RetrogeneDB ID: retro_slyc_5

Retrocopy location

• Organism: Tomato (Solanum lycopersicum)
• Coordinates: 12:65761436..65762306(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Solyc12g098120.1
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Solyc06g062430.2
• Aliases: None
• Description: None

Sequence

>retro_slyc_5
ATGACTATCCAACTAGAGGGAAAAAAAATCCAAGACCAAGACCAATTTATGGTGCCTCAAACAAATGCATTTGGACATGA
TTTTAGGGACTACAACAATGCACAAAGTGAAAGGCAAAAAGGGGTAGAAAAATTCTACAAAACACAACATATAAATCAAA
CCTATGATTTTGTGAAGAAAATGAGAGAAGATTACATAAAATTAGACAAAGCAAAAATGAGCATATGGGAATGTTGTGAA
TTATTAAATGATGTTGTTGATGATAGTGATCCTGATTTAGATGAACCACAAATTCAACATTTATTACAAAGTGCTGAGGC
AATTAGAAAAGATTATCCTAATGAAGATTGGTTACACTTAACAGCCTTAATTCATGATTTGGGTAAAATATTAGTTTTAC
CTAAGTTTGGTGGTTTACCTCAATGGGCTGTTGTTGGTGACACATTCCCTTTAGGATGTGCATTTGATGAATCAAATATT
CATCATAAATATTTTAAAGAAAATCAAGATTTCAACAACCCAATTTATAACACAAAAAATGGAATATATAATGATTCTAT
TGGACTAGAAAATGTCATGATGTCATGGGGTCATGATGATTATATGTACATGGTTGCTAAAGAAAATGGTACAACATTAC
CATCAGCTGGACTTTTTATTATAAGGTATCATTCATTTTATCCATTGCATAAAAATGGAGGTTATAAACATTTAATGAAT
GATGAAGATGAAGAAAATTTGAAGTGGCTTCATGTTTTTAATAAATATGATTTGTATAGTAAAAGCAAAGTTCATGTTAA
TGTGGAAGAAGTAAAACCTTATTATATGTCTTTAATTGAGAAATATTTTCCAGCAAAGCTAAGGTGGTGA

Alignment

ORF - retro_slyc_5 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.71 %
• Parental protein coverage: 90.16 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DGFAVPETNAFGHNFRDYT-VESARQQGVENFYKINHFNQTYDYVSKMRVEYAKLDKAEMSIWECCELLN
          D.F.VP.TNAFGH.FRDY....S.RQ.GVE.FYK..H.NQTYD.V.KMR..Y.KLDKA.MSIWECCELLN
Retrocopy DQFMVPQTNAFGHDFRDYNNAQSERQKGVEKFYKTQHINQTYDFVKKMREDYIKLDKAKMSIWECCELLN

Parental  DVVDDSDPDLDEPQIQHLLQSAEAIRKDYPDEDWLHLTALIHDLGKVLLLPSFGELPQWAVVGDTFPVGC
          DVVDDSDPDLDEPQIQHLLQSAEAIRKDYP.EDWLHLTALIHDLGK.L.LP.FG.LPQWAVVGDTFP.GC
Retrocopy DVVDDSDPDLDEPQIQHLLQSAEAIRKDYPNEDWLHLTALIHDLGKILVLPKFGGLPQWAVVGDTFPLGC

Parental  AFHDSIVHSKYFKENPDYNNTAYKSKFGVYSEGCGLDKVLMSWGHDDYMYLVAKENGTTLPSAGLFIIRY
          AF..S..H.KYFKEN.D.NN..Y..K.G.Y....GL..V.MSWGHDDYMY.VAKENGTTLPSAGLFIIRY
Retrocopy AFDESNIHHKYFKENQDFNNPIYNTKNGIYNDSIGLENVMMSWGHDDYMYMVAKENGTTLPSAGLFIIRY

Parental  HSFYALHKSGAYKELMNEEDKENLKWLHIFNKYDLYSKSKVQVNVEEVKPYYMSLIEKYFPAKLKW
          HSFY.LHK.G.YK.LMN.ED.ENLKWLH.FNKYDLYSKSKV.VNVEEVKPYYMSLIEKYFPAKL.W
Retrocopy HSFYPLHKNGGYKHLMNDEDEENLKWLHVFNKYDLYSKSKVHVNVEEVKPYYMSLIEKYFPAKLRW

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_5 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	PGSC0003DMG400004872	1 retrocopy	retro_stub_59,
Solanum lycopersicum	Solyc06g062430.2	1 retrocopy	retro_slyc_5 ,