RetrogeneDB ID: retro_slyc_96

Retrocopy location

• Organism: Tomato (Solanum lycopersicum)
• Coordinates: 9:48688036..48688360(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Solyc10g052660.1
• Aliases: None
• Description: None

Sequence

>retro_slyc_96
ATGGCTCCAAAGAAGGCACAAGATCCACCTCCATCTTCCAAGCCAGCAAAGTCCGACGGTGGAAAGCAGCAGAAGAAGAA
GTGGAGCAAGGAAAAGCAAAACGAAAAGGTGAACAACATGGTGTTGTTCGACAAGCCTACATACAATAATCTACTCTAAA
AATCTCCCAAGTATAAGATTATCGCTCCTTCTGTACTCTCCGATCGTATCTGGATGAGTGGATCACTAGCTAGTAAGGCA
ATTAGAGATTTGTTTGCTTGATGTTCAATTAGGATGGTATCTGCTCATGCAAGCCAGCAGAAATACACCGGGGCTACCAA
CACT

Alignment

ORF - retro_slyc_96 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.63 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAPKKAQAPPPSSKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDKSTYDKLLSEAPKYKLITPSVLSDRL
          MAPKKAQ.PPPSSKPAKS.GGKQ.KKKWSK.KQ.EKVNNMVLFDK.TY..LL...PKYK.I.PSVLSDR.
Retrocopy MAPKKAQDPPPSSKPAKSDGGKQQKKKWSKEKQNEKVNNMVLFDKPTYNNLL*KSPKYKIIAPSVLSDRI

Parental  RISGSLARKAIRDLMARGSIRMVSAHASQQIYTRATNT
          ..SGSLA.KAIRDL.A..SIRMVSAHASQQ.YT.ATNT
Retrocopy WMSGSLASKAIRDLFA*CSIRMVSAHASQQKYTGATNT

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_96 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 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Solanum lycopersicum	Solyc10g052660.1	1 retrocopy	retro_slyc_96 ,