RetrogeneDB ID: retro_slyc_67

Retrocopy location

• Organism: Tomato (Solanum lycopersicum)
• Coordinates: 2:15325612..15326044(+)
• Located in intron of: Solyc02g014150.2

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Solyc12g036250.1
• Aliases: None
• Description: None

Sequence

>retro_slyc_67
AGGCCTAGAAGTTTTGACTCGGAGGCTAGAAAGATATGCTGGTCCAAAGCAGAGAAAGTTCCAGGTCGAGATCCTGAGAG
GTGGAGAAAAGATGTAGCTGGCAACATTATTGGCAAGCGATTCCACAGCTGCCAAGGTTGCCTCTGCTTTGAGTATGATC
ACATTGTTCCCTTCTCTAAAGGTGGTGATTCAGTGTCAGATAACTGTCAAATTCTTCAAACAAGGGTGAATAGATCTAAA
GCAGACAAGGTTGCAGTTGACACAAAACATTTGAAAGGATATTCTTGTGACATCAACTTCAGCGACAATGACCTTGACAA
GATTGAGATGGCTGTTTATGGGGATATTAAGCGGTCAGACAATCAATGCCGTGTTCAAACAATAGATGAAATAATGGGGA
AATACAAGTCCAAGAATGGCATTGCTAGCTGC

Alignment

ORF - retro_slyc_67 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.58 %
• Parental protein coverage: 78.26 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RARSFDGEAKRMCWAKAETVPGRHPERWRKDSAGNILCKRLFNCQGCLCFEYDHIIPFSKGGESIAENCQ
          R.RSFD.EA...CW.KAE.VPGR.PERWRKD.AGNI..KR...CQGCLCFEYDHI.PFSKGG.S...NCQ
Retrocopy RPRSFDSEARKICWSKAEKVPGRDPERWRKDVAGNIIGKRFHSCQGCLCFEYDHIVPFSKGGDSVSDNCQ

Parental  ILQTRVNRLKSNKDEIDVSRLKSYSCDIKFTVKELDVIEMAVYGDVLRPGKQCRCRTVAEMLGQYKSKDR
          ILQTRVNR.K..K...D...LK.YSCDI.F....LD.IEMAVYGD..R...QCR..T..E..G.YKSK..
Retrocopy ILQTRVNRSKADKVAVDTKHLKGYSCDINFSDNDLDKIEMAVYGDIKRSDNQCRVQTIDEIMGKYKSKNG

Parental  TAPC
          .A.C
Retrocopy IASC

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_67 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	PGSC0003DMG400015000	1 retrocopy	retro_stub_98,
Solanum lycopersicum	Solyc12g036250.1	1 retrocopy	retro_slyc_67 ,