Ccdc88a (coiled coil domain containing 88A) - Rat Genome Database

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Gene: Ccdc88a (coiled coil domain containing 88A) Rattus norvegicus
Analyze
Symbol: Ccdc88a
Name: coiled coil domain containing 88A
RGD ID: 1306694
Description: Enables G-protein gamma-subunit binding activity. Predicted to be involved in several processes, including activation of protein kinase B activity; intracellular signal transduction; and regulation of plasma membrane bounded cell projection organization. Located in COPI-coated Golgi to ER transport vesicle. Orthologous to human CCDC88A (coiled-coil domain containing 88A); INTERACTS WITH 1,3-dinitrobenzene; 2,3,7,8-tetrachlorodibenzodioxine; bisphenol A.
Type: protein-coding
RefSeq Status: MODEL
Previously known as: Akt-phosphorylation enhancer; Ape; Galpha-interacting vesicle-associated protein; girdin; GIV; Hkrp1; Hook-related protein 1; LOC305605; RGD1306694; similar to hypothetical protein
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.214103,104,091 - 103,256,112 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl14103,103,513 - 103,252,368 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.014113,771,093 - 113,936,376 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl14113,867,209 - 113,932,263 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.014113,437,642 - 113,602,573 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.414110,376,486 - 110,525,468 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.114110,402,673 - 110,553,099 (+)NCBI
Celera14101,981,223 - 102,133,399 (+)NCBICelera
Cytogenetic Map14q22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

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. Identification and characterization of GIV, a novel Galpha i/s-interacting protein found on COPI, endoplasmic reticulum-Golgi transport vesicles. Le-Niculescu H, etal., J Biol Chem. 2005 Jun 10;280(23):22012-20. Epub 2005 Mar 4.
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
Additional References at PubMed
PMID:15753085   PMID:15882442   PMID:16139227   PMID:16266428   PMID:19211784   PMID:19778506   PMID:20157114   PMID:20462955   PMID:21415395   PMID:21954290   PMID:23509302   PMID:24211587  
PMID:25012178   PMID:25187647   PMID:27621449   PMID:27623382   PMID:27864364  


Genomics

Comparative Map Data
Ccdc88a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.214103,104,091 - 103,256,112 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl14103,103,513 - 103,252,368 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.014113,771,093 - 113,936,376 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl14113,867,209 - 113,932,263 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.014113,437,642 - 113,602,573 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.414110,376,486 - 110,525,468 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.114110,402,673 - 110,553,099 (+)NCBI
Celera14101,981,223 - 102,133,399 (+)NCBICelera
Cytogenetic Map14q22NCBI
CCDC88A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38255,287,842 - 55,419,856 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl255,287,842 - 55,419,895 (-)EnsemblGRCh38hg38GRCh38
GRCh37255,514,978 - 55,646,992 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36255,368,482 - 55,500,467 (-)NCBINCBI36Build 36hg18NCBI36
Build 34255,426,630 - 55,558,614NCBI
Celera255,355,473 - 55,487,467 (-)NCBICelera
Cytogenetic Map2p16.1NCBI
HuRef255,250,032 - 55,382,309 (-)NCBIHuRef
CHM1_1255,444,983 - 55,577,340 (-)NCBICHM1_1
T2T-CHM13v2.0255,285,045 - 55,417,059 (-)NCBIT2T-CHM13v2.0
Ccdc88a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391129,323,521 - 29,460,808 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1129,323,658 - 29,460,808 (+)EnsemblGRCm39 Ensembl
GRCm381129,373,405 - 29,510,808 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1129,373,658 - 29,510,808 (+)EnsemblGRCm38mm10GRCm38
MGSCv371129,273,775 - 29,410,812 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361129,273,775 - 29,410,812 (+)NCBIMGSCv36mm8
Celera1131,739,265 - 31,872,126 (+)NCBICelera
Cytogenetic Map11A3.3NCBI
Ccdc88a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542427,617,833 - 27,771,385 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495542427,617,833 - 27,771,385 (+)NCBIChiLan1.0ChiLan1.0
CCDC88A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12A56,585,354 - 56,716,197 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2A56,589,221 - 56,715,362 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02A55,445,060 - 55,576,479 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
CCDC88A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11056,167,907 - 56,300,974 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1056,170,479 - 56,300,908 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1056,119,423 - 56,257,932 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01057,166,787 - 57,305,336 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1057,173,896 - 57,305,357 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11056,867,913 - 57,007,335 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01057,147,148 - 57,286,241 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01057,437,657 - 57,577,292 (-)NCBIUU_Cfam_GSD_1.0
Ccdc88a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440629226,767,303 - 26,901,093 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364911,669,983 - 1,804,221 (-)EnsemblSpeTri2.0
SpeTri2.0NW_0049364911,670,192 - 1,804,056 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CCDC88A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl385,811,127 - 85,941,864 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1385,811,043 - 85,971,162 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2390,618,672 - 90,725,605 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CCDC88A
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11451,484,886 - 51,615,066 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1451,484,906 - 51,610,654 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604560,105,043 - 60,235,398 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Ccdc88a
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248336,116,686 - 6,260,211 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248336,117,260 - 6,260,211 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Ccdc88a
592 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:184
Count of miRNA genes:103
Interacting mature miRNAs:109
Transcripts:ENSRNOT00000005388, ENSRNOT00000005487, ENSRNOT00000067591
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
634328Hc5Hypercalciuria QTL 52.3urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)1458184885103184885Rat
1582259Gluco23Glucose level QTL 233.10.0008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1470053989104886043Rat
1641900Alcrsp11Alcohol response QTL 11alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)1470053989104886043Rat

