RetrogeneDB ID: retro_vvin_146

Retrocopy location

• Organism: Grape (Vitis vinifera)
• Coordinates: 4:14879794..14880728(+)
• Located in intron of: VIT_04s0043g00750

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: VIT_02s0087g00650
• Aliases: None
• Description: None

Sequence

>retro_vvin_146
TCGCTTATCCCATTGAATTCTGCACTTTCAAAATTTTCATATTCTCTTACTTAGGAACAGTTATCTACTTCTTCTGATAC
AATGTCCTTCTTGTCTGCAAAGTCAACTCTGTCATCATACTTTGCACCTATACATTCGAATATAATAAACATGTCTTCAT
TTCCTTCATCTTATCAAGACGTTAGTACCACTTAAGCTCCAATTACTAGTAAAATAGTTTCTGATCTGGTATCGGTGCCT
ACTATCCATCCCCTGCATCATTCTACATCCACAATTGGGGGTTCCACCTCTAGCCTCCTTTTGACTCTACCACCAACTTT
ATTAAGTCCTGATCAATTAGCACAATCCATGCCATCCATGCTTTCTTCCTCACAGAAAGTATACCTTGATCAGATGAATA
AGGTTGCTCCAACATCAACATCTCCTAATACTCTGAGCACAATGTCTACTCCAGTACTTCAAGCACCATTGTTGCCATTG
CCAGCCTCTACTCAACAATCTTAGAAGTCTACTATGCAGTTCACTGAAGAATTTTATTTTATAGCGATGAATGAAATGTT
TAAAAGGGATGGAGTTTGGGGTTATCTTAGAAAGGCAAAGCAAAAGGATGAAAAGGAAGGGATGAAAGACAATGCACTTG
GTCAAGGCTTGGGTGACAGATAGGGTCATAGACTAGTACCCAAATCAAATGCTAAACACGCTTATAATAAGGATGAGTTG
TTTGACAAGATTTCTTGTAATTCTCATGCCCGCGGGACTAGGAATGGACAGAACAGGTTCTTTATGCGAATGAAGATGGA
TACTGAGACTTTTGGAAATTTTCAACAGAGACCTCATCTAGGTTAAGGTGGCTACAAAGCTGGGCGTGGGGAGAACTACA
GTGGCTCATATAATTGGAAAAGAGGATTTGCCAGTGGATGGAATTGGGGGTGGT

Alignment

ORF - retro_vvin_146 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.65 %
• Parental protein coverage: 60.74 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SLIPLNSALSKFSSSLTQEQFSTSSDTMSFLSAKATLPSYSAPVNSNIINMSSFPSSYQDVNTTEAPITG
          SLIPLNSALSKFS.SLT.EQ.STSSDTMSFLSAK.TL.SY.AP..SNIINMSSFPSSYQDV.TT.APIT.
Retrocopy SLIPLNSALSKFSYSLT*EQLSTSSDTMSFLSAKSTLSSYFAPIHSNIINMSSFPSSYQDVSTT*APITS

Parental  KIVSDLVSVPPIHPLHHSASTIGGSTSGLLLTPPPTLLTPDQLAQPMSSMLSSSQKVYPDQRDKVAPTST
          KIVSDLVSVP.IHPLHHS.STIGGSTS.LLLT.PPTLL.PDQLAQ.M.SMLSSSQKVY.DQ..KVAPTST
Retrocopy KIVSDLVSVPTIHPLHHSTSTIGGSTSSLLLTLPPTLLSPDQLAQSMPSMLSSSQKVYLDQMNKVAPTST

Parental  SPNTLSTMSTPALQAPLLPLPASAQQSQKSAVQFTEEFDFIAMNERFKKDEVWGYLGKAKQRDEKEGMED
          SPNTLSTMSTP.LQAPLLPLPAS.QQS.KS..QFTEEF.FIAMNE.FK.D.VWGYL.KAKQ.DEKEGM.D
Retrocopy SPNTLSTMSTPVLQAPLLPLPASTQQS*KSTMQFTEEFYFIAMNEMFKRDGVWGYLRKAKQKDEKEGMKD

Parental  NALGQGLGDREGYGQVPKSDAKPAYNKDEFFDTISCNSHARGTRNGQNRFSARMKMDTETFGNFQQRPHL
          NALGQGLGDR.G...VPKS.AK.AYNKDE.FD.ISCNSHARGTRNGQNRF..RMKMDTETFGNFQQRPHL
Retrocopy NALGQGLGDR*GHRLVPKSNAKHAYNKDELFDKISCNSHARGTRNGQNRFFMRMKMDTETFGNFQQRPHL

Parental  GYGGYRAGRGENYRGSYNRGRGFAYG-GRGGG
          G.GGY.AGRGENY.GSYN..RGFA.G.G.GGG
Retrocopy G*GGYKAGRGENYSGSYNWKRGFASG>GIGGG

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_146 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_02s0087g00650	1 retrocopy	retro_vvin_146 ,