RetrogeneDB ID: retro_slyc_89

Retrocopy location

• Organism: Tomato (Solanum lycopersicum)
• Coordinates: 7:50320585..50320993(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Solyc06g067880.2
• Aliases: None
• Description: None

Sequence

>retro_slyc_89
ATAAATATAAATGGAAGTAGTTTGGTTGGTGCTGCCATTAAAGCTCCTCGAATGAACTCCAAAAATCTTATTAGTACTGT
TTTTTGTGAAGCGGTTGCTATATATGGTGTGGGCATCATTCTTCGAAACAAAGCTCGATAGTGTACCTGACTCATAGTTT
TATGCACCAGAATCTCCTAGAGGTGGCTATGTAGTGTTTGCTTTTGGATCATTGTGGGCTTTATTAATCTTGTATGTGGG
TTGTGCATTGGAATAATTGGAAGGAACTGTGCGTTATTTGATGCACAGAACTCATCATTTATTGTTAAAATCGTCGTAAT
TGAGAGTTTTGGTAGTTTACTTGGGCTTTTCGGTGTTATTGTGGGAATTATCATGTAAGCTCAAGCCACTTTGCCATCCT
AGGGTGCA

Alignment

ORF - retro_slyc_89 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.29 %
• Parental protein coverage: 77.97 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  IYITGSSLIGAAIKAPRITSKNLISVIFCEAVAIYGVIVAIIL-QTKLESVPASQIYAPESLRAGYAIFA
          I.I.GSSL.GAAIKAPR..SKNLIS..FCEAVAIYGV...IIL..TKL.SVP.S..YAPES.R.GY..FA
Retrocopy ININGSSLVGAAIKAPRMNSKNLISTVFCEAVAIYGV--GIIL>ETKLDSVPDS*FYAPESPRGGYVVFA

Parental  SG-IIVGFANLVCGLCVGIIGSSCALSDAQNSSLFVKILVIEIFGSALGLFGVIVGIIMSAQASWPSKGA
          .G.IIVGF.NLVCGLC.GIIG..CAL.DAQNSS..VKI.VIE.FGS.LGLFGVIVGIIM.AQA..PS.GA
Retrocopy FG<IIVGFINLVCGLCIGIIGRNCALFDAQNSSFIVKIVVIESFGSLLGLFGVIVGIIM*AQATLPS*GA

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_89 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Solanum lycopersicum	Solyc06g067880.2	1 retrocopy	retro_slyc_89 ,