Ervfrd-1 (endogenous retrovirus group FRD member 1, envelope) - Rat Genome Database

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Gene: Ervfrd-1 (endogenous retrovirus group FRD member 1, envelope) Rattus norvegicus
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Symbol: Ervfrd-1
Name: endogenous retrovirus group FRD member 1, envelope
RGD ID: 1563240
Description: Predicted to be involved in syncytium formation by plasma membrane fusion. Predicted to act upstream of or within labyrinthine layer development and myoblast fusion. Predicted to be located in membrane. Orthologous to human ERVFRD-1 (endogenous retrovirus group FRD member 1, envelope); INTERACTS WITH 3,7-dihydropurine-6-thione; 6-propyl-2-thiouracil; bisphenol A.
Type: protein-coding
RefSeq Status: REVIEWED
Previously known as: endogenous retrovirus group FRD member 1; envelope glycoprotein syncytin-A; Gm52; Syna; syncytin a
RGD Orthologs
Human
Mouse
Bonobo
Dog
Green Monkey
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81227,787,680 - 27,794,732 (+)NCBIGRCr8
mRatBN7.21222,151,211 - 22,158,264 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1222,151,211 - 22,158,264 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1223,294,443 - 23,301,347 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01223,905,524 - 23,912,428 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01222,972,115 - 22,979,027 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01225,161,130 - 25,168,182 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1225,161,130 - 25,168,182 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01227,161,524 - 27,168,576 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41223,220,471 - 23,222,327 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1223,915,041 - 23,922,023 (+)NCBICelera
Cytogenetic Map12q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
membrane  (IEA)

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. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:14557543   PMID:15644441   PMID:19564597   PMID:23492904   PMID:27589388  


Genomics

Comparative Map Data
Ervfrd-1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81227,787,680 - 27,794,732 (+)NCBIGRCr8
mRatBN7.21222,151,211 - 22,158,264 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1222,151,211 - 22,158,264 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1223,294,443 - 23,301,347 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01223,905,524 - 23,912,428 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01222,972,115 - 22,979,027 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01225,161,130 - 25,168,182 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1225,161,130 - 25,168,182 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01227,161,524 - 27,168,576 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41223,220,471 - 23,222,327 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1223,915,041 - 23,922,023 (+)NCBICelera
Cytogenetic Map12q12NCBI
ERVFRD-1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38611,102,489 - 11,111,725 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl611,102,324 - 11,111,845 (-)EnsemblGRCh38hg38GRCh38
GRCh37611,102,722 - 11,111,958 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36611,210,708 - 11,219,945 (-)NCBINCBI36Build 36hg18NCBI36
Celera612,331,189 - 12,340,538 (-)NCBICelera
Cytogenetic Map6p24.2NCBI
HuRef611,034,168 - 11,043,517 (-)NCBIHuRef
CHM1_1611,104,822 - 11,114,171 (-)NCBICHM1_1
T2T-CHM13v2.0610,970,408 - 10,979,644 (-)NCBIT2T-CHM13v2.0
Syna
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm395134,586,108 - 134,605,891 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl5134,587,000 - 134,589,025 (-)EnsemblGRCm39 Ensembl
GRCm385134,557,254 - 134,577,038 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl5134,558,146 - 134,560,171 (-)EnsemblGRCm38mm10GRCm38
MGSCv375135,034,110 - 135,035,963 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv365134,842,867 - 134,844,720 (-)NCBIMGSCv36mm8
Celera5131,565,945 - 131,567,798 (-)NCBICelera
Cytogenetic Map5G2NCBI
cM Map574.67NCBI
ERVFRD-1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2525,749,397 - 25,758,717 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1621,739,431 - 21,748,751 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0610,940,832 - 10,950,152 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1611,216,488 - 11,225,808 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl611,217,693 - 11,219,309 (-)Ensemblpanpan1.1panPan2
LOC119881605
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ROS_Cfam_1.0918,735,394 - 18,791,155 (-)NCBIROS_Cfam_1.0
ERVFRD-1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11761,033,479 - 61,042,781 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1761,039,949 - 61,041,559 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604411,133,315 - 11,142,617 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0

