RetrogeneDB ID: retro_vvin_56

Retrocopy location

• Organism: Grape (Vitis vinifera)
• Coordinates: 11:7216581..7217034(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: VIT_04s0023g00600
• Aliases: None
• Description: None

Sequence

>retro_vvin_56
ACAAACACCTGCTGCAGCCATCCTCTTTACCGTGAATCAGATCTTATTAATGAGAATGCGCTTGGAGTGCGGAATGCTGC
ACAAAGAAAGCTATTGGGTGAACTCGGCATTCCTGCTGAAGAGGCATCTATTGATCAGTTCACTCCACTGGGCTGCATGC
TTTACACGGCACCATCGGATGGCAAGTGGGGAGAGCATGAATTTGATTATCTACTCTTCACTGTCCGAGATACTAATGTG
AATCCAAACCCTGATGAAGTTGCTGATGTTAAGTATATGTCCCGGAATGATCTGAAAGAGCTGTAGAGGAAAACGGATGT
TGGTGAGGAAGGTCTGAAGCTATTCCCTTGGTTCAGACTGGTGGTCGACAACTTCTTCTTCAAGTGGTGGGACCATGTTG
AGAAGGGGACCCTCCTTGAAGCTACAGATATGAAAACCATTCACAAGTTGACT

Alignment

ORF - retro_vvin_56 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.08 %
• Parental protein coverage: 51.54 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TNTCCSHPLYRESELIDENALGVRNAAQRKLLDELGIPAEDAPVDQFTPLGRMLYKAPSDGKWGEHELDY
          TNTCCSHPLYRES.LI.ENALGVRNAAQRKLL.ELGIPAE.A..DQFTPLG.MLY.APSDGKWGEHE.DY
Retrocopy TNTCCSHPLYRESDLINENALGVRNAAQRKLLGELGIPAEEASIDQFTPLGCMLYTAPSDGKWGEHEFDY

Parental  LLFIVRDVNVNPNPDEVADVKYVSRNDLKELLRKADAGEEGLKLSPWFRLVVDNFLFKWWDHVEKGTLLE
          LLF.VRD.NVNPNPDEVADVKY.SRNDLKEL.RK.D.GEEGLKL.PWFRLVVDNF.FKWWDHVEKGTLLE
Retrocopy LLFTVRDTNVNPNPDEVADVKYMSRNDLKEL*RKTDVGEEGLKLFPWFRLVVDNFFFKWWDHVEKGTLLE

Parental  AADMKTIHKLT
          A.DMKTIHKLT
Retrocopy ATDMKTIHKLT

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_56 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_04s0023g00600	1 retrocopy	retro_vvin_56 ,