RetrogeneDB ID:

retro_slyc_4

Retrocopy
location
Organism:Tomato (Solanum lycopersicum)
Coordinates:6:48340000..48342565(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:Solyc06g082560.1
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:Solyc03g115230.2
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_slyc_4
ATGATGAATAATCCTGAAAATTTTACTGACAAGACAAATGAGGCTGTTGGTGAGGCACATGAACTGGCTGTATCAGCAGG
GAATGCTCAGTTGACACCTCTGCATATTGCTTTGGTTTTATTATCTGATCACAGTGGTATTTTCTGGCAAGCAATCGTAA
ATGCTGCTGGCATAGAAGATACAGCTAATGGTGTTCAAAGGGTGTTTAATCAAGCTAAGAAGAAAATCCCTTCTCAGTTA
CCACCACCTGATCAAGTTCCACCAAGTACTTCACTTAATAAGGTGCTGCTACGAGCACAATCGTTGCAGAAGTCTCGTGG
TGATAGCCATTTGGCAGTTGATCTGTTGATTTTAGGCCTTCTGGAAGATTCACAAATTGTTCATCTTTTGAACGACTCTG
GTCTTAGTGCAGCAGGAGTGAAATCAGAAGTTGAGAAACTTAGAGGAAAAGATGGAAAGGATGTGGAAAGTGCGACCACA
TTCCAAGCTCTTAACACCTATGGTCGTGATCTCGTGGAACAAGCAGGAAAACTTGATCCTGTGATTGGTAGGGATGAAGA
AATTCGAAGAGTGATTCGGATTCTATCGAGGAGGACAAAGAACAATCCGGTGCTTATTGGTGAGCCTGGTGTTGGTAAAA
CAGCTGTAGTTGAAGGGCTAGCACAAAGGATTGTTCGAGGCGATGTTCCAAGTAATTTGGCTGATGTCAGGGTGATCGCA
TTGGATATGGGAGCACTCATTGCTGGAACAAAGTACAGAGGTGAATTTGAAGAGAGGTTGAAGGATGTTCTCAAGGAAGT
GGAAGATGCACAAGGGAAAGTAACTCTCTTCATTGATGAGATACACTTGGTTTTAGGTGCTGGTAGGATTGAAGGGTCAA
TGGATGCTGCTAATTTGTTCAAGCCAATGCTTGCTAGGGGCCAATTAAGGTGCATTGGTGCGACAACTATGGAAGAGTAT
AGCAAGTATGTGGAGAAGGATGCTGCATTTGAAAGGCGTTTCCAGCAGGTATATGTCGCTGAGCCTAGCATTCCCGATAC
TATAAGTATCCTTAGAGGGTTGAAGGAGAAGTATGAAGGCCATCATGGTGTCAAAATTCAGGATAGGGCTCTTGTTATTG
