RetrogeneDB ID: retro_vvin_117

Retrocopy location

• Organism: Grape (Vitis vinifera)
• Coordinates: 18:11791396..11791599(-)
• Located in intron of: VIT_18s0001g13810

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: VIT_04s0023g01310
• Aliases: None
• Description: None

Sequence

>retro_vvin_117
ATGGCATTTTGTACACTAGCCTCCAATAAATGCCAATCAGAGGGTTTGAACCAGGTCAAGAACTACTGCCATCACCTGCA
AAGGCCAGTGTACACACGAGAGCAGGATGGTCGCTGCTCCATTTCTCACTTGAGAGCCCTCCTATTTTCCTTAAAACATC
AACAGGTAAGGTTTCAAGAACTCTCACAAGAACAAATTCCTCA

Alignment

ORF - retro_vvin_117 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.12 %
• Parental protein coverage: 66.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAFCTLASNKYQSIGL-EPGQELLPSSAKANAHTRVGWLLPHFSLASPPVFLKTSTVKKGQVAAATGDN
          MAFCTLASNK.QS.GL.EPGQELLPS.AKA..HTR.GW.L.HFSL.SPP.FLKTST.K.......T...
Retrocopy MAFCTLASNKCQSEGL<EPGQELLPSPAKASVHTRAGWSLLHFSLESPPIFLKTSTGKVSRTLTRTNSS

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_117 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_04s0023g01310	1 retrocopy	retro_vvin_117 ,