RetrogeneDB ID: retro_vvin_123

Retrocopy location

• Organism: Grape (Vitis vinifera)
• Coordinates: 18_random:2271178..2271530(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: VIT_19s0014g03450
• Aliases: None
• Description: None

Sequence

>retro_vvin_123
GGTGGATATTTGCTATGGAAAAGAAAAATAGATAAAAGCAACAACAACTCGTTTCTCTGCACCAGGGCTTGGGATGGATT
GTGGTTCAACCCTAGGGGATATTGTGCAAACTTTCTTTCAGAGGTTGTTCATTTCACCGCAAATGGCTGGGGAGGCAATG
AAGGGGAGCTTTTTGATTGTGGAGGTCATGACTTCTAAAGGTTTTAAGGTTTTGGCCACCTCCTAGAGCACCACGACATG
ATACAGTACAACTTGGAACCTGAGAGCGTCTTCTTGCTTTCTGTGAAGCTTATAAAGAAGCTCCCCAGTAGGTTCATTCA
CCAGACCAGTCGTGGGTTCCACTCCTGGATAT

Alignment

ORF - retro_vvin_123 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.61 %
• Parental protein coverage: 52.17 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GGYVA-GKEKWVKAAAARLSAPGLGMDCGSTPGDIMQTFFQGLFLSHQMVGEAIKGGFLIAEVMASKGFK
          GGY...GKEK..KA...R.SAPGLGMDCGST.GDI.QTFFQ.LF.S.QM.GEA.KG.FLI.EVM.SKGFK
Retrocopy GGYLL>GKEK*IKATTTRFSAPGLGMDCGSTLGDIVQTFFQRLFISPQMAGEAMKGSFLIVEVMTSKGFK

Parental  V-QPPPRVPRHDTVQAVQLGTRECLLAFCEAVQ-RSSPVGSFTRPVVGSTPGY
          V..PPPR.PRHDTVQ...LGT.E.LLAFCEA...RSSPVGSFTRPVVGSTPGY
Retrocopy V>WPPPRAPRHDTVQ---LGT*ERLLAFCEAYK<RSSPVGSFTRPVVGSTPGY

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_123 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 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Vitis vinifera	VIT_19s0014g03450	1 retrocopy	retro_vvin_123 ,