RetrogeneDB ID: retro_vvin_97

Retrocopy location

• Organism: Grape (Vitis vinifera)
• Coordinates: 16:11667694..11668606(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: VIT_11s0016g04200
• Aliases: None
• Description: None

Sequence

>retro_vvin_97
AGCTTGGGATGTTTTACTCTCTTTTCCATAATGTTTCTTTCAATAGCCAGTACATCCAAGTTGCTCAAGCTTAGAGAATT
GTGGCATTTTGGTTGATGGTCTCCAGAGATTATCTTGTGGGTAGCCGTAATGATACTCCCTTTCTTAGTTCCTTATGTTT
TTATTCATTTCTATGGGGATATTGCACGTTTCGGTATTGGGATCTTTCTCTTAATTCAGCTAATAATCATAATCAACTTC
GTTAAATGGTTGAATGATTGTTGTCGCTCCGACAAATATGCAGGGAGAGGCCATGTCCATGTGATGTTATTTGTAACTAC
AACATATGTCACATGCATAATGGGAATCATTTTAATGTATATTTGGTGTGTACCAGAACCGTCATACCTTCTTGACATTT
TCTTCATCGCTTGGACATTAGTGCTCTTTCAGCTCATGACTAATGTCTCTCTCCATCCAAAGATAGATGAAAGTCTCTTG
ACTCCAGAGCTTATGGGCATGTATGTTGTGTTCCTCTGCTGGTGTGCCATTAGAAGTGAACAACAAGAAAACAGATGCAA
TCAAGAGGCGGAATCAGCGACCAAAGCAGATTGGCTTACCATCATAAGCTTTGTTGTTGCGCTGCTTGCTGTGATCATTG
TAATACTTTCAACAGACATTGATTCCAAATGCTTTCAGTCTAGGAAGGATGACTCACAAGCTAAAGATGATGTTTCTTAT
GGTTACAACTTCTTCTACTTTGTTTGTGCCATGGGAGCCATGCATTTTTCAATGCTATTGATTGACTAGATTACTCATCA
TTTCATAAGAAAGTGGATAATTGACATGGGTTGAATGAGTACCTGAGTTAAAATAATGAACAAATGGCTGGTAGCCTGTG
TATACCTATGGTTATGTCGCACCCTAATATGG

Alignment

ORF - retro_vvin_97 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.79 %
• Parental protein coverage: 76.83 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SLGCFTFYFIMFLSTAGTSKLHKPRELWHSGWWSAKIILWVALMMLPFLVPSAFIQLYGEIAHFGAGVFL
          SLGCFT...IMFLS.A.TSKL.K.RELWH.G.WS..IILWVA.M.LPFLVP..FI..YG.IA.FG.G.FL
Retrocopy SLGCFTLFSIMFLSIASTSKLLKLRELWHFG*WSPEIILWVAVMILPFLVPYVFIHFYGDIARFGIGIFL

Parental  LIQLISIISFIKWLNDCCHSGKYADRCRIHVMLLATTAYVICIMGIILMYIWYVPEPSCLLNIFFITWTL
          LIQLI.II.F.KWLNDCC.S.KYA.R...HVML..TT.YV.CIMGIILMYIW.VPEPS.LL.IFFI.WTL
Retrocopy LIQLIIIINFVKWLNDCCRSDKYAGRGHVHVMLFVTTTYVTCIMGIILMYIWCVPEPSYLLDIFFIAWTL

Parental  VLLQLMTSVSLHPKVDESFLTPGLMGLYVVFLCWCAIRSEPPEDRCNQKVESATKADWLTIISFIVALLA
          VL.QLMT.VSLHPK.DES.LTP.LMG.YVVFLCWCAIRSE..E.RCNQ..ESATKADWLTIISF.VALLA
Retrocopy VLFQLMTNVSLHPKIDESLLTPELMGMYVVFLCWCAIRSEQQENRCNQEAESATKADWLTIISFVVALLA

Parental  MVIATFSTGIDSKCFQFRKDDTQAEDDVPYGYGFFHFVFATGAMYFSMLLIGWNTHHSIRKWTIDVGWTS
          ..I...ST.IDSKCFQ.RKDD.QA.DDV.YGY.FF.FV.A.GAM.FSMLLI...THH.IRKW.ID.G..S
Retrocopy VIIVILSTDIDSKCFQSRKDDSQAKDDVSYGYNFFYFVCAMGAMHFSMLLID*ITHHFIRKWIIDMG*MS

Parental  TWVRIVNEWLAACVYLWMLVAPIIW
          T.V.I.N.WL.ACVYLW.L....IW
Retrocopy T*VKIMNKWLVACVYLW-LCRTLIW

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_97 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_11s0016g04200	1 retrocopy	retro_vvin_97 ,