RetrogeneDB ID: retro_vvin_174

Retrocopy location

• Organism: Grape (Vitis vinifera)
• Coordinates: 8:8668914..8669348(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: VIT_18s0001g12300
• Aliases: None
• Description: None

Sequence

>retro_vvin_174
ATGGAAAACAATCAACATTCAGAGCTTTAGCATGGTCCAGAAAGGTTCTTTCATACCATAAAAGCAATTTCTCCAACTTC
TCAGGAAAGGTTATGTCGGGCTATGAATTCCATCGACCAGAGTGATAACCTGGGACCTTACAAACGTAAAATTAAGTTAC
GCTTTGCAAAACTGACTGAGGGTAGGACTTCATTAGCAGAACCAGATTTCGTGAGAGATGAAGTAGATATTGGTCCGGAG
GGTATGAACAAAGCAGTAGAAATGAAGTCACTGTTATTTCCAGGTAGAGCATGAGGAGAGGAAAGAATAATATGAAAGGT
TCCTATCCAACAGGCATTCTCAAGGTTCCCCAGCTTTCTCATGGGCTATCACATCTTAACAATACGTGTACTTCCAGCCA
AAATTATTCAGCGTGTCACTGCATTTTCACAGAG

Alignment

ORF - retro_vvin_174 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.4 %
• Parental protein coverage: 52.16 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MENYQHSELQHGPERLFSTRKAISPTSQERLCRAMNSIDLCDNLEPYECKIKLRFAKRTEGRTSSAEPDF
          MEN.QHSEL.HGPER.F.T.KAISPTSQERLCRAMNSID..DNL.PY..KIKLRFAK.TEGRTS.AEPDF
Retrocopy MENNQHSEL*HGPERFFHTIKAISPTSQERLCRAMNSIDQSDNLGPYKRKIKLRFAKLTEGRTSLAEPDF

Parental  VGDEVDIGP-GGPEQSSRNEVTVISKQSIRRRKNDMKGSHPKGILKVPQLSRGLPHLSNTCTSSQSYSQS
          V.DEVDIGP.GG.EQSSRNEVTVIS..S.RR.KN.MKGS.P.GILKVPQLS.GL.HL.NTCTSSQ.YS..
Retrocopy VRDEVDIGP<GGYEQSSRNEVTVISR*SMRRGKNNMKGSYPTGILKVPQLSHGLSHLNNTCTSSQNYSAC

Parental  AISFSQ
          ...F..
Retrocopy HCIFTE

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_174 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Vitis vinifera	VIT_18s0001g12300	3 retrocopies	retro_vvin_147, retro_vvin_174 , retro_vvin_61,