CALCOCO2 (calcium binding and coiled-coil domain 2) - Rat Genome Database

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Gene: CALCOCO2 (calcium binding and coiled-coil domain 2) Sus scrofa
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Symbol: CALCOCO2
Name: calcium binding and coiled-coil domain 2
RGD ID: 14190943
Description: ENCODES a protein that exhibits metal ion binding (inferred); protein homodimerization activity (inferred); INVOLVED IN positive regulation of autophagosome maturation (inferred); response to type II interferon (inferred); xenophagy (inferred); ASSOCIATED WITH Colorectal Neoplasms (ortholog); trichodontoosseous syndrome (ortholog); FOUND IN autophagosome (inferred); autophagosome membrane (inferred); cytoplasm (inferred); INTERACTS WITH deoxynivalenol
Type: protein-coding
RefSeq Status: MODEL
Previously known as: calcium-binding and coiled-coil domain-containing protein 2
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: Sscrofa11.1 - Pig Sscrofa11.1 Assembly
Position:
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1225,050,081 - 25,088,895 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11225,050,008 - 25,080,230 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21225,005,409 - 25,036,175 (+)NCBISscrofa10.2Sscrofa10.2susScr3
JBrowse: View Region in Genome Browser (JBrowse)
Model


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
Additional References at PubMed
PMID:14681463   PMID:30032202  


Genomics

Comparative Map Data
CALCOCO2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1225,050,081 - 25,088,895 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11225,050,008 - 25,080,230 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21225,005,409 - 25,036,175 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CALCOCO2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381748,831,035 - 48,865,245 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1748,831,018 - 48,866,522 (+)EnsemblGRCh38hg38GRCh38
GRCh371746,908,397 - 46,942,607 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361744,263,371 - 44,297,228 (+)NCBINCBI36Build 36hg18NCBI36
Celera1743,362,488 - 43,396,512 (+)NCBICelera
Cytogenetic Map17q21.32NCBI
HuRef1742,276,617 - 42,310,907 (+)NCBIHuRef
CHM1_11746,974,341 - 47,008,496 (+)NCBICHM1_1
T2T-CHM13v2.01749,694,621 - 49,728,978 (+)NCBIT2T-CHM13v2.0
Calcoco2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391195,990,195 - 96,015,362 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1195,990,152 - 96,002,790 (-)EnsemblGRCm39 Ensembl
GRCm381196,098,916 - 96,124,560 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1196,099,326 - 96,111,964 (-)EnsemblGRCm38mm10GRCm38
MGSCv371195,960,640 - 95,973,276 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361195,915,005 - 95,928,054 (-)NCBIMGSCv36mm8
Celera11105,750,331 - 105,762,857 (-)NCBICelera
Cytogenetic Map11DNCBI
cM Map1159.4NCBI
Calcoco2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81081,552,084 - 81,568,266 (-)NCBIGRCr8
mRatBN7.21081,055,467 - 81,069,298 (-)NCBImRatBN7.2mRatBN7.2
Rnor_6.01083,935,087 - 83,963,750 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01083,731,658 - 83,757,102 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41084,820,832 - 84,847,065 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1079,823,176 - 79,838,506 (-)NCBICelera
Cytogenetic Map10q26NCBI
Calcoco2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495545112,443,796 - 12,469,857 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495545112,443,262 - 12,469,608 (-)NCBIChiLan1.0ChiLan1.0
CALCOCO2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21916,237,637 - 16,271,874 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11718,203,227 - 18,237,474 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0178,671,682 - 8,705,625 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1178,858,056 - 8,891,297 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl178,858,872 - 8,891,276 (-)Ensemblpanpan1.1panPan2
CALCOCO2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1925,050,603 - 25,078,147 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl925,050,690 - 25,077,557 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha924,514,436 - 24,541,796 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0925,845,530 - 25,873,110 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl925,845,631 - 25,873,692 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1924,613,433 - 24,640,979 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0924,873,840 - 24,901,366 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0925,002,881 - 25,030,259 (+)NCBIUU_Cfam_GSD_1.0
Calcoco2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440560224,465,867 - 24,499,885 (+)NCBIHiC_Itri_2
SpeTri2.0NW_00493649012,576,752 - 12,609,273 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CALCOCO2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11669,242,720 - 69,274,364 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1669,251,963 - 69,273,384 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366607740,342,413 - 40,375,248 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Calcoco2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247955,265,141 - 5,283,719 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247955,259,976 - 5,281,958 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in CALCOCO2
1138 total Variants

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 hemolymphoid system musculoskeletal system nervous system renal system reproductive system respiratory system
High
Medium 10 4 3 5 2 23 2 3 3
Low
Below cutoff

Sequence


RefSeq Acc Id: ENSSSCT00000019097   ⟹   ENSSSCP00000018591
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl1225,050,081 - 25,080,227 (+)Ensembl
RefSeq Acc Id: ENSSSCT00000079098   ⟹   ENSSSCP00000062512
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl1225,050,093 - 25,080,180 (+)Ensembl
RefSeq Acc Id: ENSSSCT00000080801   ⟹   ENSSSCP00000067388
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl1225,050,092 - 25,088,895 (+)Ensembl
RefSeq Acc Id: XM_003131552   ⟹   XP_003131600
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.11225,050,008 - 25,080,230 (+)NCBI
Sequence:
RefSeq Acc Id: XP_003131600   ⟸   XM_003131552
- UniProtKB: A0A4X1UN75 (UniProtKB/TrEMBL),   A0A8D0PH39 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSSSCP00000018591   ⟸   ENSSSCT00000019097
RefSeq Acc Id: ENSSSCP00000067388   ⟸   ENSSSCT00000080801
RefSeq Acc Id: ENSSSCP00000062512   ⟸   ENSSSCT00000079098
Protein Domains
SKICH   UBZ1-type


