RetrogeneDB - Retrocopy retro_oana

                        
>retro_oana_80
GAGCCTAAATGGCACCCTCCCTGGAAATTATACAGGGTTATAATAGGCCACCAAGGGTGGGTTCATTGTGTTGCAGTAGA

TTGTACTAACGAGTGGTTTGCAACTGGGGGGAATGATAGGCTTATAAAAATTTGGGATTTGGCTACATGTCAGCTGAAGC

TTTCTCTGACAGGACACGTTAATTCTGTGCGTGACATAAAGATTTCAGAAAAAAACCCATATTTATTCAGTTGTGGGGAA

GACAACACCGTTAAGTGTTGGGATATAGAACAAAATAAAGTTATACGAAGCTATCACGGTCATTTATCAGGCGTTTATTG

TCTAGCGATACATCCTGCCATTGATATTTTAATTAGTGGTGGACGCGATGCGGTAGTTAGGGTGTGGGACATTCGCACGA

AGCAAGCGATACATGTTTTGGGGGGTCATGCAGGAACGGTAATGAGCATTTTGAGTCAGGCAGATGAGCCCCAAATAATT

TCGGGGTCCCAGGACAAAACTGTAAAATTGTGGGACCTGACTGCAGGAAAATGTAGAGTTACACTTACAAACCACAAAAA

AAGCATCCGTGCCATGGCTCTACATCCAAGAGAGTATTGTTTTTCCACGTGCTCTTCTGATAACATAAAAATTTGGAAGT

GCCCTGAAGGTGTTTTTTGCCGAAATTTGGATGGTCACAATTCAATCGTAAACTGTTGTGCGATTAAAGACGACGGGGAT

AGCACTACATTGGTGGCAGGATCAAATAACGGGCAACTACATTTTTGGGATTGGGCTAGTGGATACAAGTTTCAAACCTT

GGAGAGCATAGTCCAACGTGGTTCTATGGAAAGCGAAAACGGCATTTTCGCTTGCGCTTTCGATAAAAGTGAGTCTCGTT

TAATTACAGCGGAATGTGACAAAACAATAAAAATTTGGAAAGAAGACGACGCTGCCACTCCCGAGTCGCATCCCATTATG

TGGAAACCA

ORF - retro_oana_80 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	61.61 %
Parental protein coverage:	62.02 %
Number of stop codons detected:	0
Number of frameshifts detected:	0

Retrocopy - Parental Gene Alignment:

                                ParentalKPQWHPPWKLYRVISGHLGWVRCIAVEPGNQWFVTGSADRTIKIWDLASGKLKLSLTGHISTVRGVIVSG
.P.WHPPWKLYRVI.GH.GWV.C.AV...N.WF.TG..DR.IKIWDLA...LKLSLTGH...VR....S.
RetrocopyEPKWHPPWKLYRVIIGHQGWVHCVAVDCTNEWFATGGNDRLIKIWDLATCQLKLSLTGHVNSVRDIKISE
ParentalRSPYLFSCGEDKQVKCWDLEYNKVIRHYHGHLSAVYGLDLHPTIDVLVTCSRDSTARIWDVRTKASVHTL
..PYLFSCGED..VKCWD.E.NKVIR.YHGHLS.VY.L..HP.ID.L....RD...R.WD.RTK...H.L
RetrocopyKNPYLFSCGEDNTVKCWDIEQNKVIRSYHGHLSGVYCLAIHPAIDILISGGRDAVVRVWDIRTKQAIHVL
ParentalAGHTNAVATVKCQAAEPQIITGSHDTTIRLWDLVAGKTRVTLTNHKKSVRAVVLHPRHYTFASGSPDNIK
.GH...V.....QA.EPQII.GS.D.T..LWDL.AGK.RVTLTNHKKS.RA..LHPR.Y.F...S.DNIK
RetrocopyGGHAGTVMSILSQADEPQIISGSQDKTVKLWDLTAGKCRVTLTNHKKSIRAMALHPREYCFSTCSSDNIK
ParentalQWKFPDGNFIQNLSGHNAIINTLAVNSDG---VLVSGADNGTMHLWDWRTGYNFQRVHAAVQPGSLDSES
.WK.P.G.F..NL.GHN.I.N..A...DG....LV.G..NG..H.WDW..GY.FQ.....VQ.GS..SE.
RetrocopyIWKCPEGVFCRNLDGHNSIVNCCAIKDDGDSTTLVAGSNNGQLHFWDWASGYKFQTLESIVQRGSMESEN
ParentalGIFACAFDQSESRLLTAEADKTIKVYREDDTATEETHPVSWKP
GIFACAFD.SESRL.TAE.DKTIK...EDD.AT.E.HP..WKP
RetrocopyGIFACAFDKSESRLITAECDKTIKIWKEDDAATPESHPIMWKP

