RetrogeneDB ID: retro_vvin_110

Retrocopy location

• Organism: Grape (Vitis vinifera)
• Coordinates: 17_random:408500..408979(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: VIT_04s0008g02290
• Aliases: None
• Description: None

Sequence

>retro_vvin_110
ATGTTTAAGGAAGTTGTTTTCTCGATAAAGTTTTTGCTTCTTGACCACTACTCTCCTTCTTCGCCTTCTTTGCGAAAATT
GTTTTATTCAGTTGTATGTTAGGTTGCTACTATTTTGAGGACTAGATACACTGTTCCCAGGTTCTGGCTTGCTAGGTTAA
GGTTTTTTGAATAGTCTGAATCCATGTGACTAATTCTTCTGAGAATGAGAACTTGAAGAGTTGCATTGTTGGTGCTAGGC
AACAGCTAAACCATGTAGAGAATCCATCTGAAGCTTCAGAAACAGCGGAAAATATGGCTAATAGAGGATACATTTTCGAG
GGACATCTAATTGTGGATCCCAAGCCTCCAAGACCTCAATGGCTGGTGCAATTTAACCTCTTGATAGCTACTGCTACACT
TTCTAACTTAGAAATCAGCCAATGGTCTTACAAAAATAATAATATCACATCAGAAAATGTTGCTAGTATACTTTTACAG

Alignment

ORF - retro_vvin_110 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.49 %
• Parental protein coverage: 54.95 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MFEEAVLSIKSLLVDHYSSSSPSLRKLFYSVVCRVATILRTRYTAPGFWLSGLRLFEQAESM-VTDSSEK
          MF.E.V.SIK.LL.DHYS.SSPSLRKLFYSVVC.VATILRTRYT.P.FWL..LR.FE..ESM.VT.SSE.
Retrocopy MFKEVVFSIKFLLLDHYSPSSPSLRKLFYSVVC*VATILRTRYTVPRFWLARLRFFE*SESM<VTNSSEN

Parental  ENLKSCIAGARQQLNHVENLSEASETTENRANRGYLFEGHLTVDPEPPRPQWLVQSNNLLTAAATLSNLE
          ENLKSCI.GARQQLNHVEN.SEASET.EN.ANRGY.FEGHL.VDP.PPRPQWLVQ..NLL.A.ATLSNLE
Retrocopy ENLKSCIVGARQQLNHVENPSEASETAENMANRGYIFEGHLIVDPKPPRPQWLVQF-NLLIATATLSNLE

Parental  -SANGLT-ENNNITSENAASILLQ
          .SANGLT..NNNITSEN.ASILLQ
Retrocopy >SANGLT<KNNNITSENVASILLQ

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_110 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_04s0008g02290	1 retrocopy	retro_vvin_110 ,