Efemp1 (EGF containing fibulin extracellular matrix protein 1) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models   new Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Gene: Efemp1 (EGF containing fibulin extracellular matrix protein 1) Ictidomys tridecemlineatus
Analyze
Symbol: Efemp1
Name: EGF containing fibulin extracellular matrix protein 1
RGD ID: 12686414
Description: ENCODES a protein that exhibits calcium ion binding (inferred); epidermal growth factor receptor activity (inferred); epidermal growth factor receptor binding (inferred); INVOLVED IN negative regulation of neuron projection development (ortholog); positive regulation of cell population proliferation (ortholog); positive regulation of cell projection organization (ortholog); ASSOCIATED WITH adenocarcinoma (ortholog); adenoma (ortholog); Animal Mammary Neoplasms (ortholog); FOUND IN basement membrane (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: EGF containing fibulin like extracellular matrix protein 1; EGF-containing fibulin-like extracellular matrix protein 1
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: SpeTri2.0 - Squirrel SpeTri2.0 Assembly
Position:
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440629226,356,792 - 26,411,638 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364912,159,096 - 2,214,677 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049364912,159,654 - 2,214,480 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References
Additional References at PubMed
PMID:22301074  


Genomics

Comparative Map Data
Efemp1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440629226,356,792 - 26,411,638 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364912,159,096 - 2,214,677 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049364912,159,654 - 2,214,480 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
EFEMP1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38255,865,967 - 55,923,782 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl255,865,967 - 55,924,139 (-)EnsemblGRCh38hg38GRCh38
GRCh37256,093,102 - 56,150,917 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36255,946,606 - 56,004,436 (-)NCBINCBI36Build 36hg18NCBI36
Build 34256,004,748 - 56,060,856NCBI
Celera255,933,455 - 55,991,286 (-)NCBICelera
Cytogenetic Map2p16.1NCBI
HuRef255,828,195 - 55,886,081 (-)NCBIHuRef
CHM1_1256,023,033 - 56,081,234 (-)NCBICHM1_1
T2T-CHM13v2.0255,862,877 - 55,920,674 (-)NCBIT2T-CHM13v2.0
Efemp1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391128,803,154 - 28,876,743 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1128,803,204 - 28,876,743 (+)EnsemblGRCm39 Ensembl
GRCm381128,853,154 - 28,926,743 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1128,853,204 - 28,926,743 (+)EnsemblGRCm38mm10GRCm38
MGSCv371128,753,205 - 28,826,743 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361128,767,773 - 28,826,737 (+)NCBIMGSCv36mm8
Celera1131,227,166 - 31,304,265 (+)NCBICelera
Cytogenetic Map11A3.3NCBI
cM Map1116.32NCBI
Efemp1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr814106,811,769 - 106,890,961 (+)NCBIGRCr8
mRatBN7.214102,610,813 - 102,690,027 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl14102,610,908 - 102,690,018 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx14106,946,350 - 107,025,480 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.014108,182,972 - 108,262,217 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.014104,655,396 - 104,734,632 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.014113,202,382 - 113,294,993 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl14113,202,419 - 113,295,014 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.014112,892,387 - 112,902,495 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.014112,961,348 - 112,984,803 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.414109,733,625 - 109,828,630 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.114109,759,971 - 109,854,973 (+)NCBI
Celera14101,510,577 - 101,587,921 (+)NCBICelera
Cytogenetic Map14q22NCBI
Efemp1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542427,181,099 - 27,240,446 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495542427,181,717 - 27,240,067 (+)NCBIChiLan1.0ChiLan1.0
EFEMP1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21270,407,006 - 70,464,773 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12A70,410,928 - 70,468,816 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02A56,017,678 - 56,076,059 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12A57,155,000 - 57,212,500 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2A57,155,000 - 57,212,500 (-)Ensemblpanpan1.1panPan2
EFEMP1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11056,632,801 - 56,694,872 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1056,579,899 - 56,787,187 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1056,589,822 - 56,651,875 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01057,637,641 - 57,699,724 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1057,637,642 - 57,699,051 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11057,338,037 - 57,400,109 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01057,617,689 - 57,679,576 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01057,909,175 - 57,970,591 (-)NCBIUU_Cfam_GSD_1.0
EFEMP1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl385,407,677 - 85,473,252 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1385,407,677 - 85,473,251 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2390,132,118 - 90,197,711 (+)NCBISscrofa10.2Sscrofa10.2susScr3
EFEMP1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11450,989,553 - 51,048,149 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1450,989,795 - 51,048,708 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604560,671,542 - 60,729,463 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Efemp1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248335,654,016 - 5,723,519 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248335,654,805 - 5,722,185 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSSTOT00000029584   ⟹   ENSSTOP00000015099
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
SpeTri2.0 EnsemblNW_0049364912,159,096 - 2,214,677 (-)Ensembl
RefSeq Acc Id: XM_013357223   ⟹   XP_013212677
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
HiC_Itri_2NW_02440629226,356,792 - 26,411,638 (+)NCBI
SpeTri2.0NW_0049364912,159,654 - 2,214,480 (-)NCBI
Sequence:
RefSeq Acc Id: XM_040271030   ⟹   XP_040126964
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
HiC_Itri_2NW_02440629226,356,813 - 26,411,638 (+)NCBI
RefSeq Acc Id: XM_040271031   ⟹   XP_040126965
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
HiC_Itri_2NW_02440629226,359,881 - 26,411,638 (+)NCBI
RefSeq Acc Id: XM_040271032   ⟹   XP_040126966
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
HiC_Itri_2NW_02440629226,356,814 - 26,411,638 (+)NCBI
RefSeq Acc Id: XM_040271033   ⟹   XP_040126967
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
HiC_Itri_2NW_02440629226,357,949 - 26,411,638 (+)NCBI
Protein Sequences
Protein RefSeqs XP_013212677 (Get FASTA)   NCBI Sequence Viewer  
  XP_040126964 (Get FASTA)   NCBI Sequence Viewer  
  XP_040126965 (Get FASTA)   NCBI Sequence Viewer  
  XP_040126966 (Get FASTA)   NCBI Sequence Viewer  
  XP_040126967 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSSTOP00000015099.1
GenBank Protein KAG3267300 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: XP_013212677   ⟸   XM_013357223
- Peptide Label: isoform X2
- UniProtKB: I3MSK4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_040126964   ⟸   XM_040271030
- Peptide Label: isoform X1
RefSeq Acc Id: XP_040126966   ⟸   XM_040271032
- Peptide Label: isoform X4
RefSeq Acc Id: XP_040126967   ⟸   XM_040271033
- Peptide Label: isoform X4
RefSeq Acc Id: XP_040126965   ⟸   XM_040271031
- Peptide Label: isoform X3
RefSeq Acc Id: ENSSTOP00000015099   ⟸   ENSSTOT00000029584
Protein Domains
EGF-like


