RetrogeneDB ID: retro_vvin_31

Retrocopy location

• Organism: Grape (Vitis vinifera)
• Coordinates: Un:8913646..8914420(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: VIT_00s0186g00100
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: VIT_02s0012g01770
• Aliases: None
• Description: None

Sequence

>retro_vvin_31
ATGTCAGCTTCCCAGTTGACCACCCAGATGGCTTCCGTGGCGCCCCTACCACTCTCGCTAGCTGATCATGGCATCAAGAC
GATTGTCGAGGTTTATAAGGACGAGCCTAGAAACCCCAAGTATGCTTTCAAGCATTTTTTATTTAGTGCTCAAGGGCAGC
CTCGGTTTGGAGTGAGCTTGTGCCTCTTTGTTGATTGCCTCAACACTCTCTTAGTTCCCGGGCACTCAAATATTATTGAA
ATTCAATATCCGGAACTAGATATGCAACTTTTTCTCAAGTCTGTTGATTCCATGGATGCTTGCATTTATGGAGAGATCAG
AACAAGGATCCCGGATACAATTTCATGGGACTACAACTTTGAACATGCTGGAAGTACTCCTCTCAGTTTCACTCTCAACT
CTACAGCATTGAAAGAAGCCATTAACGACCTTGAATGGCCAGGATCTAGCATCCAGATAACCTTGGAACCAATTCCCCCT
TCAATTACCTTTAGAGGTGAAGGCCATGGAGACTTACAGATAGATTTTATATATTATGTGAACACCGATCTTTTGATTGC
TGTCCATAGTGATCACAGAGTCTCTTACAGACACAAGTATAAGTTTATTCGTGCAACAACTTCAAACATACCTAGCAGTG
TCACCAGAGATAATCGAGGAAGCAAGTTGACTATTGGGGAAAGTGGAGATCACCTTACCAGAGCCGCTAAGGTGTTGAAA
AAACTTAGTGGCCAAATCCCTGTTTTCTTTAAAGTGAGGAACACCGTGCAGTAG

Alignment

ORF - retro_vvin_31 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.35 %
• Parental protein coverage: 62.33 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FVQYEYSAQGRPRFGVSLSLFVNCLNTFSVPGRSNMIEIRYPGPDMQLLLKSVDSMDACIYAEIRTRIPD
          F.....SAQG.PRFGVSL.LFV.CLNT..VPG.SN.IEI.YP..DMQL.LKSVDSMDACIY.EIRTRIPD
Retrocopy FKHFLFSAQGQPRFGVSLCLFVDCLNTLLVPGHSNIIEIQYPELDMQLFLKSVDSMDACIYGEIRTRIPD

Parental  TISWDYNFEPAGSTPLSFTVKSAALKEAIDDLEWPGSSIQITLEPVPPSVTFRGEGHGDLQIDFMYYANT
          TISWDYNFE.AGSTPLSFT..S.ALKEAI.DLEWPGSSIQITLEP.PPS.TFRGEGHGDLQIDF.YY.NT
Retrocopy TISWDYNFEHAGSTPLSFTLNSTALKEAINDLEWPGSSIQITLEPIPPSITFRGEGHGDLQIDFIYYVNT

Parental  DLLIAFHCDHRVSYRYKYKFLRATTSNIPSSVIRDNRGSKLTIGRGG
          DLLIA.H.DHRVSYR.KYKF.RATTSNIPSSV.RDNRGSKLTIG..G
Retrocopy DLLIAVHSDHRVSYRHKYKFIRATTSNIPSSVTRDNRGSKLTIGESG

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_31 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_02s0012g01770	1 retrocopy	retro_vvin_31 ,