RetrogeneDB ID: retro_slyc_9

Retrocopy location

• Organism: Tomato (Solanum lycopersicum)
• Coordinates: 9:61771534..61774009(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Solyc09g064490.1
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Solyc06g083720.1
• Aliases: None
• Description: None

Sequence

>retro_slyc_9
ATGTCTCGTGAAAATCTTAGCAAAACCATCAGCTCCTCTCTCACTTTTAATGATACTCGTGAGGAAGAGCTCATAAATTT
CACGAGTTTCTTCTTCAACACTCATATTTCAATTCTCTTCAAATACCCCACATTCATTCTTCTAACAAATATGCACTCTT
CGATGGGATACAGTACTCAATCATTCTCATGTCTATGTCTTTTACTGTGTTTTGTTTGCATACAAGCTCAAGATTTGCAA
ACTTATATAGTTCAGTTGCATCCACATGGAGCAACAAGAACCCCTTTTAGCTCTAAACAACAATGGCACTTTTCTTTCCT
TGCAAAAGCAGTTTCCTCTGGAGAACAAGACTCGTCTTCTCGTCTTTTGTACTCTTACCATTCTGCGATGGAAGGTTTTG
CAGCTCGGCTCACTGAAGATGAGGTTGAGTTGTTAAGGGAATGTAAGGATGTGTTATCGATACGTGCTGAGAGGAGGCTT
GAAGTTCAGACCACTTATTCCTATAAGTTCTTGGGATTAAGTCCGACGAGAGAAGGAGCTTGGTTGAAGTCTGGATTTGG
TCGAGGGGCGATTATTGGAGTGTTGGATACTGGAGTTTGGCCAGAAAGTCCAAGTTTTGATGATCATGGGATGCCACCTG
CTCCACAGAAGTGGAGGGGTATTTGCCAAGGAGGACAGGATTTTAATTCTTCTAGTTGCAATCGCAAGCTTATTGGTGCG
AGGTTTTTCAGAAAAGGACATCGTGTGGCTTCAATGACATCGTCACCAGATGCAGTGGAGGAATATGTGTCGCCACGGGA
TTCCCATGGCCATGGTACACATACAGCATCCACTGCTGGAGGAGCTACAGTTCCATTGGCTGGGGTGCTCAGAAATGGAG
CAGGGGAGGCTCGAGGGATGGCCCCCGGTGGCCACATTGCGATATATAAAGTATGCTGGTTCAGTGGTTGTTACAGCTCT
GATATACTTGCAGCAATGGATGTAGCCATCAGAGATGGAGTAGACATATTGTCACTCTCACTTGGTGGCTTCCCTATTCC
ACTTTATGATGATACGATTGCCATTGGAAGTTTCCGAGCCATGGAGCATGGAATTTCAGTTATATGTGCAGCAGGGAATA
ATGGACCAATCCAAAGTTCAGTAGCCAACGGTGCTCCTTGGATTGCCACTATTGGTGCTAGCACACTTGACAGGAGATTT
CCAGCATCAGTTCAGTTAGGCAATGGAAAGTTCCTGTACGGAGAATCTTTGTACCCTGGGAAGAAAGTTCCTAGCTCTCG
GAAGAGTCTTGAGATCGTTTATATCAGAGATAAGGACAAGGGAAGTGAATTTTGCTTGAGAGGAACGCTATCAAAAGCAC
AAGTCCGAGGGAAAATGGTTGTGTGTGATAGGGGAGTCAATGGAAGGGCAGAAAAAGGCCAGGTTGTGAAGGAGGCAGGT
GGTGCTGCCATGATCTTAGCAAATACAGCAATAAATTTGGAGGAAGATTCTGTCGATGTCCATGTCCTCCCGGCAACGTT
GATTGGCTTCGATGAATCAATTCAATTACAAAACTACCTGAACTCAACAAAAAGACCAACAGCTCGATTCCTATTTGGAG
GAATGGTAATAGGAAAGTCTAGAGCACCTGCAGTAGCTCAGTTTTCGTCAAGGGGGCCAAGCTATACTGATCCTTCAATT
CTCAAACCTGATTTGATTGCTCCAGGGGTAAACATAATTGCCGCATGGCCACAAAACTTAGGCCCCAGTGGTCTTCCCGA
GGATTCACGAAGAGTAAATTTCACTGTTATGTCAGGGACTTCAATGGCGTGTCCTCATGTGAGTGGAATTGCCGCATTGC
TCCATTCAGCTCATCCTAAATGGACTCCAGCAGCAATAAGATCCGCATTAGTGACCACTGCAGATACAGCTGATCATTTG
GGAAAACCAATCATGGATGGAGATGCACCAGCTAAATTTTTTGCAGCTGGAGCTGGACAAGTGAACCCCGGAAGAGCCAT
TGATCCTGGATTGATATATGACATCCAGGTTGATGAATATATCACTCATCTTTGCACTATCGGATACAGAAATTCTGAAG
TCTTCAGCATTACTCATAGGAATGTAAGCTGCCATGACATTTTACAGAAGAACAGGGGTTTCAGCCTAAATTACCCCTCG
ATTTCAATAACTTTCAGGAAAGGAATGACTAGAAAGATGATCAAGAGGAGAGTAACAAATGTGGGGAACCCTAATTCTAC
TTACTCAGTTGACGTTGTGGCACCTGAGGGAGTCAAAGTGAGAGTGAAGCCACGCCGTCTGATATTTAAACATGTGAATC
AAAGCTTAAGCTATAGAGTTTGGTTTATATCACGAAAGAAAATAGAGTCTAAAAGGATGAGCTTCGCAGAGGGGCAATTG
ACATGGTTAGGTGTACGAAACAAAGCCACGAAAGTTAGGAGTCCTATTTCCGTCACATGGGCATCAATGAAGTGA