Markers in Region
RH128278  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.214103,114,153 - 103,114,339 (+)MAPPERmRatBN7.2
mRatBN7.2X106,466,185 - 106,466,371 (+)MAPPERmRatBN7.2
Rnor_6.0X114,127,696 - 114,127,881NCBIRnor6.0
Rnor_6.014113,781,616 - 113,781,801NCBIRnor6.0
Rnor_5.014113,448,165 - 113,448,350UniSTSRnor5.0
Rnor_5.0X112,573,674 - 112,573,859UniSTSRnor5.0
RGSC_v3.4X35,694,598 - 35,694,783UniSTSRGSC3.4
RGSC_v3.414110,386,185 - 110,386,370UniSTSRGSC3.4
Celera14101,991,520 - 101,991,705UniSTS
CeleraX105,879,207 - 105,879,392UniSTS
Cytogenetic Map14q22UniSTS
RH133705  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.214103,255,748 - 103,255,957 (+)MAPPERmRatBN7.2
Rnor_6.014113,935,831 - 113,936,039NCBIRnor6.0
Rnor_5.014113,602,210 - 113,602,418UniSTSRnor5.0
RGSC_v3.414110,528,659 - 110,528,867UniSTSRGSC3.4
Celera14102,132,854 - 102,133,062UniSTS
Cytogenetic Map14q22UniSTS
RH143665  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.214103,253,154 - 103,253,388 (+)MAPPERmRatBN7.2
Rnor_6.014113,933,237 - 113,933,470NCBIRnor6.0
Rnor_5.014113,599,616 - 113,599,849UniSTSRnor5.0
RGSC_v3.414110,526,065 - 110,526,298UniSTSRGSC3.4
Celera14102,130,260 - 102,130,493UniSTS
RH 3.4 Map14744.98UniSTS
Cytogenetic Map14q22UniSTS
BE106537  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.214103,119,907 - 103,120,094 (+)MAPPERmRatBN7.2
Rnor_6.014113,797,237 - 113,797,423NCBIRnor6.0
Rnor_5.014113,463,858 - 113,464,044UniSTSRnor5.0
RGSC_v3.414110,391,940 - 110,392,126UniSTSRGSC3.4
Celera14101,997,270 - 101,997,456UniSTS
Cytogenetic Map14q22UniSTS


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 34 22 6 16 6 2 2 74 26 41 11 2
Low 3 9 33 33 3 33 6 8 9 6
Below cutoff 2 2 2 1

