RetrogeneDB ID: retro_slyc_54

Retrocopy location

• Organism: Tomato (Solanum lycopersicum)
• Coordinates: 1:59909026..59909266(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Solyc01g094470.2
• Aliases: None
• Description: None

Sequence

>retro_slyc_54
ATATCGAAGAAAAATAATTTGGGTTGCCGAAAAAAACAGCACAACTTCAATCTTCAGAGGGAAAATGAGGAAGAAAAACT
AGCAAAGAAGCTACAAGCAAAAAGGAACAAGATGAAGGTGGATGGTAAGGACAAGAAGTTTAAAGGTGGTAATGGATTTT
AAGTTGATAAGAAAAAAATGAAGACAAGGATGACTTCATTAGCCAAAGCTAAAGCTGCATAAGCAATGGAGATTGAAAAA

Alignment

ORF - retro_slyc_54 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.54 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSKKNDLGRRKKQHEFNLRREKEEKEKLAKKLQAKKNKMKVDGKDKKKKGGNGFQVGKKKLKTRMTPLAK
          .SKKN.LG....QH.FNL.RE.EE.EKLAKKLQAK.NKMKVDGKDKK.KGGNGF.V.K...KTRMT.LAK
Retrocopy ISKKNNLGCXXXQHNFNLQRENEE-EKLAKKLQAKRNKMKVDGKDKKFKGGNGF*VDKXXXKTRMTSLAK

Parental  AKAAQAMEIEK
          AKAA.AMEIEK
Retrocopy AKAA*AMEIEK

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_54 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 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Solanum lycopersicum	Solyc01g094470.2	2 retrocopies	retro_slyc_50, retro_slyc_54 ,