Ccdc85c (coiled-coil domain containing 85C) - Rat Genome Database

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Gene: Ccdc85c (coiled-coil domain containing 85C) Mus musculus
Analyze
Symbol: Ccdc85c
Name: coiled-coil domain containing 85C
RGD ID: 1613682
MGI Page MGI
Description: Involved in cerebral cortex development. Acts upstream of or within several processes, including Notch signaling pathway; establishment of cell polarity; and radial glial cell differentiation. Located in apical junction complex. Is expressed in brain; brain pia mater; brain subventricular zone; diencephalon; and telencephalon. Used to study hydrocephalus. Orthologous to human CCDC85C (coiled-coil domain containing 85C).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: coiled-coil domain-containing protein 85C; EG668158; Gm265; Gm9010; hhy
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
GRCm3912108,169,858 - 108,244,111 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl12108,169,861 - 108,241,684 (-)EnsemblGRCm39 Ensembl
GRCm3812108,203,599 - 108,277,852 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl12108,203,602 - 108,275,425 (-)EnsemblGRCm38mm10GRCm38
MGSCv3712109,444,555 - 109,513,627 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3612108,654,152 - 108,723,483 (-)NCBIMGSCv36mm8
Celera12109,446,564 - 109,515,546 (-)NCBICelera
Cytogenetic Map12F1NCBI
cM Map1259.23NCBI
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

Molecular Function

Phenotype Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Pathological characteristics of Ccdc85c knockout rats: a rat model of genetic hydrocephalus. Konishi S, etal., Exp Anim. 2020 Jan 29;69(1):26-33. doi: 10.1538/expanim.19-0005. Epub 2019 Jul 23.
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12520002   PMID:14610273   PMID:15283996   PMID:21873635   PMID:22056358   PMID:29669786   PMID:32325033   PMID:37352102   PMID:38355793  


