RetrogeneDB ID: retro_slyc_65

Retrocopy location

• Organism: Tomato (Solanum lycopersicum)
• Coordinates: 12:9084565..9084828(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Solyc06g069520.2
• Aliases: None
• Description: None

Sequence

>retro_slyc_65
AAATCGTACAAGGCTTCACTCGTTGGTCCACTAGATCTTCCTATAGATTACTACAACATCATAGTTGTTATCTTCGGCGT
CTTTGGTGCCACATTAATTATCAGATACAAGATTTGTTAGAAACTGTTATTATATTCAATGTGCAATCCATTGCTAACAT
AAGGAATATGAAAAATGATCTTAAGCAAATCTCAATGGCTATGATGTTTCGTATCACGAATCTCATGACAAACTACTTGG
GCGTTAGTTGTTGGGAAAGCAAG

Alignment

ORF - retro_slyc_65 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.29 %
• Parental protein coverage: 84.31 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KPYKPSPVAPQDLPIDYSGFIAVICGVFGA--MFRYKICSWL-AIIFSAQSLANMRNMENDLKQISMAMM
          K.YK.S.V.P.DLPIDY...I.VI.GVFGA....RYKIC..L..IIF..QS.AN.RNM.NDLKQISMAMM
Retrocopy KSYKASLVGPLDLPIDYYNIIVVIFGVFGATLIIRYKIC*KL<VIIFNVQSIANIRNMKNDLKQISMAMM

Parental  FGIMGLMTNYLGVGPRGSK
          F.I..LMTNYLGV....SK
Retrocopy FRITNLMTNYLGVSCWESK

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_65 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 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Solanum lycopersicum	Solyc06g069520.2	4 retrocopies	retro_slyc_65 , retro_slyc_85, retro_slyc_86, retro_slyc_87,