RetrogeneDB - Retrocopy retro_slyc

                        
>retro_slyc_19
ATGAGAAATTGGAACTTTATTGTGTTTCTCTGTCTTGCTTTCGTATTGAGAGTTGAATCCTTCAAGTTTCATAGGATTGA

TCAACACGTTGAAAGGATCTCCGGAAGTGCTGGTGATGTGTTGGAGGATGATCCTACAGGTAGGTTGAAAGTTTTTGTAT

ATGAGCTTCCAAGCAAATATAACAAGAAAACTGTGCAGAGGGACTCGCGATGCCTCAGTCATATGTTTGCTGCTGAGATA

TATATGCATCAGTTTCTGTTATCCAGTCCTGTTCGAACACTTGATCCAGAGGAAGCAGATTGGTTTTACACTCCAGTTTA

CACAACTTGTGAGTACTTGACACCACATGGTCATCCTTTACCTTTCAACTCACCACGTATGATGAGAAGCGCGATTCAGC

TTATTGCTTCTAGCTGGCCATACTGGAACAGGACACAAGGGGGTGATCATTTCTTCATTGTACCACATGATTTTGGTGCA

TGTTTCCATTTTCAAGAAGAGAAAGCTATTGGAAGAGGTATTCTTCCGTTGCTCCATCGTGCTACCTTGGTTCAAACTTT

TGGACAACGGAATCATGTTTGTTTGAAGGAAGGATCGATAACTATTCCTCCGTATGCTCCTCCACAGAAAATTCAGTCTC

ATTTGATCTCTCCTGATACACCAAGATCCATATTTGTCTATTTCCGTGGCTTGTTTTATGACAAAAGAAATGATCCTAAA

GGCGGGTACTATGCAAGAGGCGCTCGAGCAGCAGTGTGGGAGAACTTTAAGGACAATCCACTCTTTGATATTTCTACAGA

TCATCCAACTACATACTACGAAGACATGCAACGAGCTATCTTTTGCTTGTGCCCTCTCGGATGGGCTCCATGGAGTCCTA

GATTGGTTGAAGCTGTTGTATTCGGATGCATCCCCGTTATAATAGCAGATGACATTGTCTTGCCATTTGCTGACGCGATC

CCATGGGAAGATATAGGATTGTTCGTAGCGGAGAAGGATGTCCCATATTTGGATAACATTCTTACTTCTGTTCCACCACA

AGAAATACTGAGGAAGCAGAGATTGCTCGCCAATCCTTCAATGAAGCAGGCTATGTTATTTCTACAACCTGCTCAACCAG

GTGATGCTTTCCACCAAATCTTGAATGGACTTGCTCGTAAATTACCCAATCATCACAAGACTATATACGGAGACAACAAC

GTCTTAAACTGGACTGCTGGTCCAGTTGCTGATCTAAAACCTTGGTAG

ORF - retro_slyc_19 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	86.59 %
Parental protein coverage:	100.0 %
Number of stop codons detected:	0
Number of frameshifts detected:	0

Retrocopy - Parental Gene Alignment:

                                ParentalMFAAEIYMHRFLLSSPVRTLNPEEADWFYTPVYTTCD-LTPNGLPLPFKSPRMMRSAIQLIASNWPYWNR
MFAAEIYMH.FLLSSPVRTL.PEEADWFYTPVYTTC..LTP.G.PLPF.SPRMMRSAIQLIAS.WPYWNR
RetrocopyMFAAEIYMHQFLLSSPVRTLDPEEADWFYTPVYTTCEYLTPHGHPLPFNSPRMMRSAIQLIASSWPYWNR
ParentalTEGADHFFIVPHDFAACFHYQEEKAIGRGILPLLQRSTLVQTFGQRNHVCLKDGSITIPPYAPPQKMQSH
T.G.DHFFIVPHDF.ACFH.QEEKAIGRGILPLL.R.TLVQTFGQRNHVCLK.GSITIPPYAPPQK.QSH
RetrocopyTQGGDHFFIVPHDFGACFHFQEEKAIGRGILPLLHRATLVQTFGQRNHVCLKEGSITIPPYAPPQKIQSH
ParentalFIPPDIPRSIFVYFRGLFYDVGNDPEGGYYARGARAAVWENFKDNPLFDISTEHPTTYYEDMQRAIFCLC
.I.PD.PRSIFVYFRGLFYD..NDP.GGYYARGARAAVWENFKDNPLFDIST.HPTTYYEDMQRAIFCLC
RetrocopyLISPDTPRSIFVYFRGLFYDKRNDPKGGYYARGARAAVWENFKDNPLFDISTDHPTTYYEDMQRAIFCLC
ParentalPLGWAPWSPRLVEAVIFGCIPVIIADDIVLPFADAIPWEEIGVFVDEKDVPNLDTILTSIPPEEILRKQR
PLGWAPWSPRLVEAV.FGCIPVIIADDIVLPFADAIPWE.IG.FV.EKDVP.LD.ILTS.PP.EILRKQR
RetrocopyPLGWAPWSPRLVEAVVFGCIPVIIADDIVLPFADAIPWEDIGLFVAEKDVPYLDNILTSVPPQEILRKQR
ParentalLLANPSMKQAMLFPQPAQSGDAFHQILNGLARKLP-HDRTVFLTPGQKILNWTAGPVGDLKPW
LLANPSMKQAMLF.QPAQ.GDAFHQILNGLARKLP.H..T.........LNWTAGPV.DLKPW
RetrocopyLLANPSMKQAMLFLQPAQPGDAFHQILNGLARKLPNHHKTIY--GDNNVLNWTAGPVADLKPW

