RetrogeneDB ID: retro_slyc_66

Retrocopy location

• Organism: Tomato (Solanum lycopersicum)
• Coordinates: 12:22150530..22151240(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Solyc06g048500.1
• Aliases: None
• Description: None

Sequence

>retro_slyc_66
ATTAGTTACATTCCCCATTTTTTTCTTAATGAGAAGGTTTTACCTTTTAAAATGATTGATCAATCTAGTTTGAGTGTTTA
TTTGAAAGGAACAGAGAAACCGCCAATATTAAAAGTCTACGTGGAAGAAACTCCTATCGAGGAGGATCATAATGTAGACA
AAGGCCAACAAGATAAGTTTAATGATTAATTTCATCCTGCGAACATGAAAAATCCTGATGATGAAATTGGAATAGGTGAA
GGTGAAGCTCAACGTGAAGGGTCGGACCTTAAGAGCAAGTTTCCTCCCACACCTATAGTAGACAAAAACAATCATGTGCT
TCTCAAACTTCACATGTGAATAATGTTAGACATGATGAAACAGGATTCTATAAGGGAATGACATTCAAGAACAACCAAGA
ACTGGCAAATTCATTGAAAATTGCTTGGTTGAAAAAATATTTTAGACTGAAAAAGGTGATGAATTCTTGTAATGTGTTTT
TTTTTAAATGCTCGTATCCAAATTAAAATTGGTGGCAGCGTTTTGTGAAATTTACAAGTAGTGACAGGTTTGACATTAGA
ATCTATGAAAAGTACCATATTTGTGGTTCAGAGCATGTTACAAGCCATAATCCCCACACGGGAAAAGCCATAGGTAAGTA
CTTTGAAAATAGGTTTCCCAATGGTAAAGGCCCATCCACAAGAGACATGTCAATTCAACTCCGCACAGAA

Alignment

ORF - retro_slyc_66 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.58 %
• Parental protein coverage: 66.39 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSYIPHFFHNEKVLPFGITDQSSLSVYLRGTGKPLILRVYVEINPIKEDHNVYQGQQDMFNEEFDPTDMN
          .SYIP....NEKVLPF...DQSSLSVYL.GT.KP.IL.VYVE..PI.EDHNV..GQQD.FN..F.P..M.
Retrocopy ISYIPXXXLNEKVLPFKMIDQSSLSVYLKGTEKPPILKVYVEETPIEEDHNVDKGQQDKFND*FHPANMK

Parental  KLDNEIGISEGKGLTEGSDLESNFPSTPTVGSNN-PHTSQSSRVKNVRDDEIGFYKGMTFKNKQELANSL
          ..D.EIGI.EG....EGSDL.S.FP.TP.V..NN....SQ.S.V.NVR.DE.GFYKGMTFKN.QELANSL
Retrocopy NPDDEIGIGEGEAQREGSDLKSKFPPTPIVDKNN<SCASQTSHVNNVRHDETGFYKGMTFKNNQELANSL

Parental  KIACLKKDFRLKKVINSRNVFFFKCSYPNCNWWLRAVKFTSSDMFAIRIYEKYHTCGSEHLTSHNPHAAT
          KIA.LKK.FRLKKV.NS.NV...KCSYPN.NWW.R.VKFTSSD.F.IRIYEKYH.CGSEH.TSHNPH...
Retrocopy KIAWLKKYFRLKKVMNSCNVXXXKCSYPN*NWWQRFVKFTSSDRFDIRIYEKYHICGSEHVTSHNPHTG-

Parental  KVIGSKTALSLDENGREKYLLHMLIQVNPE
          K.IG.K.......NG.......M.IQ...E
Retrocopy KAIG-KYFENRFPNGKGPSTRDMSIQLRTE

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_66 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	Solyc06g048500.1	1 retrocopy	retro_slyc_66 ,