RetrogeneDB ID:

retro_slyc_23

Retrocopy
location
Organism:Tomato (Solanum lycopersicum)
Coordinates:9:3123570..3124074(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:Solyc09g009720.1
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:Solyc05g054550.2
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_slyc_23
ATGGCTTCTTCACAAGCCGCTCTTCTCCTCCAAAAACAGCTCAAAGACCTAAACCGTCATCCCGTCGACGGCTTTTCTGC
CGGTTTAGTCGACGAGAACAACGTTTTTGAATGGAGTATCTCAATCATCGGTCCACCGGAAACTTTATTCGACGGCGGAT
TTTTCAACGCTACAATGAGTTTTCCGACGGATTACCCTAACAATCCACCGACGGTGAAATTCACAACGGAGATCTGGCAT
CCGAATGTTTATTCTGACGGTAGGGTTTGTATATCGATTCTTCATCCACCAGGTGATGATCCGAATCATTATGAGCTAGC
GAGTGAGCGGTGGACGCCGGTTCATACGGTGGAGAGCATTATGCTGAGTATAATTTCGATGCTTACCAGTCCGAACGATG
AATCGCCGGCGAATGTTGATGCGGCTAAGGAATGGAGGGATAATAGGGCGGAATTTGTGAAGAAGGTGAAGAGATGCGTG
AGGAAATCACAAGAGATGTTGTGA

ORF - retro_slyc_23 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 85.37 %
Parental protein coverage: 96.47 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalSQASLLLQKQLKDLCKKPVDGFSAGLVDESNLFEWSVTIIGPPETLYDGGFFNAIMSFPQNYPNSPPTVK
SQA.LLLQKQLKDL...PVDGFSAGLVDE.N.FEWS..IIGPPETL.DGGFFNA.MSFP..YPN.PPTVK
RetrocopySQAALLLQKQLKDLNRHPVDGFSAGLVDENNVFEWSISIIGPPETLFDGGFFNATMSFPTDYPNNPPTVK
ParentalFTSEIWHPNVYSDGKVCISILHPPGDDPNGYELASERWSPVHTVESIMLSIISMLSSPNDESPANVEAAK
FT.EIWHPNVYSDG.VCISILHPPGDDPN.YELASERW.PVHTVESIMLSIISML.SPNDESPANV.AAK
RetrocopyFTTEIWHPNVYSDGRVCISILHPPGDDPNHYELASERWTPVHTVESIMLSIISMLTSPNDESPANVDAAK
ParentalEWRDNRDEFKKKVSRCVRRSQEMM
EWRDNR.EF.KKV.RCVR.SQEM.
RetrocopyEWRDNRAEFVKKVKRCVRKSQEML

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_23 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 tuberosum PGSC0003DMG4010235271 retrocopy
Solanum lycopersicum Solyc05g054550.2 1 retrocopy
retro_slyc_23 ,



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