Genomics

Comparative Map Data
Ccdc85c
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3912108,169,858 - 108,244,111 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl12108,169,861 - 108,241,684 (-)EnsemblGRCm39 Ensembl
GRCm3812108,203,599 - 108,277,852 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl12108,203,602 - 108,275,425 (-)EnsemblGRCm38mm10GRCm38
MGSCv3712109,444,555 - 109,513,627 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3612108,654,152 - 108,723,483 (-)NCBIMGSCv36mm8
Celera12109,446,564 - 109,515,546 (-)NCBICelera
Cytogenetic Map12F1NCBI
cM Map1259.23NCBI
CCDC85C
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381499,500,190 - 99,604,207 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1499,500,190 - 99,604,207 (-)EnsemblGRCh38hg38GRCh38
GRCh371499,966,527 - 100,070,544 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361499,046,540 - 99,140,110 (-)NCBINCBI36Build 36hg18NCBI36
Celera1480,032,485 - 80,125,607 (-)NCBICelera
Cytogenetic Map14q32.2NCBI
HuRef1480,161,003 - 80,254,066 (-)NCBIHuRef
CHM1_11499,915,361 - 100,008,351 (-)NCBICHM1_1
T2T-CHM13v2.01493,731,756 - 93,835,650 (-)NCBIT2T-CHM13v2.0
Ccdc85c
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr86132,877,851 - 132,948,744 (-)NCBIGRCr8
mRatBN7.26127,113,440 - 127,184,328 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl6127,113,442 - 127,184,371 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.06132,113,806 - 132,183,434 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.06141,284,186 - 141,353,658 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.46132,572,485 - 132,641,431 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera6124,672,684 - 124,742,377 (-)NCBICelera
Cytogenetic Map6q32NCBI
Ccdc85c
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543820,853,560 - 20,909,510 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495543820,851,085 - 20,909,512 (-)NCBIChiLan1.0ChiLan1.0
CCDC85C
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v215100,666,643 - 100,760,232 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11499,883,139 - 99,976,695 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01480,134,889 - 80,229,717 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11499,458,198 - 99,550,546 (-)NCBIpanpan1.1PanPan1.1panPan2
CCDC85C
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1867,930,372 - 68,006,689 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl867,929,555 - 68,004,891 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha867,450,734 - 67,528,156 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0868,214,408 - 68,291,855 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl868,215,298 - 68,292,190 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1867,875,375 - 67,952,761 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0867,941,872 - 68,019,111 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0868,338,989 - 68,416,468 (-)NCBIUU_Cfam_GSD_1.0
Ccdc85c
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244086406,693,763 - 6,765,570 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366043,319,799 - 3,388,781 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049366043,316,898 - 3,388,687 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CCDC85C
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl7120,514,491 - 120,597,318 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.17120,514,488 - 120,597,409 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.27128,124,329 - 128,148,522 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CCDC85C
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12477,470,947 - 77,560,425 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2477,471,048 - 77,560,331 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605364,606,196 - 64,701,019 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Ccdc85c
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247344,310,607 - 4,366,209 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247344,310,662 - 4,366,209 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Ccdc85c
2473 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:159
Count of miRNA genes:151
Interacting mature miRNAs:158
Transcripts:ENSMUST00000136175
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
1300883Ath21_matherosclerosis 21 (mouse)Not determined1285961579119961683Mouse
39128213Lwq23_mliver weight QTL 10 (mouse)1280956708113383533Mouse
12910532Nrq10a_mnoise-induced hearing loss resistant QTL 10a (mouse)1292750025120092757Mouse
12910533Nrq10_mnoise-induced hearing loss resistant QTL 10 (mouse)1292750025120092757Mouse
1357463Vtbt14_mvertebral trabecular bone trait 14 (mouse)Not determined1292936097120092757Mouse
12910790Pwgrq7_mpre-weaning growth rate QTL 7 (mouse)1290937367108645308Mouse
1301269Sluc12_msusceptibility to lung cancer 12 (mouse)Not determined1296860337120092757Mouse
4142007Chlq17_mcirculating hormone level QTL 17 (mouse)Not determined1288052874120092757Mouse
25823169Hrsq8_mhost response to SARS QTL 8, log titer (mouse)1281696245108495368Mouse
4142002Tbqt3_mtibia bone quality traits 3 (mouse)Not determined1235285496109936243Mouse
11039526Ccc1_mcolitis susceptibility in the Collaborative Cross 1 (mouse)1293528334111028223Mouse
1300545Lifespan3_mlife span 3 (mouse)Not determined1288052874120092757Mouse
4141610Tailaq1_mtail length adjusted QTL 1 (mouse)Not determined80956708113383533Mouse
1301836Heal5_mwound healing/regeneration 5 (mouse)Not determined1289939031120092757Mouse
13524846Ppiq11_mprepulse inhibition QTL 11 (mouse)1282666396116666396Mouse
10412156Nociq3_mnociceptive sensitivity inflammatory QTL 3 (mouse)Not determined1286396075114831653Mouse
1301879Insq10_minsulin QTL 10 (mouse)Not determined1283532075117532224Mouse
13524842Ppiq10a_mprepulse inhibition QTL 10a (mouse)1277512220111512220Mouse
10402491Dipa4_mdrug induced psychomotor activation 4 (mouse)Not determined1291222515120092757Mouse
1301492Dbsty3_mdiabesity 3 (mouse)Not determined1283532075117532224Mouse
4141335W6q10_mweight 6 weeks QTL 10 (mouse)Not determined80956708113383533Mouse
1302138Im6_mimmunoregulatory 6 (mouse)Not determined1296860337120092757Mouse
5491194Mobq3_mmultigenic obesity QTL 3 (mouse)Not determined1289664071120092757Mouse
1301308Prdt4_mprion disease incubation time 4 (mouse)Not determined1288308354120092757Mouse
1301922Bbaa6_mB.burgdorferi-associated arthritis 6 (mouse)Not determined1290308268120092757Mouse
1302177Dps2_mdelta power in slow-wave sleep 2 (mouse)Not determined1294146064120092757Mouse
10412075Nils1_mneointima lesion size 1 (mouse)Not determined12102024665120092757Mouse
27226793Feml10_mfemur length 10, 5 week (mouse)1268346774113363620Mouse
1300973Abmm_mantibody mediated myocarditis (mouse)Not determined1293264461120092757Mouse
4142401Egq10_mearly growth QTL 10 (mouse)Not determined80956708113383533Mouse
13524849Ppiq11a_mprepulse inhibition QTL 11a (mouse)1280989143114989143Mouse

