Efhc2 (EF-hand domain containing 2) - Rat Genome Database

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Gene: Efhc2 (EF-hand domain containing 2) Rattus norvegicus
Analyze
Symbol: Efhc2
Name: EF-hand domain containing 2
RGD ID: 1563388
Description: Predicted to be involved in flagellated sperm motility and regulation of neuron projection development. Predicted to act upstream of or within cellular response to leukemia inhibitory factor. Predicted to be located in axonemal microtubule and ciliary basal body. Predicted to be active in axonemal A tubule inner sheath and sperm flagellum. Predicted to colocalize with microtubule. Orthologous to human EFHC2 (EF-hand domain containing 2); INTERACTS WITH 6-propyl-2-thiouracil; aflatoxin B1; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: EF-hand domain (C-terminal) containing 2; EF-hand domain-containing family member C2; LOC302507; RGD1563388; similar to EF-hand domain (C-terminal) containing 2
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X7,943,603 - 8,144,073 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 EnsemblX7,943,725 - 8,144,215 (+)EnsemblGRCr8
mRatBN7.2X5,360,499 - 5,564,004 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX5,360,617 - 5,560,970 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_UtxX5,413,662 - 5,613,947 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X8,889,453 - 9,089,753 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X5,209,641 - 5,409,978 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X5,825,551 - 6,026,398 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX5,825,711 - 6,026,398 (+)Ensemblrn6Rnor6.0
Rnor_5.0X6,650,703 - 6,850,893 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4X16,981,096 - 17,181,453 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
CeleraX5,856,308 - 6,056,659 (+)NCBICelera
Cytogenetic MapXq11NCBI
JBrowse:




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. GOA pipeline RGD automated data 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:20439489  


Genomics

Comparative Map Data
Efhc2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X7,943,603 - 8,144,073 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 EnsemblX7,943,725 - 8,144,215 (+)EnsemblGRCr8
mRatBN7.2X5,360,499 - 5,564,004 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX5,360,617 - 5,560,970 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_UtxX5,413,662 - 5,613,947 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X8,889,453 - 9,089,753 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X5,209,641 - 5,409,978 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X5,825,551 - 6,026,398 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX5,825,711 - 6,026,398 (+)Ensemblrn6Rnor6.0
Rnor_5.0X6,650,703 - 6,850,893 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4X16,981,096 - 17,181,453 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
CeleraX5,856,308 - 6,056,659 (+)NCBICelera
Cytogenetic MapXq11NCBI
EFHC2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X44,147,872 - 44,343,672 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblX44,146,255 - 44,343,850 (-)Ensemblhg38GRCh38
GRCh37X44,007,118 - 44,202,918 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36X43,892,072 - 44,087,867 (-)NCBIBuild 36Build 36hg18NCBI36
Build 34X43,764,164 - 43,959,172NCBI
CeleraX48,146,906 - 48,342,688 (-)NCBICelera
Cytogenetic MapXp11.3NCBI
HuRefX41,736,053 - 41,929,823 (-)NCBIHuRef
CHM1_1X44,040,187 - 44,235,928 (-)NCBICHM1_1
T2T-CHM13v2.0X43,554,179 - 43,750,009 (-)NCBIT2T-CHM13v2.0
Efhc2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X16,998,288 - 17,186,291 (-)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblX16,998,288 - 17,185,607 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm38X17,132,049 - 17,320,049 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX17,132,049 - 17,319,368 (-)Ensemblmm10GRCm38
MGSCv37X16,709,175 - 16,896,494 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36X16,289,095 - 16,476,292 (-)NCBIMGSCv36mm8
CeleraX14,747,753 - 14,934,751 (-)NCBICelera
Cytogenetic MapXA1.2NCBI
cM MapX12.34NCBI
Efhc2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555163,867,535 - 4,036,293 (+)Ensembl
ChiLan1.0NW_0049555163,867,542 - 4,036,049 (+)NCBIChiLan1.0ChiLan1.0
EFHC2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2X45,792,932 - 45,992,444 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1X45,796,296 - 45,995,822 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0X36,598,626 - 36,793,524 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1X44,422,431 - 44,616,413 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX44,422,431 - 44,617,327 (-)EnsemblpanPan2panpan1.1
EFHC2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X38,133,964 - 38,297,285 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX38,134,891 - 38,329,080 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_TashaX25,361,813 - 25,556,979 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0X38,222,098 - 38,417,403 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 EnsemblX38,221,731 - 38,417,400 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1X38,262,643 - 38,457,722 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0X38,245,996 - 38,437,899 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0X38,341,240 - 38,536,547 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Efhc2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X30,438,344 - 30,616,267 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493650210,278,816 - 10,457,086 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_00493650210,279,094 - 10,456,994 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
EFHC2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX39,403,692 - 39,597,512 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1X39,407,390 - 39,597,537 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X43,742,330 - 44,008,987 (-)NCBISscrofa10.2Sscrofa10.2susScr3
EFHC2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X41,315,664 - 41,513,778 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 EnsemblX41,317,034 - 41,513,669 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_0236660766,532,952 - 6,735,932 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Efhc2
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1X4,703,847 - 4,900,147 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Efhc2
1319 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:161
Count of miRNA genes:118
Interacting mature miRNAs:130
Transcripts:ENSRNOT00000037360
Prediction methods:Microtar, Miranda, Pita, 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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
70165Bp64Blood pressure QTL 645.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)X400149344939387Rat
731181Uae27Urinary albumin excretion QTL 272.70.0059urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)X197044046970440Rat
70166Bp65Blood pressure QTL 655.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)X400149314046933Rat
631666Iddm5Insulin dependent diabetes mellitus QTL 5blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)X811148653111486Rat
634325Bw13Body weight QTL 130body mass (VT:0001259)body weight (CMO:0000012)X400149324470521Rat

