RetrogeneDB ID:

retro_slyc_37

Retrocopy
location
Organism:Tomato (Solanum lycopersicum)
Coordinates:3:8858834..8860814(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:Solyc03g044330.1
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:Solyc06g059880.2
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_slyc_37
ATGGCGGCTGCTGCCTCACCATCTCCATGTTTCTCCAAAACCCTACCTCCATCTTCCTCCAAATCTTCCACCATTCTACC
TAGATCTACCTTCTCTTTCCACAATCACCCACAAAAAGCCTCACCCCTTCATCTCATCCACGCTCAACATAATCGTCGTG
GTTTTGCCGTTGCCAATGTCGTCATATCCACTACCACCCATAACGACGTTTCTGAACCTGAAACATTCGTTTCCCGTTTC
GCCCCTGACGAACCCAGAAAGGGTTGTGATGTTCTTGTGGAGGCACTTGAAAGGGAAGGTGTTACGGATGTATTTGCATA
CCCAGGAGGTGCTTCTATGGAGATTCATCAAGCTTTGACACGTTCGAATATTATTCGTAATGTGCTACCACGTCATGAGC
AAGGTGGTGTGTTTGCTGCAGAGGGTTACGCACGGGCTACTGGGTTCCCTGGTGTTTGCATTGCTACCTCTGGTCCCGGA
GCTACAAATCTTGTTAGTGGTCTTGCGGATGCTTTGTTAGATAGTATTCCGATTGTTGCTATTACAGGTCAAGTGCCAAG
GAGGATGATTGGTACTGATGCGTTCCAGGAAACGCCTATTGTTGAGGTAACGAGATCTATTACGAAGCATAATTATCTTG
TTATGGATGTAGAAGATATTCCTAGGGTTGTTCGTGAAGCATTTTTTCTTGCGAAATCGGGACGGCCTGGCCCAGTTTTG
ATTGATGTACCTAAGGATATTCAGCAACAATTGGTGATACCTAATTGGGATCAGCCAATGAGGTTGCCTGGTTACATGTC
TAGGTTACCTAAATTGCCTAATGAAATGCTTTTGGAACAAATTGTTAGGCTGATTTCCGAGTCGAAGAAGCCTGTTTTGT
ATGTGGGTGGTGGGTGTTCGCAATCAAGTGAGGAGCTGAGACGATTTGTGGAGCTTACAGGTATTCCTGTAGCGAGTACT
TTGATGGGTCTTGGAGCTTTTCCAACTGGGGATGAGCTTTCACTTCAAATGTTGGGTATGCATGGAACTGTGTATGCTAA
TTATGCTGTGGATAGTAGTGATTTGTTGCTTGCATTTGGGGTGAGGTTTGATGATCGAGTTACTGGTAAATTGGAAGCTT
TTGCTAGTCGAGCGAAAATTGTCCACATTGATATTGATTCGGCAGAGATTGGAAAAAACAAGCAACCTCATGTTTCCATT
TGTGCAGATATCAAGTTGGCATTACAGGGTTTGAATTCCATATTGGAGGGTAAAGAAGGTAAGATGAAGTTAGATTTTTC
TGCCTGGAGGCAGGAGTTAACGGAGCAGAAGATGAAGTACCCACTGAATTTTAAGACTTTTGGTGATGCCATCCCTCCAC
AATATGCTATTCAGGTTCTTGATGAGTTAACTAACGGAAATGCCATTATTAGTACTGGTGTGGGGCAACACCAGATGTGG
GCTGCCCAATACTATAAGTACAAAAAGCCACGCCAATGGTTGACATCTGGTGGATTAGGAGCAATGGGATTTGGTTTGCC
TGCTGCTATAGGTGCGGCTGTTGGGAGACCGGGTGAGATTGTGGTTGACATTGACGGTGATGGGAGTTTTATCATGAATG
TGCAAGAGTTAGCAACAATTAAGGTGGAGAATCTCCCAGTTAAGATTATGTTGCTGAATAATCAACACTTGGGAATGGTG
GTTCAATGGGAGGATCGATTCTATAAAGCTAACAGAGCACACACTTACTTGGGTGACCCTTCTAACGAGGAAGAGATCTT
CCCTAATATGTTGAAATTTGCAGAGGCTTGTGGCGTACCTGCTGCAAGAGTGTCACACAGGGATGATCTTAGAGCTGCCA
TTCAAAAGATGTTAGACACTCCTGGGCCATACTTGTTGGATGTGATTGTACCTCATCAGGAGCACGTTCTACCTATGATT
CCCAGCGGTGGTGCTTTCAAAGATGTGATCACGGAGGGCGATGGGAGATGTTCCTATTGA

