RetrogeneDB ID: retro_slyc_35

Retrocopy location

• Organism: Tomato (Solanum lycopersicum)
• Coordinates: 8:63259500..63260571(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Solyc08g079790.1
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Solyc05g052790.2
• Aliases: None
• Description: None

Sequence

>retro_slyc_35
ATGGTGGAGGCACAGTCATGGACTACAAGAAGGGGAAGCAATCCAAGATTGGAGTCACCCCAAGATCAAGTCTTGGATAT
GCCAGTAACCCCAACTGCTGAAATCAGGCAGCAACAGTATTCTAATGGTGGGATAACTTCTTTGGTGTCACCAAATGTAC
TTACTGCTCTTATAATTGCTTCTTGGTACTGTTCAAATATTGGGGTGTTGTTGCTAAACAAGTATCTTTTGAGTTTTTAT
GGTTATCGTTACCCAATATTCTTGACTATGTTGCATATGTTGTCATGTGCTACTTATAGTTTAGTTGCTATTAAGTGGCT
GGAAGTTGTTCCTTTCCAGCAGATACATAGCAGGAAACAGTTCTTCAAGATTCTTGCTTTGAGTGCTATTTTTTGTTTTT
CTGTTGTTTGTGGTAATACTTCATTGAGGTACCTTCCTGTATCGTTTAATCAAGCAATTGGTGCTACTACCCCATTTTTT
ACTGCTATTTTTGCTTTTGTGATTACTTGTAAGAAAGAAACTGCTGAGGTTTATTTAGCTCTTGTCCCTGTGGTTCTTGG
TATTGTTTTGGCTAGCAATAGTGAGCCATTGTTCCATTTGTTTGGGTTCTTGATGGCTTTAGGTTCAACTGCTGGGAGAG
CCTTGAAATCTGTTGTTCAGGGGTTGTTGTTATCCTCTGATGCTGAGAAATTGCACTCTATGAATCTGTTATTATACATG
GCTCCAATGGCAGCAATGATTTTGCTTCCTTTTACACTATACATAGAGGGGAATGTAGCTGCAGTTACAGTGGAGAAAGC
TAAGGGAGATGGATTTATGGTTTTCTTGTTGATTGGTAATGCCACAGTTGCTTATTTGGTGAACTTGACTAATTTCTTGG
TTACTAAGCATACAAGTGCCTTGACACTGCAAGTTTTGGGGAATGCCAAGGCTGCAGTGGCTGCAGTGGTGTCAGTTTTG
ATATTCAGGAATCCAGTGAACATCATGGGCATAACAGGATTTGCTGTGACTGTAATGGGTGTGGTGCTTTACAGTGAGGC
AAAGAAGAGATCTAAAGTAACAGCACACTGA

Alignment

ORF - retro_slyc_35 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.69 %
• Parental protein coverage: 98.06 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SGQFFTIGLVTAWYSSNIGVLLLNKYLLSNYGFKYPIFLTMCHMTACSLLSYIAIAWMKMVPMQTIRSRV
          S....T......WY.SNIGVLLLNKYLLS.YG..YPIFLTM.HM..C...S..AI.W...VP.Q.I.SR.
Retrocopy SPNVLTALIIASWYCSNIGVLLLNKYLLSFYGYRYPIFLTMLHMLSCATYSLVAIKWLEVVPFQQIHSRK

Parental  QFMKISALSLIFCTSVVSGNISLRYLPVSFNQAIGATTPFFTAVFAYLMTFKREAWLTYVTLIPVVTGVI
          QF.KI.ALS.IFC.SVV.GN.SLRYLPVSFNQAIGATTPFFTA.FA...T.K.E....Y..L.PVV.G..
Retrocopy QFFKILALSAIFCFSVVCGNTSLRYLPVSFNQAIGATTPFFTAIFAFVITCKKETAEVYLALVPVVLGIV

Parental  IASGGEPSFHLFGFIICIGATAARALKSVLQGILLSSEGEKLNSMNLLLYMAPIAVVFLLPATLVMEENV
          .AS..EP.FHLFGF....G.TA.RALKSV.QG.LLSS..EKL.SMNLLLYMAP.A...LLP.TL..E.NV
Retrocopy LASNSEPLFHLFGFLMALGSTAGRALKSVVQGLLLSSDAEKLHSMNLLLYMAPMAAMILLPFTLYIEGNV

Parental  VGITLALARDDSRIIWLLLFNSALAYFVNLTNFLVTKHTSALTLQVLGNAKGAVAVVISILIFRNPVSVT
          ...T...A..D.....LL..N...AY.VNLTNFLVTKHTSALTLQVLGNAK.AVA.V.S.LIFRNPV...
Retrocopy AAVTVEKAKGDGFMVFLLIGNATVAYLVNLTNFLVTKHTSALTLQVLGNAKAAVAAVVSVLIFRNPVNIM

Parental  GMLGYALTVFGVILYSEAKKRSK
          G..G.A.TV.GV.LYSEAKKRSK
Retrocopy GITGFAVTVMGVVLYSEAKKRSK

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_35 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Amborella trichopoda	AMTR_s00080p00074790	1 retrocopy	retro_atri_6,
Medicago truncatula	MTR_3g070000	1 retrocopy	retro_mtru_1,
Solanum tuberosum	PGSC0003DMG401027186	1 retrocopy	retro_stub_37,
Prunus persica	PRUPE_ppa009115mg	1 retrocopy	retro_pper_41,
Solanum lycopersicum	Solyc05g052790.2	1 retrocopy	retro_slyc_35 ,
Theobroma cacao	TCM_042615	1 retrocopy	retro_tcac_6,