RetrogeneDB ID: retro_vvin_48

Retrocopy location

• Organism: Grape (Vitis vinifera)
• Coordinates: 10:18011916..18012822(+)
• Located in intron of: VIT_10s0071g01150

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: VIT_04s0023g03360
• Aliases: None
• Description: None

Sequence

>retro_vvin_48
ATGGAGACTCAATCATCTGCAAGAAGAGTCACAAGGTTACAAACCTTGGCTGCTTCAAACAAATTTCCCATCTCAAAGAA
ATTTGAAGAATCTGATGAGGGTGTGAAATCAAGAAAAAGACGTGAGAAGCAACAAGAACGGTCTACGCTCATTGATGTAA
CGAATGATTCTCCCATTGTTGGACTTTCAATGGGAAGCTTGGAAACCCCAGTGTCATCCATCGCAAAGAAAAAGAGAAAT
CAAGCCAAGATGACCCCTCAGTCTGGGGAGGCATTGCTTAGGGGTCAGGTGAAGACCCTATTGCAGAAGGTCGAAAAAGG
GCCGGGCTTTTGAGACTCTCATTGGAAGACTGCCCCTTTCTTCATGTTCAAGGTCTCATCAATTGCCCTATGCTTCTTGC
CCCAACTCCAACAAACACACCCCAAGTCTTGAATCTTACAGTGGAGCAAAGTATCAACAATAGCAGCATGACTTTGGTGA
TGCCTTCTCCAATGGGCCAAGAACTAAAGATCTCCAAGGTGGCCAGTAATATTTTTGACAGGGAGAAGAAAAAGAATATT
GAATTGGAAACAAGTCCAGTAACTCACCCTCTACTGTTGGATTTCTCTGAAAAATCAGAAATTGCAGAGTGCAAAGAGAA
GACACCCCATGAGGACAATGATGCTTCAGTTTGGTCTATTCAGGTTAATGCAAATATCAAGGACGAAGATGAATAAGAGG
CAGTCGAAGAAGAAGAAGAAGATTATCATGAAGAAATCAACTGAGGAAGAAAAATATGAAAATGATGGAGGAATTGTTGA
TGAACCGTGCGAAGGAATGAGCAAGATCAGCATGAATGAGAATAGAATACACAAGTTTAGAGGAAAGCACACCCAATTTG
TGTACAACACTGATGACAATCTTGTT

Alignment

ORF - retro_vvin_48 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.61 %
• Parental protein coverage: 90.83 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  METPSSTRRVTRSQALAASNSNIPISKKFEESDKGVKSRKRSGKQQERYALVDVTNDSPIVGVAMGSLET
          MET.SS.RRVTR.Q.LAASN...PISKKFEESD.GVKSRKR..KQQER..L.DVTNDSPIVG..MGSLET
Retrocopy METQSSARRVTRLQTLAASNK-FPISKKFEESDEGVKSRKRREKQQERSTLIDVTNDSPIVGLSMGSLET

Parental  PLSSMAKNKSNQSKMTPGSGEALLRGQVKTLLQKVE-EEAEHSKLSLEGRPILHVQGLISSPMLLAPTPA
          P.SS.AK.K.NQ.KMTP.SGEALLRGQVKTLLQKVE...A....LSLE..P.LHVQGLI..PMLLAPTP.
Retrocopy PVSSIAKKKRNQAKMTPQSGEALLRGQVKTLLQKVE<KRAGLLRLSLEDCPFLHVQGLINCPMLLAPTPT

Parental  NTPQLLNLSVEQIINNSG---VMPSPMGQELMISEVVTDIFDGKKKENIESEASPVTRSLLSDFSEKSEI
          NTPQ.LNL.VEQ.INNS....VMPSPMGQEL.IS.V...IFD..KK.NIE.E.SPVT..LL.DFSEKSEI
Retrocopy NTPQVLNLTVEQSINNSSMTLVMPSPMGQELKISKVASNIFDREKKKNIELETSPVTHPLLLDFSEKSEI

Parental  SESSECKKKTFQEDDDASVWSIQVNASIKDEDEEEA-FEEEEDYREEIE-YEEEEEEEYEENGGIVDELC
          .E...CK.KT..ED.DASVWSIQVNA.IKDEDE.EA.......Y.EEI...EE..E......GGIVDE.C
Retrocopy AE---CKEKTPHEDNDASVWSIQVNANIKDEDE*EAVXXXXXXYHEEIN>EEEKYEND----GGIVDEPC

Parental  EGMSKISVNENGIAAKSRGKHTRFVYNSDDELV
          EGMSKIS.NEN.I..K.RGKHT.FVYN.DD.LV
Retrocopy EGMSKISMNENRI-HKFRGKHTQFVYNTDDNLV

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_48 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_04s0023g03360	1 retrocopy	retro_vvin_48 ,