Efcab9 (EF-hand calcium binding domain 9) - Rat Genome Database

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Gene: Efcab9 (EF-hand calcium binding domain 9) Rattus norvegicus
Analyze
Symbol: Efcab9
Name: EF-hand calcium binding domain 9
RGD ID: 1588807
Description: Predicted to enable calcium ion binding activity and calcium ion sensor activity. Predicted to be involved in flagellated sperm motility and sperm capacitation. Predicted to be part of CatSper complex. Predicted to be active in cytoplasm and sperm principal piece. Orthologous to human EFCAB9 (EF-hand calcium binding domain 9); INTERACTS WITH bisphenol A; aristolochic acid A (ortholog); arsane (ortholog).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: EF-hand calcium-binding domain-containing protein 9; EF-hand calcium-binding domain-containing protein 9-like; hypothetical protein LOC682929; hypothetical protein LOC688481; LOC100911628; LOC688481
RGD Orthologs
Human
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81017,611,408 - 17,616,566 (-)NCBIGRCr8
mRatBN7.21017,107,123 - 17,112,282 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1017,107,123 - 17,112,289 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1021,852,847 - 21,857,904 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01021,341,450 - 21,346,507 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01016,832,035 - 16,837,089 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01017,399,291 - 17,406,915 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1017,407,979 - 17,415,251 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01017,291,887 - 17,293,606 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41017,367,983 - 17,373,610 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1016,753,816 - 16,758,829 (-)NCBICelera
Cytogenetic Map10q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction 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. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:31056283  