ORF - retro_slyc_37 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 83.76 %
Parental protein coverage: 90. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalTFTSRFLPDEPRKGCDILVEALERQGVKNVFAYPGGTTLEIHQALTRSPTIRNILPRHEQGGVFAAEGYA
TF.SRF.PDEPRKGCD.LVEALER.GV..VFAYPGG...EIHQALTRS..IRN.LPRHEQGGVFAAEGYA
RetrocopyTFVSRFAPDEPRKGCDVLVEALEREGVTDVFAYPGGASMEIHQALTRSNIIRNVLPRHEQGGVFAAEGYA
ParentalRATGFPGVCMATSGPGATNLISGLADAMADSIPIIAITGQVPRRMIGSDAFQEIPIVEVTRSITKHNYLV
RATGFPGVC.ATSGPGATNL.SGLADA..DSIPI.AITGQVPRRMIG.DAFQE.PIVEVTRSITKHNYLV
RetrocopyRATGFPGVCIATSGPGATNLVSGLADALLDSIPIVAITGQVPRRMIGTDAFQETPIVEVTRSITKHNYLV
ParentalMDVHDIPRIVREAFFLARSGRPGPVLIDVPKDVQQQMDIPNWDQPMKLPGYISRLPLPPKKTLLEQIVRL
MDV.DIPR.VREAFFLA.SGRPGPVLIDVPKD.QQQ..IPNWDQPM.LPGY.SRLP..P...LLEQIVRL
RetrocopyMDVEDIPRVVREAFFLAKSGRPGPVLIDVPKDIQQQLVIPNWDQPMRLPGYMSRLPKLPNEMLLEQIVRL
ParentalISESKKPVLYVGGGCIQSSNELRRFAQLTGIPVASTLMGLGAFPAGDELSLQMLGMHGTVYSNYAVDRSD
ISESKKPVLYVGGGC.QSS.ELRRF..LTGIPVASTLMGLGAFP.GDELSLQMLGMHGTVY.NYAVD.SD
RetrocopyISESKKPVLYVGGGCSQSSEELRRFVELTGIPVASTLMGLGAFPTGDELSLQMLGMHGTVYANYAVDSSD
ParentalLLLAFGVRFDDRVTGKLETFASRAKIVHIDIDSTEIGKNKQPHVSICTDIKLALQGLNSILMDTENALKL
LLLAFGVRFDDRVTGKLE.FASRAKIVHIDIDS.EIGKNKQPHVSIC.DIKLALQGLNSIL...E...KL
RetrocopyLLLAFGVRFDDRVTGKLEAFASRAKIVHIDIDSAEIGKNKQPHVSICADIKLALQGLNSILEGKEGKMKL
ParentalNFSPWRKELTEQKLKYPLKYKFYGDSIPPQYAIEVLDELTNGNAIITSGVGQHQMWCAQYYKYKNPMQCL
.FS.WR.ELTEQK.KYPL..K..GD.IPPQYAI.VLDELTNGNAII..GVGQHQMW.AQYYKYK.P.Q.L
RetrocopyDFSAWRQELTEQKMKYPLNFKTFGDAIPPQYAIQVLDELTNGNAIISTGVGQHQMWAAQYYKYKKPRQWL
ParentalTSSGFGAMGFGLPAAIGAAIAIPDAIVVDIDGDGSFMMNVQELATVRAENLPVKMMILNNQHLGMATQWE
TS.G.GAMGFGLPAAIGAA...P..IVVDIDGDGSF.MNVQELAT...ENLPVK.M.LNNQHLGM..QWE
RetrocopyTSGGLGAMGFGLPAAIGAAVGRPGEIVVDIDGDGSFIMNVQELATIKVENLPVKIMLLNNQHLGMVVQWE
ParentalDRFYKANRAHSYLGNPSNKARIFPNMLKFAEACDIPCAQVIHRNDVRDAIRKMLHTPGPYLLDVIVPHQE
DRFYKANRAH.YLG.PSN...IFPNMLKFAEAC..P.A.V.HR.D.R.AI.KML.TPGPYLLDVIVPHQE
RetrocopyDRFYKANRAHTYLGDPSNEEEIFPNMLKFAEACGVPAARVSHRDDLRAAIQKMLDTPGPYLLDVIVPHQE
ParentalHVLPMIPSNGAFKDVITEGDGRCSY
HVLPMIPS.GAFKDVITEGDGRCSY
RetrocopyHVLPMIPSGGAFKDVITEGDGRCSY

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_37 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 1 parental gene, and 1 retrocopy.

Species Parental gene accession Retrocopies number
Solanum lycopersicum Solyc06g059880.2 1 retrocopy
retro_slyc_37 ,


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