Efhc1 (EF-hand domain containing 1) - Rat Genome Database

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Gene: Efhc1 (EF-hand domain containing 1) Rattus norvegicus
Analyze
Symbol: Efhc1
Name: EF-hand domain containing 1
RGD ID: 1587365
Description: Predicted to enable alpha-tubulin binding activity. Predicted to be involved in several processes, including cerebral cortex cell migration; cilium-dependent cell motility; and mitotic spindle organization. Predicted to be located in microtubule cytoskeleton and neuronal cell body. Predicted to be active in axonemal A tubule inner sheath and mitotic spindle. Human ortholog(s) of this gene implicated in juvenile absence epilepsy 1 and juvenile myoclonic epilepsy. Orthologous to human EFHC1 (EF-hand domain containing 1); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil; aflatoxin B1.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: EF-hand domain (C-terminal) containing 1; EF-hand domain-containing protein 1; LOC301295; similar to EF-hand domain-containing protein 1
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
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
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

References - curated
# Reference Title Reference Citation
1. 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.
2. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
3. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:15258581   PMID:15632090   PMID:15670853   PMID:19191033   PMID:19734894   PMID:22926142   PMID:28370826  


Genomics

Comparative Map Data
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
(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
(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
(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
(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

Variants

.
Variants in Efhc1
211 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:16
Count of miRNA genes:16
Interacting mature miRNAs:16
Transcripts:ENSRNOT00000017393
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
70226Eae4Experimental allergic encephalomyelitis QTL 4nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)9125661317Rat
9589055Scfw5Subcutaneous fat weight QTL 55.550.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)9137999212Rat
7411592Foco8Food consumption QTL 87.40.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)9137999212Rat
9589158Gluco65Glucose level QTL 656.820.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)9137999212Rat
1300124Cm4Cardiac mass QTL 43.55heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)9140594091Rat
1298088Edpm11Estrogen-dependent pituitary mass QTL 112.5pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)9143718459Rat
1641911Alcrsp13Alcohol response QTL 13response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)9143718459Rat
10054125Srcrt7Stress Responsive Cort QTL 73.330.0011blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)9187073594Rat
1331757Cdexp1CD45RC expression in CD8 T cells QTL 14.3CD8-positive T cell quantity (VT:0008077)blood CD45RC(high) CD8 T cell count to CD45RC(low) CD8 T cell count ratio (CMO:0001990)9102453767509080Rat
1354650Despr5Despair related QTL 54.010.0017locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)9125408446254084Rat
2303559Gluco54Glucose level QTL 542blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)9125408446254084Rat
61425Cia15Collagen induced arthritis QTL 154.6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)9510982642921101Rat
631211Bw4Body weight QTL45.31retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)9510982650109826Rat
11353947Bp392Blood pressure QTL 392arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)9728325252283252Rat
9589133Insul26Insulin level QTL 2617.960.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)9895256053952560Rat
7411609Foco16Food consumption QTL 1625.60.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)9895256053952560Rat
1600365Mcs20Mammary carcinoma susceptibility QTL 203mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)91353377042791750Rat
724543Cm20Cardiac mass QTL 203.9heart mass (VT:0007028)calculated heart weight (CMO:0000073)91696139840594091Rat
631680Cm11Cardiac mass QTL 113.10.00089heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)92043051965430519Rat
70186Niddm26Non-insulin dependent diabetes mellitus QTL 263.87blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)92207116986369743Rat
631643Bp120Blood pressure QTL 12030.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)92207120067071200Rat
1598823Memor16Memory QTL 161.9exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)92213332249968732Rat

Markers in Region
RH127713  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2923,361,806 - 23,362,015 (+)MAPPERmRatBN7.2
Rnor_6.0927,054,223 - 27,054,431NCBIRnor6.0
Rnor_5.0925,910,395 - 25,910,603UniSTSRnor5.0
RGSC_v3.4919,681,229 - 19,681,437UniSTSRGSC3.4
Celera920,936,771 - 20,936,979UniSTS
RH 3.4 Map9238.0UniSTS
Cytogenetic Map9q13UniSTS
RH137899  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2923,374,842 - 23,375,071 (+)MAPPERmRatBN7.2
Rnor_6.0927,067,239 - 27,067,467NCBIRnor6.0
Rnor_5.0925,923,078 - 25,923,306UniSTSRnor5.0
RGSC_v3.4919,694,057 - 19,694,285UniSTSRGSC3.4
Celera920,949,981 - 20,950,209UniSTS
RH 3.4 Map9228.6UniSTS
Cytogenetic Map9q13UniSTS


