Efcab10 (EF-hand calcium binding domain 10) - Rat Genome Database

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Gene: Efcab10 (EF-hand calcium binding domain 10) Rattus norvegicus
Analyze
Symbol: Efcab10
Name: EF-hand calcium binding domain 10
RGD ID: 1307943
Description: Predicted to enable calcium ion binding activity. Orthologous to human EFCAB10 (EF-hand calcium binding domain 10); INTERACTS WITH 6-propyl-2-thiouracil; bisphenol A; copper atom.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: EF-hand calcium-binding domain-containing protein 10; LOC362727; RGD1307943
RGD Orthologs
Human
Mouse
Bonobo
Dog
Squirrel
Pig
Green Monkey
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8655,731,902 - 55,738,821 (+)NCBIGRCr8
mRatBN7.2650,004,479 - 50,011,398 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl650,004,479 - 50,011,398 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx650,309,027 - 50,315,996 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0650,623,962 - 50,630,931 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0650,062,942 - 50,069,893 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0652,702,304 - 52,709,223 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl652,702,544 - 52,709,223 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0662,323,316 - 62,330,235 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4651,741,044 - 51,747,963 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1651,744,407 - 51,751,089 (+)NCBI
Celera649,194,412 - 49,201,339 (+)NCBICelera
Cytogenetic Map6q16NCBI
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

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Comparative Map Data
Efcab10
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8655,731,902 - 55,738,821 (+)NCBIGRCr8
mRatBN7.2650,004,479 - 50,011,398 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl650,004,479 - 50,011,398 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx650,309,027 - 50,315,996 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0650,623,962 - 50,630,931 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0650,062,942 - 50,069,893 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0652,702,304 - 52,709,223 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl652,702,544 - 52,709,223 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0662,323,316 - 62,330,235 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4651,741,044 - 51,747,963 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1651,744,407 - 51,751,089 (+)NCBI
Celera649,194,412 - 49,201,339 (+)NCBICelera
Cytogenetic Map6q16NCBI
EFCAB10
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh387105,565,124 - 105,581,493 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl7105,565,120 - 105,600,875 (-)EnsemblGRCh38hg38GRCh38
GRCh377105,205,571 - 105,221,940 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 367104,992,689 - 105,009,177 (-)NCBINCBI36Build 36hg18NCBI36
Celera7100,010,699 - 100,027,094 (-)NCBICelera
Cytogenetic Map7q22.3NCBI
HuRef799,563,858 - 99,580,241 (-)NCBIHuRef
CHM1_17105,138,892 - 105,155,283 (-)NCBICHM1_1
T2T-CHM13v2.07106,879,330 - 106,895,701 (-)NCBIT2T-CHM13v2.0
CRA_TCAGchr7v27104,566,137 - 104,582,536 (-)NCBI
Efcab10
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391233,444,824 - 33,451,268 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1233,444,853 - 33,451,266 (+)EnsemblGRCm39 Ensembl
GRCm381233,394,825 - 33,401,269 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1233,394,854 - 33,401,267 (+)EnsemblGRCm38mm10GRCm38
MGSCv371234,079,719 - 34,086,134 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361233,980,101 - 33,986,516 (+)NCBIMGSCv36mm8
Celera1234,839,250 - 34,845,770 (+)NCBICelera
Cytogenetic Map12A3NCBI
cM Map1214.34NCBI
EFCAB10
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v26142,415,837 - 142,432,528 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan17190,685,805 - 190,702,289 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0797,556,418 - 97,571,987 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.17110,285,036 - 110,301,514 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl7110,285,036 - 110,301,501 (-)Ensemblpanpan1.1panPan2
EFCAB10
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11814,833,401 - 14,844,081 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1814,833,472 - 14,845,956 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1814,484,482 - 14,495,115 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01815,135,732 - 15,146,558 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1815,135,758 - 15,148,449 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11814,921,898 - 14,932,520 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01814,844,769 - 14,855,466 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01815,124,870 - 15,135,501 (+)NCBIUU_Cfam_GSD_1.0
Efcab10
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440511857,181,530 - 57,188,497 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493647918,305,334 - 18,314,449 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493647918,305,335 - 18,312,252 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PUS7
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl9105,419,056 - 105,445,682 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.19105,424,408 - 105,445,667 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.29116,193,298 - 116,213,600 (-)NCBISscrofa10.2Sscrofa10.2susScr3
EFCAB10
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12174,490,873 - 74,505,942 (-)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604229,411,131 - 29,424,270 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0

