Ccdc12 (coiled-coil domain containing 12) - Rat Genome Database

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Gene: Ccdc12 (coiled-coil domain containing 12) Rattus norvegicus
Analyze
Symbol: Ccdc12
Name: coiled-coil domain containing 12
RGD ID: 1306081
Description: Predicted to be part of U2-type spliceosomal complex and post-mRNA release spliceosomal complex. Orthologous to human CCDC12 (coiled-coil domain containing 12); PARTICIPATES IN spliceosome pathway; INTERACTS WITH 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: coiled-coil domain-containing protein 12; LOC363151; RGD1306081; similar to hypothetical protein MGC23918
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
GRCr88119,513,007 - 119,564,802 (+)NCBIGRCr8
mRatBN7.28110,635,276 - 110,686,417 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl8110,635,710 - 110,686,417 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx8116,250,487 - 116,300,903 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.08114,449,682 - 114,500,102 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.08112,292,481 - 112,342,901 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.08118,925,682 - 118,977,038 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl8118,926,478 - 118,977,051 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.08118,266,868 - 118,317,922 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.48115,037,916 - 115,088,622 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.18115,057,428 - 115,108,076 (+)NCBI
Celera8109,919,879 - 109,970,448 (+)NCBICelera
Cytogenetic Map8q32NCBI
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

Biological Process

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Splicing and beyond: the many faces of the Prp19 complex. Chanarat S and Strasser K, Biochim Biophys Acta. 2013 Oct;1833(10):2126-34. doi: 10.1016/j.bbamcr.2013.05.023. Epub 2013 Jun 3.
2. 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.
3. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
5. Comprehensive gene review and curation RGD comprehensive gene curation
Additional References at PubMed
PMID:35352799  


