RetrogeneDB - Retrocopy retro_sita

                        
>retro_sita_16
ATGGCAGCTGCCACAGCCGTGTTCGCCGCAACCAGCGCCAGAGCCACCGCTCCTCTCCTTCACCGCAGCCGGACCCGGAA

CTACTCGTGCGGCCTTGCGACTGCGGGGCCGTCGCCGTCGCCGTCGTCGTGTGCCAGTGCCAATGTCCGCCGGCGCCGCC

CGATACCGGCGTCGTCTTGCGGCGTCCATGGACGCGGCCCCCTCGTCCCCGCGTCCGACCACTGGGGCAACTGGACCTTC

CTCCTGACCACCGCCGCGCTGGGCATCTGGTCGGAGAAGCGGACCCCGGTGGGGAAGGCGCTTAGCGGGGCGCTGGTGAG

CGTGCTGCTGGGTCTCGCGGCCAGCAGCGCCGGCGTGGTGGCGGCGGACGCCCCGGCGTACCGCGTGGTGCTCGACTACC

TCCTGCCGCTCGCCATCCCGCTGCTGCTCTTCCGCGCCGACCTCCGCCGCGTGCTCCGCTCCACCGGCGCGCTGCTGCTG

GCCTTCCTGCTCGGGTCCGCGGCGACGGCGGCGGGTACGGTGGTGGCGTTCCTCCTCGTCCCGATGCGGTCGCTGGGCCC

GGACAACTGGAAGATCGCGGCGGCGCTGATGAGCCGCCACATCGGGGGCGCCGTCAACTACGTTGCCGTCTCCGAAGCTC

TCGGGGTCTCCCCGTCGGTGCTGGCGGCCGGGCTCGCCGCCGACAACATCATCTGCGCGCTCTACTTCACGAGCCTCTTC

GCACTGGCCGCCAAGATCCCCAAGGAAGACCCAACGGGGAGCGACGGCGAGTCCGTGGCCGGCGACGACAGCAGCAGCAG

CAGCAGCAGCAGCCACAGCGCCGTGGCCATGGCGGCCGCGTTCGCCATATGTAAGGCGGGGAAGCTGGCGGCGGCCGCGC

TGGGCATACAAGGGGGAAGCCTCCCCTGCATAACAGTGGTCTCGGTGGCTCTGGCGACGCTGTTCCCCTCGCAGATCGGG

AAGCTGGCGCCGTCGGGCGAGGCCATGGCCGTGGTCCTGATGCAGGTGTTCTTCGCCGTAGTGGGAACCAACGGAAGCGT

CGGCAACGTCCTCGACACGACGCCTGCCATATTCGCCTTCGCCTTCGTGCAAATCGCCGTGCACCTCCTGCTGACCCTGG

GCGTCGGCAAGCTGCTCGGCATCGACCGCAAGCTGCTGCTGATCGCGTCCAACGCCAACGTGGGCGGCCCGACCACCGCC

TGCGGGATGGCCACCGCCAAGGGGTGGTCCTCTCTGGTGGTTCCGGGGATCCTCGCCGGCATCTTGGGCATCGCCATCGC

CACCTTCGCGGGAATCGCCTTCGGCGTGCTCGTCCTCAAACGCATGTAG

ORF - retro_sita_16 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	63.23 %
Parental protein coverage:	84.56 %
Number of stop codons detected:	0
Number of frameshifts detected:	0

Retrocopy - Parental Gene Alignment:

                                ParentalPAIAAGDHWGNWAFLLSAAAFGTWSEEKTSWGAALSGALVSILAGLAATAAGLISPGAPAHGAVMEYLLP
P...A.DHWGNW.FLL..AA.G.WSE..T..G.ALSGALVS.L.GLAA..AG.....APA...V..YLLP
RetrocopyPLVPASDHWGNWTFLLTTAALGIWSEKRTPVGKALSGALVSVLLGLAASSAGVVAADAPAYRVVLDYLLP
ParentalAAVPLLLLGADLRRVVRTTGDLLKAFLIGSVATIIGTTVAYLLVPMRSLGHDSWKIAAALMGSYIGGAVN
.A.PLLL..ADLRRV.R.TG.LL.AFL.GS.AT..GT.VA.LLVPMRSLG.D.WKIAAALM...IGGAVN
RetrocopyLAIPLLLFRADLRRVLRSTGALLLAFLLGSAATAAGTVVAFLLVPMRSLGPDNWKIAAALMSRHIGGAVN
ParentalFVAVSEALGITPSVVAAGVAADNLISALYFMILFSLASKIPAEPKNAATDGRKDGGEPEGDGRFSVLNGG
.VAVSEALG..PSV.AAG.AADN.I.ALYF..LF.LA.KIP.E......DG....G........S.....
RetrocopyYVAVSEALGVSPSVLAAGLAADNIICALYFTSLFALAAKIPKEDP-TGSDGESVAGD-DSSSSSSSSHSA
ParentalAAIALSFVICKAGSAIADRLGFQGGTLPCVTALVVFLATAFPGQLGKLAPAGETMALILMQLFFTVVGAN
.A.A..F.ICKAG...A..LG.QGG.LPC.T...V.LAT.FP.Q.GKLAP.GE.MA..LMQ.FF.VVG.N
RetrocopyVAMAAAFAICKAGKLAAAALGIQGGSLPCITVVSVALATLFPSQIGKLAPSGEAMAVVLMQVFFAVVGTN
ParentalGNVVDAVTKAPSVFAFALVQVSVHLAVLLGVGKLVGLDRKPLLIASNANIGGPTTAAAMATAKGWSSLIV
G.V.......P..FAFA.VQ..VHL...LGVGKL.G.DRK.LLIASNAN.GGPTTA..MATAKGWSSL.V
RetrocopyGSVGNVLDTTPAIFAFAFVQIAVHLLLTLGVGKLLGIDRKLLLIASNANVGGPTTACGMATAKGWSSLVV
ParentalPGILVGIFGISIATFLGIGFGMLVLRRM
PGIL.GI.GI.IATF.GI.FG.LVL.RM
RetrocopyPGILAGILGIAIATFAGIAFGVLVLKRM

