C2cd4c (C2 calcium-dependent domain containing 4C) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Behavioral & Substance Use Disorder Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Advanced Search (OLGA)
Gene: C2cd4c (C2 calcium-dependent domain containing 4C) Rattus norvegicus
Analyze
Symbol: C2cd4c
Name: C2 calcium-dependent domain containing 4C
RGD ID: 1561354
Description: Predicted to be active in cytosol. Orthologous to human C2CD4C (C2 calcium dependent domain containing 4C); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: C2 calcium-dependent domain-containing protein 4C; Fam148c; family with sequence similarity 148, member C; hypothetical protein LOC500798; LOC500798; RGD1561354; similar to Hypothetical LOC237397
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8710,742,534 - 10,746,033 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl710,742,545 - 10,751,973 (+)EnsemblGRCr8
mRatBN7.2710,090,651 - 10,095,426 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl710,092,138 - 10,095,421 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx712,973,299 - 12,975,457 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0714,851,385 - 14,853,543 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0712,711,194 - 12,713,354 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0712,973,338 - 12,978,980 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl712,974,169 - 12,976,330 (+)Ensemblrn6Rnor6.0
Rnor_5.0713,142,884 - 13,146,383 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4711,608,670 - 11,610,831 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera78,264,486 - 8,266,647 (+)NCBICelera
Cytogenetic Map7q11NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
cytosol  (ISO)

References

References - curated
# Reference Title Reference Citation
1. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:27349930  


Genomics

Comparative Map Data
C2cd4c
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8710,742,534 - 10,746,033 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl710,742,545 - 10,751,973 (+)EnsemblGRCr8
mRatBN7.2710,090,651 - 10,095,426 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl710,092,138 - 10,095,421 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx712,973,299 - 12,975,457 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0714,851,385 - 14,853,543 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0712,711,194 - 12,713,354 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0712,973,338 - 12,978,980 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl712,974,169 - 12,976,330 (+)Ensemblrn6Rnor6.0
Rnor_5.0713,142,884 - 13,146,383 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4711,608,670 - 11,610,831 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera78,264,486 - 8,266,647 (+)NCBICelera
Cytogenetic Map7q11NCBI
C2CD4C
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3819405,445 - 409,147 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl19405,443 - 409,147 (-)Ensemblhg38GRCh38
GRCh3719405,445 - 409,147 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3619356,443 - 364,234 (-)NCBIBuild 36Build 36hg18NCBI36
Celera19405,821 - 409,548 (+)NCBICelera
Cytogenetic Map19p13.3NCBI
HuRef19174,453 - 177,414 (-)NCBIHuRef
CHM1_119403,286 - 407,013 (-)NCBICHM1_1
T2T-CHM13v2.019353,898 - 357,600 (-)NCBIT2T-CHM13v2.0
C2cd4c
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391079,442,688 - 79,449,859 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1079,442,688 - 79,449,859 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm381079,606,854 - 79,614,025 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1079,606,854 - 79,614,025 (-)Ensemblmm10GRCm38
MGSCv371079,069,599 - 79,076,770 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361079,009,983 - 79,017,129 (-)NCBIMGSCv36mm8
Celera1080,620,220 - 80,627,391 (-)NCBICelera
Cytogenetic Map10C1NCBI
cM Map1039.72NCBI
C2cd4c
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554957,236,627 - 7,243,099 (+)Ensembl
ChiLan1.0NW_0049554957,236,627 - 7,243,099 (+)NCBIChiLan1.0ChiLan1.0
C2CD4C
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2204,712,133 - 4,716,777 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1193,956,193 - 3,960,811 (-)NCBINHGRI_mPanPan1
PanPan1.119356,073 - 359,067 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl19357,716 - 358,981 (-)EnsemblpanPan2panpan1.1
C2CD4C
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12058,027,422 - 58,029,144 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2058,027,399 - 58,029,105 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha2057,830,231 - 57,831,902 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.02058,770,492 - 58,772,163 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
UMICH_Zoey_3.12057,824,381 - 57,826,052 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02058,304,278 - 58,305,949 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02058,507,742 - 58,509,413 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
C2cd4c
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118217,749,706 - 217,752,328 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493658883,703 - 84,971 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_00493658882,455 - 85,000 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
C2CD4C
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl277,849,526 - 77,850,788 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1277,847,876 - 77,852,373 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
C2CD4C
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.16141,694 - 149,393 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl6143,327 - 144,592 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_0236660818,977,667 - 8,981,567 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
C2cd4c
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248287,999,273 - 8,002,683 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046248287,999,179 - 8,002,462 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
C2cd4c
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v11155,261,727 - 155,264,635 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in C2cd4c
85 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:57
Count of miRNA genes:56
Interacting mature miRNAs:57
Transcripts:ENSRNOT00000010555
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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61410Bw19Body weight QTL 196.20.001body mass (VT:0001259)body weight (CMO:0000012)7166965846669658Rat
1300176Hrtrt10Heart rate QTL 103.19heart pumping trait (VT:2000009)heart rate (CMO:0000002)7123748937Rat
9590102Sffal5Serum free fatty acids level QTL 58.620.001blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)7721609752216097Rat
1578652Bmd15Bone mineral density QTL 155.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)71051708662346019Rat
1643004Pain2Pain QTL 21mechanical nociception trait (VT:0002734)self mutilation severity score (CMO:0002145)71011291699900612Rat
2290372Gluco33Glucose level QTL 332.71blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)7131777942Rat
1300149Cm6Cardiac mass QTL 64.09heart mass (VT:0007028)heart left ventricle weight to body weight ratio (CMO:0000530)71104117804Rat
631503Bp102Blood pressure QTL 1021.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7170952746709527Rat
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)71509236116977875Rat
9590142Scort5Serum corticosterone level QTL 524.40.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)7132612984Rat
1582260Bw72Body weight QTL 723.20.0043body mass (VT:0001259)body weight (CMO:0000012)7139960528Rat
1582261Bw69Body weight QTL 693.20.0048body mass (VT:0001259)body weight (CMO:0000012)7139960528Rat
1582262Bw75Body weight QTL 7530.0038body mass (VT:0001259)body weight (CMO:0000012)7139960528Rat
2298547Neuinf5Neuroinflammation QTL 53.7nervous system integrity trait (VT:0010566)spinal cord Cd74 protein level (CMO:0002131)71011291660150541Rat
10059592Kidm45Kidney mass QTL 453.950.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)7946087754460877Rat
2298550Neuinf6Neuroinflammation QTL 63.3nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)7129716167Rat
1300138Hrtrt9Heart rate QTL 94.72heart pumping trait (VT:2000009)heart rate (CMO:0000002)71049882055498820Rat
724560Plsm3Polydactyly-luxate syndrome (PLS) morphotypes QTL 30.0003tibia length (VT:0004357)tibia length (CMO:0000450)7134650782Rat
7411566Bw136Body weight QTL 13610.40.001body mass (VT:0001259)body weight gain (CMO:0000420)7132612984Rat


