Ccin (calicin) - Rat Genome Database

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Gene: Ccin (calicin) Mus musculus
Analyze
Symbol: Ccin
Name: calicin
RGD ID: 1617144
MGI Page MGI
Description: Predicted to enable ubiquitin-like ligase-substrate adaptor activity. Involved in spermatogenesis. Located in cytoskeletal calyx. Human ortholog(s) of this gene implicated in spermatogenic failure 91. Orthologous to human CCIN (calicin).
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: 4933417A14Rik
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39443,983,504 - 43,985,533 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl443,983,483 - 43,985,423 (+)EnsemblGRCm39 Ensembl
GRCm38443,983,504 - 43,985,533 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl443,983,483 - 43,985,423 (+)EnsemblGRCm38mm10GRCm38
MGSCv37443,996,376 - 43,998,405 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36444,004,604 - 44,006,633 (+)NCBIMGSCv36mm8
Celera444,004,720 - 44,006,749 (+)NCBICelera
Cytogenetic Map4B1NCBI
cM Map423.08NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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

Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
References

References - curated
# Reference Title Reference Citation
1. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:10349636   PMID:11042159   PMID:11076861   PMID:11217851   PMID:12466851   PMID:12477932   PMID:16141072   PMID:16141073   PMID:21267068   PMID:21565611   PMID:21873635   PMID:35793634  
PMID:36546111  


Genomics

Comparative Map Data
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 Ensembl
GRCm38443,983,504 - 43,985,533 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl443,983,483 - 43,985,423 (+)EnsemblGRCm38mm10GRCm38
MGSCv37443,996,376 - 43,998,405 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36444,004,604 - 44,006,633 (+)NCBIMGSCv36mm8
Celera444,004,720 - 44,006,749 (+)NCBICelera
Cytogenetic Map4B1NCBI
cM Map423.08NCBI
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 (+)EnsemblGRCh38hg38GRCh38
GRCh37936,169,385 - 36,171,331 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36936,159,391 - 36,161,320 (+)NCBINCBI36Build 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
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8563,002,427 - 63,004,314 (+)NCBIGRCr8
mRatBN7.2558,206,676 - 58,208,563 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl558,206,633 - 58,208,951 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx560,188,596 - 60,190,483 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0562,007,409 - 62,009,296 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0561,976,733 - 61,978,620 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0559,452,348 - 59,454,235 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl559,452,348 - 59,454,233 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0563,974,871 - 63,976,758 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4560,445,684 - 60,447,571 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1560,445,862 - 60,447,748 (+)NCBI
Celera556,785,152 - 56,787,039 (+)NCBICelera
Cytogenetic Map5q22NCBI
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 (+)Ensemblpanpan1.1panPan2
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_Tasha
ROS_Cfam_1.01153,743,935 - 53,746,473 (+)NCBIROS_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_1.0
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 (+)EnsemblSpeTri2.0SpeTri2.0 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 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
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 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
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_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Ccin
77 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:69
Count of miRNA genes:65
Interacting mature miRNAs:67
Transcripts:ENSMUST00000095107
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 (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1301203Alcp8_malcohol preference locus 8 (mouse)Not determined41739516051395290Mouse
1301586Stheal3_msoft tissue heal 3 (mouse)Not determined42865844262658566Mouse
10401115Pgia35_mproteoglycan induced arthritis 35 (mouse)Not determined41256237746562509Mouse
39128211Lwq22_mliver weight QTL 22 (mouse)41789261688982216Mouse
1301786Bpq3_mblood pressure QTL 3 (mouse)Not determined44240224076402381Mouse
4141555Nbwa2_mNZB and NZW autoimmunity 2 (mouse)Not determined41789251551892635Mouse
10412178Habiir2_mhyperoxic acute lung injury imprinted region 2 (mouse)Not determined43945212663283678Mouse
1300574Im2_mimmunoregulatory 2 (mouse)Not determined42807768262077816Mouse
12880405Jcdq1_mjoint cartilage degeneration QTL 1 (mouse)41256237746562509Mouse
4142318Lyr2_mlymphoma resistance 2 (mouse)Not determined1401045763283678Mouse
1301697Sluc18_msusceptibility to lung cancer 18 (mouse)Not determined42237344856373612Mouse
1357453Kidq4_mkidney weight QTL 4 (mouse)Not determined41789261688982216Mouse
4142047Mvwf3_mmodifier of von Willebrand factor 3 (mouse)Not determined14010457117072206Mouse
11567249Elorr3_methanol induced loss of righting response 3 (mouse)43722677156268235Mouse
1357877Synch1_msynechia 1 (mouse)Not determined42870992562710107Mouse
1300977Mopkd1_mmodifier of polycystic kidney disease progression 1 (mouse)Not determined43655083970550967Mouse
25440481Moaq1_mmodifier of alien QTL 1 (mouse)41950000046000000Mouse
1301237Alcp7_malcohol preference locus 7 (mouse)Not determined41739516051395290Mouse
4141911W6q15_mweight 6 weeks QTL 15 (mouse)Not determined1789261688982216Mouse
1302075Bdln6_mbody length 6 (mouse)Not determined42237344856373612Mouse
4142290Ssrq9_mstress response QTL 9 (mouse)Not determined3439516046332776Mouse
1301437Scon1_msucrose consumption 1 (mouse)Not determined42237344856373612Mouse
1300769Pcyts2_mplasmacytoma susceptibility 2 (mouse)Not determined42211194456112145Mouse
1301792Hdlq10_mHDL QTL 10 (mouse)Not determined43585970769859853Mouse
1301990Arvm1_mautoimmune renal vasculitis 1 (mouse)Not determined42933264663332776Mouse
1302116Bbaa1_mB.burgdorferi-associated arthritis 1 (mouse)Not determined43825093072251078Mouse
1302058Hrtfm3_mheart failure modifier 3 (mouse)Not determined42211194456112145Mouse
1302184Aaom1_mautoimmune aoritis in MRL mice 1 (mouse)Not determined42432229946332776Mouse
26884449Sklq2_mskull length QTL 2, 5 week (mouse)436700000128993793Mouse
27226724Tibw2_mtibia width 2, proximal, 10 week (mouse)443000000108357197Mouse


