RetrogeneDB ID: retro_vvin_7

Retrocopy location

• Organism: Grape (Vitis vinifera)
• Coordinates: 11:13298241..13298823(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: VIT_11s0065g00100
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: VIT_17s0000g08460
• Aliases: None
• Description: None

Sequence

>retro_vvin_7
ATGGATATGGCGACGAGCTCATCTGATGTAGCCATTGAAGGACTGAGGCCGCTTCTGAGTGATAAGGAAGGTCTGGATGA
CATAGCTACAGAAAAAATTGAGAAGTTGACCGCTAAGTTGCAAGAACAAGAGCAAGATCATAAGGAGTGTGATCCTTTCG
AGAGGATTAAAGACGGGTTTATTCACTTCAAAATCCACTATTTCGGCAAGTATCTAGATTACTATAAACAACTTGCAGAA
GGGCAGCACCCCAAGTTTCTGGTGTTTGCGTGCTCTGACTCCCGCGTTAGCCCCTCTCATGTCCTGAACTTCAGGCCAGG
GAAAGCCTTCACGTGCAGGAACGTTGCTAACTCGGTTCCTGCATTTAACCAATTGAGATACTCAGGAGTTGGTGCAGTCA
TTGAATATGCAGTCAAGTATCTTGAGGTGGAGAACATCCTGATCATAAGGCATAGTCGTTGTGGTGGGACAGAGGCCCTT
ATGTCTCTTCCTGCTGATGGAACTACTTCCAATGACTTCATCGATGACTGGGTCAAAATTGCTTTACCGGCCAGGCAAGA
TGAACGAGATATGGCAGCCTAA

Alignment

ORF - retro_vvin_7 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.17 %
• Parental protein coverage: 71.26 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDMATSSSDVAIEGLRPLLSDKEGLDEIAAAKIEKLTAELQEQEQEQDHECDPVERIKDGFIHFKIHHFD
          MDMATSSSDVAIEGLRPLLSDKEGLD.IA..KIEKLTA.LQEQEQ....ECDP.ERIKDGFIHFKIH.F.
Retrocopy MDMATSSSDVAIEGLRPLLSDKEGLDDIATEKIEKLTAKLQEQEQDHK-ECDPFERIKDGFIHFKIHYFG

Parental  KYPDYYKQLAEGQHPKFLVFACSDSRVSPSHVLNFKPGEAFMCRNIANLVPAFNQLRYSGVGAVIEYAVK
          KY.DYYKQLAEGQHPKFLVFACSDSRVSPSHVLNF.PG.AF.CRN.AN.VPAFNQLRYSGVGAVIEYAVK
Retrocopy KYLDYYKQLAEGQHPKFLVFACSDSRVSPSHVLNFRPGKAFTCRNVANSVPAFNQLRYSGVGAVIEYAVK

Parental  HLEVENILVIGHSRCGGIEALMSLPADGTTSNDFIDDWVKIALPAK
          .LEVENIL.I.HSRCGG.EALMSLPADGTTSNDFIDDWVKIALPA.
Retrocopy YLEVENILIIRHSRCGGTEALMSLPADGTTSNDFIDDWVKIALPAR

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_7 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 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Triticum aestivum	TRAES3BF026200060CFD_g	2 retrocopies	retro_taes_12, retro_taes_207,
Vitis vinifera	VIT_17s0000g08460	1 retrocopy	retro_vvin_7 ,