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 7 8 32 10
Low 3 43 48 32 19 32 7 10 67 27 9 1 7
Below cutoff 9 9 9 1 1 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000017393   ⟹   ENSRNOP00000017393
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl923,375,840 - 23,414,283 (+)Ensembl
Rnor_6.0 Ensembl927,068,443 - 27,107,709 (+)Ensembl
RefSeq Acc Id: NM_001122947   ⟹   NP_001116419
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8930,872,263 - 30,910,703 (+)NCBI
mRatBN7.2923,375,840 - 23,414,283 (+)NCBI
Rnor_6.0927,068,505 - 27,107,713 (+)NCBI
Rnor_5.0925,924,344 - 25,962,902 (+)NCBI
RGSC_v3.4919,695,815 - 19,750,261 (+)RGD
Celera920,938,313 - 20,989,329 (+)RGD
Sequence:
RefSeq Acc Id: XM_039083193   ⟹   XP_038939121
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8930,872,238 - 30,910,698 (+)NCBI
mRatBN7.2923,375,815 - 23,414,283 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001116419 (Get FASTA)   NCBI Sequence Viewer  
  XP_038939121 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM18644 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000017393
  ENSRNOP00000017393.4
Reference Protein Sequences
RefSeq Acc Id: NP_001116419   ⟸   NM_001122947
- UniProtKB: D3ZD71 (UniProtKB/TrEMBL),   A6JJ88 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000017393   ⟸   ENSRNOT00000017393
RefSeq Acc Id: XP_038939121   ⟸   XM_039083193
- Peptide Label: isoform X1
- UniProtKB: A6JJ88 (UniProtKB/TrEMBL)
Protein Domains
DM10   EF-hand

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZD71-F1-model_v2 AlphaFold D3ZD71 1-648 view protein structure

Transcriptome

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

Promoters
RGD ID:13696574
Promoter ID:EPDNEW_R7099
Type:initiation region
Name:Efhc1_1
Description:EF-hand domain containing 1
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_6.0927,068,444 - 27,068,504EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1587365 AgrOrtholog
BioCyc Gene G2FUF-28020 BioCyc
Ensembl Genes ENSRNOG00000042729 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000017393 ENTREZGENE
  ENSRNOT00000017393.8 UniProtKB/TrEMBL
Gene3D-CATH 2.30.29.170 UniProtKB/TrEMBL
  EF-hand UniProtKB/TrEMBL
InterPro DUF_DM10 UniProtKB/TrEMBL
  EF-hand-like_dom UniProtKB/TrEMBL
  EF_hand_Ca-bd UniProtKB/TrEMBL
  EFHC1/EFHC2/EFHB UniProtKB/TrEMBL
KEGG Report rno:301295 UniProtKB/TrEMBL
NCBI Gene 301295 ENTREZGENE
PANTHER EF-HAND DOMAIN-CONTAINING PROTEIN 1 UniProtKB/TrEMBL
  PTHR12086 UniProtKB/TrEMBL
Pfam DUF1126 UniProtKB/TrEMBL
  EF-hand_7 UniProtKB/TrEMBL
PhenoGen Efhc1 PhenoGen
PROSITE DM10 UniProtKB/TrEMBL
  EF_HAND_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000042729 RatGTEx
SMART DM10 UniProtKB/TrEMBL
Superfamily-SCOP SSF47473 UniProtKB/TrEMBL
UniProt A6JJ88 ENTREZGENE, UniProtKB/TrEMBL
  D3ZD71 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-04-13 Efhc1  EF-hand domain containing 1  Efhc1  EF-hand domain (C-terminal) containing 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-04 Efhc1  EF-hand domain (C-terminal) containing 1  LOC301295  similar to EF-hand domain-containing protein 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-01-09 LOC301295  similar to EF-hand domain-containing protein 1  LOC684521  similar to EF-hand domain-containing protein 1  Data merged from RGD:1589164 1643240 APPROVED
2006-11-19 LOC301295  similar to EF-hand domain-containing protein 1      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-19 LOC684521  similar to EF-hand domain-containing protein 1      Symbol and Name status set to provisional 70820 PROVISIONAL