Markers in Region
D12Mit233  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm3812108,256,256 - 108,256,405UniSTSGRCm38
MGSCv3712109,494,466 - 109,494,615UniSTSGRCm37
Celera12109,496,407 - 109,496,548UniSTS
Cytogenetic Map12F1UniSTS
cM Map1252.0UniSTS
Whitehead Genetic1247.0UniSTS
Whitehead_YAC12 UniSTS
B3K(I)  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm3812108,239,451 - 108,239,601UniSTSGRCm38
MGSCv3712109,477,661 - 109,477,811UniSTSGRCm37
Celera12109,479,625 - 109,479,775UniSTS
Cytogenetic Map12F1UniSTS
cM Map1252.84UniSTS


Expression

RNA-SEQ Expression


Sequence


Ensembl Acc Id: ENSMUST00000136175   ⟹   ENSMUSP00000125757
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl12108,172,604 - 108,241,392 (-)Ensembl
GRCm38.p6 Ensembl12108,206,345 - 108,275,133 (-)Ensembl
Ensembl Acc Id: ENSMUST00000222310   ⟹   ENSMUSP00000152421
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl12108,169,861 - 108,241,684 (-)Ensembl
GRCm38.p6 Ensembl12108,203,602 - 108,275,425 (-)Ensembl
RefSeq Acc Id: NM_001159910   ⟹   NP_001153382
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm3912108,169,859 - 108,241,652 (-)NCBI
GRCm3812108,203,600 - 108,275,393 (-)NCBI
MGSCv3712109,444,555 - 109,513,627 (-)RGD
Celera12109,446,564 - 109,515,546 (-)RGD
cM Map12 ENTREZGENE
Sequence:
RefSeq Acc Id: XM_006516158   ⟹   XP_006516221
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm3912108,169,858 - 108,244,111 (-)NCBI
GRCm3812108,203,599 - 108,277,852 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006516159   ⟹   XP_006516222
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm3912108,169,858 - 108,244,111 (-)NCBI
GRCm3812108,203,599 - 108,277,852 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006516160   ⟹   XP_006516223
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm3912108,169,858 - 108,244,111 (-)NCBI
GRCm3812108,203,599 - 108,277,852 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006516161   ⟹   XP_006516224
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm3912108,169,858 - 108,244,111 (-)NCBI
GRCm3812108,203,599 - 108,277,852 (-)NCBI
Sequence:
RefSeq Acc Id: NP_001153382   ⟸   NM_001159910
- UniProtKB: E9Q6B2 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006516224   ⟸   XM_006516161
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_006516223   ⟸   XM_006516160
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_006516222   ⟸   XM_006516159
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006516221   ⟸   XM_006516158
- Peptide Label: isoform X1
- UniProtKB: A0A217FL83 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSMUSP00000152421   ⟸   ENSMUST00000222310
Ensembl Acc Id: ENSMUSP00000125757   ⟸   ENSMUST00000136175

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-E9Q6B2-F1-model_v2 AlphaFold E9Q6B2 1-420 view protein structure

Promoters
RGD ID:8679192
Promoter ID:EPDNEW_M17627
Type:initiation region
Name:Ccdc85c_1
Description:Mus musculus coiled-coil domain containing 85C , 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
GRCm3812108,275,393 - 108,275,453EPDNEW
RGD ID:6822790
Promoter ID:MM_KWN:12680
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:3T3L1_Day3,   BoneMarrow_2Hour,   BoneMarrow_4Hour,   Brain,   ES_Cell,   Kidney,   Liver,   Lung
Transcripts:NM_001159910
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv3612109,513,506 - 109,514,627 (-)MPROMDB

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:3644008 AgrOrtholog
Ensembl Genes ENSMUSG00000084883 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Transcript ENSMUST00000136175 ENTREZGENE
  ENSMUST00000136175.3 UniProtKB/TrEMBL
  ENSMUST00000222310 ENTREZGENE
  ENSMUST00000222310.2 UniProtKB/Swiss-Prot
InterPro CCDC85 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report mmu:668158 UniProtKB/Swiss-Prot
MGD MGI:3644008 ENTREZGENE
NCBI Gene 668158 ENTREZGENE
PANTHER COILED-COIL DOMAIN-CONTAINING PROTEIN 85C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR13546 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam CCDC85 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Ccdc85c PhenoGen
UniProt A0A217FL83 ENTREZGENE, UniProtKB/TrEMBL
  CC85C_MOUSE UniProtKB/Swiss-Prot, ENTREZGENE