Genomics

Comparative Map Data
Efcab9
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81017,611,408 - 17,616,566 (-)NCBIGRCr8
mRatBN7.21017,107,123 - 17,112,282 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1017,107,123 - 17,112,289 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1021,852,847 - 21,857,904 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01021,341,450 - 21,346,507 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01016,832,035 - 16,837,089 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01017,399,291 - 17,406,915 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1017,407,979 - 17,415,251 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01017,291,887 - 17,293,606 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41017,367,983 - 17,373,610 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1016,753,816 - 16,758,829 (-)NCBICelera
Cytogenetic Map10q12NCBI
EFCAB9
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh385172,194,172 - 172,203,454 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl5172,194,172 - 172,203,454 (+)EnsemblGRCh38hg38GRCh38
GRCh375171,621,176 - 171,630,458 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 365171,553,782 - 171,570,743 (+)NCBINCBI36Build 36hg18NCBI36
Celera5167,653,587 - 167,662,872 (+)NCBICelera
Cytogenetic Map5q35.1NCBI
HuRef5166,716,995 - 166,726,283 (+)NCBIHuRef
CHM1_15171,053,835 - 171,063,704 (+)NCBICHM1_1
T2T-CHM13v2.05172,734,472 - 172,743,747 (+)NCBIT2T-CHM13v2.0
Efcab9
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540824,988,212 - 24,993,963 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495540824,987,401 - 24,993,284 (+)NCBIChiLan1.0ChiLan1.0
EFCAB9
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v24167,333,910 - 167,359,342 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan15165,473,450 - 165,483,200 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v05167,545,205 - 167,554,563 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.15174,461,056 - 174,470,489 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl5174,461,056 - 174,470,489 (+)Ensemblpanpan1.1panPan2
EFCAB9
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1440,055,027 - 40,076,789 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl440,055,159 - 40,076,729 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha440,001,892 - 40,023,564 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0440,428,550 - 40,450,227 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl440,444,434 - 40,450,501 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1440,243,974 - 40,265,642 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0440,433,762 - 40,455,436 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0440,943,872 - 40,965,549 (-)NCBIUU_Cfam_GSD_1.0
Efcab9
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440721394,359,430 - 94,364,093 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366093,082,264 - 3,086,721 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049366093,082,136 - 3,086,721 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
EFCAB9
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1651,987,768 - 52,007,563 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11651,987,090 - 51,996,019 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21656,427,488 - 56,437,225 (-)NCBISscrofa10.2Sscrofa10.2susScr3
EFCAB9
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12374,360,052 - 74,369,105 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2374,360,551 - 74,368,822 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660344,253,617 - 4,263,104 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Efcab9
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462473317,813,429 - 17,818,512 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462473317,813,381 - 17,818,562 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Efcab9
9 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:15
Count of miRNA genes:15
Interacting mature miRNAs:15
Transcripts:ENSRNOT00000005509
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
6893352Bw100Body weight QTL 1000.330.6body mass (VT:0001259)body weight (CMO:0000012)11590666560906665Rat
9589136Insul27Insulin level QTL 2710.460.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)101147401056474010Rat
631564Apr3Acute phase response QTL 33.9blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)101527595560275955Rat
8662860Vetf10Vascular elastic tissue fragility QTL 10artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)10615418273453136Rat
2313066Bss63Bone structure and strength QTL 631.40.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)10538701450387014Rat
631554Bp133Blood pressure QTL 1330.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1074336463851208Rat
2313064Bmd71Bone mineral density QTL 710.90.0001tibia mineral mass (VT:1000283)compact volumetric bone mineral density (CMO:0001730)10538701450387014Rat
70223Bp57Blood pressure QTL 575arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)10180676123Rat
1354587Kidm21Kidney mass QTL 213.3kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)101502851360430477Rat
6893350Bw99Body weight QTL 990.870.16body mass (VT:0001259)body weight (CMO:0000012)11590666560906665Rat
634329Pia15Pristane induced arthritis QTL 153.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10124158324Rat
1578761Stresp21Stress response QTL 213.3thymus mass (VT:0004954)thymus wet weight (CMO:0000855)10637574651375746Rat
2293680Bss40Bone structure and strength QTL 405.660.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)10135225947Rat
7387235Uae41Urinary albumin excretion QTL 415.260.1874urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)10129497586Rat
2298544Neuinf9Neuroinflammation QTL 94.6nervous system integrity trait (VT:0010566)spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)10580199062146030Rat
10401803Kidm50Kidney mass QTL 50kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1041834445418344Rat
737820Alc9Alcohol consumption QTL 92.2consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)10514402719233348Rat
2313081Bss64Bone structure and strength QTL 641.30.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)10538701450387014Rat
631828Alc5Alcohol consumption QTL 52.4consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)10514402717245662Rat
634327Hc4Hypercalciuria QTL 42.4urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)10138328221Rat
2313095Bss62Bone structure and strength QTL 621.50.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)10538701450387014Rat
1576304Schws7Schwannoma susceptibility QTL 70.0115nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)10476552719816042Rat
7411611Foco17Food consumption QTL 1718.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)10142315980Rat
2301967Cm73Cardiac mass QTL 734.55heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)101448701189062041Rat
2303118Mamtr7Mammary tumor resistance QTL 70.003mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)109658275104670812Rat
631268Cia21Collagen induced arthritis QTL 213.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1014487011104060283Rat
9590268Scort13Serum corticosterone level QTL 133.260.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)101147401056474010Rat
2313104Bss61Bone structure and strength QTL 610.90.0001tibia area (VT:1000281)tibia midshaft cross-sectional area (CMO:0001717)10538701450387014Rat
61427Cia16Collagen induced arthritis QTL 163.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10635789696121100Rat
9590310Scort19Serum corticosterone level QTL 196.30.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)101147401056474010Rat
2316949Gluco60Glucose level QTL 603.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1014487011107057807Rat


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
7 9 19 38 37 40 14 25 14 4 101 58 24 15 40 26

