LOC100152206 (C2 calcium-dependent domain-containing protein 4A) - 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 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   new 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
Gene: LOC100152206 (C2 calcium-dependent domain-containing protein 4A) Sus scrofa
Analyze
Symbol: LOC100152206
Name: C2 calcium-dependent domain-containing protein 4A
RGD ID: 13916931
Description: INVOLVED IN positive regulation of acute inflammatory response (ortholog); regulation of cell adhesion (ortholog); regulation of vascular permeability involved in acute inflammatory response (ortholog); ASSOCIATED WITH Bloom syndrome (ortholog); colorectal cancer (ortholog); esophageal atresia (ortholog); FOUND IN nucleolus (ortholog); nucleoplasm (ortholog); nucleus (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: C2 calcium dependent domain containing 4A; C2CD4A
RGD Orthologs
Human
Mouse
Rat
Bonobo
Dog
Squirrel
Green Monkey
Alliance Genes
More Info more info ...
Latest Assembly: Sscrofa11.1 - Pig Sscrofa11.1 Assembly
Position:
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.11109,920,142 - 109,927,760 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21121,350,026 - 121,357,241 (-)NCBISscrofa10.2Sscrofa10.2susScr3
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
nucleolus  (ISO)
nucleoplasm  (ISO)
nucleus  (ISO)

References

Genomics

Comparative Map Data
LOC100152206
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.11109,920,142 - 109,927,760 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21121,350,026 - 121,357,241 (-)NCBISscrofa10.2Sscrofa10.2susScr3
C2CD4A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381562,066,977 - 62,070,917 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1562,066,977 - 62,070,917 (+)EnsemblGRCh38hg38GRCh38
GRCh371562,359,176 - 62,363,116 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361560,146,468 - 60,150,408 (+)NCBINCBI36Build 36hg18NCBI36
Celera1539,248,417 - 39,252,360 (+)NCBICelera
Cytogenetic Map15q22.2NCBI
HuRef1539,181,752 - 39,185,695 (+)NCBIHuRef
CHM1_11562,478,698 - 62,482,638 (+)NCBICHM1_1
T2T-CHM13v2.01559,870,950 - 59,874,893 (+)NCBIT2T-CHM13v2.0
C2cd4a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39967,737,814 - 67,739,612 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl967,737,771 - 67,739,612 (-)EnsemblGRCm39 Ensembl
GRCm38967,830,532 - 67,832,330 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl967,830,489 - 67,832,330 (-)EnsemblGRCm38mm10GRCm38
MGSCv37967,678,339 - 67,680,137 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36967,629,653 - 67,630,992 (-)NCBIMGSCv36mm8
Celera965,054,577 - 65,061,773 (-)NCBICelera
Cytogenetic Map9CNCBI
cM Map936.77NCBI
C2cd4a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8877,348,161 - 77,359,996 (-)NCBIGRCr8
mRatBN7.2868,467,017 - 68,469,781 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl868,466,664 - 68,470,031 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx873,998,359 - 74,001,099 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0872,271,314 - 72,274,052 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0870,111,989 - 70,114,672 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0873,671,516 - 73,686,344 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl873,672,295 - 73,673,317 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0878,000,889 - 78,013,038 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4872,185,410 - 72,186,432 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera873,226,443 - 73,241,060 (+)NCBICelera
Cytogenetic Map8q24NCBI
C2CD4A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21651,322,191 - 51,332,641 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11555,498,210 - 55,508,658 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01541,020,652 - 41,031,100 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11559,319,618 - 59,320,527 (+)NCBIpanpan1.1PanPan1.1panPan2
C2CD4A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13026,783,282 - 26,787,016 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3026,699,502 - 26,702,888 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.03026,953,827 - 26,957,208 (+)NCBIROS_Cfam_1.0
UMICH_Zoey_3.13026,891,311 - 26,894,701 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.03026,951,342 - 26,954,741 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.03027,195,078 - 27,204,128 (+)NCBIUU_Cfam_GSD_1.0
C2cd4a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024408640104,994,265 - 105,002,973 (+)NCBIHiC_Itri_2
SpeTri2.0NW_00493647122,847,090 - 22,850,006 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
C2CD4A
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12621,453,198 - 21,458,225 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2621,455,439 - 21,456,554 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666048119,930,021 - 119,934,654 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0

Variants

.
Variants in LOC100152206
166 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
Low 5 3 1 15 1 2 2
Below cutoff 3 2 4 1 6 1 1 1

Sequence


Reference Sequences
RefSeq Acc Id: XM_013992909   ⟹   XP_013848363
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.11109,920,142 - 109,927,760 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs XP_013848363 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSSSCP00000032799
  ENSSSCP00000032799.1
Reference Protein Sequences
RefSeq Acc Id: XP_013848363   ⟸   XM_013992909
- Sequence:


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSSSCG00000004573 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSSSCT00000040741 ENTREZGENE
  ENSSSCT00000040741.2 UniProtKB/TrEMBL
InterPro C2_Ca-dependent_4 UniProtKB/TrEMBL
NCBI Gene LOC100152206 ENTREZGENE
PANTHER PTHR47226 UniProtKB/TrEMBL
  PTHR47226:SF5 UniProtKB/TrEMBL
UniProt A0A286ZMJ7_PIG UniProtKB/TrEMBL