RetrogeneDB ID: retro_vvin_169

Retrocopy location

• Organism: Grape (Vitis vinifera)
• Coordinates: 7:7351152..7351461(-)
• Located in intron of: VIT_07s0005g04230

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: VIT_05s0020g04110
• Aliases: None
• Description: None

Sequence

>retro_vvin_169
CCATCCTCCATGCTCATCAAATTCAACCATGCCTCCTCACAAGCAAGATCAGAAACAGTTTCTTCTAGCGAACAACCACC
GCCCGACACCACCAACCCCCAGCAGCCACCCTCACTCTCATAGTCACCTCAGTCGATCCCTCATCTTCTTCCTCCCGTGC
CTAAGGCGAGCACTAAATTTGGAGATGCGTGTGCGTTTAATATGCTGACGTCAGAAATGATCAACGACAGGCTTGCCATG
GTTGGCTTTGTTGTAGCAATGGGTGTGGAAATATGGAGGGTGTGGGAGAAGTTTGAAGCAAATGGAAAC

Alignment

ORF - retro_vvin_169 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.48 %
• Parental protein coverage: 53.3 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PPRSVLRLQRSAVQVRCTKEDGQIERPPPVTTNPQQPPSLSQSRQPIPPPPPPPAPKVSTKFGDVFAFSG
          P............Q.R........E.PPP.TTNPQQPPSLS.S.Q.I.P...PP.PK.STKFGD..AF..
Retrocopy PSSMLIKFNHASSQAR-SETVSSSEQPPPDTTNPQQPPSLS*SPQSI-PHLLPPVPKASTKFGDACAFNM

Parental  PAPERINGRLAMVGFVAAMGAEIWKGEDVFAQISN
          ...E.IN.RLAMVGFV.AMG.EIW.....F....N
Retrocopy LTSEMINDRLAMVGFVVAMGVEIWRVWEKFEANGN

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_169 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 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Vitis vinifera	VIT_05s0020g04110	2 retrocopies	retro_vvin_169 , retro_vvin_54,