RetrogeneDB ID: retro_vvin_87

Retrocopy location

• Organism: Grape (Vitis vinifera)
• Coordinates: 14:13007258..13007867(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: VIT_05s0020g04620
• Aliases: None
• Description: None

Sequence

>retro_vvin_87
ATGGCCACCAACCTGCCTGAAGGTTACGCCGGTGACTTCTTGGAGCAAAATTCTCGCAATTCTCTCCTATTCTGGACACG
ACCCTTATATTCTAGTAATGGGTTCTACCATGGCGCTGCGGCTGAGTTTAGGCGATGGCTCAATCCACTTCGTCGGAGGC
GGCTTCCAAGGGTCGGTCTTTCCGTTAGGCCTGAGCTTGGAGAGCGGGATTACAACGACATAGGCGGCGTCGGGAAGTGA
CGAGAGGTTTTCAAGGTGACGTTGATGCCAGAATTTTTTCAGGGAGGAGCGAGAGAGAGTCGATGCATTTGGATGGTTCA
TTTTCGGCATATGGACATGCACAGTCTCTCTCATTCCGACTCGTCGTTCCTCAGATCCACCAAGCTTTTCACGGCCAGCC
AACTCTTGTCTGAATTATTGCTGCACTACACCTGCCTGCTACTCGCCCAAGGATGCGTGTTTGGTGTGGACAAGTCACTG
ACCCTCACAGCGTTGTTGGGATGTTACGTAGAGAGAGGATAGCAGGAAGAGTGAAAGCTTTGCAAGAACTTGTCCTGCCT
CAACAAGACGTGTAAGGCTGCAGTGCTTGATGAATTTGTGGATTGTGTG

Alignment

ORF - retro_vvin_87 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.53 %
• Parental protein coverage: 64.86 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MATNPPEGYADDFLEQ-ILAIPSYPGHDPNMVGTGSTMVLQLSSGDGSGHVAGGGFQGPVFPLGLSLESG
          MATN.PEGYA.DFLEQ.ILAI.SY.GHDP.....GSTM.L.LS.GDGS.H..GGGFQG.VFPLGLSLESG
Retrocopy MATNLPEGYAGDFLEQ>ILAILSYSGHDPYILVMGSTMALRLSLGDGSIHFVGGGFQGSVFPLGLSLESG

Parental  IPATQVAPGSGERF-RDDVDARGSSGRSERESVHLDGLFPAYGHVQSLSVRPAVPQVHQAFHGQPTPVPI
          I..T..A.GS.ERF...DVDAR..SGRSERES.HLDG.F.AYGH.QSLS.R..VPQ.HQAFHGQPT.V.I
Retrocopy ITTT*AASGSDERF>QGDVDARIFSGRSERESMHLDGSFSAYGHAQSLSFRLVVPQIHQAFHGQPTLV*I

Parental  TAAPHPPAIRPRVRARRGQATDPHSIAERLRRERIAERMKALQELV-PSS-NKTDRAAMLDEIVDYV
          .AA.H.PA.RPR.R...GQ.TDPHS....LRRERIA.R.KALQELV.P.S.NKT..AA.LDE.VD.V
Retrocopy IAALHLPATRPRMRVWCGQVTDPHSVVGMLRRERIAGRVKALQELV<PAS<NKTCKAAVLDEFVDCV

Legend:

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

Expression

RNA-Seq

Vitis vinifera was not studied using RNA-Seq expression data.

ChIP-Seq

Vitis vinifera was not studied using ChIP-Seq data.

EST

Vitis vinifera was not studied using EST data.

TSS

Vitis vinifera was not studied using FANTOM5 data.

Lab

retro_vvin_87 was not experimentally validated.

Homology

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.

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Vitis vinifera	VIT_05s0020g04620	2 retrocopies	retro_vvin_134, retro_vvin_87 ,