RetrogeneDB ID: retro_vvin_170

Retrocopy location

• Organism: Grape (Vitis vinifera)
• Coordinates: 7:10269935..10270423(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: VIT_00s0179g00190
• Aliases: None
• Description: None

Sequence

>retro_vvin_170
TCTGATGCAGAGCAATCCAATTCGCTTTTAGGAGAAGACATTCAAACGCCTGCATTTTTAGAGACAAAAGCGCTTGCTTC
TATTAACTTATGGACGAACAGTGCTCAAGCTAGATCAAATGCTCACTGCGATCCACACCATGATCTTCTATGCATAATTG
ATGGCTGCAAGCAAGTTGTTTTATGGCCCCCTTCTGCAAGTCTCTTGTTATATCCAATGCCTATATATGGAGAGGCCTCA
AACCATAGTTCTGTGGCTTTAGAGGAACCTGATTTTTCAATTCATCCAAGAGCCGAACACTCAATGAAGCACTCTCAGAA
GGTTATTCTTCATGCAGGAGATGCACTGTTCATTCCTGGAGGCTGGTTCCATCAAGTGGATAGTAATGATCCGACTATTG
CTGTTAACTTCTGTGGTGGTCAAACATAACGTCCAGCCTGTCAGAACACATGGATGCATATTATTTGAGGAGAATATTGA
GGAGGATT

Alignment

ORF - retro_vvin_170 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.37 %
• Parental protein coverage: 50.94 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NDDKVQLATLIEDIQTPAFLETKTLASINLWMNSAQARSSTHYDPHHNLLCIIAGCKQVVLWPPSASPLL
          .D.......L.EDIQTPAFLETK.LASINLW.NSAQARS..H.DPHH.LLCII.GCKQVVLWPPSAS.LL
Retrocopy SDAEQSNSLLGEDIQTPAFLETKALASINLWTNSAQARSNAHCDPHHDLLCIIDGCKQVVLWPPSASLLL

Parental  YPMPIYGEASNHSSVALEDPDFSIHPRAEHSMKHSQKVILHAGDALFIPEGWFHQVDSNDLTIAVNF-WW
          YPMPIYGEASNHSSVALE.PDFSIHPRAEHSMKHSQKVILHAGDALFIP.GWFHQVDSND.TIAVNF..W
Retrocopy YPMPIYGEASNHSSVALEEPDFSIHPRAEHSMKHSQKVILHAGDALFIPGGWFHQVDSNDPTIAVNF<LW

Parental  RSNITSSLSEHMDAYYLRRILRRL
          .SNITSSLSEHMDAYYLRRILRR.
Retrocopy WSNITSSLSEHMDAYYLRRILRRI

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_170 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_00s0179g00190	3 retrocopies	retro_vvin_150, retro_vvin_170 , retro_vvin_43,