Efcab3 Gene Detail

Summary

• Symbol
  Efcab3
• Name
  EF-hand calcium binding domain 3
• Synonyms
  4921510J17Rik

• Feature Type
  protein coding gene
• IDs
  MGI:1918144
  NCBI Gene: 70894
• Alliance
  gene page
• Transcription Start Sites
  3 TSS

Location &
Maps

• Sequence Map
  Chr11:104954418-105008363 bp, + strand

  From Ensembl annotation of GRCm39
  

• View this region in JBrowse
  
  

• Genome Browsers
  Ensembl | UCSC | NCBI

• Genetic Map
  Chromosome 11, 68.61 cM, cytoband E1
• Mapping Data
  2 experiments

Strain
Comparison

• SNPs within 2kb
  1823 from dbSNP Build 142
• Strain Annotations
  18

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_1918144	protein coding gene	Chr11:104899811-105008363 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0019280	protein coding gene	Chr11:108126610-108326806 (+)
A/J	MGP_AJ_G0019248	protein coding gene	Chr11:103502531-103695825 (+)
AKR/J	MGP_AKRJ_G0019217	protein coding gene	Chr11:106658381-106845839 (+)
BALB/cJ	MGP_BALBcJ_G0019222	protein coding gene	Chr11:103941423-104135849 (+)
C3H/HeJ	MGP_C3HHeJ_G0019031	protein coding gene	Chr11:107069575-107129295 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0019672	protein coding gene	Chr11:111624394-111684594 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0017297	protein coding gene	Chr11:100867476-101055177 (+)
CAST/EiJ	MGP_CASTEiJ_G0018585	protein coding gene	Chr11:107964539-108174641 (+)
CBA/J	MGP_CBAJ_G0019000	protein coding gene	Chr11:116245943-116317709 (+)
DBA/2J	MGP_DBA2J_G0019112	protein coding gene	Chr11:103010667-103204866 (+)
FVB/NJ	MGP_FVBNJ_G0019103	protein coding gene	Chr11:102662252-102715074 (+)
LP/J	MGP_LPJ_G0019182	protein coding gene	Chr11:108585814-108794282 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0019133	protein coding gene	Chr11:115542597-115602150 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0019709	protein coding gene	Chr11:107255218-107317181 (+)
PWK/PhJ	MGP_PWKPhJ_G0018350	protein coding gene	Chr11:104096983-104293085 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0018140	protein coding gene	Chr11:106870954-107066130 (+)
WSB/EiJ	MGP_WSBEiJ_G0018635	protein coding gene	Chr11:107083747-107284362 (+)

Homology

• Human Ortholog
  EFCAB3, EF-hand calcium binding domain 3

• Vertebrate Orthologs
  2

Vertebrate Orthology Source

Alliance of Genome Resources

• Human Ortholog
  EFCAB3, EF-hand calcium binding domain 3
  
• Links
  HGNC:26379

  NCBI Gene ID: 146779

  neXtProt AC: NX_Q8N7B9

  UniProt: Q8N7B9

  
  
• Chr Location
  17q23.2; chr17:62370218-62416479 (+)  GRCh38.p7

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• Alliance of Genome Resources
  Efcab3 stringent orthology
  1 human;1 mouse;1 rat
  
• HCOP
  vertebrate homology predictions: EFCAB3
• Gene Tree
  Efcab3
  

Mutations,
Alleles, and
Phenotypes

• Phenotype Summary
  5 phenotypes from 2 alleles in 2 genetic backgrounds
  5 phenotype references
  

• All Mutations and Alleles
  5
• Endonuclease-mediated
  1
• Targeted
  4
• Incidental Mutations
  Mutagenetix , APF , CvDC
• Find Mice (IMSR)
  12 strains or lines available
• Comparison Matrix
  Gene Expression + Phenotype

Male mice homozygous for a mutation are viable and show normal fertility.

Gene Ontology
(GO)
Classifications

• All GO Annotations
  2
• GO References
  2

Expression

• Assay Results
  672
• cDNA Data
  10

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

• Other Mouse Links
  Allen Institute
  GEO
  Expression Atlas

Interactions

• Efcab3 interacts with 31 markers (Mir1a-1, Mir1a-2, Mir133b, ...) View All

Sequences &
Gene Models

• All Sequences
  51
• RefSeq
  16
• UniProt
  3
• CCDS
  CCDS36355.1

• Ensembl
  ENSMUSG00000020690 (Evidence)
• NCBI Gene
  70894

Representative Sequences			Length	Strain/Species
genomic	ENSMUSG00000020690	Ensembl Gene Model | MGI Sequence Detail	53946	C57BL/6J

Protein
Information

• UniProt
  3 Sequences
• Protein Ontology
  PR:000029437 EF-hand calcium-binding domain-containing protein 3
  (term hierarchy)
• InterPro Domains
  IPR018247 EF-Hand 1, calcium-binding site
  IPR002048 EF-hand domain
  IPR011992 EF-hand domain pair
  IPR043520 SPT21/EFCAB3

Molecular
Reagents

• All nucleic 10

  cDNA 10

  
  

  Microarray probesets 3

References

• Summaries
  All 27

  Gene Ontology 2

  Phenotypes 5
• Earliest
  J:65060 Kawai J, et al., Functional annotation of a full-length mouse cDNA collection. Nature. 2001 Feb 8;409(6821):685-90
• Latest
  J:267883 Lilue J, et al., Sixteen diverse laboratory mouse reference genomes define strain-specific haplotypes and novel functional loci. Nat Genet. 2018 Nov;50(11):1574-1583

TSS for Efcab3:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr105420	Chr11:104982686-104982710 (+)	28,280 bp
Tssr105421	Chr11:104983020-104983027 (+)	28,606 bp
Tssr105422	Chr11:104983039-104983070 (+)	28,637 bp