EFHC1 (EF-hand domain containing 1) - 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: EFHC1 (EF-hand domain containing 1) Chlorocebus sabaeus
Analyze
Symbol: EFHC1
Name: EF-hand domain containing 1
RGD ID: 18414150
Description: ENCODES a protein that exhibits alpha-tubulin binding (inferred); calcium ion binding (inferred); INVOLVED IN cerebral cortex cell migration (inferred); cilium-dependent cell motility (inferred); mitotic cytokinesis (inferred); ASSOCIATED WITH absence epilepsy (ortholog); childhood absence epilepsy (ortholog); epilepsy (ortholog); FOUND IN axonemal A tubule inner sheath (ortholog); cilium (ortholog); neuronal cell body (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: EF-hand domain-containing protein 1
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: ChlSab1.1 - Green Monkey 1.1 Assembly
Position:
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11720,011,684 - 20,083,639 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1720,011,530 - 20,083,592 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604452,324,800 - 52,398,569 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
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

References
Additional References at PubMed
PMID:22301074   PMID:30032202  


Genomics

Comparative Map Data
EFHC1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11720,011,684 - 20,083,639 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1720,011,530 - 20,083,592 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604452,324,800 - 52,398,569 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
EFHC1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38652,420,342 - 52,497,198 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl652,362,123 - 52,529,886 (+)EnsemblGRCh38hg38GRCh38
GRCh37652,285,140 - 52,361,996 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36652,392,953 - 52,468,542 (+)NCBINCBI36Build 36hg18NCBI36
Build 34652,393,070 - 52,465,177NCBI
Celera653,946,143 - 54,021,738 (+)NCBICelera
Cytogenetic Map6p12.2NCBI
HuRef652,116,296 - 52,191,906 (+)NCBIHuRef
CHM1_1652,287,207 - 52,362,796 (+)NCBICHM1_1
T2T-CHM13v2.0652,259,137 - 52,336,010 (+)NCBIT2T-CHM13v2.0
Efhc1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39121,021,776 - 21,061,065 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl121,021,850 - 21,061,065 (+)EnsemblGRCm39 Ensembl
GRCm38120,951,553 - 20,990,841 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl120,951,626 - 20,990,841 (+)EnsemblGRCm38mm10GRCm38
MGSCv37120,941,707 - 20,980,922 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36120,936,839 - 20,975,992 (+)NCBIMGSCv36mm8
Celera120,826,576 - 20,865,461 (+)NCBICelera
Cytogenetic Map1A4NCBI
cM Map16.5NCBI
Efhc1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8930,872,238 - 30,910,703 (+)NCBIGRCr8
mRatBN7.2923,375,815 - 23,414,283 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl923,375,840 - 23,414,283 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx931,867,029 - 31,905,726 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0936,987,734 - 37,026,420 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0935,302,944 - 35,341,647 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0927,068,505 - 27,107,713 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl927,068,443 - 27,107,709 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0925,924,344 - 25,962,902 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4919,695,815 - 19,750,261 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera920,938,313 - 20,989,329 (+)NCBICelera
Cytogenetic Map9q13NCBI
Efhc1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554115,624,053 - 5,677,534 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554115,624,510 - 5,676,165 (-)NCBIChiLan1.0ChiLan1.0
EFHC1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2566,885,919 - 66,959,754 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1662,762,852 - 62,836,780 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0651,972,041 - 52,044,219 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1653,239,474 - 53,311,798 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl653,239,474 - 53,344,404 (+)Ensemblpanpan1.1panPan2
EFHC1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11220,068,287 - 20,131,621 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1220,067,881 - 20,131,619 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1219,965,029 - 20,028,364 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01220,567,201 - 20,630,760 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1220,566,156 - 20,630,767 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11220,072,968 - 20,136,374 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01220,176,667 - 20,240,190 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01220,315,041 - 20,378,596 (+)NCBIUU_Cfam_GSD_1.0
Efhc1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494655,559,021 - 55,613,066 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364768,347,086 - 8,401,224 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049364768,347,907 - 8,401,224 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
EFHC1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl746,239,230 - 46,348,667 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1746,244,915 - 46,320,261 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.27133,966,766 - 134,041,685 (+)NCBISscrofa10.2Sscrofa10.2susScr3
Efhc1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248553,611,176 - 3,677,675 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248553,611,016 - 3,677,813 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2