                            

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

                        

RNA-Seq - click to see more details

(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain	0 .00 RPM	41 .51 RPM
SRP007412_cerebellum	0 .00 RPM	33 .66 RPM
SRP007412_heart	0 .09 RPM	36 .04 RPM
SRP007412_kidney	0 .00 RPM	37 .01 RPM
SRP007412_liver	0 .00 RPM	25 .31 RPM
SRP007412_testis	0 .00 RPM	122 .87 RPM

ChIP-Seq - click to see more details

Ornithorhynchus anatinus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_oana_80 retrocopy.

TSS - click to see more details

Ornithorhynchus anatinus was not studied using FANTOM5 data.

Lab - click to see more details

retro_oana_80 was not experimentally validated.

Retrocopy orthology:

Ornithorhynchus anatinus 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
Choloepus hoffmanni	ENSCHOG00000001013	1 retrocopy	retro_chof_579,
Myotis lucifugus	ENSMLUG00000008318	1 retrocopy	retro_mluc_812,
Ornithorhynchus anatinus	ENSOANG00000005295	1 retrocopy	retro_oana_80 ,

	RetrogeneDB ID:	retro_oana_80
Retrocopy location	Organism:	*Platypus (Ornithorhynchus anatinus)*
	Coordinates:	Contig49450:2935..3904(+)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	PLRG1
	Ensembl ID:	ENSOANG00000005295
	Aliases:	None
	Description:	pleiotropic regulator 1 [Source:HGNC Symbol;Acc:9089]

Parental	KPQWHPPWKLYRVISGHLGWVRCIAVEPGNQWFVTGSADRTIKIWDLASGKLKLSLTGHISTVRGVIVSG
	.P.WHPPWKLYRVI.GH.GWV.C.AV...N.WF.TG..DR.IKIWDLA...LKLSLTGH...VR....S.
Retrocopy	EPKWHPPWKLYRVIIGHQGWVHCVAVDCTNEWFATGGNDRLIKIWDLATCQLKLSLTGHVNSVRDIKISE

Parental	RSPYLFSCGEDKQVKCWDLEYNKVIRHYHGHLSAVYGLDLHPTIDVLVTCSRDSTARIWDVRTKASVHTL
	..PYLFSCGED..VKCWD.E.NKVIR.YHGHLS.VY.L..HP.ID.L....RD...R.WD.RTK...H.L
Retrocopy	KNPYLFSCGEDNTVKCWDIEQNKVIRSYHGHLSGVYCLAIHPAIDILISGGRDAVVRVWDIRTKQAIHVL

Parental	AGHTNAVATVKCQAAEPQIITGSHDTTIRLWDLVAGKTRVTLTNHKKSVRAVVLHPRHYTFASGSPDNIK
	.GH...V.....QA.EPQII.GS.D.T..LWDL.AGK.RVTLTNHKKS.RA..LHPR.Y.F...S.DNIK
Retrocopy	GGHAGTVMSILSQADEPQIISGSQDKTVKLWDLTAGKCRVTLTNHKKSIRAMALHPREYCFSTCSSDNIK

Parental	QWKFPDGNFIQNLSGHNAIINTLAVNSDG---VLVSGADNGTMHLWDWRTGYNFQRVHAAVQPGSLDSES
	.WK.P.G.F..NL.GHN.I.N..A...DG....LV.G..NG..H.WDW..GY.FQ.....VQ.GS..SE.
Retrocopy	IWKCPEGVFCRNLDGHNSIVNCCAIKDDGDSTTLVAGSNNGQLHFWDWASGYKFQTLESIVQRGSMESEN

Parental	GIFACAFDQSESRLLTAEADKTIKVYREDDTATEETHPVSWKP
	GIFACAFD.SESRL.TAE.DKTIK...EDD.AT.E.HP..WKP
Retrocopy	GIFACAFDKSESRLITAECDKTIKIWKEDDAATPESHPIMWKP

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

RetrogeneDB ID:

retro_oana_80