Expression

RNA-SEQ Expression


Sequence


Ensembl Acc Id: ENSMUST00000095107   ⟹   ENSMUSP00000092725
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl443,983,483 - 43,985,423 (+)Ensembl
GRCm38.p6 Ensembl443,983,483 - 43,985,423 (+)Ensembl
RefSeq Acc Id: NM_001002787   ⟹   NP_001002787
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39443,983,504 - 43,985,533 (+)NCBI
GRCm38443,983,504 - 43,985,533 (+)ENTREZGENE
MGSCv37443,996,376 - 43,998,405 (+)RGD
Celera444,004,720 - 44,006,749 (+)RGD
cM Map4 ENTREZGENE
Sequence:
Protein Sequences
Protein RefSeqs NP_001002787 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAI50950 (Get FASTA)   NCBI Sequence Viewer  
  AAI50953 (Get FASTA)   NCBI Sequence Viewer  
  BAC26835 (Get FASTA)   NCBI Sequence Viewer  
  EDL02436 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSMUSP00000092725
  ENSMUSP00000092725.2
GenBank Protein Q8CDE2 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_001002787   ⟸   NM_001002787
- UniProtKB: Q8CDE2 (UniProtKB/Swiss-Prot),   B2RX51 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSMUSP00000092725   ⟸   ENSMUST00000095107
Protein Domains
BACK   BTB

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q8CDE2-F1-model_v2 AlphaFold Q8CDE2 1-588 view protein structure

Promoters
RGD ID:6883264
Promoter ID:EPDNEW_M5083
Type:initiation region
Name:Ccin_1
Description:Mus musculus calicin , mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38443,983,479 - 43,983,539EPDNEW
RGD ID:6835025
Promoter ID:MM_KWN:37403
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:ES_Cell,   Spleen
Transcripts:NM_001002787
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv36443,995,386 - 43,997,352 (+)MPROMDB

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:3045316 AgrOrtholog
Ensembl Genes ENSMUSG00000070999 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSMUST00000095107 ENTREZGENE
  ENSMUST00000095107.3 UniProtKB/Swiss-Prot
Gene3D-CATH 1.25.40.420 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  2.120.10.80 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro BACK UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  BTB/POZ_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Calicin_BTB_POZ UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Kelch-typ_b-propeller UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Kelch_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SKP1/BTB/POZ_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report mmu:442829 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGD MGI:3045316 ENTREZGENE
NCBI Gene 442829 ENTREZGENE
PANTHER CALICIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  KELCH PROTEIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam BACK UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  BTB UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Kelch_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Kelch_6 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Ccin PhenoGen
PROSITE BTB UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART BACK UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  BTB UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Kelch UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF117281 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF54695 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt B2RX51 ENTREZGENE, UniProtKB/TrEMBL
  CALI_MOUSE UniProtKB/Swiss-Prot, ENTREZGENE