CAGCTCAGCTTTCATCTCGATACATTACAGGTCGACATTTGCCTGATAAGGCTATTGACTTAGTTGATGAGGCTAGTGCA
AATGTGAGGGTTCAGCTTGATAGTCAGCCAGAAGAAATAGATAATCTTGAAAGGAAGAGGATTCAGCTACAAGTTGAACA
CCATGCTCTTGAAAAGGAAAAAGATAAGGCTAGCAAAGCTCGACTTGTTGAAGTGAGGAAAGAGCTTGATGATTCGAGGG
ACAAACTCCAGCCTTTGATGATGAGGTATAACAAGGAGAAGGAACGGATTGATGAGCTTCGAAGGCTTAAGCAAAAGCGC
GATGCACTGACCTATGCTTTACAAGACGCTGAAAGGAGATATGATCTTGCCAGAGCAGCAGATCTTAGATATGGTGCCAT
CCAAGATGTGGAAGCTGCAATAGCCAATCTTGAGAGTAGCACAGATGAGAGTAGAATGTTAACAGAGACTGTTGGACCCG
ATCAGATTGCGGAAGTAGTTAGTCGCTGGACTGGAATTCCTGTCTCTAGGCTTGGGCAGAATGAGAAGGAGAAATTGATT
GGTCTTGCTGATAGATTGCACCAAAGAGTTGTGGGGCAAGATGAAGCTGTAAAAGCTGTTACTGAGGCTGTGTTGAGGTC
TAGAGCTGGATTAGGAAGGCCACAACAACCAACTGGTTCATTCCTTTTCTTGGGGCCAACTGGTGTTGGAAAGACAGAAC
TTGCTAAAGCTCTTGCTGAGCAGCTCTTTGATGATGACAAATTGATGGTCAGAATCGACATGTCCGAATACATGGAGCAA
CATTCTGTTGCCAGGTTGATTGGGGCTCCACCAGGTTATGTCGGACATGAGGAAGGAGGACAACTTACCAAAGCTGTAAG
GAGGCGACCTTACAGTGTTGTGCTTTTCGACGAAGTTGAAAAAGCTCATCCAACTGTGTTTAATGCCTTGCTTCAAGTGT
TGGATGATGGTAGATTAACTGATGGTCAAGGTCGTACTGTTGATTTCACCAACACTGTGATCATTATGACCTCAAATTTG
GGAGCGGAATATCTCTTGTCAGGTACCCGCGAAATGGTCATGCAGGATGTGAGGAAGCAATTTAAGCCTGAGTTACTGAA
CAGGCTCGATGAGGTTCTAGTGTTTGATCCTTTATCACACGATCAGTTGAGGCAAGTCTGCCGTCACCAACTGAAAGATG
TGGCAGGCCGTTTAGCTGAGAGGGGTATTGCATTGGGCGTTACTGAGGCCGCATTAGATGTCGTACTTGCACAAAGCTAT
GATCCGGTGTACGGTGCAAGGCCTATTAGGAGGTGGTTGGAGAAGAAAGTTGTAACGGAGTTATCAAAGATGCTTGTCAA
GGAGGAAATTAATGAGAATTCCACCGTGTACATAGATGCCAGACGTGGCGACAAAGATCTAACTTATAGGGTGCATGGAG
AATAA