Sequence


Ensembl Acc Id: ENSRNOT00000005509   ⟹   ENSRNOP00000005509
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1017,107,123 - 17,112,289 (-)Ensembl
Rnor_6.0 Ensembl1017,407,979 - 17,415,251 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000101715   ⟹   ENSRNOP00000086575
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1017,107,815 - 17,112,245 (-)Ensembl
RefSeq Acc Id: NM_001191091   ⟹   NP_001178020
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81017,611,472 - 17,616,566 (-)NCBI
mRatBN7.21017,107,187 - 17,112,282 (-)NCBI
Rnor_6.01017,399,355 - 17,406,915 (-)NCBI
Rnor_5.01017,291,887 - 17,293,606 (-)NCBI
Celera1016,753,816 - 16,758,829 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039086853   ⟹   XP_038942781
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81017,611,408 - 17,616,330 (-)NCBI
mRatBN7.21017,107,123 - 17,112,030 (-)NCBI
RefSeq Acc Id: XM_039086855   ⟹   XP_038942783
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81017,611,408 - 17,615,160 (-)NCBI
mRatBN7.21017,107,123 - 17,110,873 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001178020 (Get FASTA)   NCBI Sequence Viewer  
  XP_038942781 (Get FASTA)   NCBI Sequence Viewer  
  XP_038942783 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000005509.3
  ENSRNOP00000086575.1
RefSeq Acc Id: NP_001178020   ⟸   NM_001191091
- UniProtKB: D3ZFC8 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000005509   ⟸   ENSRNOT00000005509
RefSeq Acc Id: XP_038942781   ⟸   XM_039086853
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038942783   ⟸   XM_039086855
- Peptide Label: isoform X2
Ensembl Acc Id: ENSRNOP00000086575   ⟸   ENSRNOT00000101715
Protein Domains
EF-hand

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZFC8-F1-model_v2 AlphaFold D3ZFC8 1-216 view protein structure

Transcriptome

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

Promoters
RGD ID:13697091
Promoter ID:EPDNEW_R7616
Type:single initiation site
Name:Efcab9_1
Description:EF-hand calcium binding domain 9
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_6.01017,415,288 - 17,415,348EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1588807 AgrOrtholog
BioCyc Gene G2FUF-25625 BioCyc
Ensembl Genes ENSRNOG00000004142 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000005509.5 UniProtKB/TrEMBL
  ENSRNOT00000101715.1 UniProtKB/TrEMBL
Gene3D-CATH EF-hand UniProtKB/TrEMBL
InterPro EF-hand-like_dom UniProtKB/TrEMBL
  EF_hand_Ca-bd UniProtKB/TrEMBL
  EFCAB9 UniProtKB/TrEMBL
KEGG Report rno:688481 UniProtKB/TrEMBL
NCBI Gene 688481 ENTREZGENE
PANTHER EF-HAND CALCIUM-BINDING DOMAIN-CONTAINING PROTEIN 9 UniProtKB/TrEMBL
  PTHR47065 UniProtKB/TrEMBL
PhenoGen Efcab9 PhenoGen
PROSITE EF_HAND_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000004142 RatGTEx
Superfamily-SCOP SSF47473 UniProtKB/TrEMBL
UniProt A0A8I6A6I3_RAT UniProtKB/TrEMBL
  D3ZFC8 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-07-21 Efcab9  EF-hand calcium binding domain 9  LOC100911628  EF-hand calcium-binding domain-containing protein 9-like  Data merged from RGD:6491503 737654 APPROVED
2013-05-24 Efcab9  EF-hand calcium binding domain 9  LOC682929  hypothetical protein LOC682929  Data merged from RGD:1592815 1643240 APPROVED
2012-07-05 LOC100911628  EF-hand calcium-binding domain-containing protein 9-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2008-10-23 Efcab9  EF-hand calcium binding domain 9  LOC688481  hypothetical protein LOC688481  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-20 LOC682929  hypothetical protein LOC682929      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-19 LOC688481  hypothetical protein LOC688481      Symbol and Name status set to provisional 70820 PROVISIONAL