RetrogeneDB ID: retro_vvin_133

Retrocopy location

• Organism: Grape (Vitis vinifera)
• Coordinates: 2:15412726..15413349(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: VIT_06s0004g02480
• Aliases: None
• Description: None

Sequence

>retro_vvin_133
ATGATCGCATGTGGGCAAGATCCTATTGTTGTTCGGTGGGGTCTCCGGCTTCTGATGATGATCCGTTTTCTAAGTGCGGG
TATGGTGGCACCATTGTGCAAAATGATGTAAGTTATTATGATGGATAACATTTAAAGGAAGATCGTTATGATAATGAATG
TGGCAATGCGGAGAATGGTGAGATTATCGAACATGCTCTTTAAGAAGAACTATCACAACTTGCTATTGACGAAACAGCTA
GATTTTCACATGAAGTGGTAGAGGATTTGCAAGTATCTATTCTTCCAAAAGAATGGCCCGATCAATCTATGGAAAATTAT
GGATTTAGGCATGAGAGCGGCCAGAAAGATATAGATGGTATGGGACTTTCTAGTTCATGTTCTAGTCCTGACGAAAAGTC
ACACAATGGGGAGGGTTGGTCATATTCTCTAGATCTGACAGATGAGAATGCACTCGATGGTGAAGTAGGCAAAATATTAA
ATCAGATGGTCTCTATTCCTCATGTTCCTAAAATCAATGGAGAAATACCCTCTCTTGATGAAACAACTCTCGATCATCAG
AGACCGTTGGACTGATTGCGGTTATTTGGTATGGCGGAGCTTAAAGTTTAGGGAGATGGTAAT

Alignment

ORF - retro_vvin_133 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.43 %
• Parental protein coverage: 58.76 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MITYEQDPDVVRWGLQLF-DGDPFSNCGYGGTIVQNDVSYYDGPYFKEDHYDNECSNVENDEIIAHALQE
          MI...QDP.VVRWGL.L..D.DPFS.CGYGGTIVQNDVSYYDG...KED.YDNEC.N.EN.EII.HAL.E
Retrocopy MIACGQDPIVVRWGLRLL<DDDPFSKCGYGGTIVQNDVSYYDG*HLKEDRYDNECGNAENGEIIEHAL*E

Parental  ELSQLAVDEAAGLSHEVVEDLQVSIFPEEWPDQSMGNYGFGHESGQEDTDDMGLSSSCSSPDEKSYNGED
          ELSQLA.DE.A..SHEVVEDLQVSI.P.EWPDQSM.NYGF.HESGQ.D.D.MGLSSSCSSPDEKS.NGE.
Retrocopy ELSQLAIDETARFSHEVVEDLQVSILPKEWPDQSMENYGFRHESGQKDIDGMGLSSSCSSPDEKSHNGEG

Parental  WSYSLDLTDEYALDDEVGKILNQMVPVPHVPKINGEIPSLDEATLDHQRLLDRLQLFDLVELKVQGDGN
          WSYSLDLTDE.ALD.EVGKILNQMV..PHVPKINGEIPSLDE.TLDHQR.LD.L.LF...ELKV.GDGN
Retrocopy WSYSLDLTDENALDGEVGKILNQMVSIPHVPKINGEIPSLDETTLDHQRPLD*LRLFGMAELKV*GDGN

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_133 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_06s0004g02480	1 retrocopy	retro_vvin_133 ,