RetrogeneDB ID: retro_vvin_8

Retrocopy location

• Organism: Grape (Vitis vinifera)
• Coordinates: 16:826921..827689(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: VIT_16s0039g01380
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: VIT_14s0068g01460
• Aliases: None
• Description: None

Sequence

>retro_vvin_8
ATGAGCACTTCTACAGGTGATTTCTATGTTAAGAAATTCCTATCTTACCACTGGAGGTCCATTAGCTCAAGGCGGGCCCC
AATATTCAATAATCTGAGCTCAATGGGGAAACTTCTAGCAGATGCACTAGGATATTATCACTTTGACAATGATAGTTTGG
TTGAGGAAGCTTGCGGTGGTGAGTCTGCTGCCAAGTCTTTAAAAGAGCAAGATGAGGAGGAATTTCGTGACTCTGAGACT
GAAGTATTGAAGCAGTTATCATCCAGGGGTCAGTTGGCGGTTTGTGCTGGAAATGGTTCAGTTCATAGCTCAATTAATCT
GGCACTTCTGAGACATGGAATTTCAATATGGATTGATGTACCGATAGAAATGGTTGCCAAGAACGTGATAGAAGAAGGGG
TTCAAATTCCTGTAACAGAATTATCTACTGCAGAATCTTATTCTGAGACGGGTGGTAACCAGGTGTTAGCTCAGCTAGTT
ATGGTGTATGAAGAAAGGAAAGGTGGATATGCAACAGCAGATGCATCAGTTTCACTCCAAAAAGTAGCTTCCCAATTAAG
TTACGATGACTTGGATGCAGTAACCACTGAAGACATGACTATGGAGGTTCTTAAAGAGATACAAAGACTGGCCAGACTAA
AGAAGATGAAAAGAGACCTTTGTTTTCTGCAAGCATTACGTCCACTCTGGCACCCACTTCTAGCATGGCATGCATGGCCA
CCTTTGATCCAAGTGTCATTCCCCATTTTTCCATCTTTAACTTTTTAA

Alignment

ORF - retro_vvin_8 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.56 %
• Parental protein coverage: 61.31 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TNVGKLLADALRYYHFDSDSLVEEACGGESAAKSLKEQDEKGFHDSETEVLKQLSSMGRLVVCAGDGLVQ
          ...GKLLADAL.YYHFD.DSLVEEACGGESAAKSLKEQDE..F.DSETEVLKQLSS.G.L.VCAG.G.V.
Retrocopy SSMGKLLADALGYYHFDNDSLVEEACGGESAAKSLKEQDEEEFRDSETEVLKQLSSRGQLAVCAGNGSVH

Parental  SSTNLALLRHGISIWIDVPIEMVAKNMIEEGVQIPVTELSTAESYSETGDNQVFAQLAVVYEEMKGGYAT
          SS.NLALLRHGISIWIDVPIEMVAKN.IEEGVQIPVTELSTAESYSETG.NQV.AQL..VYEE.KGGYAT
Retrocopy SSINLALLRHGISIWIDVPIEMVAKNVIEEGVQIPVTELSTAESYSETGGNQVLAQLVMVYEERKGGYAT

Parental  ADASVSLQKVASQLGYDDLDAVTTEDMAMEVLKEIQRLTRLKKMMEE
          ADASVSLQKVASQL.YDDLDAVTTEDM.MEVLKEIQRL.RLKKM...
Retrocopy ADASVSLQKVASQLSYDDLDAVTTEDMTMEVLKEIQRLARLKKMKRD

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_8 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_14s0068g01460	1 retrocopy	retro_vvin_8 ,