RetrogeneDB ID: retro_slyc_28

Retrocopy location

• Organism: Tomato (Solanum lycopersicum)
• Coordinates: 6:38174982..38175594(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Solyc06g060210.1
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Solyc02g093530.2
• Aliases: None
• Description: None

Sequence

>retro_slyc_28
ATGTCGTACAATTACATGTTCAAATTCATAATTGTGGGAGAAACCGGAGTGGGAAAAACTTGCCTGCTTTACCAATTGAC
ATCGGCGCGATTTAAACCGGTTTACGAGGTCACAATCGGAGCTGAATTCGGATCCAGAACGATCACCGTCGATCAGAAGC
CAATTAAGCTGCAAATATGGGACACGGCGGGACAGGAAAAGTTCCGATCACTCACGAGATATTTTTACAGAGGCGCTGTT
GGGGCTTTGCTAGTTTACGACGTGACTAAGCGGCAAACTTTCCAGCAACTCCCGAATTGGCTCGAGGATTTACGAAAACA
CGGCGATGAGAAATTGACGGTAATGGTGGTGGGGAACAAGTGCGATCTGGATGAAGAAACTAGGGCTGTTAGTAAGGAGG
AAGGCGAGGAATTTGCGAAGAGGAATAAGTGTTTGTTCATGGAAGTATCAGCTAGAACGGCGAAGAATGTGGAGGCGGCG
TTCGGAAGCGCGGCGGAAGAAATATGTGAGAAGATCGGAAAAGGGGATTTTGGGACGGTGGAGGGATATAAGGGGATTAC
AATTGGGAATTGGAGAGGAAAAAGTAAAAGATTTTACTCATGTTGTTTTTGA

Alignment

ORF - retro_slyc_28 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.42 %
• Parental protein coverage: 90.52 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSYDYLFKYIIIGDTGVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMVTIDGKPIKLQIWDTAGQESFRS
          MSY.Y.FK.II.G.TGVGK.CLL.Q.T..RF.PV...TIG.EFG.R..T.D.KPIKLQIWDTAGQE.FRS
Retrocopy MSYNYMFKFIIVGETGVGKTCLLYQLTSARFKPVYEVTIGAEFGSRTITVDQKPIKLQIWDTAGQEKFRS

Parental  ITRSYYRGAAGALLVYDITRRETFNHLASWLEDARQHANPNMTIMLVGNKSDLSHR-RAVSKEEGEQFAK
          .TR..YRGA.GALLVYD.T.R.TF..L..WLED.R.H.....T.M.VGNK.DL....RAVSKEEGE.FAK
Retrocopy LTRYFYRGAVGALLVYDVTKRQTFQQLPNWLEDLRKHGDEKLTVMVVGNKCDLDEETRAVSKEEGEEFAK

Parental  ENGLLFLEASARTAQSVEEAFIQTAAKILQKIQEGVFDVSNESSGIKVGYGR
          .N..LF.E.SARTA..VE.AF...A..I..KI..G.F.......GI..G..R
Retrocopy RNKCLFMEVSARTAKNVEAAFGSAAEEICEKIGKGDFGTVEGYKGITIGNWR

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_28 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	Solyc02g093530.2	1 retrocopy	retro_slyc_28 ,