RetrogeneDB ID:

retro_vvin_146

Retrocopy
location
Organism:Grape (Vitis vinifera)
Coordinates:4:14879794..14880728(+)
Located in intron of:VIT_04s0043g00750
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:VIT_02s0087g00650
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_vvin_146
TCGCTTATCCCATTGAATTCTGCACTTTCAAAATTTTCATATTCTCTTACTTAGGAACAGTTATCTACTTCTTCTGATAC
AATGTCCTTCTTGTCTGCAAAGTCAACTCTGTCATCATACTTTGCACCTATACATTCGAATATAATAAACATGTCTTCAT
TTCCTTCATCTTATCAAGACGTTAGTACCACTTAAGCTCCAATTACTAGTAAAATAGTTTCTGATCTGGTATCGGTGCCT
ACTATCCATCCCCTGCATCATTCTACATCCACAATTGGGGGTTCCACCTCTAGCCTCCTTTTGACTCTACCACCAACTTT
ATTAAGTCCTGATCAATTAGCACAATCCATGCCATCCATGCTTTCTTCCTCACAGAAAGTATACCTTGATCAGATGAATA
AGGTTGCTCCAACATCAACATCTCCTAATACTCTGAGCACAATGTCTACTCCAGTACTTCAAGCACCATTGTTGCCATTG
CCAGCCTCTACTCAACAATCTTAGAAGTCTACTATGCAGTTCACTGAAGAATTTTATTTTATAGCGATGAATGAAATGTT
TAAAAGGGATGGAGTTTGGGGTTATCTTAGAAAGGCAAAGCAAAAGGATGAAAAGGAAGGGATGAAAGACAATGCACTTG
GTCAAGGCTTGGGTGACAGATAGGGTCATAGACTAGTACCCAAATCAAATGCTAAACACGCTTATAATAAGGATGAGTTG
TTTGACAAGATTTCTTGTAATTCTCATGCCCGCGGGACTAGGAATGGACAGAACAGGTTCTTTATGCGAATGAAGATGGA
TACTGAGACTTTTGGAAATTTTCAACAGAGACCTCATCTAGGTTAAGGTGGCTACAAAGCTGGGCGTGGGGAGAACTACA
GTGGCTCATATAATTGGAAAAGAGGATTTGCCAGTGGATGGAATTGGGGGTGGT

ORF - retro_vvin_146 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 83.65 %
Parental protein coverage: 60.74 %
Number of stop codons detected: 5
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalSLIPLNSALSKFSSSLTQEQFSTSSDTMSFLSAKATLPSYSAPVNSNIINMSSFPSSYQDVNTTEAPITG
SLIPLNSALSKFS.SLT.EQ.STSSDTMSFLSAK.TL.SY.AP..SNIINMSSFPSSYQDV.TT.APIT.
RetrocopySLIPLNSALSKFSYSLT*EQLSTSSDTMSFLSAKSTLSSYFAPIHSNIINMSSFPSSYQDVSTT*APITS
ParentalKIVSDLVSVPPIHPLHHSASTIGGSTSGLLLTPPPTLLTPDQLAQPMSSMLSSSQKVYPDQRDKVAPTST
KIVSDLVSVP.IHPLHHS.STIGGSTS.LLLT.PPTLL.PDQLAQ.M.SMLSSSQKVY.DQ..KVAPTST
RetrocopyKIVSDLVSVPTIHPLHHSTSTIGGSTSSLLLTLPPTLLSPDQLAQSMPSMLSSSQKVYLDQMNKVAPTST
ParentalSPNTLSTMSTPALQAPLLPLPASAQQSQKSAVQFTEEFDFIAMNERFKKDEVWGYLGKAKQRDEKEGMED
SPNTLSTMSTP.LQAPLLPLPAS.QQS.KS..QFTEEF.FIAMNE.FK.D.VWGYL.KAKQ.DEKEGM.D
RetrocopySPNTLSTMSTPVLQAPLLPLPASTQQS*KSTMQFTEEFYFIAMNEMFKRDGVWGYLRKAKQKDEKEGMKD
ParentalNALGQGLGDREGYGQVPKSDAKPAYNKDEFFDTISCNSHARGTRNGQNRFSARMKMDTETFGNFQQRPHL
NALGQGLGDR.G...VPKS.AK.AYNKDE.FD.ISCNSHARGTRNGQNRF..RMKMDTETFGNFQQRPHL
RetrocopyNALGQGLGDR*GHRLVPKSNAKHAYNKDELFDKISCNSHARGTRNGQNRFFMRMKMDTETFGNFQQRPHL
ParentalGYGGYRAGRGENYRGSYNRGRGFAYG-GRGGG
G.GGY.AGRGENY.GSYN..RGFA.G.G.GGG
RetrocopyG*GGYKAGRGENYSGSYNWKRGFASG>GIGGG

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_146 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 1 parental gene, and 1 retrocopy.

Species Parental gene accession Retrocopies number
Vitis vinifera VIT_02s0087g00650 1 retrocopy
retro_vvin_146 ,



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