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 4 58 144 91 89 59 75 59 6 313 162 9 125 74 92 30 14 14

Sequence


Ensembl Acc Id: ENSRNOT00000010555   ⟹   ENSRNOP00000010555
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl710,092,138 - 10,095,421 (+)Ensembl
Rnor_6.0 Ensembl712,974,169 - 12,976,330 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000142919   ⟹   ENSRNOP00000109429
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl710,742,545 - 10,751,973 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000168277   ⟹   ENSRNOP00000103507
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl710,742,552 - 10,751,973 (+)Ensembl
RefSeq Acc Id: NM_001109285   ⟹   NP_001102755
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8710,742,534 - 10,744,695 (+)NCBI
mRatBN7.2710,091,921 - 10,094,083 (+)NCBI
Rnor_6.0712,974,169 - 12,976,330 (+)NCBI
Rnor_5.0713,142,884 - 13,146,383 (+)NCBI
RGSC_v3.4711,608,670 - 11,610,831 (+)RGD
Celera78,264,486 - 8,266,647 (+)RGD
Sequence:
RefSeq Acc Id: XM_006240985   ⟹   XP_006241047
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8710,742,539 - 10,746,033 (+)NCBI
mRatBN7.2710,090,651 - 10,095,426 (+)NCBI
Rnor_6.0712,973,338 - 12,978,980 (+)NCBI
Rnor_5.0713,142,884 - 13,146,383 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001102755 (Get FASTA)   NCBI Sequence Viewer  
  XP_006241047 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL89418 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000103507.1
  ENSRNOP00000109429
  ENSRNOP00000109429.1
RefSeq Acc Id: NP_001102755   ⟸   NM_001109285
- UniProtKB: D3ZLU0 (UniProtKB/TrEMBL),   A6K8Z8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006241047   ⟸   XM_006240985
- Peptide Label: isoform X1
- Sequence:
Ensembl Acc Id: ENSRNOP00000010555   ⟸   ENSRNOT00000010555
Ensembl Acc Id: ENSRNOP00000109429   ⟸   ENSRNOT00000142919
Ensembl Acc Id: ENSRNOP00000103507   ⟸   ENSRNOT00000168277
Protein Domains
C2

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZLU0-F1-model_v2 AlphaFold D3ZLU0 1-422 view protein structure

Transcriptome

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

Promoters
RGD ID:13695058
Promoter ID:EPDNEW_R5582
Type:single initiation site
Name:C2cd4c_1
Description:C2 calcium-dependent domain containing 4C
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_6.0712,974,187 - 12,974,247EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1561354 AgrOrtholog
BioCyc Gene G2FUF-34875 BioCyc
Ensembl Genes ENSRNOG00000008026 Ensembl
  ENSRNOG00000073081 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000142919 ENTREZGENE
  ENSRNOT00000142919.1 UniProtKB/TrEMBL
  ENSRNOT00000168277.1 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.150 UniProtKB/TrEMBL
InterPro C2_Ca-dep UniProtKB/TrEMBL
  C2_domain_sf UniProtKB/TrEMBL
  C2C4C/C2C4D UniProtKB/TrEMBL
KEGG Report rno:500798 UniProtKB/TrEMBL
NCBI Gene 500798 ENTREZGENE
PANTHER PTHR46291 UniProtKB/TrEMBL
  PTHR46291:SF5 UniProtKB/TrEMBL
Pfam PF00168 UniProtKB/TrEMBL
PhenoGen C2cd4c PhenoGen
PROSITE PS50004 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000008026 RatGTEx
  ENSRNOG00000073081 RatGTEx
SMART SM00239 UniProtKB/TrEMBL
Superfamily-SCOP SSF49562 UniProtKB/TrEMBL
UniProt A0ABK0LDH7_RAT UniProtKB/TrEMBL
  A6K8Z8 ENTREZGENE, UniProtKB/TrEMBL
  D3ZLU0 ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2011-08-02 C2cd4c  C2 calcium-dependent domain containing 4C  Fam148c  family with sequence similarity 148, member C  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-07 Fam148c  family with sequence similarity 148, member C  RGD1561354_predicted  RGD1561354 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1561354_predicted  RGD1561354 (predicted)  LOC500798  similar to Hypothetical LOC237397  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC500798  similar to Hypothetical LOC237397      Symbol and Name status set to provisional 70820 PROVISIONAL