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSSTOG00000025148 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSSTOT00000029584.2 UniProtKB/TrEMBL
Gene3D-CATH Laminin UniProtKB/TrEMBL
InterPro cEGF UniProtKB/TrEMBL
  EGF-like_Ca-bd_dom UniProtKB/TrEMBL
  EGF-like_dom UniProtKB/TrEMBL
  EGF-type_Asp/Asn_hydroxyl_site UniProtKB/TrEMBL
  EGF_Ca-bd_CS UniProtKB/TrEMBL
  Growth_fac_rcpt_cys_sf UniProtKB/TrEMBL
NCBI Gene Efemp1 ENTREZGENE
PANTHER EGF-CONTAINING FIBULIN-LIKE EXTRACELLULAR MATRIX PROTEIN 1 UniProtKB/TrEMBL
  EGF-LIKE DOMAIN-CONTAINING PROTEIN UniProtKB/TrEMBL
Pfam cEGF UniProtKB/TrEMBL
  EGF_CA UniProtKB/TrEMBL
PROSITE ASX_HYDROXYL UniProtKB/TrEMBL
  EGF_2 UniProtKB/TrEMBL
  EGF_3 UniProtKB/TrEMBL
  EGF_CA UniProtKB/TrEMBL
SMART EGF UniProtKB/TrEMBL
  EGF_CA UniProtKB/TrEMBL
Superfamily-SCOP SSF57184 UniProtKB/TrEMBL
UniProt I3MSK4 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2017-10-17 Efemp1  EGF containing fibulin extracellular matrix protein 1    EGF containing fibulin like extracellular matrix protein 1  Symbol and/or name change 5135510 APPROVED