,388 - 36,171,334 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl936,169,388 - 36,171,334 (+)Ensemblhg38GRCh38
GRCh37936,169,385 - 36,171,331 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36936,159,391 - 36,161,320 (+)NCBIBuild 36Build 36hg18NCBI36
Build 34936,159,390 - 36,161,320NCBI
Celera936,102,976 - 36,104,918 (+)NCBICelera
Cytogenetic Map9p13.3NCBI
HuRef936,123,296 - 36,125,238 (+)NCBIHuRef
CHM1_1936,169,794 - 36,171,736 (+)NCBICHM1_1
T2T-CHM13v2.0936,191,394 - 36,193,340 (+)NCBIT2T-CHM13v2.0
Ccin
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39443,983,504 - 43,985,533 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl443,983,483 - 43,985,423 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm38443,983,504 - 43,985,533 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl443,983,483 - 43,985,423 (+)Ensemblmm10GRCm38
MGSCv37443,996,376 - 43,998,405 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36444,004,604 - 44,006,633 (+)NCBIMGSCv36mm8
Celera444,004,720 - 44,006,749 (+)NCBICelera
Cytogenetic Map4B1NCBI
cM Map423.08NCBI
Ccin
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_0049581516 - 1,111 (+)NCBIChiLan1.0ChiLan1.0
CCIN
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21188,411,833 - 88,424,872 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1988,417,770 - 88,430,809 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0936,014,394 - 36,021,056 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1936,815,577 - 36,822,204 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl936,820,373 - 36,822,139 (+)EnsemblpanPan2panpan1.1
CCIN
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11152,637,580 - 52,640,121 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1151,228,265 - 51,230,803 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.01153,743,935 - 53,746,473 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
UMICH_Zoey_3.11152,246,797 - 52,249,335 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01152,268,837 - 52,271,375 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01152,970,389 - 52,972,927 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Ccin
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404947167,595,289 - 167,597,603 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365244,143,347 - 4,145,113 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049365244,143,238 - 4,145,183 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CCIN
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1236,948,636 - 236,950,402 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.11236,947,871 - 236,950,447 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21264,620,225 - 264,622,451 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CCIN
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11244,387,239 - 44,390,726 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1244,387,995 - 44,389,761 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366603841,478,897 - 41,480,841 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Ccin
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248684,536,042 - 4,537,911 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Ccin
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v112,540,481 - 2,542,391 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Ccin
5 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:12
Count of miRNA genes:12
Interacting mature miRNAs:12
Transcripts:ENSRNOT00000019887
Prediction methods: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
1298067Scl15Serum cholesterol level QTL 154.80.001blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)53801167083011670Rat
1300115Hrtrt7Heart rate QTL 72.76heart pumping trait (VT:2000009)heart rate (CMO:0000002)55266537294894052Rat
1578776Stresp18Stress response QTL 182.9thymus mass (VT:0004954)thymus wet weight (CMO:0000855)53275164977751649Rat
1549845Scl44Serum cholesterol level QTL 446blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)544924861153890773Rat
6907115Mcs29Mammary carcinoma susceptibility QTL 29mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)53800433183004331Rat
70212Niddm25Non-insulin dependent diabetes mellitus QTL 253.54blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)538207390136631402Rat
1358353Srcrtb2Stress Responsive Cort Basal QTL 23.480.003blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)52367149379046465Rat
1331801Rf33Renal function QTL 334.149kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)548523123134369373Rat
1598807Glom12Glomerulus QTL 122.7kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)53801167083011670Rat
1302786Kidm8Kidney mass QTL 828.15kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)53801167083011670Rat
1331782Rf36Renal function QTL 363.296kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)539019942102105896Rat
6903292Stl28Serum triglyceride level QTL 282.60.0073blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)53331167378311673Rat
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)551657967166600247Rat
1578767Stresp17Stress response QTL 174.30.01blood aldosterone amount (VT:0005346)plasma aldosterone level (CMO:0000551)53275164977751649Rat
1576312Emca8Estrogen-induced mammary cancer QTL 84.1mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)555124766172190305Rat
1641912Alcrsp18Alcohol response QTL 18response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)53998594884985948Rat
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)5692228281330203Rat
6903306Scl35Serum cholesterol QTL 352.60.0073blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)53331167378311673Rat
1576317Eutr2Estrogen induced uterine response QTL 20.01uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)53952692484526924Rat
1331773Scl26Serum cholesterol level QTL 263.065blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)54852312391770353Rat
70189Mcs5Mammary carcinoma susceptibility QTL 510.51mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)560601597137492949Rat
1331771Rf35Renal function QTL 354.36965kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)51001906491770353Rat
61359EaexExperimental allergic encephalomyelitis QTL x3nervous system integrity trait (VT:0010566)post-insult time to onset of experimental autoimmune encephalomyelitis (CMO:0001422)560511627105511627Rat
2290448Scl54Serum cholesterol level QTL 542.93blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)536460764136631402Rat
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)5706553574335773Rat
1331756Rf34Renal function QTL 344.16275kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)51001906487027358Rat
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)52602321171023211Rat
2316959Gluco59Glucose level QTL 594.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)556546393101546393Rat
1600358Mamtr5Mammary tumor resistance QTL 5mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)52367149368671493Rat


