RetrogeneDB ID: retro_vvin_58

Retrocopy location

• Organism: Grape (Vitis vinifera)
• Coordinates: 11:12962628..12963174(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: VIT_05s0124g00280
• Aliases: None
• Description: None

Sequence

>retro_vvin_58
ATGTTGAGTTCTAAGGAATTTTGGACAAATAAGACTTTGGTGGGGTCTTGGATTGGGGCAGCTTCTGTCTCTTCTGAACA
CTTCCACCGACTTTGCTTCTTCTGAACTCGCAAGAAGAGGAATCAGTGCTCTAACTTCTCAGTCTTTTCTAAATTATGTT
CTCTTAGCAATTGTCTATGGAACCACTATGATTCTCCAAAAGAAAGCTTTAAAGGCAACATGGTATTATCACATAGTTCT
TGCATAGGTGGATGTGGAGACCAATTTTCTTGTGGTAAAAGCGTACCATTACACTTCTGTAACAAGTGTCATGCTGCTGG
GATTGTAAAACAATCCCGTGTGCCATAATTTTTACCTGGTTTTTCTTGAAGACAAAGTACAGATTTAAAAAAATTAACCG
GTGCAGCAATCTGTATTGTTAGTCTTGTTATTGTCATCTTTTCATATGTTCATGCAAGTGACAGAGCAGAAGAGAGTAAC
CCTCTGAAATGGGATTTGTTTGTGATTGTTGGGTCTATTCTCTATGCTACCAGCAATGTTAGTGAG

Alignment

ORF - retro_vvin_58 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.26 %
• Parental protein coverage: 50.7 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MLSSKEFWTKKTLVG-LGLGQFLSLLITSTGFSSSELARRGINVPTSQSFLNYVLLAIVYGITMILRKRA
          MLSSKEFWT.KTLVG.LGLGQ.LSLL.TST.F.SSELARRGI...TSQSFLNYVLLAIVYG.TMIL.K.A
Retrocopy MLSSKEFWTNKTLVG>LGLGQLLSLLNTSTDFASSELARRGISALTSQSFLNYVLLAIVYGTTMILQKKA

Parental  LKAKWYYYVVLALVDVEANFLVVKAYQYTSITSVMLL-DCFTIPCVIIFTRFFLKTKYRI-KKLTGASIC
          LKA.WYY..VLA.VDVE.NFLVVKAY.YTS.TSVMLL.DC.TIPC.IIFT.FFLKTKYR....LTGA.IC
Retrocopy LKATWYYHIVLA*VDVETNFLVVKAYHYTSVTSVMLL>DCKTIPCAIIFTWFFLKTKYRF>XXLTGAAIC

Parental  IAGIVIVIFSDVHASDRAGGNSPLKGDLLVIAGSILYAVSNVSE
          I...VIVIFS.VHASDRA....PLK.DL.VI.GSILYA.SNVSE
Retrocopy IVSLVIVIFSYVHASDRAEESNPLKWDLFVIVGSILYATSNVSE

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_58 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_05s0124g00280	1 retrocopy	retro_vvin_58 ,