Genomics

Comparative Map Data
Ccdc12
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr88119,513,007 - 119,564,802 (+)NCBIGRCr8
mRatBN7.28110,635,276 - 110,686,417 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl8110,635,710 - 110,686,417 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx8116,250,487 - 116,300,903 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.08114,449,682 - 114,500,102 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.08112,292,481 - 112,342,901 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.08118,925,682 - 118,977,038 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl8118,926,478 - 118,977,051 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.08118,266,868 - 118,317,922 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.48115,037,916 - 115,088,622 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.18115,057,428 - 115,108,076 (+)NCBI
Celera8109,919,879 - 109,970,448 (+)NCBICelera
Cytogenetic Map8q32NCBI
CCDC12
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38346,921,730 - 46,981,994 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl346,921,726 - 46,982,010 (-)EnsemblGRCh38hg38GRCh38
GRCh37346,963,220 - 47,023,484 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36346,938,225 - 46,993,242 (-)NCBINCBI36Build 36hg18NCBI36
Build 34346,938,224 - 46,993,243NCBI
Celera346,901,718 - 46,956,791 (-)NCBICelera
Cytogenetic Map3p21.31NCBI
HuRef347,006,349 - 47,066,597 (-)NCBIHuRef
CHM1_1346,913,314 - 46,973,900 (-)NCBICHM1_1
T2T-CHM13v2.0346,938,112 - 46,998,350 (-)NCBIT2T-CHM13v2.0
Ccdc12
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm399110,483,376 - 110,540,661 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl9110,485,571 - 110,540,674 (+)EnsemblGRCm39 Ensembl
GRCm389110,654,308 - 110,711,593 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl9110,656,503 - 110,711,606 (+)EnsemblGRCm38mm10GRCm38
MGSCv379110,559,007 - 110,614,097 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv369110,501,319 - 110,556,370 (+)NCBIMGSCv36mm8
Celera9110,386,535 - 110,441,389 (+)NCBICelera
Cytogenetic Map9F2NCBI
cM Map960.37NCBI
Ccdc12
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542025,212,422 - 25,257,741 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495542025,212,888 - 25,257,733 (+)NCBIChiLan1.0ChiLan1.0
CCDC12
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2246,878,280 - 46,935,992 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1346,883,049 - 46,940,761 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0346,822,128 - 46,882,217 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1347,923,673 - 47,981,073 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl347,923,673 - 47,978,660 (-)Ensemblpanpan1.1panPan2
CCDC12
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12041,838,497 - 41,889,902 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2041,834,095 - 41,890,482 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2041,754,749 - 41,806,149 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02042,321,311 - 42,372,466 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2042,321,335 - 42,376,002 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12041,563,007 - 41,614,141 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02041,963,968 - 42,015,100 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02042,244,929 - 42,296,066 (+)NCBIUU_Cfam_GSD_1.0
Ccdc12
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118201,154,789 - 201,207,178 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936596703,943 - 756,362 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936596707,841 - 756,285 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CCDC12
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1329,786,091 - 29,846,688 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11329,785,581 - 29,846,683 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21333,064,788 - 33,120,575 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CCDC12
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1228,326,480 - 8,384,985 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl228,326,798 - 8,381,938 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666041158,764,128 - 158,820,769 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Ccdc12
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462473074,308,926 - 74,354,904 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462473074,307,144 - 74,354,904 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Ccdc12
343 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:38
Count of miRNA genes:36
Interacting mature miRNAs:37
Transcripts:ENSRNOT00000028426
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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1581557Eae16Experimental allergic encephalomyelitis QTL 163.8nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)88462195110921472Rat
631650Stl6Serum triglyceride level QTL 640.0019blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)810378157112202585Rat
1554321Bmd3Bone mineral density QTL 37.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)840952565123900184Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)846531639119088626Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)846531639119088626Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)absolute change in systolic blood pressure (CMO:0000607)846531639119088626Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)846531639119088626Rat
2303171Bp331Blood pressure QTL 3315.570.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)861290298119084929Rat
631653Bp125Blood pressure QTL 1253.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)866142385111142385Rat
631210Bw3Body weight QTL35.9mesenteric fat pad mass (VT:0010427)mesenteric fat pad weight to body weight ratio (CMO:0000654)869349194112783834Rat
1300171Bp184Blood pressure QTL 1843.66arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)870513503118219066Rat
8694446Bw170Body weight QTL 17012.070.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)871888757116888757Rat
9590292Uminl3Urine mineral level QTL 33.620.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)871888757116888757Rat
8694200Abfw4Abdominal fat weight QTL 49.070.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)871888757116888757Rat
8694392Bw161Body weight QTL 1618.060.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)871888757116888757Rat
1549909Stresp11Stress response QTL 116.830.0019stress-related behavior trait (VT:0010451)number of approaches toward negative stimulus before onset of defensive burying response (CMO:0001960)873473045118473045Rat
2300181Bmd55Bone mineral density QTL 555.70.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)876468691121468691Rat
61437Cia6Collagen induced arthritis QTL 6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)882460758122812818Rat
2313400Anxrr25Anxiety related response QTL 25aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)889265192114019816Rat
738011Anxrr9Anxiety related response QTL 96.1exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)893535351123900184Rat
1358893Bp263Blood pressure QTL 2635.01arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)893965141123900184Rat
1358903Bp252Blood pressure QTL 25270.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)893965141123900184Rat
738014Anxrr15Anxiety related response QTL 153.60.005locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)895718998123900184Rat
2300182Bmd56Bone mineral density QTL 565.4femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)895718998123900184Rat
724539Cm19Cardiac mass QTL 192.6heart mass (VT:0007028)calculated heart weight (CMO:0000073)8100149864120994388Rat

Markers in Region
RH129303  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.28110,686,144 - 110,686,364 (+)MAPPERmRatBN7.2
Rnor_6.08118,976,766 - 118,976,985NCBIRnor6.0
Rnor_5.08118,317,650 - 118,317,869UniSTSRnor5.0
RGSC_v3.48115,088,350 - 115,088,569UniSTSRGSC3.4
Celera8109,970,176 - 109,970,395UniSTS
RH 3.4 Map946.9UniSTS
Cytogenetic Map8q32UniSTS


