RetrogeneDB ID: retro_slyc_83

Retrocopy location

• Organism: Tomato (Solanum lycopersicum)
• Coordinates: 5:56571707..56571949(+)
• Located in intron of: Solyc05g044480.2

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Solyc09g090610.2
• Aliases: None
• Description: None

Sequence

>retro_slyc_83
AAAGACTCTGTCAATTATTTAACTTCACCTTATGTTAGGGACATGGTTATGCCCATTGTCAACAAGGGTAAGCCAGATCT
TACGAAGAAGGTTATGCCTGCTGTCATTGTTCGCAAGCCATGGCATAGAAAAGGCTTTGTTAACATGTACCTTGAAGATA
ATGCTGTGGTGATTGTGAGTCCAAAGAGTGAAACGGAAGGGTCTGCAATTACTTCCCAATTGGGAAAGTGTGTGCTGATC
TT

Alignment

ORF - retro_slyc_83 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.86 %
• Parental protein coverage: 59.29 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KGRLNRLPSACVGDMVMATVKKGKPDLRKKVMPAVIVRQRKPWRRKDGVFMYFEDNAGVIVNPKGEMKGS
          K...N.L.S..V.DMVM..V.KGKPDL.KKVMPAVIVR..KPW.RK..V.MY.EDNA.VIV.PK.E..GS
Retrocopy KDSVNYLTSPYVRDMVMPIVNKGKPDLTKKVMPAVIVR--KPWHRKGFVNMYLEDNAVVIVSPKSETEGS

Parental  AITG-PIGKECADL
          AIT..PIGK.CADL
Retrocopy AITS<PIGKVCADL

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_83 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 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Medicago truncatula	MTR_7g098290	1 retrocopy	retro_mtru_54,
Solanum tuberosum	PGSC0003DMG400017151	2 retrocopies	retro_stub_123, retro_stub_87,
Solanum lycopersicum	Solyc06g083780.2	1 retrocopy	retro_slyc_58,
Solanum lycopersicum	Solyc09g090610.2	1 retrocopy	retro_slyc_83 ,