RetrogeneDB ID: retro_slyc_58

Retrocopy location

• Organism: Tomato (Solanum lycopersicum)
• Coordinates: 10:46550358..46550621(-)
• Located in intron of: Solyc10g049740.1

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Solyc06g083780.2
• Aliases: None
• Description: None

Sequence

>retro_slyc_58
AAAGACTCTGTACATTATTTAACTTCAGCTTATGTTGGAGACATGATAACGCCCACTGTCAACAAGGGTAAACCAGATCT
TATGAAGAAGGTTATGCCTGCTATTATTGTTGGCAAGCCATGGCATAGAAAGGGCGTTGTTAACATGTACTTTGAAGATA
ATGTTGTGGTGATTGTGAGTCCAAAGGGTGAAACGCGGAAGGGTCTGCAATCACTTGCCCAATTGGAAAAGAGTGTGCTG
ATCTTTGACCTAGGATCGCTAGT

Alignment

ORF - retro_slyc_58 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.23 %
• Parental protein coverage: 63.57 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KGRLNRLPSACVGDMVMATVKKGKPDLRKKVMPAVIVRQRKPWRRKDGVFMYFEDNAGVIVNPKGE-MKG
          K.....L.SA.VGDM...TV.KGKPDL.KKVMPA.IV...KPW.RK..V.MYFEDN..VIV.PKGE..KG
Retrocopy KDSVHYLTSAYVGDMITPTVNKGKPDLMKKVMPAIIV--GKPWHRKGVVNMYFEDNVVVIVSPKGETRKG

Parental  -SAITGPIGKECADLWPRIAS
          .SAIT.PIGKECADL.PRIAS
Retrocopy <SAITCPIGKECADL*PRIAS

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_58 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.

---

Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Solanum lycopersicum	Solyc06g083780.2	1 retrocopy	retro_slyc_58 ,
Solanum lycopersicum	Solyc09g090610.2	1 retrocopy	retro_slyc_83,