RetrogeneDB ID: retro_vvin_47

Retrocopy location

• Organism: Grape (Vitis vinifera)
• Coordinates: 10:12572410..12573150(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: VIT_07s0141g00830
• Aliases: None
• Description: None

Sequence

>retro_vvin_47
AAACTCGATGGTCCTAGCCACTGCTACATTGACGGTGATGACTGCACCTCTAGTGGCATGGCCCTTAAGAGCGTCGATGT
CGCAACTCTCGAAAATCTCTATGTTGATTTGGTTCTCAATGTTCCAGAATTGCCTCCTGCGTCATTTCTCGATCGAAAGG
CTTACATAGAGTGGTTGGGGGCGTCTCCTCCTGATAAGAAATACTAGGAAGCTGGTGGTAACTGCAATATGGCTATTGCT
GCAAAAAGACTGGGACTTTGTTATATAACAATTGGTCATGTGGGTAATGAAATCTATGGAGACTCCCTTCTTGATGTGCT
TCATGATGAGGAATTGATATGGTTGGGATGAATGAAGATACCGATGTTGTTGTTGGTGCTAGTGCCTCGTATGAAACTCT
TCTATTCTGGGTTTTAATTGAACATGTGCAAAAACATGGTTTTTGTAGTTGAGTTGATTTTAGTAAGGAACCTGCATTCG
GCTAGATGAGCAAACTATCCAGAGAAATAAAGCTGACCATAAGAAAGTCAAAGATCCTGTTCTGTAATGGTTATGGTTTT
GATGAACTGTACCCTAGTTTGATTATATCTGCTTTGAACTATGTTGTTGAAGTTGGAACTTCAGTTTTCTTTAATCTTGG
ACCACATGGGAAAAGTCTTTCTGTTGGAACACCTGAACAACAAAGAGCACTAGGCCAATTCTTGACGATGAGCGATGTTC
TACTCTTAACATCTGATGAG

Alignment

ORF - retro_vvin_47 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.87 %
• Parental protein coverage: 53.81 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QLSVPSHCYTAGGDCTSGGVALKSVDVATLGNLCVDLVLNVPELPPASFLDRKAYMERLAASPPDKKYWE
          .L..PSHCY..G.DCTS.G.ALKSVDVATL.NL.VDLVLNVPELPPASFLDRKAY.E.L.ASPPDKKY.E
Retrocopy KLDGPSHCYIDGDDCTSSGMALKSVDVATLENLYVDLVLNVPELPPASFLDRKAYIEWLGASPPDKKY*E

Parental  AGGNCNMAIAAKRLGLCCVTIGHVGNEIYGDFLLDVLHDE-GIDTVGMNEDTDVVDSASASYETLLCWVL
          AGGNCNMAIAAKRLGLC..TIGHVGNEIYGD.LLDVLHDE.GID.VGMNEDTDVV..ASASYETLL.WVL
Retrocopy AGGNCNMAIAAKRLGLCYITIGHVGNEIYGDSLLDVLHDE<GIDMVGMNEDTDVVVGASASYETLLFWVL

Parental  VDPLQRHGFCSRADFSKEPAFSWMSKLSREVKMAIRKSKILFCNGYGFDELSPSLIISALDYAVEVGTSV
          ....Q.HGFCS..DFSKEPAF..MSKLSRE.K..IRKSKILFCNGYGFDEL.PSLIISAL.Y.VEVGTSV
Retrocopy IEHVQKHGFCS*VDFSKEPAFG*MSKLSREIKLTIRKSKILFCNGYGFDELYPSLIISALNYVVEVGTSV

Parental  FFDPGPRGKSLSVGTPEQQRALGQFLTMSDVLLLTSDE
          FF..GP.GKSLSVGTPEQQRALGQFLTMSDVLLLTSDE
Retrocopy FFNLGPHGKSLSVGTPEQQRALGQFLTMSDVLLLTSDE

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_47 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_07s0141g00830	1 retrocopy	retro_vvin_47 ,