RetrogeneDB ID:

retro_slyc_27

Retrocopy
location
Organism:Tomato (Solanum lycopersicum)
Coordinates:4:59557850..59559350(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:Solyc04g072580.1
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:Solyc07g045160.2
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_slyc_27
ATGGGATCATTGGTTGATAGTTTTGCTTTGCATAATTTGAACAAGAAAATCGTGATGGGTGACAATGGTTATGTTTTTGA
AGACGTTCCTCATTTGTCTGATTACATTCCTAGTCTTCCTACGTATCCTAATCCATTGAAGAAAAATCCTTCCTATTCAG
TCGTCAATCAGTATTTTGTCGATGAAGATGATACAGTTGCTCAAAATATTGTTGTCCGCAAGAACAGTCCAAGAGGGATA
CATTTTCGTCGAGCTGGTCCTTCCCAAGACGTTTATTTTAAGGCGGATGATGTTAATGCATGTATTGTAACATGTGGAGG
TTTATGCCCTGGTCTCAATACAGTTATCAGGGAAATAGTATGTGGCTTGTACTCTATGTATGGTGTAGCAAGAGTCATGG
GGATAGATGGAGGATATCGAGGTTTCTATTCCAAAAACACGATTCCATTGACACCTAACGTTGTGAATGATATCCATAAA
CGTGGTGGAACGATTCTTGGGTCATCTCGAGGAGGTCATGTTACTAAGAAGATAGTAGATAGCATTCAGGATCGAGGAAT
TAATCAGGTTTATATAATTGGAGGAGATGGAACGCTTAAAGGAGCATCGTTGATATTTGAGGAAATTACGAGGCGTGGTC
TAAATGTTGTAGTTGTTGGAATCCCCAAGACAATAGATAACGATATACCAGTTATTGACAAGTCTTTTGGTTTTGATTCT
GCGGTTGAGGAAGCTCAACGTGCTATTAGTGCTGCTCATGTTGAAGCTACGAGTTTTGAGAATGGAATTGGGGTTGTGAA
GTTAATGGGACGGGATAGTGGGTTTATAGCAATGTATGCTAGTCTTGCTAGTCGAGATGTTGATTGTTGTTTGATTCCAG
AATCCTGTTTCTATCTTGAAGGACGCGGTGGACTGTTTGAGTATATCGAACAAAGGCTGAAAGAGAATGGACACATGGTT
ATCGTTGTAGCTGAAGGTGTTGGACAAGATGATGAGCAAGTTGATGTTGGTTTATGGATATCGACAAGGATAAAGGAGCA
TTTTTCGAAAGAAAAGAAGATGATGATCAATCTGAAGTATATAGATCCAACATACATGATTCGGGCTATTGCAAGTAATG
CATCTGATAATATGTATTGCACTCATCTTGCTCAAAGCGCGGTACATGGAGCAATGGCTGGGTACACAGGCTTTACGGTT
GGTCCTGTCAACAACACACATGCTTACATACCCTTTGATAGAATCACTGAGAAACAAAACAAGGTTGACATTACAGACAT
GATGTGGGCACAACTTCTATCTTCAACTAATCAACCTAGCTTCTTGTCAACAGCGAGATCAGCTGATAATATTGAAGCAA
ACAAGGACGAAGAACCACCTATTCAATTATCAGATGAAGAAACAAATCAACTTAGCTTCTTGACAACCAGAGTCGATATA
AATGAAGCAAACAAGAACAAAGAACCACCTACTGAATTATCAGATGGAGAAACAAATTAA

ORF - retro_slyc_27 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 87.34 %
Parental protein coverage: 64.49 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalKKIVIGDDGYVLEDVPHLSDYIPNLPTYTNPLQHNPSYSVVKQYFVNEDDTVAEKVVVHKNSPRGIHFRR
KKIV.GD.GYV.EDVPHLSDYIP.LPTY.NPL..NPSYSVV.QYFV.EDDTVA...VV.KNSPRGIHFRR
RetrocopyKKIVMGDNGYVFEDVPHLSDYIPSLPTYPNPLKKNPSYSVVNQYFVDEDDTVAQNIVVRKNSPRGIHFRR
ParentalAGPCQKVYFEPDDVYACIVTCGGLCPGLNTVIREIVCGLHYMYGVSRVMGIDGGYRGFYSKNTIPLTPKV
AGP.Q.VYF..DDV.ACIVTCGGLCPGLNTVIREIVCGL..MYGV.RVMGIDGGYRGFYSKNTIPLTP.V
RetrocopyAGPSQDVYFKADDVNACIVTCGGLCPGLNTVIREIVCGLYSMYGVARVMGIDGGYRGFYSKNTIPLTPNV
ParentalVNNIHKRGGTILGTSRGGHVTKKIVDSIQDRGINQVYIIGGDGTQRGAAVIFEEIRRRGLNVAVAGIPKT
VN.IHKRGGTILG.SRGGHVTKKIVDSIQDRGINQVYIIGGDGT..GA..IFEEI.RRGLNV.V.GIPKT
RetrocopyVNDIHKRGGTILGSSRGGHVTKKIVDSIQDRGINQVYIIGGDGTLKGASLIFEEITRRGLNVVVVGIPKT
ParentalIDNDIPVIDKSFGFDSAVEEAQRAISAAHVEATSFENGIGLVKLMGRDSGFIAMYATLASRDVDCCLIPE
IDNDIPVIDKSFGFDSAVEEAQRAISAAHVEATSFENGIG.VKLMGRDSGFIAMYA.LASRDVDCCLIPE
RetrocopyIDNDIPVIDKSFGFDSAVEEAQRAISAAHVEATSFENGIGVVKLMGRDSGFIAMYASLASRDVDCCLIPE
ParentalSPFYLEGSGGLFEYIEHRLKDNGHMVIVIAEGAGQE
S.FYLEG.GGLFEYIE.RLK.NGHMVIV.AEG.GQ.
RetrocopySCFYLEGRGGLFEYIEQRLKENGHMVIVVAEGVGQD

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






Solanum lycopersicum was not studied using RNA-Seq expression data.
Solanum lycopersicum was not studied using ChIP-Seq data.
Solanum lycopersicum was not studied using EST data.
Solanum lycopersicum was not studied using FANTOM5 data.
retro_slyc_27 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 3 parental genes, and 3 retrocopies.

Species Parental gene accession Retrocopies number
Oryza longistaminata KN540365.1_FG0011 retrocopy
Solanum tuberosum PGSC0003DMG4000174131 retrocopy
Solanum lycopersicum Solyc07g045160.2 1 retrocopy
retro_slyc_27 ,



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