RetrogeneDB - Retrocopy retro_rnor

                        
>retro_rnor_2323
TGGGAAACCCTGAGGGTGTCCCTCACAAAAGGCCTCCTGCACTGTGAGCAAAAGGGACTTATGAGACTCTAGCATGATTT

AGAATAATGCATCTCATTTCCCACACTGTCCTGTTACTCCGGATGGGTGGTAGATCACATCCCACCCACCACCTCACACC

ACAAGCCAGATATGGCACCCGCTTGGATAATTCACCATCCTCTAGATCTGCTGCAGGCCAAAACCAATCCTCACTCCTTA

AGTCTCCTGGCACAAGTACCCTGCAATCCCCTCACCCTCAACAGCAAATGGAACCCATAGCACTCATGAGTCCCTGTTCA

CAGACCCTATGGCGCTTCAGTGCTCTCGGGCTATCAGAGTGGAGGGTTGCATCTGAAACTACAAATTGGCCAGCAGAAGG

AGAGCAGCAGAGGGCCTGAGGCTGCAGCAGGAGGAGCAAGAGAGGAAGGTGGGAGCCCTCTCAGAGATGGCATGCCAACA

GCTGGAGAGGTTTGACCAGCTGAGGGAGCAGAAGCTGCAGAAGGACTTCCGGGGCTTCCAGGGCAGGATGGAGAAGGGTC

GCAGAGAAGCCCTGGACCGTCAGAAGAAGCTGAAAGCTGAGCATGGCCTCAGAGCCAAGCTTCTCACCCTAAAACTTGGA

GAGGCTAAGCAGCAGCAGCACAAGAAGCAGGCAGAGTAGGAGCGGCTTCCTGAGGAGGAAGGCCAGATCTGTGTGCGTAG

CCTGTACCCCCTGCAAGAGGAGGTCCTGTCTCAACCAGCAGCTGGAGGCCTCCTTTCAGCAGCACAGAGACCTCCTGAAC

GTGGACCTGTCTGCCTTCCAGAGCCGGGGCAAGCAGCTGTGCGGCTTCATCTCCGGACTCCTTCCCACCACCTTGGACAC

TGGCTATCCCACAGCAGAGAATCATGCTGAGGCTGAGGGAGCCCTGCAGGAAATGAGGGACCTCCTCATCCATTTAGAGC

AGGAGATCTCCAGAGCCACCTAAGTGAAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGCCTGCATCAAGCAACAGGAGTCA

CAGGGCCCTCAGCGCCCAAGGGCTCCTGCCCAGACCTCTGCCACCAGCCCAAGCCCAGCAGGGACTCAGGCGAAGAAAGA

CCTGCAGGTGCAGTTCCAGGATGGGACGATGCACTGGTACCAGCAACTTCAGGATGCTTCTGCCAAATGCGAGTTGGCCT

TTGAGGACCTGAGCAGCAGCAAGGACAGTCAGGACAGAAGGATCAAGATGGACTTGCAGAAGGCAGCCACCATCCCAGTG

AGCCAGATCTCCAGCAGCGCAGGTTCAAAGCTCAAGGAGGTCTTTGACAAACTCCATAGCCTGCTCTCTGGACAGCCTGT

GCAATCTGGTGGGCCTCCCATGTCTGTCACTCTTAACCCTCAGGGGCTGGACCTTGTCCAGTACAAAGTGGCAGAGAAGT

TCGACAAGCAAGGGGAGTTGAAGTGGCCTCTCACCCCAAAGCGCCTTTCCCCATTGCGGCCGTGGCCTCTGGGATCTGGA

TGCTCCACCCCAGAGTGGGAGACCTCATCCTCGATCAGCTCCACAGGCAGCATCCCTACTCCGTTTCTTTGTACCCAGCC

TTTAAGGAAGCGATGGGTTTGACGATTATTAATGGAAGCTTGCCTACAAATTGACATATTCCAAGGTTGAGCAACATGAC

AATATTCTAAAACAGATGGCTGGGATGATTCATTTATCTGCCACAATCATCCCGTTCCAGCGGCCTGACAAAAGCAGGTC

AGAACCTCACACTCATGGCTTACATTATGACTGGTGGTCATTGGCATAGGCCTTAAACTTGGAGCCTTTCCTGGATGTGA

TAGCCACTCTCCTGTTTGACGTCCTGGAGGTGTGTGGGACTGCCCTCGTGAAGCAGTACCAGGTCCGGTATGGAAGATGG

TCCTTGTCACTAGAGAGGACTACTTGCCCAGAGTTAAAGCCATCCTGAGCTCAGGATAGATGGGATCTCTGATGCATCTG

CAGCAGTTCTTGGACAAATGTCTGCAGCACAGGGAGTCCCTGTCCCCAGAGGTTTTCTGAAGTCATCATTCTGGAGTTCT

ORF - retro_rnor_2323 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	64.35 %
Parental protein coverage:	99.0 %
Number of stop codons detected:	8
Number of frameshifts detected:	7

