RetrogeneDB ID: retro_vvin_73

Retrocopy location

• Organism: Grape (Vitis vinifera)
• Coordinates: 13:10811900..10812877(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: VIT_02s0033g01110
• Aliases: None
• Description: None

Sequence

>retro_vvin_73
ATGGATAAGTATACAATAATCAAGGAAGTTGGTGATAGGACATTTGGAAGTGTTTAGCGAGCAATAAATAAGCAGATTGG
TGAAGTTGTTGCTTTAAAAAAGATGAAAAGAAAATATTATTCTTGGGAAGAATGTTTAAATCTGAAAGAAGTCAAGTCAT
TGAGAAAGATGAACCACCCAAACATTGTGAAACTCAAGGAAGTCTTTAGGAAAAATGATATTTTGTACTTTGTGTTTGAA
TACATGGAATGCAACCTTTACCAACTTATGAAAGATCGATTGAAGCTTTTTTTCGAAACTGAAGTTTGAAATTGGTGTTT
TCAAGTGTTCCAAGGTCTTGCTTACATGCACAGGCGTGGATATTTTCATCACAACCTCAAGCTAGAGAACTTGTTGGTTA
CCAAAGATGTAACAAAAATTATTGATTTTGGTCTTGGTCGAGAGATCAATTCTCAACCACCATACATAGAATAAGTCTCT
ACGCGTTGGTATCAAGTTCTAGAGGTTCTACTTCAATCATCCACATTGGGTTTTGCAATTGATATGTGGGCAATAGGTGC
TATCATGGCTTAATTGTTTGCTCTCCATCATCTCTTTCTAGGATCGAGTGAAGAAGATGAAATTTACAAAATATGCAATG
TTATACGTAGTCCAACTTGGAATTCATTGACCAAGGGACTTAAACTTGCTAATGCTATTAACTACCAATTCCCACAATTT
TCTAGTGTTCATCTCTATGTATTGATACCATCTGCAAGTGAGGATGCAATTAGCCTTATTACTTGACTTTGTTCATGGGA
TCCCTGCAAGAGGCCAATAGCCTTGGAGGCTCTTTAGCATCATTTCTTTAAGAGTAGCTTTTATATCCCACCATCCCTTC
ATCCTCAAACTGCTGTGACTAGGACACCTCCATCTAGTAAAAAAATGGAGCTTTGGAGCAGAAATGTGCTAGGAGGTGTT
CAACGCAAGTTGGAAAT

Alignment

ORF - retro_vvin_73 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.04 %
• Parental protein coverage: 72.12 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MDKYTIIKEVGDGTFGSVWRAINKQTGEVVAIKKMKRKYYSWEECLNLREVKSLRKMNHPNIVKLREVFR
          MDKYTIIKEVGD.TFGSV.RAINKQ.GEVVA.KKMKRKYYSWEECLNL.EVKSLRKMNHPNIVKL.EVFR
Retrocopy MDKYTIIKEVGDRTFGSV*RAINKQIGEVVALKKMKRKYYSWEECLNLKEVKSLRKMNHPNIVKLKEVFR

Parental  ENDILYFVFEYMECNLYQLMKDRLKLFSETEVRNWCFQVFQGLAYMHRRGYFHRDLKPENLLVTKDVIKI
          .NDILYFVFEYMECNLYQLMKDRLK...ETEV.NWCFQVFQGLAYMHRRGYFH..LK.ENLLVTKDV.KI
Retrocopy KNDILYFVFEYMECNLYQLMKDRLKXXXETEV*NWCFQVFQGLAYMHRRGYFHHNLKLENLLVTKDVTKI

Parental  ADFGLAREINSQPPYTEYVSTRWYRAPEVLLQSSTYGSAVDMWAMGAIMAELFTLRPLFPGSSEADEIYK
          .DFGL.REINSQPPY.E.VSTRWY...EVLLQSST.G.A.DMWA.GAIMA.LF.L..LF.GSSE.DEIYK
Retrocopy IDFGLGREINSQPPYIE*VSTRWYQVLEVLLQSSTLGFAIDMWAIGAIMA*LFALHHLFLGSSEEDEIYK

Parental  ICSVMGSPTWNSWAEGLKLANAINYQFPQFSSIHLSVLIPSASEDAISLITSLCSWDPCKRPTALEALQH
          IC.V..SPTWNS...GLKLANAINYQFPQFSS.HL.VLIPSASEDAISLIT.LCSWDPCKRP.ALEAL.H
Retrocopy ICNVIRSPTWNSLTKGLKLANAINYQFPQFSSVHLYVLIPSASEDAISLIT*LCSWDPCKRPIALEAL*H

Parental  PFFQSCFYVPPSLRPRTAVTRTPPSG-ETKGALDQKSGRRYSRATSN
          .FF.S.FY.PPSL.P.TAVTRTPPS.....GAL.QK..RR.S....N
Retrocopy HFFKSSFYIPPSLHPQTAVTRTPPSS<XXXGALEQKCARRCSTQVGN

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_73 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Solanum tuberosum	PGSC0003DMG400018466	1 retrocopy	retro_stub_34,
Solanum lycopersicum	Solyc08g005470.2	1 retrocopy	retro_slyc_24,
Vitis vinifera	VIT_02s0033g01110	1 retrocopy	retro_vvin_73 ,