RetrogeneDB ID: retro_slyc_2

Retrocopy location

• Organism: Tomato (Solanum lycopersicum)
• Coordinates: 1:83809519..83810338(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Solyc01g090180.2
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Solyc11g072550.1
• Aliases: None
• Description: None

Sequence

>retro_slyc_2
ATGGGTAGCCAAATGGCTGTCCCTGTGAATGAGACCTTCTTCATATCACATGGTTCCCCAATGCTATCCATAGATGATTC
GTTACCTGCCAGACATTTCTTGAAATGCTTCAACCAGAAAGTCTTCACCCAGAAACCCAATTCAATTTTGGTGATATCTG
GTCATTGGGAGACTTCAGAGCCTACTGTGAATTGCATCACTGGCCTGAATGACACTATTTACGACTTCTACGGCTTCCCA
GAACAGATGTACCAGCTGAAATATCAAGCACCAGGAGCTCCAAAATTAGCGAAAAGGGTGAAGGAACTGCTCAAGTCATC
TGGCTTCAATCGAGTGCACGAAGACAATAACCGGGGCCTGGATCATGGTGCATGGGTGCCTCTTATGCTCATGTATCCAG
GGGCTGACATCCCAGTTTGCCAGCTTTCTGTCCAGACAAAGAAGGATGGAACTCATCATTTTAACATTGGGAAAGCATTG
GCCCCTCTCAAGGAAGAGGGTGTCCTCATAGTTGGTTCTGGATCTGCAACTCACAACTTGAGGGCTTTGCGCGACACTGC
TGGCGTCGCTTCTTGGGCTATGGATTTTGACAATTGGCTTAAGGAGTCCCTTGTTAATGGAAGGTATGAAGATGTCAACA
ACTATATGACAAAAGCACCTTGTGCCAAAATTGCACACCCATGGCCTGATCACCTGTATCCATTACATGTAGCAATGGGT
GCAGCAGGTGAAAATGCCAAAGCTGAACTTATTCATCACAGCTGGAGCAATCATGCTCTTTCTTACGCCTCCTACAAGTT
TGAGTCACAGCTAAAGTAG

Alignment

ORF - retro_slyc_2 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.14 %
• Parental protein coverage: 95.64 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PVKETFFISHGSPTLSIDESLPARNFLKSFKQKFLMNQKPNSILVISAHWETSEPTVNSIRGRNDTIHDF
          PV.ETFFISHGSP.LSID.SLPAR.FLK.F.QK....QKPNSILVIS.HWETSEPTVN.I.G.NDTI.DF
Retrocopy PVNETFFISHGSPMLSIDDSLPARHFLKCFNQK-VFTQKPNSILVISGHWETSEPTVNCITGLNDTIYDF

Parental  YGFPKSMYQLKYPAPGSPELAKRVKDVLMASGFPIVHEDKKRGLDHGAWVPLMLMYPEADIPVCQLSVQP
          YGFP..MYQLKY.APG.P.LAKRVK..L..SGF..VHED..RGLDHGAWVPLMLMYP.ADIPVCQLSVQ.
Retrocopy YGFPEQMYQLKYQAPGAPKLAKRVKELLKSSGFNRVHEDNNRGLDHGAWVPLMLMYPGADIPVCQLSVQT

Parental  NRDGTYHYNLGKALASLKDEGVLIIGSGSATHNLRALGPSKNVSSWALEFDNWLKDALLSGRHQDVNNYD
          ..DGT.H.N.GKALA.LK.EGVLI.GSGSATHNLRAL.....V.SWA..FDNWLK..L..GR..DVNNY.
Retrocopy KKDGTHHFNIGKALAPLKEEGVLIVGSGSATHNLRALRDTAGVASWAMDFDNWLKESLVNGRYEDVNNYM

Parental  MKAPHAKVAHPWPEHIYPLHVALGAAGEGVNGELIHHSWDLGALSYASYRFPS
          .KAP.AK.AHPWP.H.YPLHVA.GAAGE....ELIHHSW...ALSYASY.F.S
Retrocopy TKAPCAKIAHPWPDHLYPLHVAMGAAGENAKAELIHHSWSNHALSYASYKFES

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_2 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	PGSC0003DMG400025377	1 retrocopy	retro_stub_54,
Solanum lycopersicum	Solyc11g072550.1	1 retrocopy	retro_slyc_2 ,