RetrogeneDB ID: retro_slyc_101

Retrocopy location

• Organism: Tomato (Solanum lycopersicum)
• Coordinates: 9:63125882..63126184(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Solyc06g069090.2
• Aliases: None
• Description: None

Sequence

>retro_slyc_101
CTTATAAAGTCTGAGCAGCTAATCTTGTCAAGCAAAGCAAAGTAAATTATTGCCACCAGTTTGACAGTGAGACCTCTCAA
GAGAGATTCGGCTTCTCAATGACACCACAACAAATTTCTTTCATCTATTCATAATCTCATATTAAAGGACTTGATTCTTA
CAACATATATTGTTAGGAAGCATACTAGGTATTATGTTGATGGTTCAAAGATAATGAATTATTACTTGATCCCTAGGAAC
GAAACAACACCAAGTAAAAGTTGGAGGCCTTTTCAACAGTTCACGAAAAGCTTTCAAGTAAA

Alignment

ORF - retro_slyc_101 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.96 %
• Parental protein coverage: 52.88 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LVRELEKKFSGKDVIFIATRRIVRPPKRGSAAQRPRTRTLTSVHDAILEDLVVPAEIVGKRTRYRVDGSK
          L........S.K....IAT...VRP.KR.SA.Q......L.S.H..IL.DL.....IV.K.TRY.VDGSK
Retrocopy LIKSEQLILSSKAK*IIATSLTVRPLKRDSASQ*HHNKFLSSIHNLILKDLILTTYIVRKHTRYYVDGSK

Parental  IMKVY-LDPKERNNTEYKLETFSAVYRKLSGK
          IM..Y.LDP.ERNNT..KLE.FS.V..KLS.K
Retrocopy IMNYY<LDP*ERNNTK*KLEAFSTVHEKLSSK

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_101 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Solanum tuberosum	PGSC0003DMG400028781	1 retrocopy	retro_stub_156,
Solanum lycopersicum	Solyc06g069090.2	1 retrocopy	retro_slyc_101 ,