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSSSCG00000017543 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
  ENSSSCG00015057352 UniProtKB/TrEMBL
  ENSSSCG00025005883 UniProtKB/TrEMBL
  ENSSSCG00030059916 UniProtKB/TrEMBL
  ENSSSCG00035003141 UniProtKB/TrEMBL
  ENSSSCG00040066361 UniProtKB/TrEMBL
  ENSSSCG00045036793 UniProtKB/TrEMBL
  ENSSSCG00050055148 UniProtKB/TrEMBL
  ENSSSCG00055006245 UniProtKB/TrEMBL
  ENSSSCG00060052211 UniProtKB/TrEMBL
  ENSSSCG00070018634 UniProtKB/TrEMBL
Ensembl Transcript ENSSSCT00000019097 ENTREZGENE
  ENSSSCT00000019097.5 UniProtKB/TrEMBL
  ENSSSCT00000079098.2 UniProtKB/TrEMBL
  ENSSSCT00000080801.2 UniProtKB/TrEMBL
  ENSSSCT00015076418.1 UniProtKB/TrEMBL
  ENSSSCT00015076513.1 UniProtKB/TrEMBL
  ENSSSCT00025007852.1 UniProtKB/TrEMBL
  ENSSSCT00025007864.1 UniProtKB/TrEMBL
  ENSSSCT00025007874.1 UniProtKB/TrEMBL
  ENSSSCT00030083628.1 UniProtKB/TrEMBL
  ENSSSCT00030083645.1 UniProtKB/TrEMBL
  ENSSSCT00035003891.1 UniProtKB/TrEMBL
  ENSSSCT00035003893.1 UniProtKB/TrEMBL
  ENSSSCT00040090608.1 UniProtKB/TrEMBL
  ENSSSCT00040090725.1 UniProtKB/TrEMBL
  ENSSSCT00040090824.1 UniProtKB/TrEMBL
  ENSSSCT00045063344.1 UniProtKB/TrEMBL
  ENSSSCT00045063393.1 UniProtKB/TrEMBL
  ENSSSCT00050075232.1 UniProtKB/TrEMBL
  ENSSSCT00050075237.1 UniProtKB/TrEMBL
  ENSSSCT00050075240.1 UniProtKB/TrEMBL
  ENSSSCT00055012104.1 UniProtKB/TrEMBL
  ENSSSCT00055012167.1 UniProtKB/TrEMBL
  ENSSSCT00060071051.1 UniProtKB/TrEMBL
  ENSSSCT00060071055.1 UniProtKB/TrEMBL
  ENSSSCT00060071064.1 UniProtKB/TrEMBL
  ENSSSCT00070036783.1 UniProtKB/TrEMBL
  ENSSSCT00070036795.1 UniProtKB/TrEMBL
  ENSSSCT00070036799.1 UniProtKB/TrEMBL
  ENSSSCT00070036805.1 UniProtKB/TrEMBL
Gene3D-CATH 1.10.287.1490 UniProtKB/TrEMBL
  2.60.40.2840 UniProtKB/TrEMBL
  6.20.250.40 UniProtKB/TrEMBL
InterPro CALCOCO1/2_Zn_UBZ1 UniProtKB/TrEMBL
  SKICH UniProtKB/TrEMBL
KEGG Report ssc:100523089 UniProtKB/TrEMBL
NCBI Gene CALCOCO2 ENTREZGENE
PANTHER CALCIUM-BINDING AND COILED-COIL DOMAIN-CONTAINING PROTEIN 2 UniProtKB/TrEMBL
  SKICH DOMAIN-CONTAINING PROTEIN UniProtKB/TrEMBL
Pfam SKICH UniProtKB/TrEMBL
PROSITE ZF_UBZ1 UniProtKB/TrEMBL
UniProt A0A4X1UL33_PIG UniProtKB/TrEMBL
  A0A4X1UN75 ENTREZGENE, UniProtKB/TrEMBL
  A0A4X1UPT4_PIG UniProtKB/TrEMBL
  A0A4X1UQE7_PIG UniProtKB/TrEMBL
  A0A5G2QKC1_PIG UniProtKB/TrEMBL
  A0A5G2QZL4_PIG UniProtKB/TrEMBL
  A0A8D0PH39 ENTREZGENE, UniProtKB/TrEMBL
  A0A8D0QKT2_PIG UniProtKB/TrEMBL
  A0A8D1JBD1_PIG UniProtKB/TrEMBL
  A0A8D1JIA3_PIG UniProtKB/TrEMBL
  A0A8D2BN00_PIG UniProtKB/TrEMBL
  F1RWF7_PIG UniProtKB/TrEMBL
VGNC ID VGNC:86141 ENTREZGENE