Alignment

ORF - retro_slyc_9 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.63 %
• Parental protein coverage: 99.22 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FYFLCFLLCFIPLLQAQNFRTYIVQLHPQHASTRTPFSSKLQWHLSFLENFISSGE-NSSSRLLYSYHSA
          F..LC.LLCF....QAQ...TYIVQLHP.H..TRTPFSSK.QWH.SFL....SSGE..SSSRLLYSYHSA
Retrocopy FSCLCLLLCFV-CIQAQDLQTYIVQLHP-HGATRTPFSSKQQWHFSFLAKAVSSGEQDSSSRLLYSYHSA

Parental  FEGFAALLSENELKALKKSNDVLSIYPERKLEVQTTYSYKFLGLSPTKEGTWLKSGFGRGAIIGVLDTGI
          .EGFAA.L.E.E...L....DVLSI..ER.LEVQTTYSYKFLGLSPT.EG.WLKSGFGRGAIIGVLDTG.
Retrocopy MEGFAARLTEDEVELLRECKDVLSIRAERRLEVQTTYSYKFLGLSPTREGAWLKSGFGRGAIIGVLDTGV

Parental  WPESPSFVDHGMSPIPKKWKGICQEGKNFNSSSCNRKLIGARFFQIGHMMASKISKSIDFVEDYVSPRDS
          WPESPSF.DHGM.P.P.KW.GICQ.G..FNSSSCNRKLIGARFF..GH..AS..S.S.D.VE.YVSPRDS
Retrocopy WPESPSFDDHGMPPAPQKWRGICQGGQDFNSSSCNRKLIGARFFRKGHRVASMTS-SPDAVEEYVSPRDS

Parental  EGHGTHTASTAGGAPVPMASVLGNGAGEARGMAPGAHIAIYKVCWSSGCYSSDILAAMDVAIRDGVDILS
          .GHGTHTASTAGGA.VP.A.VL.NGAGEARGMAPG.HIAIYKVCW.SGCYSSDILAAMDVAIRDGVDILS
Retrocopy HGHGTHTASTAGGATVPLAGVLRNGAGEARGMAPGGHIAIYKVCWFSGCYSSDILAAMDVAIRDGVDILS

