RetrogeneDB ID: retro_vvin_65

Retrocopy location

• Organism: Grape (Vitis vinifera)
• Coordinates: 12:6973960..6974466(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: VIT_18s0001g00210
• Aliases: None
• Description: None

Sequence

>retro_vvin_65
AGAGACACTGCTATTGAATTGGTTCAAGAACTTGACTCGAGGAGGTTGGATCTTGTTATGGCGGAGTAAGTGTTGGGTTA
ATGGGTTTGGTTTCTTATGAAGTTCATCGTGGCGGTGGACATATACTTGGAATCATCCCCAAAACTCTGATGTGCAAAGA
GATAACTGGGGAAACAGTAAGAGAGGTTTGACCCATAGCCGACATGCACCAAAGGAAAGCTGAGATGGCCCACCATTCAG
ATTGTTTTACCGCCTCATCAGGTGGCTATGGAACATTGGAGGAGTTATTGAAAGTCATCACATGGGCCCAACTTGGAATC
CATGACAAGCCTATGGGTTTGCTGAATGTGGATGGCTACTACAACCATCTCCTTACTTTCATCGAAAAAACCGTGGATAA
TGGCTTCATCAAGCCCTCTCAACATCACATTATCGTCTTTGCTCCAAACGCAAGAGAACCCGTTCAAAAACTCAAGGAAT
ACGTGTTTGTGCATACTGAAATAGTG

Alignment

ORF - retro_vvin_65 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.53 %
• Parental protein coverage: 77.17 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RDAAIELAQELVSRRLDLV-YGGGSVGLMGLVSQEVHRGGGHVLGIIPKTLMCKEITGETVGEVRPVADM
          RD.AIEL.QEL.SRRLDLV.YGG.SVGLMGLVS.EVHRGGGH.LGIIPKTLMCKEITGETV.EV.P.ADM
Retrocopy RDTAIELVQELDSRRLDLV<YGGVSVGLMGLVSYEVHRGGGHILGIIPKTLMCKEITGETVREV*PIADM

Parental  HQRKAEMARHSDCFIALPGGYGTLEELLEVITWAQLGIHDKPVGLLNVDGYYNYLLTFIDKAVDDGFIKP
          HQRKAEMA.HSDCF.A..GGYGTLEELL.VITWAQLGIHDKP.GLLNVDGYYN.LLTFI.K.VD.GFIKP
Retrocopy HQRKAEMAHHSDCFTASSGGYGTLEELLKVITWAQLGIHDKPMGLLNVDGYYNHLLTFIEKTVDNGFIKP

Parental  SQRHIIVSAPNARELVQKLEEYVPVHDGVV
          SQ.HIIV.APNARE.VQKL.EYV.VH...V
Retrocopy SQHHIIVFAPNAREPVQKLKEYVFVHTEIV

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_65 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,