RetrogeneDB ID: retro_slyc_33

Retrocopy location

• Organism: Tomato (Solanum lycopersicum)
• Coordinates: 3:10779886..10780684(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Solyc03g044890.1
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Solyc11g012410.1
• Aliases: None
• Description: None

Sequence

>retro_slyc_33
ATGGAAGAGTTTGTTGATGTTGCAATTGAAGCAGCTAAGAAAGCCGGAGAGATAATTCGTCATGGATTCTACAAGAGTAA
GCATATTGAGCACAAAGGAGTTGTTGATTTAGTGACAGAGACTGATAAGGCATGTGAAGTTTTAATTTTTAATCATCTGA
AGCAATGTTTTCCTAGTCATAAGTTCATTGGTGAAGAAACAACTGCTGCTGCTTCTGGAAATTTTGAGCTTACTGATGAA
CCAACTTGGATAGTTGATCCACTTGATGGAACTACTAACTTTGTGCATGGCTTCCCTTTTGTTTGTGTATCTATCGGTCT
CACAATTGAAAAGAAACCAGTGGTTGGTGTTGTTTACAACCCAATCATCGACGAGCTTTTCACTGCAATCTATGGGAGAG
GTGCTTTTCTTAATGGGAAGTCCATCAGAGTATCTTCAGAGTCTCAACTTGTAAAAGCTCTTGTTGCTACAGAGGTTGGA
ACAAACAGGGATAAGGCAATTGTAGATGCTACTACAGGAAGAATTAATAGAGTGATTTTCAAGGTTAGGTCCCTCAGGAT
GTCTGGTTCTTGTGCATTAAATCTATGTGGAGTGGCGTGTGGAAGGCTTGATCTCTTCTATGAAATTGAATTTGGTGGTC
CGTGGGATGTCGCAGCTGGTGCTCTCATAGTCATAGAAGCTGGAGGACTCGTTCTTGATCCATCTGGTTCCGAATTTGAC
CTAACAGCTCGACGTGTAGCTGCTACAAACGCTCATCTCAAGGACGCTTTTATCAACGCCTTGAATGAATCAGAATGA

Alignment

ORF - retro_slyc_33 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.31 %
• Parental protein coverage: 97.76 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VEQFLDVAVEAAKKAGEIIREGFYKTKHVEHKGMVDLVTETDKACEDFIFNHLKQRFPSHKFIGEETTAA
          .E.F.DVA.EAAKKAGEIIR.GFYK.KH.EHKG.VDLVTETDKACE..IFNHLKQ.FPSHKFIGEETTAA
Retrocopy MEEFVDVAIEAAKKAGEIIRHGFYKSKHIEHKGVVDLVTETDKACEVLIFNHLKQCFPSHKFIGEETTAA

Parental  C-GNFELTDEPTWIVDPLDGTTNFVHGFPFVCVSIGLTIEKKPTVGVVYNPIIDELFTGIDGKGAFLNGK
          ..GNFELTDEPTWIVDPLDGTTNFVHGFPFVCVSIGLTIEKKP.VGVVYNPIIDELFT.I.G.GAFLNGK
Retrocopy ASGNFELTDEPTWIVDPLDGTTNFVHGFPFVCVSIGLTIEKKPVVGVVYNPIIDELFTAIYGRGAFLNGK

Parental  PIKVSSQSELVKALLATEAGTNRDKLVVDATTGRINSLLFKVRSLRMCGSCALNLCGVACGRLDLFYELE
          .I.VSS.S.LVKAL.ATE.GTNRDK..VDATTGRIN...FKVRSLRM.GSCALNLCGVACGRLDLFYE.E
Retrocopy SIRVSSESQLVKALVATEVGTNRDKAIVDATTGRINRVIFKVRSLRMSGSCALNLCGVACGRLDLFYEIE

Parental  FGGPWDVAGGAVIVKEAGGFVFDPSGSEFDLTARRVAATNAHLKDAFIKALNE
          FGGPWDVA.GA.IV.EAGG.V.DPSGSEFDLTARRVAATNAHLKDAFI.ALNE
Retrocopy FGGPWDVAAGALIVIEAGGLVLDPSGSEFDLTARRVAATNAHLKDAFINALNE

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_33 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	PGSC0003DMG400013285	1 retrocopy	retro_stub_49,
Solanum lycopersicum	Solyc11g012410.1	1 retrocopy	retro_slyc_33 ,