RetrogeneDB ID:

retro_vvin_28

Retrocopy
location
Organism:Grape (Vitis vinifera)
Coordinates:18:5617416..5618736(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:VIT_18s0001g07340
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:VIT_13s0084g00820
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_vvin_28
ATGGATATCTTCACTGCATTTGTCTTCCTCACTCTTGTGGTTTCAACCACCAAAGCTTTTGATCCCTGTGCTTCCCCTTC
TTCGGAATCCAAGGGCTCGGATCTTTCGGTGATCCATGTGTATGGCCAATGCTCTCCCTTCAACCAGCACAAGGCTGGGT
CCTGGGTGAACACCGTCATCAACATGGCCTCAAAAGACCCAGCACGCGTCACCTACTTGTCCAGCCTAGTTGCATCCCCC
AAGGCCACCTCTGTCCCAATTGCGTCTGGGCAACAGGTCCTCAACATTGGCAACTACGTGGTGCGAGTCAAACTGGGCAC
TCCCGGTCAGCTTATGTTCATGGTTCTTGACACCAGCAGAGACGCCGCATGGGTCCCATGCGCCGACTGCGCCGGCTGCT
CCTCCCCCACCTTCTCCCCCAACACTTCTTCCACTTACGCTTCACTCCAATGCTCTGTGCCCCAGTGCACCCAGGTCCGT
GGCCTCTCGTGCCCCACCACGGGTACTGCTGCATGCTTCTTCAACCAAACCTATGGGGGAGATTCCTCCTTCTCCGCCAT
GCTCTCACAGGATTCTCTCGGCTTGGCGGTTGACACTCTTCCCAGCTACTCTTTCGGCTGCGTCAACGCTGTCTCCGGCT
CGACCCTTCCGCCGCAGGGGCTCCTGGGGCTGGGTCGTGGGCCCATGTCGTTGCTCTCACAATCCGGGTCTCTATACTCT
GGTGTCTTCTCCTACTGTTTTCCCAGTTTCAAATCATACTACTTCTCTGGCTCCTTACGCCTCGGACCCCTGGGTCAACC
CAAGAACATCAGAACCACCCCACTCCTCCGAAACCCGCACCGACCCACTCTCTACTACGTCAACCTAACCGGAGTCAGCG
TCGGCCGAGTTTTGGTGCCGGTGGCGCCAGAGCTACTGGCATTTGACCCAAACACCGGCGCCGGTACCATAATTGACTCA
GGTACAGTCATAACTCGGTTCGTGGAACCAGTATACGCGGCCATCAGGGACGAATTCAGGAAGCAGGTGAAAGGACCATT
TGCAACGATAGGGGCATTCGATACGTGTTTCGCAGCAACAAATGAGGACATAGCACCCCCGGTAACGTTCCATTTCACAG
GAATGGACCTGAAGTTGCCGCTGGAGAACACACTGATACACAGCAGCGCAGGGTCGTTGGCATGCTTGGCAATGGCAGCA
GCGCCCAACAACGTCAACTCGGTGCTGAACGTTATAGCGAATCTACAGCAGCAGAATCTTAGGATTATGTTTGATGTCAC
CAACTCTCGTCTGGGAATTGCTCGTGAGCTGTGTAACTAG

ORF - retro_vvin_28 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 56.02 %
Parental protein coverage: 96.11 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalLFLSLALGLTQP--NCETPD---QGSTLQVLHVYSPCSPFRPKEPLSWEESVLQMQAKDKARLQFLSSLV
.FL.L....T.....C..P.....GS.L.V.HVY..CSPF......SW...V..M..KD.AR...LSSLV
RetrocopyVFLTLVVSTTKAFDPCASPSSESKGSDLSVIHVYGQCSPFNQHKAGSWVNTVINMASKDPARVTYLSSLV
ParentalA--RKSVVPIASGRQIVQNPTYIVRAKIGTPAQTMLMAMDTSSDVAWIPCNGCLGCSSTLFNSPASTTYK
A......VPIASG.Q......Y.VR.K.GTP.Q.M.M..DTS.D.AW.PC..C.GCSS..F....S.TY.
RetrocopyASPKATSVPIASGQQVLNIGNYVVRVKLGTPGQLMFMVLDTSRDAAWVPCADCAGCSSPTFSPNTSSTYA
ParentalSLGCQAAQCKQ---VPKPTCGGGVCSFNLTYGG-SSLAANLSQDTITLATDAVPGYSFGCIQKATGGSLP
SL.C...QC.Q......PT.G...C.FN.TYGG.SS..A.LSQD...LA.D..P.YSFGC.....G..LP
RetrocopySLQCSVPQCTQVRGLSCPTTGTAACFFNQTYGGDSSFSAMLSQDSLGLAVDTLPSYSFGCVNAVSGSTLP
ParentalAQGLLGLGRGPLSLLSQTQNLYQSTFSYCLPSFKSLNFSGSLRLGPVGQPKRIKYTPLLKNPRRPSLYFV
.QGLLGLGRGP.SLLSQ...LY...FSYC.PSFKS..FSGSLRLGP.GQPK.I..TPLL.NP.RP.LY.V
RetrocopyPQGLLGLGRGPMSLLSQSGSLYSGVFSYCFPSFKSYYFSGSLRLGPLGQPKNIRTTPLLRNPHRPTLYYV
ParentalNLMAVRVGRRVVDVPPGSFTFNPSTGAGTIFDSGTVFTRLVTPAYIAVRDAFRNRV-GRNLTVTSLGGFD
NL..V.VGR..V.V.P....F.P.TGAGTI.DSGTV.TR.V.P.Y.A.RD.FR..V.G...T........
RetrocopyNLTGVSVGRVLVPVAPELLAFDPNTGAGTIIDSGTVITRFVEPVYAAIRDEFRKQVKGPFATIGAFDTCF
ParentalTCYTVPIAAPTITFMFTGMNVTLPPDNLLIHSTAGSTTCLAMAAAPDNVNSVLNVIANLQQQNHRLLYDV
......IA.P..TF.FTGM...LP..N.LIHS.AGS..CLAMAAAP.NVNSVLNVIANLQQQN.R...DV
RetrocopyAATNEDIAPP-VTFHFTGMDLKLPLENTLIHSSAGSLACLAMAAAPNNVNSVLNVIANLQQQNLRIMFDV
ParentalPNSRLGVARELC
.NSRLG.ARELC
RetrocopyTNSRLGIARELC

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






Vitis vinifera was not studied using RNA-Seq expression data.
Vitis vinifera was not studied using ChIP-Seq data.
Vitis vinifera was not studied using EST data.
Vitis vinifera was not studied using FANTOM5 data.
retro_vvin_28 was not experimentally validated.

Retrocopy orthology:
Vitis vinifera does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

Parental genes homology:
Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species Parental gene accession Retrocopies number
Brassica oleracea Bo8g0836401 retrocopy
Brassica rapa Bra0148191 retrocopy
Medicago truncatula MTR_8g0395401 retrocopy
Populus trichocarpa POPTR_0001s065601 retrocopy
Prunus persica PRUPE_ppa005966mg1 retrocopy
Theobroma cacao TCM_0451111 retrocopy
Vitis vinifera VIT_13s0084g00820 1 retrocopy
retro_vvin_28 ,



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