RetrogeneDB ID: retro_vvin_24

Retrocopy location

• Organism: Grape (Vitis vinifera)
• Coordinates: 15:12372333..12373023(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: VIT_15s0021g01750
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: VIT_17s0000g08710
• Aliases: None
• Description: None

Sequence

>retro_vvin_24
ATGGACCAACTGTACGGTCTTTACTCTCCCTCCTCCTCCGATTACCATCACCCGCCTCCATTTCCGCCGAAAAATCTGAT
TTCTCCATCTCATTACCCGAATTTTAATTCTCCTGCGCCATTTCCGATCTTTGGATTCGACCAGCTGTTGTCGGCGTCGT
CTGTGGCGGTCTCTGATGCAACTTCCATGGTGGCTCAAATTCAAGGAGGAGGTTCTGGAGATGAGGTTTCCAGTGCTATT
CGAACCCAAATCGCTACTCATCCTCTCTATCCTAAACTTCTCCATGCTTACATCGAGTGCCAGAAGGTCGGAGCGCCACC
GGAGGTGGCGTATCTGTTGGAAGAAATCAGGAGAGGAAGCGAGCTTTGTAGAAGAAACACCGTTTCCACTTGCTTGGGTG
CGGATCCCGAGCTGGATGAGTTCATGGAAACCTACTGCAATGTACTAATGAAATATAAATCGGATCTCGCCAGGCCTTTC
GATGAAGCCACCGCGTTTCTGAACAACATAGAGACGCAGCTCAATACTCTCTGCAATGGTGCTTCCCGAAGCTACGTTTC
CGACGAAGTAGCTAGGTCATTAGAGGAAGGCTTAGAGGAAGTAGAGGGTGGGAAGTTGAAGACATGGAGGAGTACAAGGA
GTGTGGCCTTCACAAATGAAATACTAAGCAAGAAGAGGTGTCTGAACTAA

Alignment

ORF - retro_vvin_24 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.14 %
• Parental protein coverage: 70.22 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDQLYGLHSPSSSDYHHPPPFPPENLISPSHYPNFNSPAPFPIFGSDQLLSASSLVVSDAASMVAEIQGG
          MDQLYGL.SPSSSDYHHPPPFPP.NLISPSHYPNFNSPAPFPIFG.DQLLSASS..VSDA.SMVA.IQGG
Retrocopy MDQLYGLYSPSSSDYHHPPPFPPKNLISPSHYPNFNSPAPFPIFGFDQLLSASSVAVSDATSMVAQIQGG

Parental  GSGEEVSSAIRAKIATHPLYPKLLHAYIECQKVGAPPEVAYLLEEIRRGSELCRRNAVSTCLGADPELDE
          GSG.EVSSAIR..IATHPLYPKLLHAYIECQKVGAPPEVAYLLEEIRRGSELCRRN.VSTCLGADPELDE
Retrocopy GSGDEVSSAIRTQIATHPLYPKLLHAYIECQKVGAPPEVAYLLEEIRRGSELCRRNTVSTCLGADPELDE

Parental  FMETYCDILVKYKSDLARPFDEATAFLNNIETQLNTLCNGASRSYVSDEAAGSSEEDLSGGEVEVQECLQ
          FMETYC..L.KYKSDLARPFDEATAFLNNIETQLNTLCNGASRSYVSDE.A.S.EE.L...E........
Retrocopy FMETYCNVLMKYKSDLARPFDEATAFLNNIETQLNTLCNGASRSYVSDEVARSLEEGLEEVEGGKLKTWR

Parental  TTENQELKDKLLRK
          .T.........L.K
Retrocopy STRSVAFTNEILSK

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_24 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_17s0000g08710	1 retrocopy	retro_vvin_24 ,