RetrogeneDB ID: retro_slyc_17

Retrocopy location

• Organism: Tomato (Solanum lycopersicum)
• Coordinates: 9:3455756..3457964(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Solyc09g010050.1
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Solyc09g074680.2
• Aliases: None
• Description: None

Sequence

>retro_slyc_17
ATGAGCGAGGTGAAGATTATCGAGTTTGAGGATGGATGGGAATTTATGGAGAAGGGAATCACTAAGTTGAAGAAAATTTT
ACAAGAAGAAGAAGAAATTTGTTTCGATTCCGAAGAGTATATGATGCTCTATACAACAATATTCAACATGTGTACACAGA
GTATGCCGCCGCCATATATTAATAATCACTCAAAACAGTTGTATGAAAACTACAAGCAAGTATTTGTAGAATACATCGAT
TCTACTGTACTGCCCTGTTTACGAGACAGACACGATGAGTTCCTATTGAAGGAGATTGTGAAACGATGGGCGAATCACAA
AGTTATGATTCGGTGGCTCTCGCGTTTCTTCCAATACCTGGAACGTTTTTTTATTAATGCAAAATCTCTACCTGGACTCA
AGGAAGTTGGTTTGATGTGTTTTCGTGATCTGGTTTACGAGGAATTGAAAGTTAAAGCTAGAGATGTGGTTTTTGTGTTG
ATTGAACGAGAACGAGATGGGGAGAAGATTGACAGAAGTTTATTGAAGAGTGTGGTTGATATATTCGTTGCAGTTGGGAT
GGGGAATATGGAGTGCTACGTGAATGATTTTGAATTTGCAATGCTTGAAGATACTGCAGGTTATTACTCTCGTAAAGCTT
CAAGTTGGATTGGGGAAGATTCGTGTCCTGATTATATGTTGAACGCAGAGGAGTGTTTGAAGAAGGAGAAAGAGAGAGTA
TCGAATTATCTCCATGTTGTTAGTGAGTCGAAACTTTTAGAGAAAGTGCGATATGAATTGTTGGTTGTATATACGAATCA
GTTACTCGAGAAGGAGCATTCTGGAATTCGAGTATTGCTTAGAGATGATAAGGTAGATGATTTATCTCGAATGTATAGGC
TGTTCTACAAAATCGACAAGGGATTGGTACCTGTTTCAGCTATGTTTAAGCAGCACGTCGTTGCTGAAGGGATGTACTTA
GTGCAACAGGCTGATGATACGACAAATAGACAGTCTGAAACTCCCTTCTTTGTTAGGAAGGTCATTGAGCTTTACGATAA
GTATATGAGTTATGTTACGAGCTGTTTTGCTAATCACTCTCTGTTTCATAAGGCTCTCAAGGAGGCATTTGAGGTGTTTT
GTAACAAGATTGTATCGGGTTGTTCAAGTGCAGAGCTCCTTGCTTCGTATTGTGATAGTATTCTCAAGAAAGGTGGAAGT
GAAAAACTTAGTGATGATGCTATCGAGGAGACGTTGGATAAGGTGGTAAAGCTTCTCGCGTACATTAATGACAAAGACCT
TTTTGGAGAGTTCTGCAGGAAGAAGCTTTCTCGTAGATTGCTCTTTAGTAAATGTGCTAATGATGAACACGAAAGGCTTA
TGTTAACGAAGCTAAAGCAGTATTGTGGTGGACAGTTTACATCAAAGATGGAGGGAATGGTAACAGACTTGACGTTAGCT
AAGGAAAATCAGAACGATTTTCAAGAATATCTCAGCAACAACGCGAGTACTGGAATTGATCTAACTGTCACAGTACTTAC
AAGTGGGTTCTGGCCTAGCTATAAATCTTGTGATTTGAGTCTACCTGTCGAGATGGCTAAGTGTGTACAAGTCTTCAACG
AATTCTATCAGACAACAACGAAACACAGGAAACTGACATGGATTTATTCATTGGGTACGTGTAACGTCATTGGGAAGTTT
GATTCAAAAACCATTGAATTGATTCTGGGAACCTATCAGGCTGCTGTTCTGTCATTGTTTAATTCGTCAGATAGATTGAG
TTACTCGGAAATCAAAAGTCAGTTAAATTTAGCTGATGATGACTTGATCAGATTGCTTCAATCTCTTTCATGTGCTAAGT
ATAAAATTCTGATTAAAGATCCTAGCAATGCAACTGTTACATCATCTGATCATTTCGAGTTCAACTCCAAGTTCACTGAC
AGGATGAGACGGGTTAGGGTACCGTTACCTCTTGTGGATGAAAGGAAAAAGGTGGTGGAGGATGTAGGCAAAGATAGACG
TTATGCAATCGATGCATGTATAGTACGTATTATGAAGAGTCGAAAGGTTCTTCCTCATCAACAACTAGTAGCAGAGTGTG
TTGAGCAGTTGAGCTCCATGTTCAAGCCTGACTTAAAAGCAATCAAAAAGCAGATAGAAGATCTCATCACTAGAGAATAC
TTGGAAAGAGATGAAGAGAACCCAAATTTGTTCAAGTATTTAGCCTAA

