RetrogeneDB ID: retro_vvin_10

Retrocopy location

• Organism: Grape (Vitis vinifera)
• Coordinates: 2:4424612..4425671(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: VIT_02s0025g04920
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: VIT_13s0019g03270
• Aliases: None
• Description: None

Sequence

>retro_vvin_10
ATGGTGGAGGCGCAGACATGGACGACGAGGAGGGGGAGCAATCCGAGGCTGGAGACGACGGAGCAAGTGGTGGACATTCC
GGCGACGCCGCCGGGAGGCGTGCGGAATAGCGGAAACGCCATTGGATCGTTCCTGTCGCCGAATGTGTTGACGGCTCTGA
TAATTGCGTCTTGGTATTTGTCAAACATCGGCGTCCTCCTCCTCAACAAGTATCTCCTGAGCTTCTATGGCTACCGCTAC
CCAATCTTCCTGACCATGCTCCACATGCTATCGTGCGCTGGATACAGCTACGCCGCCATCAACTGGCTTGAGCTTGTACC
CCTCCAGCACATTCTGTCTCGCCGTCAGTTCCTCAAGATCTTCGCCCTCAGCGCCATCTTCTGCTTCTCCGTTGTCTGCG
GCAATACCTCTCTGAGATACCTTCCGGTGTCATTCAATCAGGCCATTGGAGCAACGACGCCGTTCTTCACCGCAATTTTC
GCCTTCTTGATTACTTGCAAGAAGGAGACTGGTGAGGTGTATTTGGCACTGTTGCCGGTGGTGTTCGGCATCGTTTTGGC
GAGTAACAGTGAGCCGTTGTTCCATCTGTTTGGGTTTTTGATTTGCATCGGATCCACTGCTGGGCGTGCTCTGAAATCAG
TGGTTCAGGGGATATTGTTGACATCAGAGGCTGAGAAGCTCCACTCAATGAATTTGCTACTGTATATGGCTCCAATGGCG
GCTTTGATTCTACTCCCGTTTACTCTTTACATAGAGGGAAATGTGGCCGCTTTCACGGTGGAGAAAGCCAGGGGGGATTC
CTTTATCATATTTTTGTTGATTGGGAATGCGACGGTGGCGTATTTGGTGAACTTGACCAACTTTTTGGTCACAAAGCACA
CCAGTGCATTGACACTGCAGGTGCTGGGGAATGCCAAAGCGGCGGTAGCAGCAGTTGTGTCGGTGTTGATTTTCCGGAAT
CCGGTGACGGTGATGGGAATGACTGGCTTTGCTGTTACAATAATGGGGGTGGTGCTTTACAGCGAGGCGAAGAAGAGATC
CAAAGTTACAACTCATTGA

Alignment

ORF - retro_vvin_10 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.67 %
• Parental protein coverage: 99.02 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SSRFFTIGLVTAWYSSNIGVLLLNKYLLSNYGFKYPIFLTMCHMTACSLLSYVAIAWMKMVPMQTIRSRV
          S....T......WY.SNIGVLLLNKYLLS.YG..YPIFLTM.HM..C...SY.AI.W...VP.Q.I.SR.
Retrocopy SPNVLTALIIASWYLSNIGVLLLNKYLLSFYGYRYPIFLTMLHMLSCAGYSYAAINWLELVPLQHILSRR

Parental  QFMKISALSLVFCASVVSGNISLRFLPVSFNQAIGATTPFFTAVFAYLMTLKREAWLTYVTLIPVVTGVI
          QF.KI.ALS..FC.SVV.GN.SLR.LPVSFNQAIGATTPFFTA.FA.L.T.K.E....Y..L.PVV.G..
Retrocopy QFLKIFALSAIFCFSVVCGNTSLRYLPVSFNQAIGATTPFFTAIFAFLITCKKETGEVYLALLPVVFGIV

Parental  IASGGEPSFHLFGFLMCIGATAARALKSVLQGILLSSEGEKLNSMNLLLYMAPIAVVFLLPATLFMEENV
          .AS..EP.FHLFGFL.CIG.TA.RALKSV.QGILL.SE.EKL.SMNLLLYMAP.A...LLP.TL..E.NV
Retrocopy LASNSEPLFHLFGFLICIGSTAGRALKSVVQGILLTSEAEKLHSMNLLLYMAPMAALILLPFTLYIEGNV

Parental  VGITLALARDDIKIVWYLLFNSALAYFVNLTNFLVTKHTSALTLQVLGNAKGAVAVVVSILIFRNPVSVT
          ...T...AR.D..I...L..N...AY.VNLTNFLVTKHTSALTLQVLGNAK.AVA.VVS.LIFRNPV.V.
Retrocopy AAFTVEKARGDSFIIFLLIGNATVAYLVNLTNFLVTKHTSALTLQVLGNAKAAVAAVVSVLIFRNPVTVM

Parental  GMLGYSLTVFGVILYSEAKKRSK
          GM.G...T..GV.LYSEAKKRSK
Retrocopy GMTGFAVTIMGVVLYSEAKKRSK

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_10 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Amborella trichopoda	AMTR_s00080p00074790	1 retrocopy	retro_atri_6,
Medicago truncatula	MTR_3g070000	1 retrocopy	retro_mtru_1,
Prunus persica	PRUPE_ppa009115mg	1 retrocopy	retro_pper_41,
Theobroma cacao	TCM_042615	1 retrocopy	retro_tcac_6,
Vitis vinifera	VIT_13s0019g03270	1 retrocopy	retro_vvin_10 ,