Sequence

Nucleotide Sequences
RefSeq Transcripts XM_001065246 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006221877 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008767113 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008767116 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008767120 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008770470 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017604844 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039092889 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039092890 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039092891 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039092892 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039092893 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039092894 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide FQ230491 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ233449 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000254 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000067591   ⟹   ENSRNOP00000063373
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl14103,104,693 - 103,249,489 (+)Ensembl
Rnor_6.0 Ensembl14113,867,209 - 113,932,263 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000095959   ⟹   ENSRNOP00000083554
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl14103,103,513 - 103,252,368 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000112813   ⟹   ENSRNOP00000086390
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl14103,103,513 - 103,252,368 (+)Ensembl
RefSeq Acc Id: XM_008770470   ⟹   XP_008768692
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.214103,104,455 - 103,256,112 (+)NCBI
Rnor_6.014113,771,093 - 113,936,376 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039092889   ⟹   XP_038948817
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.214103,104,455 - 103,249,235 (+)NCBI
RefSeq Acc Id: XM_039092890   ⟹   XP_038948818
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.214103,104,455 - 103,248,470 (+)NCBI
RefSeq Acc Id: XM_039092891   ⟹   XP_038948819
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.214103,104,091 - 103,256,108 (+)NCBI
RefSeq Acc Id: XM_039092892   ⟹   XP_038948820
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.214103,104,091 - 103,256,108 (+)NCBI
RefSeq Acc Id: XM_039092893   ⟹   XP_038948821
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.214103,104,091 - 103,256,108 (+)NCBI
RefSeq Acc Id: XM_039092894   ⟹   XP_038948822
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.214103,104,091 - 103,256,108 (+)NCBI
Reference Sequences
RefSeq Acc Id: XP_008768692   ⟸   XM_008770470
- Peptide Label: isoform X3
- UniProtKB: A0A8I6A5W7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000063373   ⟸   ENSRNOT00000067591
RefSeq Acc Id: XP_038948819   ⟸   XM_039092891
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038948820   ⟸   XM_039092892
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038948821   ⟸   XM_039092893
- Peptide Label: isoform X6
- UniProtKB: A0A8I5ZW24 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038948822   ⟸   XM_039092894
- Peptide Label: isoform X7
RefSeq Acc Id: XP_038948817   ⟸   XM_039092889
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038948818   ⟸   XM_039092890
- Peptide Label: isoform X2
RefSeq Acc Id: ENSRNOP00000083554   ⟸   ENSRNOT00000095959
RefSeq Acc Id: ENSRNOP00000086390   ⟸   ENSRNOT00000112813
Protein Domains
Calponin-homology (CH)

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZYD7-F1-model_v2 AlphaFold D3ZYD7 1-1512 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:1306694 AgrOrtholog
BioCyc Gene G2FUF-14653 BioCyc
Ensembl Genes ENSRNOG00000004057 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000063373.4 UniProtKB/TrEMBL
  ENSRNOP00000083554 ENTREZGENE
  ENSRNOP00000083554.1 UniProtKB/TrEMBL
  ENSRNOP00000086390 ENTREZGENE
  ENSRNOP00000086390.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000067591.4 UniProtKB/TrEMBL
  ENSRNOT00000095959 ENTREZGENE
  ENSRNOT00000095959.1 UniProtKB/TrEMBL
  ENSRNOT00000112813 ENTREZGENE
  ENSRNOT00000112813.1 UniProtKB/TrEMBL
Gene3D-CATH 1.10.418.10 UniProtKB/TrEMBL
InterPro CH-domain UniProtKB/TrEMBL
  CH_dom_sf UniProtKB/TrEMBL
  Girdin UniProtKB/TrEMBL
  HOOK_N UniProtKB/TrEMBL
NCBI Gene 305605 ENTREZGENE
PANTHER PTHR18947:SF30 UniProtKB/TrEMBL
Pfam HOOK_N UniProtKB/TrEMBL
PhenoGen Ccdc88a PhenoGen
PROSITE PS50021 UniProtKB/TrEMBL
UniProt A0A8I5ZW24 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6A5W7 ENTREZGENE, UniProtKB/TrEMBL
  D3ZYD7_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-07 Ccdc88a  coiled coil domain containing 88A  RGD1306694_predicted  similar to hypothetical protein (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-20 RGD1306694_predicted  similar to hypothetical protein (predicted)  LOC305605_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC305605_predicted  similar to hypothetical protein (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL