RetrogeneDB ID: retro_slyc_57

Retrocopy location

• Organism: Tomato (Solanum lycopersicum)
• Coordinates: 10:9816572..9816806(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Solyc06g007470.2
• Aliases: None
• Description: None

Sequence

>retro_slyc_57
ATACGTGATGTCTAGGTAGGTTTTTCTTTTGAATTGGACACTCTTCCTAAGCTCAATTTGAAGATGTAGTATTGTGTTTC
ATGTGCAATTCACTCCAAGGTGATTAGAGTCCATTCTTGTACTGATAGGAGAGTTTGTGAGCCTCCACAACATTTCAGGC
ACCCAAGGGATGATCTCCCAAAGATAGGTTAAGCTCCACGCCCCACAGGAGGACCTCCTGCTGCTCCACGCTCT

Alignment

ORF - retro_slyc_57 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.64 %
• Parental protein coverage: 61.42 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VRDVQEACAFELYTLPKLYLKMQYCVSCAIHSKVVRVRSRTDRRVREPPQRFRRPRDDLPKTGQAPRPAG
          .RDV.....FEL.TLPKL.LKM.YCVSCAIHSKV.RV.S.TDRRV.EPPQ.FR.PRDDLPK.G.APRP.G
Retrocopy IRDV*VGFSFELDTLPKLNLKM*YCVSCAIHSKVIRVHSCTDRRVCEPPQHFRHPRDDLPKIG*APRPTG

Parental  GPPAAPRT
          GPPAAPR.
Retrocopy GPPAAPRS

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_57 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.

---

Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Brassica oleracea	Bo8g090770	1 retrocopy	retro_bole_5,
Solanum tuberosum	PGSC0003DMG400020566	2 retrocopies	retro_stub_41, retro_stub_88,
Solanum lycopersicum	Solyc06g007470.2	1 retrocopy	retro_slyc_57 ,