RetrogeneDB ID: retro_vvin_103

Retrocopy location

• Organism: Grape (Vitis vinifera)
• Coordinates: 16:11693053..11693624(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: VIT_03s0038g00910
• Aliases: None
• Description: None

Sequence

>retro_vvin_103
TTCAAGAAAACACTTTCCACAGCCATGGAAATCCATGTGGTTGGTTTGCACCAGGTTGCCACAATGAGGTGTATGGTGAA
CCAGAGAAGAGTGAAAATGGTGGCCAAATAGATAAGAAGAGAGTTTTTCGACATGCTTCTCACCGACAAGGTTTTGCAGT
TTTCTATTCTTCTAGAGGCGGCTCTCGGAGTCGATTACTATCTCTCCTCTCTCACCACTATCATCCATGTTGAAGTCTCC
GCTAATTTGCAGGTGGTTAAATTTTATGTATCTATTTTTTTAGGATAGGAAAAGAAATGAGGTAGCCATTGCTGGTTCGA
AGTCAAAGGTTGAATATATTCGAAGTGAGTTGAGGAGGCATATGAAGCTACGGCTAACTCAAGAGATACGCTTCATAGAG
GATGAGTCTCTAGAGCAAGGAAGCTGGGTGATTGCAATATTGGATAGGATGAAGAATGAGAAAAAGATGGAAGAAAGCCA
AGATCAATCGTCTAAATCATCTTATTTATCTCAAGATGATGACTGGGAGGGTGATGGTGATGACCCTAATGAGAACATTA
TTCATATAAAA

Alignment

ORF - retro_vvin_103 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.39 %
• Parental protein coverage: 85.2 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FRRTLSTAVEVHVAGPHQIATVRCMANQRRVKMVAKQIRRELSDMLLTDKVLQFAVLPEAALGADRYLSS
          F..TLSTA.E.HV.G.HQ.AT.RCM.NQRRVKMVAK.IRRE..DMLLTDKVLQF..L.EAALG.D.YLSS
Retrocopy FKKTLSTAMEIHVVGLHQVATMRCMVNQRRVKMVAK*IRREFFDMLLTDKVLQFSILLEAALGVDYYLSS

Parental  LTTISDVEVSADLQVVKVYVSVFG-DEKGKEVAIAGLKSKAKYVRSELGRRMKLRLTPEIRFVEDESLER
          LTTI..VEVSA.LQVVK.YVS....D.K..EVAIAG.KSK..Y.RSEL.R.MKLRLT.EIRF.EDESLE.
Retrocopy LTTIIHVEVSANLQVVKFYVSXXX>DRKRNEVAIAGSKSKVEYIRSELRRHMKLRLTQEIRFIEDESLEQ

Parental  GSRVIAILDRIKNEKKMAGSQDQPSESSDLPQDDDWEGDGDDPDENIIYIK
          GS.VIAILDR.KNEKKM..SQDQ.S.SS.L.QDDDWEGDGDDP.ENII.IK
Retrocopy GSWVIAILDRMKNEKKMEESQDQSSKSSYLSQDDDWEGDGDDPNENIIHIK

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_103 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_03s0038g00910	1 retrocopy	retro_vvin_103 ,