RetrogeneDB ID: retro_slyc_88

Retrocopy location

• Organism: Tomato (Solanum lycopersicum)
• Coordinates: 6:46463588..46464167(-)
• Located in intron of: Solyc06g074960.2

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Solyc12g088660.1
• Aliases: None
• Description: None

Sequence

>retro_slyc_88
ATGGTTGAGCTTAAGTTTCTTGGGATGGATTTGGCTGTGTTTTGGGAACCCTTAGCAAAGATGAATTCCTGGAAAAGGAT
TGTTTGGTTCGGTTAATATCCAAGATCCTTGGATATCCTATCGTTGCTACCTCCACCACTGTTAAAGTTCCTCAGATATT
AAAAAATTGTACAGTGCAAAAGTTTAGTGTTGTGAGTTTTGAGCTTGAAGTAATTGGTTCTACCATTGCTTTAGCATATT
GTCTTCACAAAGGACTTCCATTTTCAGCATTTGGAGAGAATGCTTTTCTTTTGATTCAAGCTATCATTTTGGTGCAATCA
TCTATTAGTTTCTCAGCCTTTGGGAGGAAAACATTGATTAGAGCATTATCATATTGTGCTATAGCCCCATCTGTTTTGGC
AGGTGAAATTGATGCCATCCATTTTGAGGCTTCATATGCCTGTCAGCACACGATTTTCTTTTTGCTAGTATGCCCAAATC
TTGAAGAATTTTAAGAACAGAAGAACTGAGGAGCTAAGCTGTTTAACCTTTTTAATGAACTTTGGTGGTTCCATGTTAAG
AGTTTTTACCAGTTTTGAA

Alignment

ORF - retro_slyc_88 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.63 %
• Parental protein coverage: 83.19 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  MVELKFLGMD-FGCALGSLSNGQFPEKDCLLPLISKLLGYAIVAASTTVKLPQILKILQHKSVRGLSVVA
          MVELKFLGMD.FGC.LG.LS...F.EKDCL..LISK.LGY.IVA.STTVK.PQILK......V...SVV.
Retrocopy MVELKFLGMD<FGCVLGTLSKDEFLEKDCLVRLISKILGYPIVATSTTVKVPQILK---NCTVQKFSVVS

Parental  FELELIGYTIALSYCLHKGLPFSAFGEYLFLLIQAIILV-AIIYYF-SQPL-GMKTWMKGLLYCAVAPTV
          FELE.IG.TIAL.YCLHKGLPFSAFGE..FLLIQAIILV.AIIY.F.SQPL.G.KT....L.YCA.AP.V
Retrocopy FELEVIGSTIALAYCLHKGLPFSAFGENAFLLIQAIILV<AIIY*F<SQPL<GRKTLIRALSYCAIAPSV

Parental  LAGQINPVLFEALYASQHAI-FLCARIP-QIWKNFKGKSTGELSFLTFFMNFAGSMVRVFTSLQ
          LAG.I....FEA.YA.QH.I.FL.A..P.QI.KNFK...T.ELS.LTF.MNF.GSM.RVFTS..
Retrocopy LAGEIDAIHFEASYACQHTI<FLFASMP<QILKNFKNRRTEELSCLTFLMNFGGSMLRVFTSFE

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Solanum lycopersicum was not studied using RNA-Seq expression data.

ChIP-Seq

Solanum lycopersicum was not studied using ChIP-Seq data.

EST

Solanum lycopersicum was not studied using EST data.

TSS

Solanum lycopersicum was not studied using FANTOM5 data.

Lab

retro_slyc_88 was not experimentally validated.

Homology

Retrocopy orthology:

Solanum lycopersicum 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Solanum tuberosum	PGSC0003DMG400015434	1 retrocopy	retro_stub_134,
Solanum lycopersicum	Solyc12g088660.1	1 retrocopy	retro_slyc_88 ,