Retrocopy - Parental Gene Alignment:

                                ParentalWETLRALRNSSKGRLRYDREWLLRYEDVLEECMSLPKLSSYSGWVVDHILPNTSHHTQENAPS-SDNSPS
WETLR......KG.L......L.R....LE.C.S.P.LS.YSGWVVDHI.P.TSHH....AP...DNSPS
RetrocopyWETLRV--SLTKGLLHCEQKGLMRL*HDLE*CISFPTLSCYSGWVVDHIPPTTSHHKPDMAPA<LDNSPS
ParentalSGSASGLYQSTL-KSPVRSSPQSP-SPSTPSGTQSAHESPFTEPIALQSSRAIKVEGCIRMYELAHRMRG
S.SA.G..QS.L.KSP..S..QSP.SPST..GT.S.HES.FT.P.ALQ.SRAI.VEGCI..Y.LA.R.R.
RetrocopySRSAAGQNQSSLLKSPGTSTLQSP<SPSTANGTHSTHESLFTDPMALQCSRAIRVEGCI*NYKLASRRRA
ParentalTEGLRQWQEEQERKVQALSEMASEQLKRFDELKELKLHKEFRDLQEVMEKSTREALGHQEKLKAEHRHRA
.EGLR..QEEQERKV.ALSEMA..QL.RFD.L.E.KL.K.FR..Q..MEK..REAL..Q.KLKAEH..RA
RetrocopyAEGLRLQQEEQERKVGALSEMACQQLERFDQLREQKLQKDFRGFQGRMEKGRREALDRQKKLKAEHGLRA
ParentalKILNLKLREA-EQQRVKQAEQEQLRKEEGQIRLRSLYTLQEEVLQL-NQQLDASSQHKDLLNVDLAAFQT
K.L.LKL.EA..QQ..KQAE.E.L..EEGQI..RSLY.LQEEVL....Q......QH.DLLNVDL.AFQ.
RetrocopyKLLTLKLGEAKQQQHKKQAE*ERLPEEEGQICVRSLYPLQEEVLSQ>QQLEASFQQHRDLLNVDLSAFQS
ParentalRGNQLCGLISGIIRTTLESGYPTAENQAEAERVLQEMRDLLSNLEQEITRASEMKKKDEEEARVKLQESQ
RG.QLCG.ISG...TTL..GYPTAEN.AEAE..LQEMRDLL..LEQEI.RA..................Q
RetrocopyRGKQLCGFISGLLPTTLDTGYPTAENHAEAEGALQEMRDLLIHLEQEISRAT*VXXXXXXXXXXXCIKQQ
ParentalVQQGP---GAPTKTSAPSPSLVGTQS-EDLQVKVQDSTMQWYQQLQDASAKCVLAFEDLTSSKDSQIKKI
..QGP....AP..TSA.SPS..GTQ...DLQV..QD.TM.WYQQLQDASAKC.LAFEDL.SSKDSQ...I
RetrocopyESQGPQRPRAPAQTSATSPSPAGTQAKKDLQVQFQDGTMHWYQQLQDASAKCELAFEDLSSSKDSQDRRI
ParentalKMDLQKAATIPVSQISTIAGSKLKEVFDKIHSLLSGKPVQSGGRSVCVTLNPQGLDFVQYKLAEKFVKQG
KMDLQKAATIPVSQIS..AGSKLKEVFDK.HSLLSG.PVQSGG....VTLNPQGLD.VQYK.AEKF.KQG
RetrocopyKMDLQKAATIPVSQISSSAGSKLKEVFDKLHSLLSGQPVQSGGPPMSVTLNPQGLDLVQYKVAEKFDKQG
ParentalE-EEVASHHEAAFPIAVVASGIWMLHPKVGDLILAHLHKKCPYSVPFYPAFKEGMPL-EDYQRMLGYQVT
E..EVASH..A.FPIA.VASGIWMLHP.VGDLIL..LH...PYSV..YPAFKE.M.L..DY...L.Y..T
RetrocopyE<VEVASHPKAPFPIAAVASGIWMLHPRVGDLILDQLHRQHPYSVSLYPAFKEAMGL<DDY*WKLAYKLT
ParentalDSKVEQQDNFLKRMSGMIRLYAAIIQLQWPYGSRQEAHPHGLNHGWRWLAQILNMEPLSDVTATLLFDFL
.SKVEQ.DN.LK.M.GMI.L.A.II..Q.P..SR.E.H.HGL...W..LA..LN.EP..DV.ATLLFD.L
RetrocopyYSKVEQHDNILKQMAGMIHLSATIIPFQRPDKSRSEPHTHGLHYDWWSLA*ALNLEPFLDVIATLLFDVL
ParentalEVCGNALMKQYQVQF-WKMILLIKEDYFPRIEAITSSGQMGSFIRLKQFLEKCLQRRE-IPVPKGFLTPS
EVCG.AL.KQYQV...WKM.L...EDY.PR..AI.SSG.MGS...L.QFL.KCLQ.RE..PVP.GFL..S
RetrocopyEVCGTALVKQYQVRY<WKMVLVTREDYLPRVKAILSSG*MGSLMHLQQFLDKCLQHRE<VPVPRGFLKSS
ParentalFWRS
FW.S
RetrocopyFWSS

