RetrogeneDB ID: retro_vvin_63

Retrocopy location

• Organism: Grape (Vitis vinifera)
• Coordinates: 12:20511262..20511645(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: VIT_11s0206g00130
• Aliases: None
• Description: None

Sequence

>retro_vvin_63
ATGAAGATCACAACACTTTCTGAATTTGAAATGCAATCCGGATGGATCCGATGCGATAATCCTGACGAACACATCTAATG
TCAGCCATTTCGGGTACTTTTAAAGATCCAGCGTCAAGGAATTTATCGTTTTCATGGATCGGACAATTGTCAAAAGGACA
TCTCCCTCTCAACGCCAATTCGTCCAACATGAAGAATATAAAGTGCATTCTTACAATAGAAATGGTCTTTGTGCACTAGA
TTTTATGGATGACCACTATCCTATTCAAAGCGCATTTTCCTTGCTCAACTAGGTGCGAGATGAGTATCAAAAGAATTTTG
GTGATTCATGGAGGATTGTACAAGCAGATAACACTTAACCATGGCCCCTATTTGAATGAAGCA

Alignment

ORF - retro_vvin_63 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.95 %
• Parental protein coverage: 63.82 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MKITAL-LVLKCNPDGSDAIILANASDVGHFGYFQRSSVKEFIVFVGRTVAKRTPPSQRQSVQHEEYKVH
          MKIT.L.L.LKCNPDGSDAIIL.N.S.V.HFGYF.RSSVKEFIVF..RT..KRT.PSQRQ.VQHEEYKVH
Retrocopy MKITTL>LNLKCNPDGSDAIILTNTSNVSHFGYF*RSSVKEFIVFMDRTIVKRTSPSQRQFVQHEEYKVH

Parental  SYNRNGLCALGFMDDHYPVRSAFSLLNQVIDEYQKNFGDSWRTVQADNTQPW-PYLNEA
          SYNRNGLCAL.FMDDHYP..SAFSLLN.V.DEYQKNFGDSWR.VQADNT.PW.PYLNEA
Retrocopy SYNRNGLCALDFMDDHYPIQSAFSLLN*VRDEYQKNFGDSWRIVQADNT*PW>PYLNEA

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_63 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_11s0206g00130	1 retrocopy	retro_vvin_63 ,