RetrogeneDB ID: retro_vvin_192

Retrocopy location

• Organism: Grape (Vitis vinifera)
• Coordinates: Un:15309502..15309964(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: VIT_03s0180g00170
• Aliases: None
• Description: None

Sequence

>retro_vvin_192
ATGGACGAACCTGATCATCTTTCTCACATCCCCGTTCATCAATCTCTTGGTGGCGGTTCAGTTGCTAATTTCCTGTTGTG
GAGATGGTGATGTGGAGCGGCGACTTGTCTAATCTCTGCAGGTAGCATATGGTTTCGCTTTCGAATGAGTCGGCGATGAC
CTATTGTTTTTCGTAGCAAATGTGGTGTTGTTTTTTGTTGTGATCGTCTTTCCTATGAGCCAAATCCGCATCTATTCTTA
ATAGACTTCTGCATTTTTCTCCCTGATATGGAAATCTCTGAAGAATCTGTTGTGAAAGCTATAGATGTCATTTGAGTATG
GATCAATTATGCGTTATCAACTGCACGGGACATTACAGTTGGTAGAAACGTGAAACTCTTCCTCCAGGTTGCTTTTGGCT
TGTGGTTTGTTTCATATATTGGCAGTCTCTTCGAGTTCCTGACTACTGCCCATATTGAGGTT

Alignment

ORF - retro_vvin_192 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.36 %
• Parental protein coverage: 73.91 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MGESDHPSRISVHQALGGGSVADFLLWRRWCGAAVCLVSASSLW-FLFERAGYNLLSFVANVVLLLVVIL
          M.E.DH.S.I.VHQ.LGGGSVA.FLLWR..CGAA.CL.SA.S.W.F.FE..G..LL.FVANVVL..VVI.
Retrocopy MDEPDHLSHIPVHQSLGGGSVANFLLWRW*CGAATCLISAGSIW>FAFE*VGDDLLFFVANVVLFFVVIV

Parental  -FLWAKSASILNRPLPPLP-DMEISEESVVKAADVIRVWINYALSVARDIAVGRNVKLFLQVAFGLWVVS
          .FL.AKSASILNR.L...P.DMEISEESVVKA.DVI.VWINYALS.ARDI.VGRNVKLFLQVAFGLW.VS
Retrocopy >FL*AKSASILNRLLHFSP>DMEISEESVVKAIDVI*VWINYALSTARDITVGRNVKLFLQVAFGLWFVS

Parental  YIGSLFNFLTLVYIGV
          YIGSLF.FLT...I.V
Retrocopy YIGSLFEFLTTAHIEV

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_192 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Glycine max	GLYMA20G26480	1 retrocopy	retro_gmax_27,
Vitis vinifera	VIT_02s0025g00640	1 retrocopy	retro_vvin_116,
Vitis vinifera	VIT_03s0180g00170	1 retrocopy	retro_vvin_192 ,