RetrogeneDB ID: retro_vvin_3

Retrocopy location

• Organism: Grape (Vitis vinifera)
• Coordinates: 14:12098941..12099301(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: VIT_14s0036g01220
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: VIT_07s0005g00690
• Aliases: None
• Description: None

Sequence

>retro_vvin_3
ATGGGTATCGGTTTAGTCGTCGATGACAAAAGCAAAAAGACGAAGTGCACCGCTCCCAAATCTGATGATATCTACCTCAA
GCTCACAGTCAAGTTGTATCATTTTTTGGTACGAAAAACCGGAAGCAAGTTCAATGTTGTGACATTGAAGCGGTTCTTCA
TGAGCAAGGTTAATAAGTTGCCTTTGTTACTTTCCCGTTTGGTTCGTTTCATGGACGGAAAGAAAGGTAAGATTGTTGTG
GTTATTGGTTCTGTTACCGATGATCTCCGAGTATACGAAGTCCTTTATTTGAAAGTGACTATCCTGAGGTTCACAAAGAG
AGTAAGGGAAGGGATTGAGAGGTTGATGGTGAATGCTTGA

Alignment

ORF - retro_vvin_3 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.32 %
• Parental protein coverage: 50.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGIDLVAGGKSKRTKRTAPKSDDIYLKLLVKLYRFLVRRTGSKFNAVILKRLFMSKVNKPPLSLSRLVRY
          MGI.LV...KSK.TK.TAPKSDDIYLKL.VKLY.FLVR.TGSKFN.V.LKR.FMSKVNK.PL.LSRLVR.
Retrocopy MGIGLVVDDKSKKTKCTAPKSDDIYLKLTVKLYHFLVRKTGSKFNVVTLKRFFMSKVNKLPLLLSRLVRF

Parental  MDGKEGKIAVVVGTVTDDLRVYEVPCLKVTALRFTERARARIEK
          MDGK.GKI.VV.G.VTDDLRVYEV..LKVT.LRFT.R.R..IE.
Retrocopy MDGKKGKIVVVIGSVTDDLRVYEVLYLKVTILRFTKRVREGIER

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_3 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 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Triticum aestivum	Traes_2AS_E714D8C86	1 retrocopy	retro_taes_47,
Vitis vinifera	VIT_07s0005g00690	1 retrocopy	retro_vvin_3 ,