RetrogeneDB - Retrocopy retro_slyc

                        
>retro_slyc_7
ATGAATTCATCGTCGAAAGGATTGGAATGGAAAGAATGGTTACAAGGATGGCTTCGTTTAACATATGAGACACTGTTTCA

GAAAATTCATGCTAAACATTTACAAGAACCTTTGCCTTTACCTCCTCTCAATGGCCTAAATTGCATTGTCACAGGAGCCA

CTAGTGGCATTGGACTTGAAATTGCTAAACAATTGGCTGAGTCAGGTGCACATCTTGTTATGGCTGTAAGAAACACAAAT

CTTGCTCATCAACTCATTGAAAAATGGCAAAGAAATGAAACTGTATCGAGGCCCTTAAGCATCGATGTTATAGAACTTGA

TCTCTTTTATCTCGAGTCAGTTGTAAAATTTGCAAAAGAATGGAATTCGAGATCAAAACCTCTTCATATTCTCATCAATA

ATGCTGGAATCTATTCTATAGGACAACCACAAAAATTTACCAAAGACGGATATGAAACACATATACAAGTGAACCATCTT

GCACCTGCATTACTATCTCTTCTGCTTTTGCCTTCTTTGAAAAGAGGCTCTCCAAGCAGGATTATCAATATGAATTCCCT

TATGCATGTAATTGGCGTTGTGGATCCTCAAGATATGAATTTCTTAACCAAGAAGAATAAGTTCACAAGTAGAAAGGCAT

ACTCGAGTAGCAAATTGGCACAAATGAAGTTTAGCAGTATACTTCAAAAACTCCTAATTAATACTAATATTCATGTAATG

TGTGTAGAGCCAGGAGCTGTACGTACAAATGTTACGCGAGATCTTCCAAGAATTCTGAACATTCTTTATCAGAAAATGTT

CTTTTTCATGTTCGATGCTCAACAGGGTTCAAGAAGTGCACTTTTTGCAGCTACTGATGCTGAGATCTTGGATTATTGTG

GTGTGTTGAAAGCAGAAGGGTGTATTGGTTGTGCCTTCATTGGTTGCCATTGTAGAATTAGTGAACCTAGCAAACAAGTA

GATAATGAGAGAACCTCTTTTGAAATATGGGATAAGACTATGGAAATGGTTGGTCTTCCTGCAGGGTGTGTTGACATGAT

TCTTCAAGGTGAAGAAATTCATTGCCGCTATGGAGCTGTTAATGATCGTTAA

ORF - retro_slyc_7 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	58.1 %
Parental protein coverage:	92.99 %
Number of stop codons detected:	0
Number of frameshifts detected:	0

Retrocopy - Parental Gene Alignment:

                                ParentalAKKKTLGWMEWLRGWFYLVYEMLFQRILASHLQNPMPLPPINDVTCIVTGSTSGIGREIARQLAEAGAHV
...K.L.W.EWL.GW..L.YE.LFQ.I.A.HLQ.P.PLPP.N...CIVTG.TSGIG.EIA.QLAE.GAH.
RetrocopySSSKGLEWKEWLQGWLRLTYETLFQKIHAKHLQEPLPLPPLNGLNCIVTGATSGIGLEIAKQLAESGAHL
ParentalVMAVRSTNRAQELIRKWQEEWSGKGLPLNIEVMELDLLSLDSVARFAEAWNARMAPVHVLINNAGIFSIG
VMAVR.TN.A..LI.KWQ........PL.I.V.ELDL..L.SV..FA..WN.R..P.H.LINNAGI.SIG
RetrocopyVMAVRNTNLAHQLIEKWQRNET-VSRPLSIDVIELDLFYLESVVKFAKEWNSRSKPLHILINNAGIYSIG
ParentalEPQKFSKDGYEEHMQVNHLAPAMLSILLLPSLIRGSPSRIVNVNSTMHYVGFVDPEDMNVVSGKRKYTSV
.PQKF.KDGYE.H.QVNHLAPA.LS.LLLPSL.RGSPSRI.N.NS.MH..G.VDP.DMN....K.K.TS.
RetrocopyQPQKFTKDGYETHIQVNHLAPALLSLLLLPSLKRGSPSRIINMNSLMHVIGVVDPQDMNFLTKKNKFTSR
ParentalVGYGGSKLAQIMFSSILHKRLPAESGISVVCNTPGIVLTNVARDLPQFLQVGYRLIPYFIFNAEEGSRST
..Y..SKLAQ..FSSIL.K.L.....I.V.C..PG.V.TNV.RDLP..L...Y.....F.F.A..GSRS.
RetrocopyKAYSSSKLAQMKFSSILQKLL-INTNIHVMCVEPGAVRTNVTRDLPRILNILYQKMFFFMFDAQQGSRSA
ParentalLFAATDPQISEYCEMLKADDWPVCAYISHDCRPTNASEEAHNIETSYKVWEKTLELVGLPSDAVERLIEG
LFAATD..I..YC..LKA.....CA.I...CR....S....N..TS...W.KT.E.VGLP...V.....G
RetrocopyLFAATDAEILDYCGVLKAEGCIGCAFIGCHCRISEPSKQVDNERTSFEIWDKTMEMVGLPAGCVDMILQG
ParentalEEIKCRYG
EEI.CRYG
RetrocopyEEIHCRYG