Markers in Region
AU047346  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X5,513,885 - 5,513,991 (+)MAPPERmRatBN7.2
Rnor_6.0X5,979,058 - 5,979,163NCBIRnor6.0
Rnor_5.0X6,804,122 - 6,804,227UniSTSRnor5.0
RGSC_v3.4X17,134,367 - 17,134,472UniSTSRGSC3.4
CeleraX6,009,583 - 6,009,688UniSTS
Cytogenetic MapXq12UniSTS


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 9 55 160 87 86 55 68 55 6 322 150 11 135 93 95 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000037360   ⟹   ENSRNOP00000034132
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 EnsemblX7,943,725 - 8,144,215 (+)Ensembl
mRatBN7.2 EnsemblX5,360,617 - 5,560,970 (+)Ensembl
Rnor_6.0 EnsemblX5,825,711 - 6,026,398 (+)Ensembl
RefSeq Acc Id: NM_001106952   ⟹   NP_001100422
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X7,943,726 - 8,144,073 (+)NCBI
mRatBN7.2X5,360,617 - 5,560,970 (+)NCBI
Rnor_6.0X5,825,781 - 6,026,144 (+)NCBI
Rnor_5.0X6,650,703 - 6,850,893 (+)NCBI
RGSC_v3.4X16,981,096 - 17,181,453 (+)RGD
CeleraX5,856,308 - 6,056,659 (+)RGD
Sequence:
RefSeq Acc Id: XM_017601976   ⟹   XP_017457465
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X7,943,603 - 8,144,068 (+)NCBI
mRatBN7.2X5,360,499 - 5,564,004 (+)NCBI
Rnor_6.0X5,825,551 - 6,026,398 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001100422 (Get FASTA)   NCBI Sequence Viewer  
  XP_017457465 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL97668 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000034132
  ENSRNOP00000034132.4
RefSeq Acc Id: NP_001100422   ⟸   NM_001106952
- UniProtKB: D3ZKF6 (UniProtKB/TrEMBL),   A6JZW6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017457465   ⟸   XM_017601976
- Peptide Label: isoform X1
- Sequence:
Ensembl Acc Id: ENSRNOP00000034132   ⟸   ENSRNOT00000037360
Protein Domains
DM10

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZKF6-F1-model_v2 AlphaFold D3ZKF6 1-750 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1563388 AgrOrtholog
BioCyc Gene G2FUF-3117 BioCyc
Ensembl Genes ENSRNOG00000002986 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000037360 ENTREZGENE
  ENSRNOT00000037360.7 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
  EFHC1/EFHC2/EFHB UniProtKB/TrEMBL
KEGG Report rno:302507 UniProtKB/TrEMBL
NCBI Gene 302507 ENTREZGENE
PANTHER EF-HAND DOMAIN-CONTAINING FAMILY MEMBER C2 UniProtKB/TrEMBL
  PTHR12086 UniProtKB/TrEMBL
Pfam DUF1126 UniProtKB/TrEMBL
PhenoGen Efhc2 PhenoGen
PROSITE DM10 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000002986 RatGTEx
SMART DM10 UniProtKB/TrEMBL
Superfamily-SCOP SSF47473 UniProtKB/TrEMBL
UniProt A6JZW6 ENTREZGENE, UniProtKB/TrEMBL
  D3ZKF6 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-04-13 Efhc2  EF-hand domain containing 2  Efhc2  EF-hand domain (C-terminal) containing 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Efhc2  EF-hand domain (C-terminal) containing 2   Efhc2_predicted  EF-hand domain (C-terminal) containing 2 (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-30 Efhc2_predicted  EF-hand domain (C-terminal) containing 2 (predicted)  RGD1563388_predicted  similar to EF-hand domain (C-terminal) containing 2 (predicted)  Symbol and Name updated 1299863 APPROVED
2006-03-07 RGD1563388_predicted  similar to EF-hand domain (C-terminal) containing 2 (predicted)  LOC302507  similar to EF-hand domain (C-terminal) containing 2  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC302507  similar to EF-hand domain (C-terminal) containing 2      Symbol and Name status set to provisional 70820 PROVISIONAL