                            

                            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_19 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza longistaminata	KN538848.1_FG012	1 retrocopy	retro_olon_4,
Oryza brachyantha	OB01G51480	1 retrocopy	retro_obra_20,
Solanum tuberosum	PGSC0003DMG400014472	1 retrocopy	retro_stub_120,
Solanum lycopersicum	Solyc12g042360.1	1 retrocopy	retro_slyc_19 ,

	RetrogeneDB ID:	retro_slyc_19
Retrocopy location	Organism:	*Tomato (Solanum lycopersicum)*
	Coordinates:	5:5906879..5908127(+)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	Solyc05g012730.1
	Aliases:	None
	Status:	KNOWN_PROTEIN_CODING
Parental gene information	Parental gene summary:
	Parental gene symbol:	None
	Ensembl ID:	Solyc12g042360.1
	Aliases:	None
	Description:	None

Parental	MFAAEIYMHRFLLSSPVRTLNPEEADWFYTPVYTTCD-LTPNGLPLPFKSPRMMRSAIQLIASNWPYWNR
	MFAAEIYMH.FLLSSPVRTL.PEEADWFYTPVYTTC..LTP.G.PLPF.SPRMMRSAIQLIAS.WPYWNR
Retrocopy	MFAAEIYMHQFLLSSPVRTLDPEEADWFYTPVYTTCEYLTPHGHPLPFNSPRMMRSAIQLIASSWPYWNR

Parental	TEGADHFFIVPHDFAACFHYQEEKAIGRGILPLLQRSTLVQTFGQRNHVCLKDGSITIPPYAPPQKMQSH
	T.G.DHFFIVPHDF.ACFH.QEEKAIGRGILPLL.R.TLVQTFGQRNHVCLK.GSITIPPYAPPQK.QSH
Retrocopy	TQGGDHFFIVPHDFGACFHFQEEKAIGRGILPLLHRATLVQTFGQRNHVCLKEGSITIPPYAPPQKIQSH

Parental	FIPPDIPRSIFVYFRGLFYDVGNDPEGGYYARGARAAVWENFKDNPLFDISTEHPTTYYEDMQRAIFCLC
	.I.PD.PRSIFVYFRGLFYD..NDP.GGYYARGARAAVWENFKDNPLFDIST.HPTTYYEDMQRAIFCLC
Retrocopy	LISPDTPRSIFVYFRGLFYDKRNDPKGGYYARGARAAVWENFKDNPLFDISTDHPTTYYEDMQRAIFCLC

Parental	PLGWAPWSPRLVEAVIFGCIPVIIADDIVLPFADAIPWEEIGVFVDEKDVPNLDTILTSIPPEEILRKQR
	PLGWAPWSPRLVEAV.FGCIPVIIADDIVLPFADAIPWE.IG.FV.EKDVP.LD.ILTS.PP.EILRKQR
Retrocopy	PLGWAPWSPRLVEAVVFGCIPVIIADDIVLPFADAIPWEDIGLFVAEKDVPYLDNILTSVPPQEILRKQR

Parental	LLANPSMKQAMLFPQPAQSGDAFHQILNGLARKLP-HDRTVFLTPGQKILNWTAGPVGDLKPW
	LLANPSMKQAMLF.QPAQ.GDAFHQILNGLARKLP.H..T.........LNWTAGPV.DLKPW
Retrocopy	LLANPSMKQAMLFLQPAQPGDAFHQILNGLARKLPNHHKTIY--GDNNVLNWTAGPVADLKPW

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

RetrogeneDB ID:

retro_slyc_19