RetrogeneDB ID: retro_vvin_23

Retrocopy location

• Organism: Grape (Vitis vinifera)
• Coordinates: 9:20947768..20948305(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: VIT_09s0054g00420
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: VIT_14s0068g01370
• Aliases: None
• Description: None

Sequence

>retro_vvin_23
ATGGCTTTTATACTGGTTTCGTCGACGCTCGGGAGCTCAGATGTTCCGTTCATTGTGACCCACAAGAAGGCCTCTCTCAC
CAGGCTCAAGTCCGGTGACAAGCGAGTCTCTGTGTCCATCGACATCTGCAATCAAGGACCCACGACCGCGTATGATGTAA
GTCTCACTGATGATAGCTGGTCACAAGATGTATTTAATGTTGTCAGTGGCAACACTTCAACATCATGGGAAAGGCTTGAT
GTCGGTGGTCTTCTATCACATGCTTTTGAATTGGAGTCCAAAATGGAAGGAATGTTTTATGGTGCACCAGCAGTCATTAC
GTTCCACATCCCTACCACGGCTGCTCTGCAGGAGGCATATTCAACTCCAATATTGCCTTCAGATATCCTTGCAGTGAGAC
CTCCAGAGAAGAAGTTTGAGTGGGCTAAGAGGTTGTTGGCAAAATATGGGTCCCAAATCTCTGTGATCTCCATTGTGTAT
CTGGTCGCTAGTCCATCAAAATCCGGTGCTGGGAAAGGAAGCAAGAAGAAGAGTTAA

Alignment

ORF - retro_vvin_23 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.06 %
• Parental protein coverage: 94.71 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VALILVSSTLGSSDVPFIVAHKKASLTRLKSGAERVSVSIDIYNQGSTTAYDVSLTDDSWSQDVFNIVSG
          .A.ILVSSTLGSSDVPFIV.HKKASLTRLKSG..RVSVSIDI.NQG.TTAYDVSLTDDSWSQDVFN.VSG
Retrocopy MAFILVSSTLGSSDVPFIVTHKKASLTRLKSGDKRVSVSIDICNQGPTTAYDVSLTDDSWSQDVFNVVSG

Parental  NTSTSWERLDAGGLLSHAFELESKVEGMFYGAPAVITFRIPTTAALQEAYSTPILPLDILAVRPPEKKFE
          NTSTSWERLD.GGLLSHAFELESK.EGMFYGAPAVITF.IPTTAALQEAYSTPILP.DILAVRPPEKKFE
Retrocopy NTSTSWERLDVGGLLSHAFELESKMEGMFYGAPAVITFHIPTTAALQEAYSTPILPSDILAVRPPEKKFE

Parental  W--RLLAKYGSQISVISIVSVFVYLVASPSKSGAGKGSKKK
          W..RLLAKYGSQISVISIV....YLVASPSKSGAGKGSKKK
Retrocopy WAKRLLAKYGSQISVISIV----YLVASPSKSGAGKGSKKK

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_23 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.

---

Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Vitis vinifera	VIT_14s0068g01370	1 retrocopy	retro_vvin_23 ,