ORF - retro_slyc_4 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 91.42 %
Parental protein coverage: 81.89 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalNPEKFTHKTNEAIAEAHELAVSAGHAQLTPLHMALALLSDHSGIFWQAIVNAAGSEETANGVERVFNQAK
NPE.FT.KTNEA..EAHELAVSAG.AQLTPLH.AL.LLSDHSGIFWQAIVNAAG.E.TANGV.RVFNQAK
RetrocopyNPENFTDKTNEAVGEAHELAVSAGNAQLTPLHIALVLLSDHSGIFWQAIVNAAGIEDTANGVQRVFNQAK
ParentalKKIPSQSPAPDQVPASTSLIKVLRRAQSLQKSRGDSHLAVDLLILGLLEDSQIADLLKDSGLSAARVKSE
KKIPSQ.P.PDQVP.STSL.KVL.RAQSLQKSRGDSHLAVDLLILGLLEDSQI..LL.DSGLSAA.VKSE
RetrocopyKKIPSQLPPPDQVPPSTSLNKVLLRAQSLQKSRGDSHLAVDLLILGLLEDSQIVHLLNDSGLSAAGVKSE
ParentalVEKLRGKDGKKVESATGDTTFQALKTYGRDLVEQAGKLDPVIGRDEEIRRVIRILSRRTKNNPVLIGEPG
VEKLRGKDGK.VESA...TTFQAL.TYGRDLVEQAGKLDPVIGRDEEIRRVIRILSRRTKNNPVLIGEPG
RetrocopyVEKLRGKDGKDVESA---TTFQALNTYGRDLVEQAGKLDPVIGRDEEIRRVIRILSRRTKNNPVLIGEPG
ParentalVGKTAVVEGLAQRIVRGDVPSNLADVRLIALDMGALIAGAKYRGEFEERLKAVLKEVEDAEGKVILFIDE
VGKTAVVEGLAQRIVRGDVPSNLADVR.IALDMGALIAG.KYRGEFEERLK.VLKEVEDA.GKV.LFIDE
RetrocopyVGKTAVVEGLAQRIVRGDVPSNLADVRVIALDMGALIAGTKYRGEFEERLKDVLKEVEDAQGKVTLFIDE
ParentalIHLVLGAGRTEGSMDAANLFKPMLARGQLRCIGATTLEEYRKYVEKDAAFERRFQQVYVAEPSVPDTISI
IHLVLGAGR.EGSMDAANLFKPMLARGQLRCIGATT.EEY.KYVEKDAAFERRFQQVYVAEPS.PDTISI
RetrocopyIHLVLGAGRIEGSMDAANLFKPMLARGQLRCIGATTMEEYSKYVEKDAAFERRFQQVYVAEPSIPDTISI
ParentalLRGLKEKYEGHHGVKIQDRALVIAAQLSARYITGRHLPDKAIDLVDEACANVRVQLDSQPEEIDNLERKR
LRGLKEKYEGHHGVKIQDRALVIAAQLS.RYITGRHLPDKAIDLVDEA.ANVRVQLDSQPEEIDNLERKR
RetrocopyLRGLKEKYEGHHGVKIQDRALVIAAQLSSRYITGRHLPDKAIDLVDEASANVRVQLDSQPEEIDNLERKR
ParentalIQLEVEHHALEKEKDKASKARLVEVRKELDDLRDKLQPLMMRYKKEKERVDELRRLKQKRDELTYALQEA
IQL.VEHHALEKEKDKASKARLVEVRKELDD.RDKLQPLMMRY.KEKER.DELRRLKQKRD.LTYALQ.A
RetrocopyIQLQVEHHALEKEKDKASKARLVEVRKELDDSRDKLQPLMMRYNKEKERIDELRRLKQKRDALTYALQDA
ParentalERRYDLARAADLRYGAIQEVESAIANLESSTDESTMLTETVGPDQIAEVVSRWTGIPVSRLGQNEKEKLI
ERRYDLARAADLRYGAIQ.VE.AIANLESSTDES.MLTETVGPDQIAEVVSRWTGIPVSRLGQNEKEKLI
RetrocopyERRYDLARAADLRYGAIQDVEAAIANLESSTDESRMLTETVGPDQIAEVVSRWTGIPVSRLGQNEKEKLI
ParentalGLADRLHLRVVGQDQAVKAVAEAVLRSRAGLGRPQQPTGSFLFLGPTGVGKTELAKALAEQLFDDDKLMV
GLADRLH.RVVGQD.AVKAV.EAVLRSRAGLGRPQQPTGSFLFLGPTGVGKTELAKALAEQLFDDDKLMV
RetrocopyGLADRLHQRVVGQDEAVKAVTEAVLRSRAGLGRPQQPTGSFLFLGPTGVGKTELAKALAEQLFDDDKLMV
ParentalRIDMSEYMEQHSVARLIGAPPGYVGHEEGGQLTEAVRRRPYSVVLFDEVEKAHPAVFNALLQVLDDGRLT
RIDMSEYMEQHSVARLIGAPPGYVGHEEGGQLT.AVRRRPYSVVLFDEVEKAHP.VFNALLQVLDDGRLT
RetrocopyRIDMSEYMEQHSVARLIGAPPGYVGHEEGGQLTKAVRRRPYSVVLFDEVEKAHPTVFNALLQVLDDGRLT
ParentalDGQGRTVDFTNTVIIMTSNLGAEYLLSGLSGKCTMEKAREMVMQEV
DGQGRTVDFTNTVIIMTSNLGAEYLLSG......M...R.....E.
RetrocopyDGQGRTVDFTNTVIIMTSNLGAEYLLSG-TREMVMQDVRKQFKPEL

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_4 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 Solyc03g115230.2 1 retrocopy
retro_slyc_4 ,




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