RetrogeneDB ID: retro_vvin_43

Retrocopy location

• Organism: Grape (Vitis vinifera)
• Coordinates: 10:4318011..4318550(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: VIT_00s0179g00190
• Aliases: None
• Description: None

Sequence

>retro_vvin_43
AGGCACAGACTGACAGGGTCTGATGCAGAGCAATCCAATTTGCTTTTAGGAGATGCTCTTCAACAAATTTATTTAGCACG
AGTACCAATTATGAAATGTGGAGAATGATGATAAAGTTCAACTGGAAACTTTGATAGAAGACATTCAAACACCTGCATTT
TAGAGACAAAAACACTTGTTCCTACTAACTTATGGATGACCAGTGCTCAAGCTAGATCGAGTGCTCACTACGATCCACAC
CATAATCTTCTATGCATAATTGATGGCTGCAAACAAGTTGTTTTATTTCCCCCTTTTGCAAGTCTCTTATTATATCCAAT
GCCTATATATGGAAAGGCCTCAGACCATAGTTCTGTGACTTTAGAGGAATCTGATTTTTCAATTCATCCAAGAGCCGAAC
ACTCAATGAAGCATTCTTAGAAGGTTATTCTACATGCAAGAGATGCACTGTTCATTCCTGAAGGTCGGTTCCATCAAGTG
GATAATAATGATTTTACTATTGTTGTAACTTCTGGTGGCGGTCAAACATAACGTCTAGC

Alignment

ORF - retro_vvin_43 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.15 %
• Parental protein coverage: 56.25 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  RHGLAGSDAEQSNSLLGDAPQQIYLAQVPIM-NVENDDKVQLATLIEDIQTPAF-LETKTLASINLWMNS
          RH.L.GSDAEQSN.LLGDA.QQIYLA.VPIM.NVENDDKVQL.TLIEDIQTPAF.LETKTL...NLWM.S
Retrocopy RHRLTGSDAEQSNLLLGDALQQIYLARVPIM>NVENDDKVQLETLIEDIQTPAF<LETKTLVPTNLWMTS

Parental  AQARSSTHYDPHHNLLCIIAGCKQVVLWPPSASPLLYPMPIYGEASNHSSVALEDPDFSIHPRAEHSMKH
          AQARSS.HYDPHHNLLCII.GCKQVVL.PP.AS.LLYPMPIYG.AS.HSSV.LE..DFSIHPRAEHSMKH
Retrocopy AQARSSAHYDPHHNLLCIIDGCKQVVLFPPFASLLLYPMPIYGKASDHSSVTLEESDFSIHPRAEHSMKH

Parental  SQKVILHAGDALFIPEGWFHQVDSNDLTIAV-NFWWRSNITSS
          S.KVILHA.DALFIPEG.FHQVD.ND.TI.V.NFWWRSNITSS
Retrocopy S*KVILHARDALFIPEGRFHQVDNNDFTIVV<NFWWRSNITSS

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_43 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Vitis vinifera	VIT_00s0179g00190	3 retrocopies	retro_vvin_150, retro_vvin_170, retro_vvin_43 ,