Parental  LSIGGFPVPLFEDTIAIGSFRAMERGISVICAAGNNGPIRSSVANEAPWIATIGASTLDRKFPAIIQLGN
          LS.GGFP.PL..DTIAIGSFRAME.GISVICAAGNNGPI.SSVAN.APWIATIGASTLDR.FPA..QLGN
Retrocopy LSLGGFPIPLYDDTIAIGSFRAMEHGISVICAAGNNGPIQSSVANGAPWIATIGASTLDRRFPASVQLGN

Parental  GKYVYGESLYPGKQVHNSQKVLEIVYLSDGDNGSEFCLRGSLPRAKVRGKIVVCDRGVNGRAEKGQVVKE
          GK..YGESLYPGK.V..S.K.LEIVY..D.D.GSEFCLRG.L..A.VRGK.VVCDRGVNGRAEKGQVVKE
Retrocopy GKFLYGESLYPGKKVPSSRKSLEIVYIRDKDKGSEFCLRGTLSKAQVRGKMVVCDRGVNGRAEKGQVVKE

Parental  SGGVAMILANTAVNMEEDSVDVHVLPATLIGFDESIQLQSYMNSTRKPTARIIFGGTVIGKSSAPAVAQF
          .GG.AMILANTA.N.EEDSVDVHVLPATLIGFDESIQLQ.Y.NST..PTAR..FGG.VIGKS.APAVAQF
Retrocopy AGGAAMILANTAINLEEDSVDVHVLPATLIGFDESIQLQNYLNSTKRPTARFLFGGMVIGKSRAPAVAQF

Parental  SSRGPSFTDPSILKPDMIAPGVNIIAAWPQNLGPSGLAEDSRRVNFTVLSGTSMACPHVSGIAALLHSIH
          SSRGPS.TDPSILKPD.IAPGVNIIAAWPQNLGPSGL.EDSRRVNFTV.SGTSMACPHVSGIAALLHS.H
Retrocopy SSRGPSYTDPSILKPDLIAPGVNIIAAWPQNLGPSGLPEDSRRVNFTVMSGTSMACPHVSGIAALLHSAH

Parental  PKWSPAAIKSALMTTADTTNHQGKSIMDGDTPAGLFAIGAGHVNPGRSDDPGLIYDIIAKDYITHLCTIG
          PKW.PAAI.SAL.TTADT..H.GK.IMDGD.PA..FA.GAG.VNPGR..DPGLIYDI....YITHLCTIG
Retrocopy PKWTPAAIRSALVTTADTADHLGKPIMDGDAPAKFFAAGAGQVNPGRAIDPGLIYDIQVDEYITHLCTIG

Parental  YKNSEIFSITHKNVSCHDVLQKKRGFSLNYPSISVIFKAGKTRKMITRRVTNVGSPNSTYSVEIVEPEGV
          Y.NSE.FSITH.NVSCHD.LQK.RGFSLNYPSIS..F..G.TRKMI.RRVTNVG.PNSTYSV..V.PEGV
Retrocopy YRNSEVFSITHRNVSCHDILQKNRGFSLNYPSISITFRKGMTRKMIKRRVTNVGNPNSTYSVDVVAPEGV

Parental  KVRVKPRRLVFKRVNQSLSYRVWFISRKRIGTQKRSFAEGQLMWINSRDKYQKVRSPISVAWASKK
          KVRVKPRRL.FK.VNQSLSYRVWFISRK.I.....SFAEGQL.W...R.K..KVRSPISV.WAS.K
Retrocopy KVRVKPRRLIFKHVNQSLSYRVWFISRKKIESKRMSFAEGQLTWLGVRNKATKVRSPISVTWASMK

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_9 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 lycopersicum	Solyc03g044150.2	1 retrocopy	retro_slyc_26,
Solanum lycopersicum	Solyc06g083720.1	1 retrocopy	retro_slyc_9 ,