RetrogeneDB ID: retro_slyc_91

Retrocopy location

• Organism: Tomato (Solanum lycopersicum)
• Coordinates: 8:33067227..33067432(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Solyc02g064730.2
• Aliases: None
• Description: None

Sequence

>retro_slyc_91
AATGGTCAGAAAACCAAGATGGCTCGTGAGAAGAACATCGAGAACATGAGAGGCGCAAAAGGATGCCTACTTGATGCGAA
CAAGAAGCCTTGAATATCCAGTATAGGTGTGTCTGCATACATTTATGTGCATAACATCACACGTGATGTGGAAGTAACAT
GGAGATTTATTTCATTTAAGAAAATCCAAATATCATTTTTGTTTT

Alignment

ORF - retro_slyc_91 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.34 %
• Parental protein coverage: 88.31 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NGQKAKMARERNLEKLKGAKGSQLDTNKK-AMNIQCK-VCMQTFMCTTSEVKCKEHAEAKH-PKSDLYAC
          NGQK.KMARE.N.E...GAKG..LD.NKK.A.NIQ...VC..TFMC.TS.V..K.H....H..KS....C
Retrocopy NGQKTKMAREKNIENMRGAKGCLLDANKK<ALNIQYR<VCLHTFMCITSHVMWK*HGDLFHLRKSKYHFC

Parental  F
          F
Retrocopy F

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_91 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 lycopersicum	Solyc02g064730.2	1 retrocopy	retro_slyc_91 ,
Solanum lycopersicum	Solyc04g078070.2	1 retrocopy	retro_slyc_48,