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

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Gene: Efhc1 (EF-hand domain (C-terminal) containing 1) Mus musculus
Analyze
Symbol: Efhc1
Name: EF-hand domain (C-terminal) containing 1
RGD ID: 1317535
MGI Page MGI
Description: Predicted to enable alpha-tubulin binding activity. Involved in flagellated sperm motility. Located in axoneme and neuronal cell body. Is active in axonemal A tubule inner sheath and sperm flagellum. Is expressed in several structures, including brain; epithelium; future hindbrain roof plate; spinal cord ventricular layer; and spleen. Used to study juvenile myoclonic epilepsy. 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).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: 1700029F22Rik; EF-hand domain-containing protein 1; mRib72; mRib72-1; myoc; myoclonin-1; myoclonin1
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
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
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
References

References - curated
# Reference Title Reference Citation
1. Functional annotation of a full-length mouse cDNA collection. Kawai J, etal., Nature. 2001 Feb 8;409(6821):685-90.
2. MGDs mouse GO annotations MGD data from the GO Consortium
3. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Okazaki Y, etal., Nature. 2002 Dec 5;420(6915):563-73.
4. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
5. Mouse MP Annotation Import Pipeline RGD automated import pipeline
6. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
7. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:10349636   PMID:11042159   PMID:11076861   PMID:12040188   PMID:12095989   PMID:12477932   PMID:15258581   PMID:15670853   PMID:16141072   PMID:16141073   PMID:16572395   PMID:17971504  
PMID:18164683   PMID:19147686   PMID:19191033   PMID:20015616   PMID:21267068   PMID:21677750   PMID:21873635   PMID:22226147   PMID:22926142   PMID:23213475   PMID:23756482   PMID:27467453  
PMID:29539279   PMID:33328576   PMID:37295417   PMID:37865089   PMID:37989994  


Genomics

Comparative Map Data
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
(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
(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
(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

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:182
Count of miRNA genes:174
Interacting mature miRNAs:179
Transcripts:ENSMUST00000038447, ENSMUST00000160782
Prediction methods:Miranda, Rnahybrid, Targetscan
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 (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
11039528Ccc3_mcolitis susceptibility in the Collaborative Cross 3 (mouse)13680142195051546Mouse
1301011Cplaq4_mcircadian period of locomotor activity 4 (mouse)Not determined1967344243673601Mouse
1301073Orch5_mautoimmune orchitis resistance 5 (mouse)Not determined11906535153065454Mouse
1301275Sle10_msystematic lupus erythematosus susceptibility 10 (mouse)Not determined1288219436882352Mouse
15092046Wngrme1_mweek nine growth rate, maternal effect 1 (mouse)1328014237782236Mouse
1301370Adip1_madiposity 1 (mouse)Not determined1288219436882352Mouse
13824984Twq5_mtestis weight QTL 5 (mouse)13069992184732197Mouse
15092044Wtgrme1_mweek ten growth rate, maternal effect 1 (mouse)1328014237782236Mouse
1301240Sluc15_msusceptibility to lung cancer 15 (mouse)Not determined11906535153065454Mouse
1301471Obq2_mobesity QTL 2 (mouse)Not determined1394162037941887Mouse
14700685Civq2_mcerebral infarct volume QTL 2 (mouse)11134048245340482Mouse
1301756Pgia1_mproteoglycan induced arthritis 1 (mouse)Not determined11906535153065454Mouse
1301891Alcp25_malcohol preference locus 25 (mouse)Not determined1125203185Mouse
1300834Cia20_mcollagen induced arthritis 20 (mouse)Not determined1125203185Mouse
15092055Lgrme1_mlate growth rate, maternal effect 1 (mouse)1328014237782236Mouse
4141646Fecq3_mfecundity QTL 3 (mouse)Not determined11291692026517685Mouse
12880407V125Dq2_mvitamin D active form serum level QTL 2 (mouse)11933908153339081Mouse
15092050Wsegrme1_mweek seven growth rate, maternal effect 1 (mouse)1328014237782236Mouse
15092051Wegrme1_mweek eight growth rate, maternal effect 1 (mouse)1328014237782236Mouse
15092048Wsigrme1_mweek six growth rate, maternal effect 1 (mouse)1328014237782236Mouse
1301482Morph1_mmorphine antinociception 1 (mouse)Not determined1130367747Mouse
10043970Obq23_mobesity QTL 23 (mouse)Not determined1501266539012665Mouse
10412226Alpq4_malcohol preference QTL 4 (mouse)Not determined1122976684Mouse


