RetrogeneDB ID: retro_vvin_89

Retrocopy location

• Organism: Grape (Vitis vinifera)
• Coordinates: 14:16460981..16461789(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: VIT_03s0091g00410
• Aliases: None
• Description: None

Sequence

>retro_vvin_89
CTCGCCCTGGTGCACGTTAGCACCACTGATCCTTTGCCTCACCTAAGCATCAAGGACACTCCCATTGAAACTTCTTCTGC
CCAGTATATATTGCAACAATACACAACTACCTTTAGAGGATAAAAACTACAGAACTCAATTCGAAATGCTTATGCCATGG
GGAATGTGAAGATGATAGCTTTTGAGTTTGAGACTGCAACTTGGCTTTTGAAGAACTGAGATGCCTCAAAAGATGCAAAT
TTAGGTGGGTTTGTGCTCTGGTAGATGAATCCAGACATGTGGAATGTTGAACTTGCAGTTGGGGGTAGCAAGGTTTATGC
TAGCTGCAATGGCAAGCTTATCTTAAGGCATTCACCCTGGCTGGGAGCACATTCTGCAAAGGGCTGTGTTAGGCCATTGC
ACCGAGTGCTTTAGGGCCTTGATCCAAGGATCACTGCTCGCATGTTTGCTAATGCAATATGTATTGGAGAAAACAAGATC
AATAGTGAGGATTGCTTTATTATCAGGCTATGTGCTGACCCTCAGTCATTGAATGCTAGGAGTGAAGACCTAGTAGAGAT
CATAAGACATGTTTTGTTTGAGTACTTTAGCCAAAAAACGGGTCTTCTTGTTCACGTGGAGGGTTCCCATTTTACGCGCA
TCCAATCCAATGGTGGAGATATTGTTTACTAGGAAACCATAATCAATTCATTCCTAGAAGATTATAGGCTAGTTGAAGGG
ATCATGGTAGCTCACTCTGGGTGCTCAATAGTGACCCTTTTCAGGCTTGGAGAAGATGGCGGCTACAATCACCAACCTTA
CAATGCAA

Alignment

ORF - retro_vvin_89 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.89 %
• Parental protein coverage: 56.63 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LAPVHVSTTDPLPHLSIKDTPIETSSAQYILQQYTAASGGQKLQNSIRNAYAMGKVKMIASEFETATRVL
          LA.VHVSTTDPLPHLSIKDTPIETSSAQYILQQYT....G.KLQNSIRNAYAMG.VKMIA.EFETAT..L
Retrocopy LALVHVSTTDPLPHLSIKDTPIETSSAQYILQQYTTTFRG*KLQNSIRNAYAMGNVKMIAFEFETATWLL

Parental  KNRNASKDADSGGFVLWQMNPDMWYVELAVGGSKVHAGCNGKLVWRHTPWLGAHSAKGPVRPLRRALQGL
          KN..ASKDA..GGFVLW.MNPDMW.VELAVGGSKV.A.CNGKL..RH.PWLGAHSAKG.VRPL.R.L.GL
Retrocopy KN*DASKDANLGGFVLW*MNPDMWNVELAVGGSKVYASCNGKLILRHSPWLGAHSAKGCVRPLHRVL*GL

Parental  DPRTTASMFADARCIGEKKINGEDCFILKLCADPQTLKARSEGPAEIIRHVLFGYFSQKTGLLVHMEDSH
          DPR.TA.MFA.A.CIGE.KIN.EDCFI..LCADPQ.L.ARSE...EIIRHVLF.YFSQKTGLLVH.E.SH
Retrocopy DPRITARMFANAICIGENKINSEDCFIIRLCADPQSLNARSEDLVEIIRHVLFEYFSQKTGLLVHVEGSH

Parental  LTRIQSNGGDAVYWETTINSFLEDYRPVEGIMIAHSGRSIVTLFRFGE-MAMSHTKTRME
          .TRIQSNGGD.VY.ET.INSFLEDYR.VEGIM.AHSG.SIVTLFR.GE.MA...T...M.
Retrocopy FTRIQSNGGDIVY*ETIINSFLEDYRLVEGIMVAHSGCSIVTLFRLGE>MAATITNLTMQ

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_89 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_03s0091g00410	1 retrocopy	retro_vvin_89 ,