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

endocrine system hemolymphoid system nervous system
High
Medium 20 38
Low 16 16 22
Below cutoff 4

Sequence


Reference Sequences
RefSeq Acc Id: ENSCSAT00000011155   ⟹   ENSCSAP00000009237
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
ChlSab1.1 Ensembl1720,011,530 - 20,083,592 (-)Ensembl
RefSeq Acc Id: XM_007972258   ⟹   XP_007970449
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
ChlSab1.11720,011,684 - 20,083,639 (-)NCBI
Vero_WHO_p1.0NW_02366604452,324,800 - 52,398,440 (+)NCBI
Sequence:
RefSeq Acc Id: XM_007972259   ⟹   XP_007970450
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
ChlSab1.11720,011,686 - 20,083,636 (-)NCBI
Vero_WHO_p1.0NW_02366604452,324,842 - 52,398,569 (+)NCBI
Sequence:
RefSeq Acc Id: XM_038006166   ⟹   XP_037862094
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
Vero_WHO_p1.0NW_02366604452,328,649 - 52,398,569 (+)NCBI
RefSeq Acc Id: XM_038006167   ⟹   XP_037862095
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
Vero_WHO_p1.0NW_02366604452,324,843 - 52,398,569 (+)NCBI
RefSeq Acc Id: XM_038006168   ⟹   XP_037862096
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
Vero_WHO_p1.0NW_02366604452,324,843 - 52,398,569 (+)NCBI
Protein Sequences
Protein RefSeqs XP_007970449 (Get FASTA)   NCBI Sequence Viewer  
  XP_007970450 (Get FASTA)   NCBI Sequence Viewer  
  XP_037862094 (Get FASTA)   NCBI Sequence Viewer  
  XP_037862095 (Get FASTA)   NCBI Sequence Viewer  
  XP_037862096 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSCSAP00000009237.1
Reference Protein Sequences
RefSeq Acc Id: XP_007970449   ⟸   XM_007972258
- Peptide Label: isoform X1
- UniProtKB: A0A0D9RKU8 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_007970450   ⟸   XM_007972259
- Peptide Label: isoform X2
- UniProtKB: A0A0D9RKU8 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSCSAP00000009237   ⟸   ENSCSAT00000011155
RefSeq Acc Id: XP_037862095   ⟸   XM_038006167
- Peptide Label: isoform X4
- UniProtKB: A0A0D9RKU8 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_037862096   ⟸   XM_038006168
- Peptide Label: isoform X5
- UniProtKB: A0A0D9RKU8 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_037862094   ⟸   XM_038006166
- Peptide Label: isoform X3
- UniProtKB: A0A0D9RKU8 (UniProtKB/TrEMBL)


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCSAG00000013059 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSCSAT00000011155.1 UniProtKB/TrEMBL
Gene3D-CATH 2.30.29.170 UniProtKB/TrEMBL
  EF-hand UniProtKB/TrEMBL
InterPro EF-hand-dom_pair UniProtKB/TrEMBL
  EF_hand_dom UniProtKB/TrEMBL
  EFHC1/EFHC2/EFHB UniProtKB/TrEMBL
  Uncharacterised_DM10 UniProtKB/TrEMBL
KEGG Report csab:103221365 UniProtKB/TrEMBL
NCBI Gene EFHC1 ENTREZGENE
PANTHER EF-HAND DOMAIN-CONTAINING PROTEIN 1 UniProtKB/TrEMBL
  PTHR12086 UniProtKB/TrEMBL
Pfam DUF1126 UniProtKB/TrEMBL
PROSITE DM10 UniProtKB/TrEMBL
  EF_HAND_2 UniProtKB/TrEMBL
SMART DM10 UniProtKB/TrEMBL
Superfamily-SCOP SSF47473 UniProtKB/TrEMBL
UniProt A0A0D9RKU8 ENTREZGENE, UniProtKB/TrEMBL