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
6 3 34 45 25 24 11 18 11 5 107 64 1 41 24 43 13 6 6

Sequence


Ensembl Acc Id: ENSRNOT00000019887   ⟹   ENSRNOP00000019887
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl563,000,630 - 63,008,214 (+)Ensembl
mRatBN7.2 Ensembl558,206,633 - 58,208,951 (+)Ensembl
Rnor_6.0 Ensembl559,452,348 - 59,454,233 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000124170   ⟹   ENSRNOP00000106158
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl563,000,138 - 63,010,123 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000159019   ⟹   ENSRNOP00000105972
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl563,002,379 - 63,005,254 (+)Ensembl
RefSeq Acc Id: NM_001005904   ⟹   NP_001005904
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8563,002,427 - 63,004,314 (+)NCBI
mRatBN7.2558,206,676 - 58,208,563 (+)NCBI
Rnor_6.0559,452,348 - 59,454,235 (+)NCBI
Rnor_5.0563,974,871 - 63,976,758 (+)NCBI
RGSC_v3.4560,445,684 - 60,447,571 (+)RGD
Celera556,785,152 - 56,787,039 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001005904 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH83832 (Get FASTA)   NCBI Sequence Viewer  
  EDL98782 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000019887.3
  ENSRNOP00000106158
GenBank Protein Q5XI58 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_001005904   ⟸   NM_001005904
- UniProtKB: Q5XI58 (UniProtKB/Swiss-Prot),   A6IJ62 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000019887   ⟸   ENSRNOT00000019887
Ensembl Acc Id: ENSRNOP00000106158   ⟸   ENSRNOT00000124170
Ensembl Acc Id: ENSRNOP00000105972   ⟸   ENSRNOT00000159019
Protein Domains
BACK   BTB

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q5XI58-F1-model_v2 AlphaFold Q5XI58 1-588 view protein structure

Transcriptome

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

Promoters
RGD ID:13693686
Promoter ID:EPDNEW_R4211
Type:initiation region
Name:Ccin_1
Description:calicin
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_6.0559,452,328 - 59,452,388EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1359369 AgrOrtholog
BioCyc Gene G2FUF-41480 BioCyc
Ensembl Genes ENSRNOG00000014831 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000019887.6 UniProtKB/Swiss-Prot
  ENSRNOT00000124170 ENTREZGENE
Gene3D-CATH 1.25.40.420 UniProtKB/Swiss-Prot
  2.120.10.80 UniProtKB/Swiss-Prot
  Potassium Channel Kv1.1, Chain A UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7112736 IMAGE-MGC_LOAD
InterPro BACK UniProtKB/Swiss-Prot
  BTB/POZ_dom UniProtKB/Swiss-Prot
  Calicin_BTB_POZ UniProtKB/Swiss-Prot
  Kelch-typ_b-propeller UniProtKB/Swiss-Prot
  Kelch_1 UniProtKB/Swiss-Prot
  SKP1/BTB/POZ_sf UniProtKB/Swiss-Prot
KEGG Report rno:298392 UniProtKB/Swiss-Prot
MGC_CLONE MGC:94933 IMAGE-MGC_LOAD
NCBI Gene 298392 ENTREZGENE
PANTHER LD33804P UniProtKB/Swiss-Prot
Pfam BACK UniProtKB/Swiss-Prot
  BTB UniProtKB/Swiss-Prot
  Kelch_1 UniProtKB/Swiss-Prot
  Kelch_6 UniProtKB/Swiss-Prot
PhenoGen Ccin PhenoGen
PROSITE BTB UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000014831 RatGTEx
SMART BACK UniProtKB/Swiss-Prot
  BTB UniProtKB/Swiss-Prot
  Kelch UniProtKB/Swiss-Prot
Superfamily-SCOP SSF117281 UniProtKB/Swiss-Prot
  SSF54695 UniProtKB/Swiss-Prot
UniProt A0ABK0LUU1_RAT UniProtKB/TrEMBL
  A6IJ62 ENTREZGENE, UniProtKB/TrEMBL
  CALI_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2005-07-29 Ccin  calicin      Symbol and Name status set to provisional 70820 PROVISIONAL