RetrogeneDB ID: retro_vvin_13

Retrocopy location

• Organism: Grape (Vitis vinifera)
• Coordinates: 14:25068779..25070063(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: VIT_14s0068g01350
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: VIT_15s0046g01510
• Aliases: None
• Description: None

Sequence

>retro_vvin_13
ATGAGAGATTCCAACACGGATCTGTTCGACCCAAGAACAGCCATGGATTCTGATTCCTCACCGGGATCCACACCCACGGT
TTCGTCTTGCGATTTCGGATGCGCCTTCAATGACATTAACTTCTCCCATCGGATTCTGCGGATCGAGATCATGGCGGGAG
CGCAGGATTCGAGGTCTGAAGGTGAGGGATGCACAAGCATCGCTGATTGGGCTAGGCACCGTAAGAGGAGGAGAGAGGAT
ATCAAGAAGGAGAACGGTGCAGATATTGTTACTTGTCCTGAAGAACAGATTTTAAATTGTAACCAGCCTGACGTGGATGA
TGTTGTGGCCTCTGAAAATGACGACAAAGAAGCAGTCGCGATGATTGAAGAATCTGCATCAGGTAATGAAGCTGAAGTTG
GCAATAATTCAGCCTGGAACATGGATTGTTCTACGGTCGTGAGAATTAAAACTCTACACATTAGCCCCCTTATTTTAGCT
GCAAAAAGTCCATTTTTCTACAAGCTCTTCTCAAATGAGATGAGGGAGTCAGAGCAGAGGCGTGTAACATTACGAATTAA
TGCGTCTGAGGAAGCTGCTCTCATGGAGCTCTTGAATTTCATGTATAGCAATACCCTGTCCACAAGTACAGCTCCTGGTT
CGCTGGATGTGCCGATGGCTGCTGATAAATTTGAGGTTGTGTCACGTATGAGGCACTGCAGCAGGCTCTTAAGGAACTTA
CCCATGATACCTGAATCTGCATTGCTCGGTCTAGAGCTTCCTTCTAGTGCCCTAATGGCTGAGGCAGTTCAGCCTTTGAC
AGATGTAGCCAAGCAATACCTTGCTAGTCGTTACAAAGACACAACCAAGTTTCAAGAAGAAGCGATGGCCTTACCCCTTG
TCGGGATTGAAGCAGTTTTGTCCAGTGATGATCTCCAGGTTGCGTCAGAGGATGCAGTGTATGATTTTGTGTTGAAGTGG
GCCAGGGCTCGGTACCCAAAATTGGAGGAGCGACATGAAATCCTTGGTACGCGCCTAGGCCGCTTCATCCAGTTCTCCTA
TGTGACATGCAGGAAGCTTAAGAAGGTTCTAACCTGCAATGACTTTGATCACGCCTTACATCCAAGGCTGTGCTGGAGGC
TCCATTTTTCAAGGCCGAGGCCCCTCATCGGCAGCGAAGCCTGGCTGCAGAGGACACTGCCCTCATCTACCGTTGCTTCG
TGGAGCGGGCCTACAAGTATCGTTCAGTCAAGGTTGTGGAGTTTGAATTTCCTCGACAGCCGTGTGTTGTCTACCTGGAT
CTAA

Alignment

ORF - retro_vvin_13 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.98 %
• Parental protein coverage: 66.18 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MRDSNTDLFDPRTAMDSDSSPGSTPTVSSCDFGFAFNDSNFSDRVLRIEIMAGSQDSRSEGEGCTSIADW
          MRDSNTDLFDPRTAMDSDSSPGSTPTVSSCDFG.AFND.NFS.R.LRIEIMAG.QDSRSEGEGCTSIADW
Retrocopy MRDSNTDLFDPRTAMDSDSSPGSTPTVSSCDFGCAFNDINFSHRILRIEIMAGAQDSRSEGEGCTSIADW

Parental  ARHRKRRREDIKKENGADIVACPEEQILNCNQPDVDDVVACENEDEEAVAMIEESASGDEAEVGNNSAWN
          ARHRKRRREDIKKENGADIV.CPEEQILNCNQPDVDDVVA.EN.D.EAVAMIEESASG.EAEVGNNSAWN
Retrocopy ARHRKRRREDIKKENGADIVTCPEEQILNCNQPDVDDVVASENDDKEAVAMIEESASGNEAEVGNNSAWN

Parental  MDCSTVVRIKTLHISSPILAAKSPFFYKLFSNGMRESEQRHVTLRINASEEAALMELLNFMYSNTLSTST
          MDCSTVVRIKTLHIS..ILAAKSPFFYKLFSN.MRESEQR.VTLRINASEEAALMELLNFMYSNTLSTST
Retrocopy MDCSTVVRIKTLHISPLILAAKSPFFYKLFSNEMRESEQRRVTLRINASEEAALMELLNFMYSNTLSTST

Parental  APGLLDVLMAADKFEVASCMRHCSRLLRNLSMTPESALLYLELPSSVLMAEAVQPLTDAAKQYLAGRYKD
          APG.LDV.MAADKFEV.S.MRHCSRLLRNL.M.PESALL.LELPSS.LMAEAVQPLTD.AKQYLA.RYKD
Retrocopy APGSLDVPMAADKFEVVSRMRHCSRLLRNLPMIPESALLGLELPSSALMAEAVQPLTDVAKQYLASRYKD

Parental  ITKFQEEVMALPLAGIEAVLSSDDLQVASEDAVYDFVLKWARAQYPKLEERREILGTRLGRFIRFPYMTC
          .TKFQEE.MALPL.GIEAVLSSDDLQVASEDAVYDFVLKWARA.YPKLEER.EILGTRLGRFI.F.Y.TC
Retrocopy TTKFQEEAMALPLVGIEAVLSSDDLQVASEDAVYDFVLKWARARYPKLEERHEILGTRLGRFIQFSYVTC

Parental  RKLKKVLTCNDFDHDL
          RKLKKVLTCNDFDH.L
Retrocopy RKLKKVLTCNDFDHAL

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_13 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_15s0046g01510	1 retrocopy	retro_vvin_13 ,