RetrogeneDB ID: retro_slyc_23

Retrocopy location

• Organism: Tomato (Solanum lycopersicum)
• Coordinates: 9:3123570..3124074(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Solyc09g009720.1
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Solyc05g054550.2
• Aliases: None
• Description: None

Sequence

>retro_slyc_23
ATGGCTTCTTCACAAGCCGCTCTTCTCCTCCAAAAACAGCTCAAAGACCTAAACCGTCATCCCGTCGACGGCTTTTCTGC
CGGTTTAGTCGACGAGAACAACGTTTTTGAATGGAGTATCTCAATCATCGGTCCACCGGAAACTTTATTCGACGGCGGAT
TTTTCAACGCTACAATGAGTTTTCCGACGGATTACCCTAACAATCCACCGACGGTGAAATTCACAACGGAGATCTGGCAT
CCGAATGTTTATTCTGACGGTAGGGTTTGTATATCGATTCTTCATCCACCAGGTGATGATCCGAATCATTATGAGCTAGC
GAGTGAGCGGTGGACGCCGGTTCATACGGTGGAGAGCATTATGCTGAGTATAATTTCGATGCTTACCAGTCCGAACGATG
AATCGCCGGCGAATGTTGATGCGGCTAAGGAATGGAGGGATAATAGGGCGGAATTTGTGAAGAAGGTGAAGAGATGCGTG
AGGAAATCACAAGAGATGTTGTGA

Alignment

ORF - retro_slyc_23 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.37 %
• Parental protein coverage: 96.47 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SQASLLLQKQLKDLCKKPVDGFSAGLVDESNLFEWSVTIIGPPETLYDGGFFNAIMSFPQNYPNSPPTVK
          SQA.LLLQKQLKDL...PVDGFSAGLVDE.N.FEWS..IIGPPETL.DGGFFNA.MSFP..YPN.PPTVK
Retrocopy SQAALLLQKQLKDLNRHPVDGFSAGLVDENNVFEWSISIIGPPETLFDGGFFNATMSFPTDYPNNPPTVK

Parental  FTSEIWHPNVYSDGKVCISILHPPGDDPNGYELASERWSPVHTVESIMLSIISMLSSPNDESPANVEAAK
          FT.EIWHPNVYSDG.VCISILHPPGDDPN.YELASERW.PVHTVESIMLSIISML.SPNDESPANV.AAK
Retrocopy FTTEIWHPNVYSDGRVCISILHPPGDDPNHYELASERWTPVHTVESIMLSIISMLTSPNDESPANVDAAK

Parental  EWRDNRDEFKKKVSRCVRRSQEMM
          EWRDNR.EF.KKV.RCVR.SQEM.
Retrocopy EWRDNRAEFVKKVKRCVRKSQEML

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_23 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Solanum tuberosum	PGSC0003DMG401023527	1 retrocopy	retro_stub_55,
Solanum lycopersicum	Solyc05g054550.2	1 retrocopy	retro_slyc_23 ,