RetrogeneDB ID: retro_vvin_84

Retrocopy location

• Organism: Grape (Vitis vinifera)
• Coordinates: 14:1334853..1335207(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: VIT_03s0038g03420
• Aliases: None
• Description: None

Sequence

>retro_vvin_84
CCATTGTCAAACACACACCAAAGAAGAGCAGAAATGGTTCGTCACTCTGATTTCTTCAGTGCCTTACCAGGTGGGTAGGG
AACTCTAAAGGAATTGCATGAAATCATCTCATGGGCATAGCTCGAAATCCGCGATGAACCAGTGGATTTGTTTCGTGTGG
ATGGCTACTACAACAACCTACCCACCTTCATTGACAAAGCAGTGGATAATAGCTTCATCAAATCTTCACAGCGCCACATT
ATTGTGTCTGCTCCAAATGTCAAAAAGCTATTCCAAAAGCTTGAGAAGTATGTGCCTGTGCATAATGGAGCCATTGCGAA
GACGAGGTGGGAGGTTGAACAATAGCAACATCAG

Alignment

ORF - retro_vvin_84 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.03 %
• Parental protein coverage: 51.53 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PVADMHQRKAEMARHSDCFIALPGGYGTLEELLEVITWAQLGIHDKPVGLLNVDGYYNYLLTFIDKAVDD
          P....HQR.AEM.RHSD.F.ALPGG.GTL.EL.E.I.WA.L.I.D.PV.L..VDGYYN.L.TFIDKAVD.
Retrocopy PLSNTHQRRAEMVRHSDFFSALPGG*GTLKELHEIISWA*LEIRDEPVDLFRVDGYYNNLPTFIDKAVDN

Parental  GFIKPSQRHIIVSAPNAKELVQKLEEYVPVHDGVIAKARWEVEQQQHQ
          .FIK.SQRHIIVSAPN.K.L.QKLE.YVPVH.G.IAK.RWEVEQ.QHQ
Retrocopy SFIKSSQRHIIVSAPNVKKLFQKLEKYVPVHNGAIAKTRWEVEQ*QHQ

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_84 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Vitis vinifera	VIT_03s0038g03420	1 retrocopy	retro_vvin_84 ,
Vitis vinifera	VIT_18s0001g00210	2 retrocopies	retro_vvin_65, retro_vvin_66,