RetrogeneDB ID: retro_slyc_12

Retrocopy location

• Organism: Tomato (Solanum lycopersicum)
• Coordinates: 8:56385091..56386453(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Solyc08g067310.1
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Solyc01g008850.2
• Aliases: None
• Description: None

Sequence

>retro_slyc_12
ATGGAGGAGAGACAATTGTTGTTTGACAAGTATGAAATCGGAAAGTTATTAGGTAAAGGGACTTTTGCGAAAGTGTACTA
TGGTAAAGAAGTGGAAACAGGGGAAAGTGTAGCCATTAAAGTGATAAAAAAAGATCAAGTTCAAAAAGAAGGAATGATGG
AGCAGATCACAAGAGAAATCTCAGTGATGGGGCTGGTTCGACATCCGAATATAGTTGAACTCAAAGAAGTCATGGCGACA
AAGTCTAAAATCTTCTTCATAATGGAGTATGTTAAAGGGGGTGAGCTTTTCGCAAAATTAGTATCCAAAGGCAAATTTAA
AGAAGATACAGCAAGAAAGTACTTTCAACAGTTGATAAGTGCTGTTGATTTCTGTCATAGTCGAGGTGTTTATCATCGCG
ATTTGAAGCCTGAGAACTTACTCCTTGATGAGAATGAGGACTTGAAGATATCTGATTTCGGGCTATCGGCTTTGCCTGAT
GAGCAGTTGAGTAGAAATGATGGTTTGCTTCATACACAGTGTGGGACACCAGCATATGTTGCTCCTGAGGTTTTAAGGAG
AAAAGGTTATGATGGTGCAAAGGCTGATATCTGGTCATGTGGGGTTATCTTGTATGTGCTTCTAGCTGGTTACTTGCCAT
TTCAAGATGAGAATGTGATGAACATGTACAAGAAGATCTTCAAGGCGTATTTCGAGTTCCCTCCTTGGTTTTCAATGGAT
TCGAGGCGTTTGATATCTAAACTTTTAATGGCTGATCCAGACAGGAGGATCACTATTCAAGGTATCATGAGGGTTCCATG
GTTTAGGAAGGATTTCGCCATGCCACGGGCTTTTTCAATCCAAGATTTTCAAAAGTTAGAAAATGATCATGTTGAAGAAG
GAATGAGCAGCAAACAAGGAGGAGGGGTCCTAAGGAAATCCCCTTCATCCCCTGCATTTTTCAATGCATTCGAGTTGATC
TCATCCATGTCTTCTGGTTTCGACTTGTCTAGCTTGTTTGAGATCAAAGGGAAGGCATCATCCATGTTCACTTCAAGGAG
CACTGCCCGGGATGTTATCCGTAAAATGGAGAAAATGGCTAAAGTTATGAGGTATAAGGTTTATAGGGTAAAACCATTCA
AGTTAAAGATGCAATGCCCCGAGGAAGGACGAAAAGGGCGGTTGTTGGTGACCGCTGAGGTGTTCAAGGTGGCCCCGGAA
GTCACCGTGGTCGAGCTCTCTAAGTCCTCCGGCGACACCTTGGAGTATAACAAGTTTTGTGAAGAGGAAGTTAGGCCTGC
GTTGAAGGACATTGTTTGGACATGGCAAGGGACAGGTACTGGAAATGCTGATATTGATAACAAACAGGACTTGGAGCAAT
AA

Alignment

ORF - retro_slyc_12 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.94 %
• Parental protein coverage: 95.21 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KYEVGRTIGEGTFAKVKFAKNSETGESVAIKILDKDKVLKHKMAEQIKREIATMKLIRHPHVVQLYEVMG
          KYE.G...G.GTFAKV...K..ETGESVAIK...KD.V.K..M.EQI.REI..M.L.RHP..V.L.EVM.
Retrocopy KYEIGKLLGKGTFAKVYYGKEVETGESVAIKVIKKDQVQKEGMMEQITREISVMGLVRHPNIVELKEVMA

Parental  SKTKIFIVLEFVTGGELFDKIVNHGRMREEEARKYFQQLIHTVDYCHSRGVYHRDLKPENLLLDSSGDLK
          .K.KIF...E.V.GGELF.K.V..G...E..ARKYFQQLI..VD.CHSRGVYHRDLKPENLLLD...DLK
Retrocopy TKSKIFFIMEYVKGGELFAKLVSKGKFKEDTARKYFQQLISAVDFCHSRGVYHRDLKPENLLLDENEDLK

Parental  VSDFGLSAL--SQQVRADGLLHTTCGTPNYVAPEVLNDRGYDGATADLWSCGVILFVLLAGYLPFDDSNL
          .SDFGLSAL...Q..R.DGLLHT.CGTP.YVAPEVL...GYDGA.AD.WSCGVIL.VLLAGYLPF.D.N.
Retrocopy ISDFGLSALPDEQLSRNDGLLHTQCGTPAYVAPEVLRRKGYDGAKADIWSCGVILYVLLAGYLPFQDENV

Parental  MNLYNKISAAEFTCPPWISFGAIKLITRILDPNPTTRITVPEILEDEWFKKDYRPP---VFDEIEDANLD
          MN.Y.KI..A.F..PPW.S.....LI...L...P..RIT...I....WF.KD...P.............D
Retrocopy MNMYKKIFKAYFEFPPWFSMDSRRLISKLLMADPDRRITIQGIMRVPWFRKDFAMPRAFSIQDFQKLEND

Parental  DVEAVFRDSEEYHVTERREEKPTSMNAFELIS-MSQGLNLGNLFDEQGFKRETRFTSKCPANEIISKIEE
          .VE..........V.......P...NAFELIS.MS.G..L..LF...G.K....FTS...A...I.K.E.
Retrocopy HVEEGMSSKQGGGVLRKSPSSPAFFNAFELISSMSSGFDLSSLFEIKG-KASSMFTSRSTARDVIRKMEK

Parental  AAKPLGFDVHK-KNYKMRLQNLKAGRKGNLNVSTEVFQVAPSLHMVEVRKSKGDTLEFHKF-YKNLSTCL
          .AK.....V...K..K...Q....GRKG.L.V..EVF.VAP....VE..KS.GDTLE..KF........L
Retrocopy MAKVMRYKVYRVKPFKLKMQCPEEGRKGRLLVTAEVFKVAPEVTVVELSKSSGDTLEYNKFCEEEVRPAL

Parental  DNVVW
          ...VW
Retrocopy KDIVW

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_12 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
Prunus persica	PRUPE_ppa005881mg	1 retrocopy	retro_pper_37,
Solanum lycopersicum	Solyc01g008850.2	1 retrocopy	retro_slyc_12 ,