Variants

.
Variants in Efcab10
51 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:21
Count of miRNA genes:20
Interacting mature miRNAs:21
Transcripts:ENSRNOT00000014252
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
9590290Uminl2Urine mineral level QTL 23.960.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)63878398983783989Rat
8693632Alc27Alcohol consumption QTL 272.20.791drinking behavior trait (VT:0001422)calculated ethanol drink intake rate (CMO:0001615)63432335751121479Rat
634318Bw118Body weight QTL 1183.55abdominal fat pad mass (VT:1000711)abdominal fat pad weight (CMO:0000088)63330954957730294Rat
634307Bp141Blood pressure QTL 1414arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)63523041780230417Rat
10401812Kidm54Kidney mass QTL 54kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)61436878859368788Rat
2292589Emca10Estrogen-induced mammary cancer QTL 100.048mammary gland integrity trait (VT:0010552)post-insult time to mammary tumor formation (CMO:0000345)61653614061536140Rat
634330Pia16Pristane induced arthritis QTL 163.9joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)645790088104200226Rat
10401800Kidm49Kidney mass QTL 49kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)61436878859368788Rat
1331779Rf38Renal function QTL 382.876kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)63207442872227641Rat
1300164Rf15Renal function QTL 153.12renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)6507449754641141Rat
1354632Scl29Serum cholesterol level QTL 293.74blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)63509870971636405Rat
4145119Mcs25Mammary carcinoma susceptibility QTL 250.0001mammary gland integrity trait (VT:0010552)ratio of deaths to total study population during a period of time (CMO:0001023)610894415110548006Rat
2293839Kiddil2Kidney dilation QTL 24.8kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)62086642281133036Rat
1576309Emca7Estrogen-induced mammary cancer QTL 74mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)615107216107351382Rat
9590140Scort4Serum corticosterone level QTL 414.490.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)63878398983783989Rat
9590306Scort18Serum corticosterone level QTL 182.880.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)63878398983783989Rat
1578665Bss16Bone structure and strength QTL 164.4femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)61173566972593685Rat
2293841Kiddil4Kidney dilation QTL 44.4kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)62086642281133036Rat
1641898Colcr4Colorectal carcinoma resistance QTL43.710.0007intestine integrity trait (VT:0010554)well differentiated malignant colorectal tumor surface area measurement (CMO:0002077)62033877762613667Rat
1578668Bmd14Bone mineral density QTL 143.8femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)61173566972593685Rat
6893340Cm77Cardiac mass QTL 770.260.57heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)63330954981132889Rat
70199Coreg1Compensatory renal growth QTL 111.8kidney mass (VT:0002707)compensatory renal growth score (CMO:0001894)63569161857730540Rat
2301972Bp325Blood pressure QTL 3254.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)6172227641Rat
1300143Rf14Renal function QTL 142.92renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)63443413777102317Rat
1354664Slep2Serum leptin concentration QTL 24.49blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)61653614071636405Rat


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
nervous system
renal system
reproductive system
respiratory system
2 6 6 110 37 39 9 12 9 6 92 31 93 45 60 30

Sequence


Ensembl Acc Id: ENSRNOT00000014252   ⟹   ENSRNOP00000014252
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl650,004,479 - 50,011,398 (+)Ensembl
Rnor_6.0 Ensembl652,702,544 - 52,709,223 (+)Ensembl
RefSeq Acc Id: NM_001108706   ⟹   NP_001102176
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8655,731,902 - 55,738,821 (+)NCBI
mRatBN7.2650,004,479 - 50,011,398 (+)NCBI
Rnor_6.0652,702,304 - 52,709,223 (+)NCBI
Rnor_5.0662,323,316 - 62,330,235 (+)NCBI
RGSC_v3.4651,741,044 - 51,747,963 (+)RGD
Celera649,194,412 - 49,201,339 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001102176 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM03291 (Get FASTA)   NCBI Sequence Viewer  
  EDM03292 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000014252.6
RefSeq Acc Id: NP_001102176   ⟸   NM_001108706
- UniProtKB: D4AA55 (UniProtKB/TrEMBL),   A6HB86 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000014252   ⟸   ENSRNOT00000014252
Protein Domains
EF-hand

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4AA55-F1-model_v2 AlphaFold D4AA55 1-112 view protein structure

Transcriptome

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

Promoters
RGD ID:13694551
Promoter ID:EPDNEW_R5076
Type:multiple initiation site
Name:Efcab10_1
Description:EF-hand calcium binding domain 10
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_6.0652,702,516 - 52,702,576EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1307943 AgrOrtholog
BioCyc Gene G2FUF-37838 BioCyc
Ensembl Genes ENSRNOG00000010730 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000014252.7 UniProtKB/TrEMBL
InterPro DD_EFCAB10 UniProtKB/TrEMBL
  EF-hand-like_dom UniProtKB/TrEMBL
  EF_hand_Ca-bd UniProtKB/TrEMBL
  EFC10 UniProtKB/TrEMBL
KEGG Report rno:362727 UniProtKB/TrEMBL
NCBI Gene 362727 ENTREZGENE
PANTHER EF-HAND CALCIUM-BINDING DOMAIN-CONTAINING PROTEIN 10 UniProtKB/TrEMBL
  PTHR21847 UniProtKB/TrEMBL
PhenoGen Efcab10 PhenoGen
PROSITE EF_HAND_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000010730 RatGTEx
Superfamily-SCOP Dimerization-anchoring domain of cAMP-dependent PK regulatory subunit UniProtKB/TrEMBL
  SSF47473 UniProtKB/TrEMBL
UniProt A6HB86 ENTREZGENE, UniProtKB/TrEMBL
  D4AA55 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-11-14 Efcab10  EF-hand calcium binding domain 10  RGD1307943  LOC362727   Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1307943  LOC362727   RGD1307943_predicted  LOC362727 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-20 RGD1307943_predicted  LOC362727 (predicted)  LOC362727_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC362727_predicted  LOC362727 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL