RetrogeneDB ID: retro_vvin_105

Retrocopy location

• Organism: Grape (Vitis vinifera)
• Coordinates: 17:15074405..15074657(+)
• Located in intron of: VIT_17s0053g00410

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: VIT_03s0038g03650
• Aliases: None
• Description: None

Sequence

>retro_vvin_105
ATGAGTAGAAGCTTGGGAATTCCGGTGAAGCTACTTCATGAAGCTGCAGGGCATGTGGTTACAGTGGAGCTCAAGGGTGG
AGAACTGTACAGAGGAAGCATGATCGAATGCGAAGACAACTAGAATTGCCAACTCGAAAACATCACCTTCACTGCTAAGG
ATGAAGAGGTTTTCTAACTTGAGCATGCCTTTATCCGTGGTAGCAAAGTCAGGTTCATGGTCATTCCAGATATGTTAAAG
AATGCTCCTGTT

Alignment

ORF - retro_vvin_105 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.48 %
• Parental protein coverage: 63.64 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSRSLGIPVKLLHEAAGHVVTVELKSGELYRGSMIECEDNWNCQLENITFTAKDGKVSQLEHVFIRGSKV
          MSRSLGIPVKLLHEAAGHVVTVELK.GELYRGSMIECEDN.NCQLENITFTAKD..V..LEH.FIRGSKV
Retrocopy MSRSLGIPVKLLHEAAGHVVTVELKGGELYRGSMIECEDN*NCQLENITFTAKDEEVF*LEHAFIRGSKV

Parental  RFMVIPDMLKNAPM
          RFMVIPDMLKNAP.
Retrocopy RFMVIPDMLKNAPV

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_105 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 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Vitis vinifera	VIT_03s0038g03650	2 retrocopies	retro_vvin_105 , retro_vvin_11,