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


Retrocopy-Parental alignment summary:






>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

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:

ParentalFYFLCFLLCFIPLLQAQNFRTYIVQLHPQHASTRTPFSSKLQWHLSFLENFISSGE-NSSSRLLYSYHSA
F..LC.LLCF....QAQ...TYIVQLHP.H..TRTPFSSK.QWH.SFL....SSGE..SSSRLLYSYHSA
RetrocopyFSCLCLLLCFV-CIQAQDLQTYIVQLHP-HGATRTPFSSKQQWHFSFLAKAVSSGEQDSSSRLLYSYHSA
ParentalFEGFAALLSENELKALKKSNDVLSIYPERKLEVQTTYSYKFLGLSPTKEGTWLKSGFGRGAIIGVLDTGI
.EGFAA.L.E.E...L....DVLSI..ER.LEVQTTYSYKFLGLSPT.EG.WLKSGFGRGAIIGVLDTG.
RetrocopyMEGFAARLTEDEVELLRECKDVLSIRAERRLEVQTTYSYKFLGLSPTREGAWLKSGFGRGAIIGVLDTGV
ParentalWPESPSFVDHGMSPIPKKWKGICQEGKNFNSSSCNRKLIGARFFQIGHMMASKISKSIDFVEDYVSPRDS
WPESPSF.DHGM.P.P.KW.GICQ.G..FNSSSCNRKLIGARFF..GH..AS..S.S.D.VE.YVSPRDS
RetrocopyWPESPSFDDHGMPPAPQKWRGICQGGQDFNSSSCNRKLIGARFFRKGHRVASMTS-SPDAVEEYVSPRDS
ParentalEGHGTHTASTAGGAPVPMASVLGNGAGEARGMAPGAHIAIYKVCWSSGCYSSDILAAMDVAIRDGVDILS
.GHGTHTASTAGGA.VP.A.VL.NGAGEARGMAPG.HIAIYKVCW.SGCYSSDILAAMDVAIRDGVDILS
RetrocopyHGHGTHTASTAGGATVPLAGVLRNGAGEARGMAPGGHIAIYKVCWFSGCYSSDILAAMDVAIRDGVDILS
ParentalLSIGGFPVPLFEDTIAIGSFRAMERGISVICAAGNNGPIRSSVANEAPWIATIGASTLDRKFPAIIQLGN
LS.GGFP.PL..DTIAIGSFRAME.GISVICAAGNNGPI.SSVAN.APWIATIGASTLDR.FPA..QLGN
RetrocopyLSLGGFPIPLYDDTIAIGSFRAMEHGISVICAAGNNGPIQSSVANGAPWIATIGASTLDRRFPASVQLGN
ParentalGKYVYGESLYPGKQVHNSQKVLEIVYLSDGDNGSEFCLRGSLPRAKVRGKIVVCDRGVNGRAEKGQVVKE
GK..YGESLYPGK.V..S.K.LEIVY..D.D.GSEFCLRG.L..A.VRGK.VVCDRGVNGRAEKGQVVKE
RetrocopyGKFLYGESLYPGKKVPSSRKSLEIVYIRDKDKGSEFCLRGTLSKAQVRGKMVVCDRGVNGRAEKGQVVKE
ParentalSGGVAMILANTAVNMEEDSVDVHVLPATLIGFDESIQLQSYMNSTRKPTARIIFGGTVIGKSSAPAVAQF
.GG.AMILANTA.N.EEDSVDVHVLPATLIGFDESIQLQ.Y.NST..PTAR..FGG.VIGKS.APAVAQF
RetrocopyAGGAAMILANTAINLEEDSVDVHVLPATLIGFDESIQLQNYLNSTKRPTARFLFGGMVIGKSRAPAVAQF
ParentalSSRGPSFTDPSILKPDMIAPGVNIIAAWPQNLGPSGLAEDSRRVNFTVLSGTSMACPHVSGIAALLHSIH
SSRGPS.TDPSILKPD.IAPGVNIIAAWPQNLGPSGL.EDSRRVNFTV.SGTSMACPHVSGIAALLHS.H
RetrocopySSRGPSYTDPSILKPDLIAPGVNIIAAWPQNLGPSGLPEDSRRVNFTVMSGTSMACPHVSGIAALLHSAH
ParentalPKWSPAAIKSALMTTADTTNHQGKSIMDGDTPAGLFAIGAGHVNPGRSDDPGLIYDIIAKDYITHLCTIG
PKW.PAAI.SAL.TTADT..H.GK.IMDGD.PA..FA.GAG.VNPGR..DPGLIYDI....YITHLCTIG
RetrocopyPKWTPAAIRSALVTTADTADHLGKPIMDGDAPAKFFAAGAGQVNPGRAIDPGLIYDIQVDEYITHLCTIG
ParentalYKNSEIFSITHKNVSCHDVLQKKRGFSLNYPSISVIFKAGKTRKMITRRVTNVGSPNSTYSVEIVEPEGV
Y.NSE.FSITH.NVSCHD.LQK.RGFSLNYPSIS..F..G.TRKMI.RRVTNVG.PNSTYSV..V.PEGV
RetrocopyYRNSEVFSITHRNVSCHDILQKNRGFSLNYPSISITFRKGMTRKMIKRRVTNVGNPNSTYSVDVVAPEGV
ParentalKVRVKPRRLVFKRVNQSLSYRVWFISRKRIGTQKRSFAEGQLMWINSRDKYQKVRSPISVAWASKK
KVRVKPRRL.FK.VNQSLSYRVWFISRK.I.....SFAEGQL.W...R.K..KVRSPISV.WAS.K
RetrocopyKVRVKPRRLIFKHVNQSLSYRVWFISRKKIESKRMSFAEGQLTWLGVRNKATKVRSPISVTWASMK

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

Solanum lycopersicum was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Solanum lycopersicum was not studied using ChIP-Seq data.

EST - click to see more details

Solanum lycopersicum was not studied using EST data.

TSS - click to see more details

Solanum lycopersicum was not studied using FANTOM5 data.

Lab - click to see more details

retro_slyc_9 was not experimentally validated.

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 Solyc03g044150.21 retrocopy
retro_slyc_26,
Solanum lycopersicum Solyc06g083720.1 1 retrocopy
retro_slyc_9 ,


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