RetrogeneDB ID: retro_slyc_18

Retrocopy location

• Organism: Tomato (Solanum lycopersicum)
• Coordinates: 2:28204076..28204736(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Solyc02g032310.1
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Solyc07g065820.2
• Aliases: None
• Description: None

Sequence

>retro_slyc_18
ATGCTGTCGTGCTTAGGTTCTTACCTTTCAAGGTTTTGTAATATTGATTTTGATCAATCAGCGGACCTCGACGATATTGA
TGTCCTTGCAAGAGAGACAATGTTTAGGGTCAATGAGATTGAAGCTCTTTATGAGCTCTTTAAAAAGATTAGTAGTGCAG
GGATTGGTGATGGCCTAATCATGAACAAGAAAGAGTTTCAATTGGCTATAAACAACACAAATGTGAAAGAAAGCTTCTTT
GCTGACAGAGTATTTGACTTATTTGACACAAAGCGTAAGGGAATTTTGGGCTTTAAAGAATTTGCTTGTGCACTTTCTAT
TTTCCATCCAAATTCAGCTATTGATGATAAGATTCAGTTTTCTTTTCAACTATATGACATCAAACAACAGGGGTTCATTG
AGAGAGAAGAGGTGAAACAGATGATGCTTGTTGCTCTTGCTCAGTCTAATATGAAATTTTCAGACAATGTGATTGAGAGG
ATTATTGACAATACTTTTGAAGAAGCAGATATCAATCGTGATGGAAAGATTGATAAGGAGGAATGGAGAAGTTTAGTGTT
GCGAAATCCTTCCCTTTTGAAGAATATGACTCTCCCATTTCTCACGGACATTACTACAATGTTTCCGAACTTTACCTATC
ACTCAAGAGTTGAGGACTGA

Alignment

ORF - retro_slyc_18 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.89 %
• Parental protein coverage: 99.54 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLQCLGSYLSRCCDLDFKQSGGLDDPEILARETVFSVSEIEALYELFKKISSAVIDDGLI-NKEEFQLAL
          ML.CLGSYLSR.C..DF.QS..LDD...LARET.F.V.EIEALYELFKKISSA.I.DGLI.NK.EFQLA.
Retrocopy MLSCLGSYLSRFCNIDFDQSADLDDIDVLARETMFRVNEIEALYELFKKISSAGIGDGLIMNKKEFQLAI

Parental  FKTNKKESLFADRVFDLFDTKHNGILGFEEFARALSVFHPNAPIDDKIEFSFQLYDLKQQGFIERQEVKQ
          ..TN.KES.FADRVFDLFDTK..GILGF.EFA.ALS.FHPN..IDDKI.FSFQLYD.KQQGFIER.EVKQ
Retrocopy NNTNVKESFFADRVFDLFDTKRKGILGFKEFACALSIFHPNSAIDDKIQFSFQLYDIKQQGFIEREEVKQ

Parental  MVVATLAESGMNLSDDVIESIIDKTFEEADTKHDGKIDKEEWRNLVLRHPSLLKNMTLQYLKDITTTFPS
          M....LA.S.M..SD.VIE.IID.TFEEAD...DGKIDKEEWR.LVLR.PSLLKNMTL..L.DITT.FP.
Retrocopy MMLVALAQSNMKFSDNVIERIIDNTFEEADINRDGKIDKEEWRSLVLRNPSLLKNMTLPFLTDITTMFPN

Parental  FVFHSRVED
          F..HSRVED
Retrocopy FTYHSRVED

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_18 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
Solanum tuberosum	PGSC0003DMG400022267	1 retrocopy	retro_stub_29,
Solanum lycopersicum	Solyc07g065820.2	1 retrocopy	retro_slyc_18 ,