RetrogeneDB ID: retro_vvin_131

Retrocopy location

• Organism: Grape (Vitis vinifera)
• Coordinates: 19:19891353..19892124(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: VIT_06s0009g03170
• Aliases: None
• Description: None

Sequence

>retro_vvin_131
ATGTTGAGAGTTGTTCATTTCCCACTAGGTGCATCTCTAGCTCTCGTTGCACTAAAACTATCTTTGATTCCCACTCTCAA
CCTCACATCCCCTTCAATCATTCGCAAATTCTCTTCATTTCCTTCTCTACACGCATTTCTTCCCAAAACATTCCTATTCG
GTTCACCTATCCTTTTTCTCTTGGCATAAAGAGATTCCCTCCCATGGTGGCTCAACCATGTCCTCGAGCTTCATTTAGTT
CTGAGGGCAACTCTGGAAGTGGTAGGGAAATATTGGTGCAACATCTGCTTGTTAAGGAGGATGACCTTAAGCTTCTATTG
GACCTTCAATAGAGGATTTCTGGTGGAGTAGATTTAAGTGATCTGGTTGTGGAATACTCAATTTGTCCGTATAAAGAAGA
GGATGGAATGCTTGGATGAGTGAGAAAAGGGCAAATGGTACCAGAGTTTGAGGAGGTTGCATTTAATGCACCTTTAAACA
AAGTTGTAAGGTGTAAAACAAAATTTGGATGACACTTGTTGCAAGTTATATCTAAAAGGGAAGAATCATTACTTCAAGAC
ATTCAACCCGAGGAGCTTCATGCAAAAATGCAAGATCCCATTTTTTTTTGAAGAGGTTCAGTTGATTGATGTTCGAGAAC
CTGAGGAAGTGGCTTAAGCGTCATTACCAGGTTTTTAGGTTCTTTTCCTCCAACCATTTGGGAACTGGGGACCAGAAATG
ACCACTAAATTTGATCATGAGAAGGATTCTTATCTTATGTGTCACCATGGC

Alignment

ORF - retro_vvin_131 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.49 %
• Parental protein coverage: 86.82 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MLRAAHLPPGASPALVALKLSLIPTLNLTSPSIIRKFSSFSSLHAFLPKTFLPSSP-YPLSLGLKRFPPM
          MLR..H.P.GAS.ALVALKLSLIPTLNLTSPSIIRKFSSF.SLHAFLPKTFL..SP.YP.SLG.KRFPPM
Retrocopy MLRVVHFPLGASLALVALKLSLIPTLNLTSPSIIRKFSSFPSLHAFLPKTFLFGSP<YPFSLGIKRFPPM

Parental  VAQPCPRASFSSGGNTGSGREILVQHLLVKEDDLKLLLELQQRISGGVDLSDLAVEYSICPSKEEGGMLG
          VAQPCPRASFSS.GN.GSGREILVQHLLVKEDDLKLLL.LQ.RISGGVDLSDL.VEYSICP.KEE.GMLG
Retrocopy VAQPCPRASFSSEGNSGSGREILVQHLLVKEDDLKLLLDLQ*RISGGVDLSDLVVEYSICPYKEEDGMLG

Parental  WVRKGQMVPEFEEAAFKAPLNKVVRCKTKFGWHLLQVISEREESLLQDIQPVELHAKMQD-PNFFEEVQL
          .VRKGQMVPEFEE.AF.APLNKVVRCKTKFG.HLLQVIS.REESLLQDIQP.ELHAKMQD.P...EEVQL
Retrocopy *VRKGQMVPEFEEVAFNAPLNKVVRCKTKFG*HLLQVISKREESLLQDIQPEELHAKMQD>PXXXEEVQL

Parental  IDVREPEEVAQASLPGFQVLPLQQFGNWGPEITTKFDPEKDTYLMCHHG
          IDVREPEEVA.ASLPGF.VL.LQ.FGNWGPE.TTKFD.EKD.YLMCHHG
Retrocopy IDVREPEEVA*ASLPGF*VLFLQPFGNWGPEMTTKFDHEKDSYLMCHHG

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_131 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_06s0009g03170	1 retrocopy	retro_vvin_131 ,