Expression

RNA-SEQ Expression


Sequence


Ensembl Acc Id: ENSMUST00000038447   ⟹   ENSMUSP00000042343
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl121,021,912 - 21,061,065 (+)Ensembl
GRCm38.p6 Ensembl120,951,688 - 20,990,841 (+)Ensembl
Ensembl Acc Id: ENSMUST00000160782
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl121,021,850 - 21,025,751 (+)Ensembl
GRCm38.p6 Ensembl120,951,626 - 20,955,527 (+)Ensembl
RefSeq Acc Id: NM_027974   ⟹   NP_082250
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39121,021,850 - 21,061,065 (+)NCBI
GRCm38120,951,626 - 20,990,841 (+)NCBI
MGSCv37120,941,707 - 20,980,922 (+)RGD
Celera120,826,576 - 20,865,461 (+)RGD
cM Map1 ENTREZGENE
Sequence:
RefSeq Acc Id: XR_003946579
Type: NON-CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39121,021,776 - 21,061,065 (+)NCBI
GRCm38120,951,553 - 20,990,841 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_082250 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein ACB20692 (Get FASTA)   NCBI Sequence Viewer  
  BAB24614 (Get FASTA)   NCBI Sequence Viewer  
  EDL14385 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSMUSP00000042343
  ENSMUSP00000042343.5
GenBank Protein Q9D9T8 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_082250   ⟸   NM_027974
- UniProtKB: Q9D9T8 (UniProtKB/Swiss-Prot),   B2CKC6 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSMUSP00000042343   ⟸   ENSMUST00000038447
Protein Domains
DM10   EF-hand

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q9D9T8-F1-model_v2 AlphaFold Q9D9T8 1-648 view protein structure

Promoters
RGD ID:6817636
Promoter ID:MM_KWN:236
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:BoneMarrow_4Hour,   Brain,   ES_Cell,   Kidney,   Lung,   MEF_B4,   MEF_B6,   Spleen
Transcripts:NM_027974,   OTTMUST00000074048
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv36120,941,314 - 20,941,814 (+)MPROMDB
RGD ID:6873280
Promoter ID:EPDNEW_M91
Type:initiation region
Name:Efhc1_1
Description:Mus musculus EF-hand domain (C-terminal) containing 1 , mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38120,951,618 - 20,951,678EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:1919127 AgrOrtholog
Ensembl Genes ENSMUSG00000041809 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSMUST00000038447 ENTREZGENE
  ENSMUST00000038447.6 UniProtKB/TrEMBL
Gene3D-CATH 2.30.29.170 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EF-hand UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro EF-hand-dom_pair UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EF_hand_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EFHC1/EFHC2/EFHB UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Uncharacterised_DM10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report mmu:71877 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGD MGI:1919127 ENTREZGENE
NCBI Gene 71877 ENTREZGENE
PANTHER EF-HAND DOMAIN-CONTAINING PROTEIN 1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR12086 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam DUF1126 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EF-hand_7 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Efhc1 PhenoGen
PROSITE DM10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EF_HAND_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART DM10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EFh UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF47473 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt B2CKC6 ENTREZGENE, UniProtKB/TrEMBL
  EFHC1_MOUSE UniProtKB/Swiss-Prot, ENTREZGENE