RetrogeneDB ID: retro_slyc_98

Retrocopy location

• Organism: Tomato (Solanum lycopersicum)
• Coordinates: 9:56464389..56464725(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Solyc07g063280.1
• Aliases: None
• Description: None

Sequence

>retro_slyc_98
GCAAAGAACAAAGGTGGCAAACGTAGCTCCACCACTGTACGACGCTTAAGATGCATAATTATAGGCTGAATTATGATAAG
AAGGTCAAAATATTGAAGCACAAGATCAAACAAAGCAACTTCCATCAACGAGAATACAGTCATATCTCGATGGTCAATCA
ATACTAGGTTGATTAATCTAGAGAAATTGGAATCCATTAGAGAAGAGAGACATGATCGACTTTTTAGCAACTACTATATC
ATAATGAATGGATATAATTTTCCCATTTCCCTTGTGAATGAGCGCAAGAAGAAAGGAAAAGCTCATCAACTTTGCAGTAG
CAATCTACTGGAACAA

Alignment

ORF - retro_slyc_98 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.66 %
• Parental protein coverage: 91.06 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  AKNKSGNRSSATTRRL-KMYNSRPKRDRKGKILKHEY-QSKQLPSTRIQPD-PRWFINTRVISQEKLESF
          AKNK.G.RSS.T.RRL.KM.N.R...D.K.KILKH...Q.KQLPSTRIQ....RW.INTR.I..EKLES.
Retrocopy AKNKGGKRSSTTVRRL<KMHNYRLNYDKKVKILKHKI<QTKQLPSTRIQSY<SRWSINTRLINLEKLESI

Parental  REEIQDRLSSNYNIIMNGSNLPMSLVNEHKKE-KLINLAVSLLLEQ
          REE..DRL.SNY.IIMNG.N.P.SLVNE.KK..K...L..S.LLEQ
Retrocopy REERHDRLFSNYYIIMNGYNFPISLVNERKKKGKAHQLCSSNLLEQ

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_98 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Solanum tuberosum	PGSC0003DMG400012453	1 retrocopy	retro_stub_43,
Solanum lycopersicum	Solyc07g063280.1	2 retrocopies	retro_slyc_92, retro_slyc_98 ,