Variants

.
Variants in Ervfrd-1
62 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:127
Count of miRNA genes:97
Interacting mature miRNAs:114
Transcripts:ENSRNOT00000074788
Prediction methods:Miranda, 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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
10755457Coatc14Coat color QTL 140.01759coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)12122591684Rat
6893681Bw109Body weight QTL 1092.30.004body mass (VT:0001259)body weight (CMO:0000012)12123297788Rat
1581516Cm56Cardiac mass QTL 564.20.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)12129333307Rat
1598855Bp294Blood pressure QTL 2943.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)12134851688Rat
7411660Foco28Food consumption QTL 2810.90.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12142110980Rat
9590086Insglur6Insulin/glucose ratio QTL 618.970.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)12142110980Rat
8694179Bw150Body weight QTL 1502.90.001body mass (VT:0001259)body weight gain (CMO:0000420)12142110980Rat
7411586Foco5Food consumption QTL 55.40.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12142110980Rat
7411595Foco9Food consumption QTL 940.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12142110980Rat
7411545Bw128Body weight QTL 1285.20.001body mass (VT:0001259)body weight gain (CMO:0000420)12142110980Rat
9590147Scort7Serum corticosterone level QTL 713.610.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)12142110980Rat
2303575Insul14Insulin level QTL 144blood insulin amount (VT:0001560)blood insulin level (CMO:0000349)12142450532Rat
737979Pia22Pristane induced arthritis QTL 2253.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)12144465750Rat
634351Apr5Acute phase response QTL 56.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)12144503507Rat
2302042Pia38Pristane induced arthritis QTL 383.50.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)12144503507Rat
634350Apr4Acute phase response QTL 46orosomucoid 1 amount (VT:0010541)plasma orosomucoid 1 level (CMO:0001467)12117200546172005Rat
8552918Pigfal7Plasma insulin-like growth factor 1 level QTL 7blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)12556449546669029Rat
7411547Bw129Body weight QTL 1290.001body mass (VT:0001259)body weight gain (CMO:0000420)6556449546669029Rat
7411597Foco10Food consumption QTL 100.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12556449546669029Rat
7411641Foco19Food consumption QTL 1927.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12556449546669029Rat
8552964Pigfal17Plasma insulin-like growth factor 1 level QTL 173.5blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)12556449546669029Rat
7411588Foco6Food consumption QTL 60.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12556449546669029Rat
8552912Pigfal6Plasma insulin-like growth factor 1 level QTL 65blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)12556449846669029Rat
10059594Kidm46Kidney mass QTL 463.790.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)12610757946669029Rat
1302792Scl21Serum cholesterol level QTL 213.80.0011blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)12719673046669029Rat
2293086Iddm30Insulin dependent diabetes mellitus QTL 303.82blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)12844949028302290Rat
61331Eau2Experimental allergic uveoretinitis QTL 20.0005uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)12852542328064601Rat
1300157Rf21Renal function QTL 214.4renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)12931821632103380Rat
1549829Scl48Serum cholesterol level QTL 485blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)12960327746669029Rat
2293699Bss49Bone structure and strength QTL 495.610.0001lumbar vertebra size trait (VT:0010518)lumbar vertebra trabecular cross-sectional area (CMO:0001692)121047413746669029Rat
2300186Bmd59Bone mineral density QTL 597.10.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)121047413746669029Rat
1331786Kidm11Kidney mass QTL 113.571kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)121107382524234895Rat
1331755Bp219Blood pressure QTL 2193.041arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)121107382528064557Rat
1331761Bp218Blood pressure QTL 2182.973arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)121107382545055165Rat
61404Bw120Body weight QTL 1205.1body mass (VT:0001259)body mass index (BMI) (CMO:0000105)121235161946669029Rat
1641928Alcrsp5Alcohol response QTL 5response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)121281238546669029Rat
2303569Gluco44Glucose level QTL 442blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)121281238546669029Rat
1549902Bp269Blood pressure QTL 269arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)121318273646669029Rat
1549912Bp268Blood pressure QTL 268arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)101318273646669029Rat
2302060Pia37Pristane induced arthritis QTL 376.10.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)121319815746669029Rat
61416Pia4Pristane induced arthritis QTL 48.4joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)121363552330827399Rat
61421Cia12Collagen induced arthritis QTL 124.6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)121363552335682913Rat
631543Bp83Blood pressure QTL 835.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)121555082638478808Rat
2293684Bmd26Bone mineral density QTL 264.40.0002femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)121587265332974238Rat
631560Apr1Acute phase response QTL 16.1orosomucoid 1 amount (VT:0010541)plasma orosomucoid 1 level (CMO:0001467)121914436246669029Rat
2306789Ean6Experimental allergic neuritis QTL 64.9nervous system integrity trait (VT:0010566)experimental autoimmune neuritis severity score (CMO:0001528)121961087024139202Rat
737822Alc10Alcohol consumption QTL 102.2consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)121961087040218516Rat
5684888Pia42Pristane induced arthritis QTL 42joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)121961087042828880Rat
61324Eae5Experimental allergic encephalomyelitis QTL 514nervous system integrity trait (VT:0010566)percentage of study population developing relapsing-remitting experimental autoimmune encephalomyelitis during a period of time (CMO:0001402)121961087046669029Rat
1298081Cia25Collagen induced arthritis QTL 254.7joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)121961088935682913Rat
70213Niddm27Non-insulin dependent diabetes mellitus QTL 273.72blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)121983578938193007Rat
631521Pia12Pristane induced arthritis QTL 128.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)122025941723672083Rat
7411643Foco20Food consumption QTL 200.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)122032881946669029Rat


