RetrogeneDB ID: retro_slyc_103

Retrocopy location

• Organism: Tomato (Solanum lycopersicum)
• Coordinates: SL2.40sc04407:147..1062(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Solyc09g097970.2
• Aliases: None
• Description: None

Sequence

>retro_slyc_103
AAACTGGGCCGTGTTGGCCCCGAGGTGTTTCCGATTGGCCTGGGCTGCATGGGAATGAGCGAGTTCTATGGCGCGCACGA
CGACGCGCAATCTATTCAACTTATTCATCATGCGATCGATAAAGGCGTCAACTTTATCGATACGGCTGATATCTACGGTC
CGCACACCAACGAAGAGCTGGTAGGGCGGGCGCTGGCGGGCCGGCGCGACAAGGTGGTGCTGGCCACCAAGTTCGGCATC
GTGCGCGATCCCGCCAACTCGGCCGCGCGCGGCGCCAACGGCCGTCCCGAATACGTGCGAGCCAGCTGTGACGCCAGCCT
GAAGCGGCTCGGCGTCGACCATATCGACCTGTATTACCAGCATCGCGTCGATCCGGACACGCCGATCGAGGACACGGTCG
GCGCGATGGCCGAACTGGTCAAGGCAGGCAAGGTGCGTTGGATCGGCCTGTCCGAGGCGGGCGCCGCCACGATAGAACGG
GCGCATGCCGTCCATCCGATCACCGCGCTGCAGACCGAATATTCGCTGTGGACGCGCGACGTGGACGAGAACGGCATCAT
GGCCACCTGCGAACGCCTTGGTATCGGCTTCGTGCCTTACAGCCCGCTGGGCCGCGGCTTCCTGACCGGTGCGATCCGCA
CGCCCGACGATTTCGACGCCGACGACTATCGCCGCACCAACCCGCGTTTCATGGGCGAGAACTTCGCGCGCAACCTGAAG
CTGGTCGATGCGGTGCGCGAACTGGCGGCCGCCAAGGGCTGCTCGCCTGCGCAACTGGCGCTGGCGTGGGTGCTGGCGCG
CGGCGATCATCTGGTGCCGATTCCGGGCACGCGGCGCATCGCCAACCTCGAGGACAACCTCGGCGCGCTCAATGTGGTGC
TGACCCGCGAGGATCTGTCCAATATCGACGCGGTG

Alignment

ORF - retro_slyc_103 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.03 %
• Parental protein coverage: 87.57 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KLGSEGLEVSAQGLGCMGMSAFYGPPKPDSDMVQLIHHAINSGVTFLDTSDVYGPHTNEILLGKALMGGM
          KLG..G.EV...GLGCMGMS.FYG....D....QLIHHAI..GV.F.DT.D.YGPHTNE.L.G.AL..G.
Retrocopy KLGRVGPEVFPIGLGCMGMSEFYGA-HDDAQSIQLIHHAIDKGVNFIDTADIYGPHTNEELVGRAL-AGR

Parental  RERVELATKFAVSFAEGKMQVRG---EPAYVRAACEASLKRLDVDCIDLYYQHRIDTRVPIEVTVGELKK
          R..V.LATKF...........RG....P.YVRA.C.ASLKRL.VD.IDLYYQHR.D...PIE.TVG....
Retrocopy RDKVVLATKFGIVRDPANSAARGANGRPEYVRASCDASLKRLGVDHIDLYYQHRVDPDTPIEDTVGAMAE

Parental  LVEEGKIKYIGLSEASASTIRRAHAVHPITAVQLEWSLWSRDVEED-IVPTCRELGIGIVAYSPLGRGFL
          LV..GK...IGLSEA.A.TI.RAHAVHPITA.Q.E.SLW.RDV.E..I..TC..LGIG.V.YSPLGRGFL
Retrocopy LVKAGKVRWIGLSEAGAATIERAHAVHPITALQTEYSLWTRDVDENGIMATCERLGIGFVPYSPLGRGFL

Parental  SSGPKLLEDCSNEDFRKYLPRFQGENLEHNKKLYERICQIAAKKGCTPSQLALAWVHHQGNDVCPIPGTT
          ........D....D.R...PRF.GEN...N.KL.......AA.KGC.P.QLALAWV...G....PIPGT.
Retrocopy TGAIRTPDDFDADDYRRTNPRFMGENFARNLKLVDAVRELAAAKGCSPAQLALAWVLARGDHLVPIPGTR

Parental  KIENLNQNIGALSIKLTSEDMTELESI
          .I.NL..N.GAL...LT.ED.......
Retrocopy RIANLEDNLGALNVVLTREDLSNIDAV

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_103 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
Oryza sativa indica	BGIOSGA016143	1 retrocopy	retro_oind_55,
Solanum lycopersicum	Solyc09g097970.2	1 retrocopy	retro_slyc_103 ,