Alignment

ORF - retro_slyc_17 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.64 %
• Parental protein coverage: 54.73 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EQQVFVRKLIELHDKYMAYVTNCFANNSLFHKALKEAFEVFCNKIVSGCSSAELLASFCDNILKKGGSEK
          E...FVRK.IEL.DKYM.YVT.CFAN.SLFHKALKEAFEVFCNKIVSGCSSAELLAS.CD.ILKKGGSEK
Retrocopy ETPFFVRKVIELYDKYMSYVTSCFANHSLFHKALKEAFEVFCNKIVSGCSSAELLASYCDSILKKGGSEK

Parental  LSDDDIEETLDKVVKLLAYISDKDLFAEFYRKKLSRRLLFDKSANDDHERLILTKLKQQCGGQFTSKMEG
          LSDD.IEETLDKVVKLLAYI.DKDLF.EF.RKKLSRRLLF.K.AND.HERL.LTKLKQ.CGGQFTSKMEG
Retrocopy LSDDAIEETLDKVVKLLAYINDKDLFGEFCRKKLSRRLLFSKCANDEHERLMLTKLKQYCGGQFTSKMEG

Parental  MVTDLTLARENQNHFQEYLSNNPAASPGIDLTVTVLTTGFWPSYKSSDLCLPVEMVKCVEVFKEFYQTKT
          MVTDLTLA.ENQN.FQEYLSNN..AS.GIDLTVTVLT.GFWPSYKS.DL.LPVEM.KCV.VF.EFYQT.T
Retrocopy MVTDLTLAKENQNDFQEYLSNN--ASTGIDLTVTVLTSGFWPSYKSCDLSLPVEMAKCVQVFNEFYQTTT

Parental  KHRKLTWIYSLGTCNINGKFDSKTIELILGTYQAAVLLLFNSSDRLSYSEIKSQLNLADDDLIRLLQSLS
          KHRKLTWIYSLGTCN..GKFDSKTIELILGTYQAAVL.LFNSSDRLSYSEIKSQLNLADDDLIRLLQSLS
Retrocopy KHRKLTWIYSLGTCNVIGKFDSKTIELILGTYQAAVLSLFNSSDRLSYSEIKSQLNLADDDLIRLLQSLS

Parental  CAKYKILIKEPSNRTVSSSDHFEFNSKFTDRMRRIRVPLPPVDERKKVVEDVDKDRRYAIDACIVRIMKS
          CAKYKILIK.PSN.TV.SSDHFEFNSKFTDRMRR.RVPLP.VDERKKVVEDV.KDRRYAIDACIVRIMKS
Retrocopy CAKYKILIKDPSNATVTSSDHFEFNSKFTDRMRRVRVPLPLVDERKKVVEDVGKDRRYAIDACIVRIMKS

Parental  RKVLPHQQLVLECVEQLSRMFKPDFKAIKKRIEDLITRDYLERDKENPNLFKYLA
          RKVLPHQQLV.ECVEQLS.MFKPD.KAIKK.IEDLITR.YLERD.ENPNLFKYLA
Retrocopy RKVLPHQQLVAECVEQLSSMFKPDLKAIKKQIEDLITREYLERDEENPNLFKYLA

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_17 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	Solyc09g074680.2	1 retrocopy	retro_slyc_17 ,