RetrogeneDB ID: retro_slyc_13

Retrocopy location

• Organism: Tomato (Solanum lycopersicum)
• Coordinates: 4:60544594..60545005(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Solyc04g074580.1
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Solyc05g051500.2
• Aliases: None
• Description: None

Sequence

>retro_slyc_13
ATGGCTCGTACGAAGCAAACTGCCCGTAAATCCACTGGAGGAAAGGCTCCAAGGAAGCAACTAGCCACCAAGGCCGCCAG
GAAATCTGCCCCAACAACTGGAGGAGTCAAGAAGCCTCACAGATACAGGCCTGGAACCGTTGCTCTTCGTGAAATCCGCA
AGTACCAGAAGAGTACTGAGCTATTGATCAGGAAGTTGCCATTCCAGAGGCTTGTTCGTGAAATTGCTCAGGACTTCAAG
ACTGATTTGCGTTTCCAGAGCCATGCTGTGTTGGCTTTGCAAGAGGCAGCTGAGGCTTACCTTGTTGGGCTTTTTGAAGA
TACAAATCTGTGTGCTATTCACGCCAAGCGTGTCACAATCATGCCCAAGGACATTCAGCTTGCTAGAAGGATTAGGGGTG
AAAGGGCTTAG

Alignment

ORF - retro_slyc_13 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100. %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MARTKQTARKSTGGKAPRKQLATKAARKSAPTTGGVKKPHRYRPGTVALREIRKYQKSTELLIRKLPFQR
          MARTKQTARKSTGGKAPRKQLATKAARKSAPTTGGVKKPHRYRPGTVALREIRKYQKSTELLIRKLPFQR
Retrocopy MARTKQTARKSTGGKAPRKQLATKAARKSAPTTGGVKKPHRYRPGTVALREIRKYQKSTELLIRKLPFQR

Parental  LVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA
          LVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA
Retrocopy LVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA

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_13 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 4 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Brassica rapa	Bra003745	4 retrocopies	retro_brap_3, retro_brap_36, retro_brap_54, retro_brap_55,
Medicago truncatula	MTR_1g023630	1 retrocopy	retro_mtru_31,
Medicago truncatula	MTR_4g097170	1 retrocopy	retro_mtru_5,
Solanum lycopersicum	Solyc05g051500.2	1 retrocopy	retro_slyc_13 ,