RetrogeneDB ID: retro_slyc_93

Retrocopy location

• Organism: Tomato (Solanum lycopersicum)
• Coordinates: 9:2671168..2671952(+)
• Located in intron of: Solyc09g009290.2

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Solyc01g098350.2
• Aliases: None
• Description: None

Sequence

>retro_slyc_93
ATGACTTACACGGCACTAGACACATTCTATCTTGTGGAGGAGCAGCTTAGAAACTCGCCTTCTAGGAAAGATGGAATTGA
TGAAGTTACTAAAACAGCACTTCGAATCTATGGTTGTGATCTCATCCAAGAAAGTGGGATTTTGCTCAGATTACCTCAAG
CTGTAATGGCCACTGGTCAAGTATTACTTCATCGCTTTTAGTGCAAGAAATCATTTGCCCATTTTAATGTGAATAGTATT
GCAGCTAGTTGTGTTTGGCTTGCATCAGAACTCAAAGAAGCCCGAGAAAAGCAACGCAGGTGTTTGTTGTTTTCCACAGA
ATGGAATATAAGAGAGAAAACTTACCTGTAGAACATCTGGATACATCTTCGAAAAAATATATTGATTTGAAAGCAGACCT
AATCAGAACAGAGAGGCATCTTTTAAAAGAGATGGGTTTTATCTGCCATGTCGAGCATCCTCATAAATTTATATCAAACT
ACCTTGCAACTCTTGAAACACCTGCAGAATTGAGACAAGAAGCTTGGAACCTTGCAAATGACAGTTTGCGCACAACACTC
GGTGTAAGATCAAGAATGAGGTTGTGGCCTGTGGAGTTGTATATGCTGCAGCCCGTAGATTTCAAGTGACCCTCCCAGAG
AATCCTCCTTGGTGGAAGGCATTTGATGCAGAAAAGGCTGATATTGGTGATGTTTGCGGAGTTCTCGCTCATCTTTACAG
CCTTCCAAAGGCGCAATGCATTCCTGTGTGCAAGTACGGAGGCCCCTTTGCTTCATCAAACAGA

Alignment

ORF - retro_slyc_93 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.23 %
• Parental protein coverage: 61.5 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MIYTAIDTFYLAEEQLVESPSRKDGIDDVTETALRIYGCDLVQECGILLRLPQAVMATGQVLFHRFYCKK
          M.YTA.DTFYL.EEQL..SPSRKDGID.VT.TALRIYGCDL.QE.GILLRLPQAVMATGQVL.HRF.CKK
Retrocopy MTYTALDTFYLVEEQLRNSPSRKDGIDEVTKTALRIYGCDLIQESGILLRLPQAVMATGQVLLHRF*CKK

Parental  SFARFNVKRVAASCVWLASKLEE-SPRKARQVLVVFHRMECRRENLPIEHLDTSSKKYVDLKADLIRTER
          SFA.FNV...AASCVWLAS.L.E.SPRKA.QV.VVFHRME..RENLP.EHLDTSSKKY.DLKADLIRTER
Retrocopy SFAHFNVNSIAASCVWLASELKE<SPRKATQVFVVFHRMEYKRENLPVEHLDTSSKKYIDLKADLIRTER

Parental  HLLKEMGFICHVEHPHKFISNYLATLETPAELRQEAWNLANDSLRTTLCVR-FKSEVVACGVVYAAARRF
          HLLKEMGFICHVEHPHKFISNYLATLETPAELRQEAWNLANDSLRTTL.VR..K.EVVACGVVYAAARRF
Retrocopy HLLKEMGFICHVEHPHKFISNYLATLETPAELRQEAWNLANDSLRTTLGVR<IKNEVVACGVVYAAARRF

Parental  QVPLPENPPWWKAFDADKAGIDEVCRVLAHLYSLPKAKYIPVCKEGGSFATSNR
          QV.LPENPPWWKAFDA.KA.I..VC.VLAHLYSLPKA..IPVCK.GG.FA.SNR
Retrocopy QVTLPENPPWWKAFDAEKADIGDVCGVLAHLYSLPKAQCIPVCKYGGPFASSNR

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_93 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
Prunus persica	PRUPE_ppa005678mg	1 retrocopy	retro_pper_44,
Solanum lycopersicum	Solyc01g098350.2	1 retrocopy	retro_slyc_93 ,