RetrogeneDB ID: retro_vvin_5

Retrocopy location

• Organism: Grape (Vitis vinifera)
• Coordinates: 6:19128615..19129851(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: VIT_06s0061g01300
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: VIT_12s0059g00750
• Aliases: None
• Description: None

Sequence

>retro_vvin_5
ATGCAGGCTCTATCTCCATCTCCTAATCTCAAATCCTTAATCAGGACGAGGCCGCTCGTTCCCACTCACCGCGTCGCTCC
ACACCGACTCGTGGTTCAATGTGTTTACAAATCCGACTACTCTAACTTCTCCGGCGGCGTCGGGTTCAGCCGAGCTGATT
GGCAAAGCTCTTGCGCCATCTTAGCTAGCAAGGTTGTGTCGCAGCAGCAAGACACCGAGAAGAGCGGCAACGCCGATCTG
ACCGCTGTTAATGGCCACAAGACACTAGATCTCGTCCCCATCGAGAATCTGCCCAAGCCGCTCACCATCACCGACCTCTC
ACCCGCTCCGATGCACGGCTCGGAGCTCCGTGTGGCTTACCAGGGTGTTCCCGGCGCGTACAGCGAGGCCGCCGCCGGAA
AAGCGTATCCGAACTGCGAGGCGATACCGTGTGACCAATTCGAGGTGGCGTTTCAGGCTGTGGAGCTGTGGATCGCCGAT
CGAGCTGTGCTGCCGGTGGAGAACTCGCTCGGAGGCAGCATTCACCGGAATTATGACCTCCTGCTTCGCCACCGCCTCCA
CATCGTGGGCGAGGTCCAACTTCCGGTGCACCACTGCCTGTTAGCCTTACCGGGAGTGCGAAAAGAGTACCTGACTCGCG
TGATAAGCCATCCTCAAGCCCTGGCCCAGTGCGAGCACACGCTCACCAAACTCGGCCTCAACGTCGCTCGCGAGGCCGTG
GACGACACCGCCGGAGCCGCGGAGTACGTAGCGTTGAACAACCTCCGAGATACGGCGGCGATCGCGAGCGCCCGAGCGGC
GGATCTGTACGGACTCCAGATATTGGCGGACGGCATCCAAGACGACTCGAGCAACGTGACTCGGTTCGTGATGCTTGCGC
GCGAGCCAATCATCCCTCGCACCGACCGGCCATTCAAGACCAGCATCGTATTCGCACACGACAAGGGAACGTCCGTACTG
TTCAAGGTTCTGTCAGCGTTCGCCTTCAGAAACATAAGCTTGACGAAGATCGAGAGCAGACCTCACCGAAACCGTCCGAT
CAGATTGGTGGACGACGCGAACGTGGGAACGGCAAAGCACTTCGAGTACATGTTCTACGTGGATTTCGAGGCATCCATGG
CAGAAGTCAGAGCCCAGAACGCACTGGCGGAGGTTCAAGAGTTCACATCTTTCTTGAGGGTGTTGGGGAGCTATCCTATG
GACATGACGCCTTGGTGCCCTTCTGGGGGAGATTAA

Alignment

ORF - retro_vvin_5 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.88 %
• Parental protein coverage: 78.23 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LASFPKPLSVTDISAAPKDGTKVRISYKGVPGAYSEDAALKAYPHCETVPCDEFEDAFKAVELWLAEKAV
          ....PKPL..TD.S.AP..G...R..Y.GVPGAYSE.AA.KAYP.CE..PCD.FE.AF.AVELW.A..AV
Retrocopy IENLPKPLTITDLSPAPMHGSELRVAYQGVPGAYSEAAAGKAYPNCEAIPCDQFEVAFQAVELWIADRAV

Parental  LPIENSLGGSIHRNYDLLLRHRLHIVGEVQLAVNLCLLAIPGVGIDQLRRVLSHPQALAQSDIILSKLG-
          LP.ENSLGGSIHRNYDLLLRHRLHIVGEVQL.V..CLLA.PGV....L.RV.SHPQALAQ....L.KLG.
Retrocopy LPVENSLGGSIHRNYDLLLRHRLHIVGEVQLPVHHCLLALPGVRKEYLTRVISHPQALAQCEHTLTKLGL

Parental  -VSRENVDDSAGAAQYVASHGLRDAGVVASARAAEIYGLNILAERIQDDFDNITRFLVLARDPIIPRTNK
          .V.RE.VDD.AGAA.YVA...LRD....ASARAA..YGL.ILA..IQDD..N.TRF..LAR.PIIPRT..
Retrocopy NVAREAVDDTAGAAEYVALNNLRDTAAIASARAADLYGLQILADGIQDDSSNVTRFVMLAREPIIPRTDR

Parental  LFKTSIVFTLEEGPGVLFKALAVFALRDINLTKIESRPQRKKPLRVVDDSNTGSAKYFDYLFYIDFEASM
          .FKTSIVF....G..VLFK.L..FA.R.I.LTKIESRP.R..P.R.VDD.N.G.AK.F.Y.FY.DFEASM
Retrocopy PFKTSIVFAHDKGTSVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMFYVDFEASM

Parental  AEPRAQTALAHLQEFATFLRVLGCYPMDSFP
          AE.RAQ.ALA..QEF..FLRVLG.YPMD..P
Retrocopy AEVRAQNALAEVQEFTSFLRVLGSYPMDMTP

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_5 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 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Theobroma cacao	TCM_011909	1 retrocopy	retro_tcac_23,
Vitis vinifera	VIT_12s0059g00750	1 retrocopy	retro_vvin_5 ,