RetrogeneDB ID: retro_slyc_11

Retrocopy location

• Organism: Tomato (Solanum lycopersicum)
• Coordinates: 12:5798818..5799556(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Solyc12g015790.1
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Solyc12g010210.1
• Aliases: None
• Description: None

Sequence

>retro_slyc_11
ATGGCTACTAGGCTTCAATTTGAAAAATCGAGTGAAATTGGAGTTTTCTCAAAGCTAACTAATGCATATTGTTTGTTACC
TACTGGCGGATCTGAACACTTCTACAACACATTTGAATCTGAACTGTCACAAATTATTCCGGTAATCAAAACCTCAATCG
GAGGAACGAGGATAATCGGGAGACTCTGTGCCGGAAACAGAAAAGGTCTTCTCTTACCTCACACTACTACAGATGAAGAA
TTTGATAACTTGAGAAACAATCTACCAGACGGAGTTGTAGTTAAGCGCATTGATGAGCGATTATCTGCCCTAGGAAATTG
CATAGCTTGTAATGACAATGTTGCTATGATGCATACAGATCTCGATGATGAAACTGAAGAGATGATTGGTGATGTACTTG
GTGTCGAAGTTTTCAGGCAAACAATTGCAGGGAATGCTCTTGTTGGTAGTTATTGTGCTATTTCAAACGCGGGATGCTTA
GTACATCCTCATACATCTGTGGAAGATATGTACGAACTTTCAACTCTTCTCGAGGTTCCGTTCATTGCCGGAACAGTAAA
TCGCGGTAGTGAAGCGATTGCTGCTGGATTGATTGTTAATGACTGGACGGCATTTACGGGACGAAACACTACTGCAACAG
AGGTATCTGTTATTGAACGTGTTTTCAAGCTTAGAGAGGCTGAACCTATATATATTGTTGATGAGATGAAGAGATCATTG
ATTGATAGTGATCGATAG

Alignment

ORF - retro_slyc_11 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.6 %
• Parental protein coverage: 98.77 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAIRLQFENSCEVGVFSKLTNTYSLVAIGASENFYSVFEDALPENFPVIKTSIGGTRIIGRLCAGNKNGL
          MA.RLQFE.S.E.GVFSKLTN.Y.L...G.SE.FY..FE..L....PVIKTSIGGTRIIGRLCAGN..GL
Retrocopy MATRLQFEKSSEIGVFSKLTNAYCLLPTGGSEHFYNTFESELSQIIPVIKTSIGGTRIIGRLCAGNRKGL

Parental  LLPHTTTDQELWHLRNSLPDRVVVHRIEERLSALGNCIACNDYESLAHVDLDKETEEMIADVLGVEVLRH
          LLPHTTTD.E...LRN.LPD.VVV.RI.ERLSALGNCIACND.....H.DLD.ETEEMI.DVLGVEV.R.
Retrocopy LLPHTTTDEEFDNLRNNLPDGVVVKRIDERLSALGNCIACNDNVAMMHTDLDDETEEMIGDVLGVEVFRQ

Parental  TIADNILVGSYCAFSNLGGLVHPHASIEEMTELARLLGIPVTAGTVNRGSEVIAAGMIVNDWAAFCGSDT
          TIA.N.LVGSYCA.SN.G.LVHPH.S.E.M.EL..LL..P..AGTVNRGSE.IAAG.IVNDW.AF.G..T
Retrocopy TIAGNALVGSYCAISNAGCLVHPHTSVEDMYELSTLLEVPFIAGTVNRGSEAIAAGLIVNDWTAFTGRNT

Parental  TATEVAVIDNIFKLQGAQP--SLNEIRKSVID
          TATEV.VI...FKL..A.P.....E...S.ID
Retrocopy TATEVSVIERVFKLREAEPIYIVDEMKRSLID

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_11 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
Brassica rapa	Bra007180	1 retrocopy	retro_brap_30,
Solanum lycopersicum	Solyc12g010210.1	1 retrocopy	retro_slyc_11 ,