                            

                            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_7 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
Solanum tuberosum	PGSC0003DMG400010157	1 retrocopy	retro_stub_22,
Populus trichocarpa	POPTR_0015s05560	1 retrocopy	retro_ptri_15,
Solanum lycopersicum	Solyc03g098460.2	1 retrocopy	retro_slyc_7 ,

	RetrogeneDB ID:	retro_slyc_7
Retrocopy location	Organism:	*Tomato (Solanum lycopersicum)*
	Coordinates:	12:39878865..39879957(-)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	Solyc12g042640.1
	Aliases:	None
	Status:	KNOWN_PROTEIN_CODING
Parental gene information	Parental gene summary:
	Parental gene symbol:	None
	Ensembl ID:	Solyc03g098460.2
	Aliases:	None
	Description:	None

Parental	AKKKTLGWMEWLRGWFYLVYEMLFQRILASHLQNPMPLPPINDVTCIVTGSTSGIGREIARQLAEAGAHV
	...K.L.W.EWL.GW..L.YE.LFQ.I.A.HLQ.P.PLPP.N...CIVTG.TSGIG.EIA.QLAE.GAH.
Retrocopy	SSSKGLEWKEWLQGWLRLTYETLFQKIHAKHLQEPLPLPPLNGLNCIVTGATSGIGLEIAKQLAESGAHL

Parental	VMAVRSTNRAQELIRKWQEEWSGKGLPLNIEVMELDLLSLDSVARFAEAWNARMAPVHVLINNAGIFSIG
	VMAVR.TN.A..LI.KWQ........PL.I.V.ELDL..L.SV..FA..WN.R..P.H.LINNAGI.SIG
Retrocopy	VMAVRNTNLAHQLIEKWQRNET-VSRPLSIDVIELDLFYLESVVKFAKEWNSRSKPLHILINNAGIYSIG

Parental	EPQKFSKDGYEEHMQVNHLAPAMLSILLLPSLIRGSPSRIVNVNSTMHYVGFVDPEDMNVVSGKRKYTSV
	.PQKF.KDGYE.H.QVNHLAPA.LS.LLLPSL.RGSPSRI.N.NS.MH..G.VDP.DMN....K.K.TS.
Retrocopy	QPQKFTKDGYETHIQVNHLAPALLSLLLLPSLKRGSPSRIINMNSLMHVIGVVDPQDMNFLTKKNKFTSR

Parental	VGYGGSKLAQIMFSSILHKRLPAESGISVVCNTPGIVLTNVARDLPQFLQVGYRLIPYFIFNAEEGSRST
	..Y..SKLAQ..FSSIL.K.L.....I.V.C..PG.V.TNV.RDLP..L...Y.....F.F.A..GSRS.
Retrocopy	KAYSSSKLAQMKFSSILQKLL-INTNIHVMCVEPGAVRTNVTRDLPRILNILYQKMFFFMFDAQQGSRSA

Parental	LFAATDPQISEYCEMLKADDWPVCAYISHDCRPTNASEEAHNIETSYKVWEKTLELVGLPSDAVERLIEG
	LFAATD..I..YC..LKA.....CA.I...CR....S....N..TS...W.KT.E.VGLP...V.....G
Retrocopy	LFAATDAEILDYCGVLKAEGCIGCAFIGCHCRISEPSKQVDNERTSFEIWDKTMEMVGLPAGCVDMILQG

Parental	EEIKCRYG
	EEI.CRYG
Retrocopy	EEIHCRYG

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

RetrogeneDB ID:

retro_slyc_7