                            

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

                        

RNA-Seq - click to see more details

Setaria italica was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Setaria italica was not studied using ChIP-Seq data.

EST - click to see more details

Setaria italica was not studied using EST data.

TSS - click to see more details

Setaria italica was not studied using FANTOM5 data.

Lab - click to see more details

retro_sita_16 was not experimentally validated.

Retrocopy orthology:

Setaria italica 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
Setaria italica	Si008152m.g	1 retrocopy	retro_sita_16 ,

	RetrogeneDB ID:	retro_sita_16
Retrocopy location	Organism:	*Foxtail millet (Setaria italica)*
	Coordinates:	1:3969906..3971235(-)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	Si019049m.g
	Aliases:	None
	Status:	KNOWN_PROTEIN_CODING
Parental gene information	Parental gene summary:
	Parental gene symbol:	None
	Ensembl ID:	Si008152m.g
	Aliases:	None
	Description:	None

Parental	PAIAAGDHWGNWAFLLSAAAFGTWSEEKTSWGAALSGALVSILAGLAATAAGLISPGAPAHGAVMEYLLP
	P...A.DHWGNW.FLL..AA.G.WSE..T..G.ALSGALVS.L.GLAA..AG.....APA...V..YLLP
Retrocopy	PLVPASDHWGNWTFLLTTAALGIWSEKRTPVGKALSGALVSVLLGLAASSAGVVAADAPAYRVVLDYLLP

Parental	AAVPLLLLGADLRRVVRTTGDLLKAFLIGSVATIIGTTVAYLLVPMRSLGHDSWKIAAALMGSYIGGAVN
	.A.PLLL..ADLRRV.R.TG.LL.AFL.GS.AT..GT.VA.LLVPMRSLG.D.WKIAAALM...IGGAVN
Retrocopy	LAIPLLLFRADLRRVLRSTGALLLAFLLGSAATAAGTVVAFLLVPMRSLGPDNWKIAAALMSRHIGGAVN

Parental	FVAVSEALGITPSVVAAGVAADNLISALYFMILFSLASKIPAEPKNAATDGRKDGGEPEGDGRFSVLNGG
	.VAVSEALG..PSV.AAG.AADN.I.ALYF..LF.LA.KIP.E......DG....G........S.....
Retrocopy	YVAVSEALGVSPSVLAAGLAADNIICALYFTSLFALAAKIPKEDP-TGSDGESVAGD-DSSSSSSSSHSA

Parental	AAIALSFVICKAGSAIADRLGFQGGTLPCVTALVVFLATAFPGQLGKLAPAGETMALILMQLFFTVVGAN
	.A.A..F.ICKAG...A..LG.QGG.LPC.T...V.LAT.FP.Q.GKLAP.GE.MA..LMQ.FF.VVG.N
Retrocopy	VAMAAAFAICKAGKLAAAALGIQGGSLPCITVVSVALATLFPSQIGKLAPSGEAMAVVLMQVFFAVVGTN

Parental	GNVVDAVTKAPSVFAFALVQVSVHLAVLLGVGKLVGLDRKPLLIASNANIGGPTTAAAMATAKGWSSLIV
	G.V.......P..FAFA.VQ..VHL...LGVGKL.G.DRK.LLIASNAN.GGPTTA..MATAKGWSSL.V
Retrocopy	GSVGNVLDTTPAIFAFAFVQIAVHLLLTLGVGKLLGIDRKLLLIASNANVGGPTTACGMATAKGWSSLVV

Parental	PGILVGIFGISIATFLGIGFGMLVLRRM
	PGIL.GI.GI.IATF.GI.FG.LVL.RM
Retrocopy	PGILAGILGIAIATFAGIAFGVLVLKRM

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

RetrogeneDB ID:

retro_sita_16