RetrogeneDB ID: retro_vvin_116

Retrocopy location

• Organism: Grape (Vitis vinifera)
• Coordinates: 18:3315498..3316042(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: VIT_02s0025g00640
• Aliases: None
• Description: None

Sequence

>retro_vvin_116
ATGGTTGACCACGAGGATTCAACTCATTCCCCCGTTGAACAGATGATGGAGAAGATCTCTAAGAAGATCCACAGTCACTA
CTCATCGTCTTTCTGATTCCGATAACGAGAAATCATCTCCCACAACTTTCAAAGCCAAGGTTTATCGGATCTTCGACAGG
GAAAAACCTATTCACAAGGTTCTCAACGGTGGAAAACCTATTGATGTTGTTTTGTGGGAAAAAAAAATTTCGACAGGAGT
GCTTGGTGGTGAAACTGCAGTATGGACTCTATTCGAGTTGCTTGAATACCACCTGCTAACTCTAGTATGCCATTGCTTGA
TACTCGCACTGGCAATATTATTCTTGTGGTCCAATGCAACCACCTTCATCAACAAGGCACCACCACACATTCCAGAAGTC
CACATTCCAAATGATCTAGTTCTGCAGTTTGCATCGGCTTTGAGAATTGAAATCAACCGGGGTTTTGCTATCTTGTGCAA
TATTGCATCTGGCAAAGATCTAAAGAAGTTTCTCTCAGTGATTGTTGGCTTATAAGTGGTGGCG

Alignment

ORF - retro_vvin_116 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.06 %
• Parental protein coverage: 72.22 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MADHEDSTPSPVESMMEKISEKIHGHDSSS-SDSDNEKSSPSAFKAKVYRIFGREKPVHKVLGGGKPADV
          M.DHEDST.SPVE.MMEKIS.KIH.H.SSS.SDSDNEKSSP..FKAKVYRIF.REKP.HKVL.GGKP.DV
Retrocopy MVDHEDSTHSPVEQMMEKISKKIHSHYSSS>SDSDNEKSSPTTFKAKVYRIFDREKPIHKVLNGGKPIDV

Parental  VLWRNKKISAGVLGGATAVWILFELLEYHLLTLVCHCSILALAILFLWSNATTFINKAPPHIPEVHIPED
          VLW.....S.GVLGG.TAVW.LFELLEYHLLTLVCHC.ILALAILFLWSNATTFINKAPPHIPEVHIP.D
Retrocopy VLWXXXX-STGVLGGETAVWTLFELLEYHLLTLVCHCLILALAILFLWSNATTFINKAPPHIPEVHIPND

Parental  PVLQFASALRIEINRGFTLLRNVASGKDLKKFLSVIAGLWVVS
          .VLQFASALRIEINRGF..L.N.ASGKDLKKFLSVI.GL.VV.
Retrocopy LVLQFASALRIEINRGFAILCNIASGKDLKKFLSVIVGL*VVA

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_116 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
Vitis vinifera	VIT_02s0025g00640	1 retrocopy	retro_vvin_116 ,
Vitis vinifera	VIT_03s0180g00170	1 retrocopy	retro_vvin_192,