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium
Low 1
Below cutoff 3 9 7 12 7 1 1 12 15 7 9 1

Sequence


RefSeq Acc Id: ENSRNOT00000074788   ⟹   ENSRNOP00000067387
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1222,151,211 - 22,158,264 (+)Ensembl
Rnor_6.0 Ensembl1225,161,130 - 25,168,182 (+)Ensembl
RefSeq Acc Id: NM_001014771   ⟹   NP_001014771
RefSeq Status: REVIEWED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81227,787,680 - 27,794,732 (+)NCBI
mRatBN7.21222,151,211 - 22,158,264 (+)NCBI
Rnor_6.01225,161,130 - 25,168,182 (+)NCBI
Rnor_5.01227,161,524 - 27,168,576 (+)NCBI
RGSC_v3.41223,220,471 - 23,222,327 (+)RGD
Celera1223,915,041 - 23,922,023 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001014771 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAW62447 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000067387
  ENSRNOP00000067387.1
RefSeq Acc Id: NP_001014771   ⟸   NM_001014771
- Peptide Label: precursor
- UniProtKB: Q5G5D4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000067387   ⟸   ENSRNOT00000074788

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q5G5D4-F1-model_v2 AlphaFold Q5G5D4 1-618 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:1563240 AgrOrtholog
BioCyc Gene G2FUF-19575 BioCyc
Ensembl Genes ENSRNOG00000050672 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000074788 ENTREZGENE
  ENSRNOT00000074788.2 UniProtKB/TrEMBL
Gene3D-CATH 1.10.287.210 UniProtKB/TrEMBL
InterPro TLV/ENV_coat_polyprotein UniProtKB/TrEMBL
KEGG Report rno:288602 UniProtKB/TrEMBL
NCBI Gene 288602 ENTREZGENE
PANTHER ENDOGENOUS RETROVIRUS GROUP S71 MEMBER 1 ENV POLYPROTEIN-RELATED UniProtKB/TrEMBL
  PTHR10424 UniProtKB/TrEMBL
Pfam TLV_coat UniProtKB/TrEMBL
PhenoGen Ervfrd-1 PhenoGen
RatGTEx ENSRNOG00000050672 RatGTEx
Superfamily-SCOP Virus ectodomain UniProtKB/TrEMBL
UniProt Q5G5D4 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2017-04-05 Ervfrd-1  endogenous retrovirus group FRD member 1, envelope  Ervfrd-1  endogenous retrovirus group FRD member 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2016-07-21 Ervfrd-1  endogenous retrovirus group FRD member 1  Syna  syncytin a  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2011-10-21 Syna  syncytin a  Gm52  envelope glycoprotein syncytin-A  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Gm52  envelope glycoprotein syncytin-A   Gm52_predicted  envelope glycoprotein syncytin-A (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-07 Gm52_predicted  envelope glycoprotein syncytin-A (predicted)  Gm52  envelope glycoprotein syncytin-A  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 Gm52  envelope glycoprotein syncytin-A      Symbol and Name status set to provisional 70820 PROVISIONAL