RetrogeneDB ID: retro_slyc_53

Retrocopy location

• Organism: Tomato (Solanum lycopersicum)
• Coordinates: 1:98246137..98246428(+)
• Located in intron of: Solyc01g112180.2

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Solyc02g061790.2
• Aliases: None
• Description: None

Sequence

>retro_slyc_53
AAGAGACAGGAAGAGGATGAGTATGCTTCTGGAGGCAACAATTCTCCTAAGAGACTATCCTCCAGAACCGATGATTCTGA
AGTTGTCGATCACGTCGTATTTTGTTAGATTTCTAAGAATCGGAAAGTGCCAATTAGGAATTTCAGAGGGAAGAGTATGA
TGGACATTTGAGAGTATTACTTTGAAGATGGAGAAAATGCGAGTAATAAAGGCATCTCATTGAGTATGCATTTGTGGAAT
GTTCTCAGAGATCATGCAGATGAAATTGATAAGGTTGTTTCTGAGAACAAT

Alignment

ORF - retro_slyc_53 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.2 %
• Parental protein coverage: 94.17 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KRKEENEYASEGDNPPKK-ASRTDDSDDEDAIVVCEISKNRRVTVRNFGGRVMVDIREFYVKDGKQMPGR
          KR.EE.EYAS.G.N.PK...SRTDDS...D..V.C.ISKNR.V..RNF.G..M.DI.E.Y..DG......
Retrocopy KRQEEDEYASGGNNSPKRLSSRTDDSEVVDHVVFC*ISKNRKVPIRNFRGKSMMDI*EYYFEDGEN-ASN

Parental  KGISLSMDQWNVLREHADEIDEAVAENS
          KGISLSM..WNVLR.HADEID..V.EN.
Retrocopy KGISLSMHLWNVLRDHADEIDKVVSENN

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_53 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	PGSC0003DMG400008674	1 retrocopy	retro_stub_79,
Solanum lycopersicum	Solyc02g061790.2	1 retrocopy	retro_slyc_53 ,