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 3 43 54 38 19 38 6 9 74 35 41 11 6
Low 3 3 3 2 2 2
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000028426   ⟹   ENSRNOP00000028426
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl8110,635,710 - 110,686,417 (+)Ensembl
Rnor_6.0 Ensembl8118,926,478 - 118,977,051 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000108901   ⟹   ENSRNOP00000087339
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl8110,635,710 - 110,686,417 (+)Ensembl
RefSeq Acc Id: NM_001108783   ⟹   NP_001102253
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88119,514,094 - 119,564,802 (+)NCBI
mRatBN7.28110,635,710 - 110,686,417 (+)NCBI
Rnor_6.08118,926,467 - 118,977,038 (+)NCBI
Rnor_5.08118,266,868 - 118,317,922 (+)NCBI
RGSC_v3.48115,037,916 - 115,088,622 (+)RGD
Celera8109,919,879 - 109,970,448 (+)RGD
Sequence:
RefSeq Acc Id: XM_006243970   ⟹   XP_006244032
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88119,513,007 - 119,564,801 (+)NCBI
mRatBN7.28110,635,276 - 110,686,417 (+)NCBI
Rnor_6.08118,925,682 - 118,977,038 (+)NCBI
Rnor_5.08118,266,868 - 118,317,922 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001102253 (Get FASTA)   NCBI Sequence Viewer  
  XP_006244032 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL77064 (Get FASTA)   NCBI Sequence Viewer  
  EDL77065 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000028426
  ENSRNOP00000028426.5
  ENSRNOP00000087339.1
Reference Protein Sequences
RefSeq Acc Id: NP_001102253   ⟸   NM_001108783
- UniProtKB: D4A4Z0 (UniProtKB/TrEMBL),   A6I3G1 (UniProtKB/TrEMBL),   A0A8I6A5P0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006244032   ⟸   XM_006243970
- Peptide Label: isoform X1
- UniProtKB: D4A4Z0 (UniProtKB/TrEMBL),   A6I3G1 (UniProtKB/TrEMBL),   A0A8I6A5P0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000028426   ⟸   ENSRNOT00000028426
RefSeq Acc Id: ENSRNOP00000087339   ⟸   ENSRNOT00000108901

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4A4Z0-F1-model_v2 AlphaFold D4A4Z0 1-166 view protein structure

Transcriptome

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

Promoters
RGD ID:13696334
Promoter ID:EPDNEW_R6858
Type:initiation region
Name:Ccdc12_1
Description:coiled-coil domain containing 12
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_6.08118,926,467 - 118,926,527EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1306081 AgrOrtholog
BioCyc Gene G2FUF-29060 BioCyc
Ensembl Genes ENSRNOG00000020946 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000028426 ENTREZGENE
  ENSRNOT00000028426.7 UniProtKB/TrEMBL
  ENSRNOT00000108901.1 UniProtKB/TrEMBL
InterPro mRNA_splic_Cwf18-like UniProtKB/TrEMBL
KEGG Report rno:363151 UniProtKB/TrEMBL
NCBI Gene 363151 ENTREZGENE
PANTHER COILED-COIL DOMAIN-CONTAINING PROTEIN 12 UniProtKB/TrEMBL
  PTHR31551 UniProtKB/TrEMBL
Pfam cwf18 UniProtKB/TrEMBL
PhenoGen Ccdc12 PhenoGen
RatGTEx ENSRNOG00000020946 RatGTEx
UniProt A0A8I6A5P0 ENTREZGENE, UniProtKB/TrEMBL
  A6I3G1 ENTREZGENE, UniProtKB/TrEMBL
  D4A4Z0 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Ccdc12  coiled-coil domain containing 12   Ccdc12_predicted  coiled-coil domain containing 12 (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-30 Ccdc12_predicted  coiled-coil domain containing 12 (predicted)  RGD1306081_predicted  similar to hypothetical protein MGC23918 (predicted)  Symbol and Name updated 1299863 APPROVED
2005-01-20 RGD1306081_predicted  similar to hypothetical protein MGC23918 (predicted)  LOC363151_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC363151_predicted  similar to hypothetical protein MGC23918 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL