RetrogeneDB ID:

retro_slyc_36

Retrocopy
location
Organism:Tomato (Solanum lycopersicum)
Coordinates:2:30909487..30911146(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:Solyc02g037490.1
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:Solyc03g031940.2
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_slyc_36
ATGGATCAATTGAAACCAAGTTCTGTCAATTCATCTCCTCTTACACCATTAACATTCTTGGAAAGAGCTGCTGTAGCTTA
TGGGGATAGTGTTTCCATTGTCTGTAACTCCACTACATACACCTGGTCTCAAACATTCACTCGATGTTTACTCCTCGCTT
CCTCAATTTCAACCCTCATTGGTATCAAAAAAGGCCAAGTTGTTTCGGTTTTAGCTCCTAATATTCCCGCAACGTTAGAG
CTTCAATTTGCTGTTCCAATGGCTGGTGCTGTACTCAACAACATCAACACTCGTCTCGATGCCAAAACCGTCTCTGTTCT
GCTCCAACATAGTGAATCGAAGCTCTTGTTTGTTGATTACCAGCTATATCCTTTGGTACTTCAGTCGATTTCATTGTTTC
CATCTGATGTCGACACTCCAATTCTTGTCCTAATAGAAGATGAAAACTCTGTTCCGTTTTCAACAAACTTGGATTTCGAT
CACTGTGATACTTATGATGCTATGTTGGCGAAGGGGGATTTGAATTTCAATTGGATTCGACCTGAGAATGATCGGGATGC
GATGACGTTGAACTACACTTCTGGAACAACATCCTCACCTAAAGGAGTGGTACATTCTCATAGATCTCTTTTTATCATCA
CAGTTGATTCGTTAATAGATTGGTCTGTACCAAGTCAGCCAGTGTATCTATGGACCCTCCCAATGTTCCATTCCAACGGA
TGGAGTTACACATGGGGTATGGCTGTTGTTGGTGGGACCAACATTTGTCTTCGAAAATTCGACGCTAATGTTGTGTTTCA
TGCTATCAACAAATATAATGTCACACATATGTGTGGTGCACCTGTGGTACTCACTATGCTAGCCAATTCCCCCTGTGCTA
AGCCATTACAAAACCCCGTCCACTTCCGTACTGGTGGGGCTCCTCCCCCTGCCACCATTGTCCTTCGTGTCGAATCCTTA
GGATTCATAGTGAATCACGGGTATGGGATGACAGAGGTGGCAGGGGTAGTCGTATCTTGTATTTGGAAACCAAAATGGAA
CAAATTATCTGCGAATGTGAAGGCAAAATTGAAGTCTAGACAAGGGATTAAGAGTTTAGGTATGACGGAGGTTGACGTGG
TGGATCCGGAATCTGGAGTTAGTGTAAAGAGGGATGGCGTTACAATGGGTGAAATTGTATTAAGAGGTGGATGTATAATG
TTGGGTTATTTGAAAAATGAAGAAGCTACATCAAAATGTATGAAAAACAATTGGCTTTATACAGGGGATGTAGCAGTTGT
GCATCCAGATGGGTACTTGGAAATTAAAGATAGATCTAAAGATATTATAATTAGCGGTGGTGAGAATGTAAGCAGTGTTG
AAGTAGAATCCGTACTTTATTCAAACAATTTTGTGAATGAGGCAGCAGTTGTAGCAAGACCCGATGAATTTTGGGGCGAA
ACGCCTTGTGCATTCGTGAGTCTGAAGATGGAACTGAAACTTAAACCGAAAGAGAAGGAAATTATTGATTTCTGTAGAGA
AAGATTGCCACATTATATGATACCCAAGACGGTAATTTTCATGGATGAACTACCCAAAACAGCAACTGGGAAAATTCAAA
AGTTTTCTCTAAGACAGATTGCTAATGGTATGGGGTCGTTACCTGCTAGTCGAATGTAG

ORF - retro_slyc_36 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 60.92 %
Parental protein coverage: 87.82 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalKISKGPANTCPFSPLDFLERASIVYGNCTSIVYNDTSYTWSQTYTRCKKLASSISSL-GIKKGDVVSVLS
.......N..P..PL.FLERA...YG...SIV.N.T.YTWSQT.TRC..LASSIS.L.GIKKG.VVSVL.
RetrocopyQLKPSSVNSSPLTPLTFLERAAVAYGDSVSIVCNSTTYTWSQTFTRCLLLASSISTLIGIKKGQVVSVLA
ParentalPNIPAMYELQFAVPMSGAILNNINFRLDPRTLSVLLRHSESKLVFVDYQASSLLLEAISLFPSNLQRPKL
PNIPA..ELQFAVPM.GA.LNNIN.RLD..T.SVLL.HSESKL.FVDYQ...L.L..ISLFPS....P.L
RetrocopyPNIPATLELQFAVPMAGAVLNNINTRLDAKTVSVLLQHSESKLLFVDYQLYPLVLQSISLFPSDVDTPIL
ParentalVLIEDNCGDTPLVSRNEF--YNSYENVIDEGDQHFKWIAPESEWEPMTLNYTSGTTYAPKGVLHSHRSAF
VLIED.....P......F.....Y......GD..F.WI.PE.....MTLNYTSGTT..PKGV.HSHRS.F
RetrocopyVLIEDE-NSVPFSTNLDFDHCDTYDAMLAKGDLNFNWIRPENDRDAMTLNYTSGTTSSPKGVVHSHRSLF
ParentalTMSVMGLIDWSVPKQPVFLWTLPIFHANGWGFCWAMAAVGGTNVCLRRSHDAALIYEAIQQHKVTHMCGA
...V..LIDWSVP.QPV.LWTLP.FH.NGW...W.MA.VGGTN.CLR...DA.....AI....VTHMCGA
RetrocopyIITVDSLIDWSVPSQPVYLWTLPMFHSNGWSYTWGMAVVGGTNICLRK-FDANVVFHAINKYNVTHMCGA
ParentalPVVLNMLSTYTKRKPLDSPVQILTAGAPPPAAVLDRTESLGFVISHGYGLTETGGPAVTCAWKQEWNSLT
PVVL.ML......KPL..PV...T.GAPPPA....R.ESLGF...HGYG.TE..G..V.C.WK..WN.L.
RetrocopyPVVLTMLANSPCAKPLQNPVHFRTGGAPPPATIVLRVESLGFIVNHGYGMTEVAGVVVSCIWKPKWNKLS
ParentalNSERATLKSRQGVKMVGFTDVDVVDPETGISIERNGMAVGEIVLKGGSVMLGYLKDPEGTSKCMKNDGWF
....A.LKSRQG.K..G.T.VDVVDPE.G.S..R.G...GEIVL.GG..MLGYLK..E.TSKCMKN..W.
RetrocopyANVKAKLKSRQGIKSLGMTEVDVVDPESGVSVKRDGVTMGEIVLRGGCIMLGYLKNEEATSKCMKNN-WL
ParentalYTGDVGVMHSDGYLEVKDRSKDVIICGGENISSVEIESILYKHPAVNEAAVVARPDNYWGETPCVFVSLK
YTGDV.V.H.DGYLE.KDRSKD.II.GGEN.SSVE.ES.LY....VNEAAVVARPD..WGETPC.FVSLK
RetrocopyYTGDVAVVHPDGYLEIKDRSKDIIISGGENVSSVEVESVLYSNNFVNEAAVVARPDEFWGETPCAFVSLK
ParentalNDAR-NVTEKELREFCKENLPLYMVPRTVVIQDDLPKTATGKIQKYLLRDKAKSL
........EKE...FC.E.LP.YM.P.TV...D.LPKTATGKIQK..LR..A...
RetrocopyMELKLKPKEKEIIDFCRERLPHYMIPKTVIFMDELPKTATGKIQKFSLRQIANGM

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_36 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 Solyc03g031940.2 1 retrocopy
retro_slyc_36 ,


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