                            

                            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
SRP017611_brain	0 .00 RPM	19 .70 RPM
SRP017611_kidney	0 .00 RPM	16 .33 RPM
SRP017611_liver	0 .00 RPM	7 .33 RPM

ChIP-Seq - click to see more details

Rattus norvegicus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_rnor_2323 retrocopy.

TSS - click to see more details

Rattus norvegicus was not studied using FANTOM5 data.

Lab - click to see more details

retro_rnor_2323 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_rnor_2323 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Microcebus murinus	ENSMICG00000017640	1 retrocopy	retro_mmur_1261,
Myotis lucifugus	ENSMLUG00000007379	1 retrocopy	retro_mluc_171,
Mus musculus	ENSMUSG00000019715	2 retrocopies	retro_mmus_3505, retro_mmus_460,
Rattus norvegicus	ENSRNOG00000015237	1 retrocopy	retro_rnor_2323 ,

	RetrogeneDB ID:	retro_rnor_2323
Retrocopy location	Organism:	*Rat (Rattus norvegicus)*
	Coordinates:	6:119465851..119467931(+)
	Located in intron of:	ENSRNOG00000010227
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	Gle1
	Ensembl ID:	ENSRNOG00000015237
	Aliases:	Gle1, Gle1l
	Description:	Nucleoporin GLE1 [Source:UniProtKB/Swiss-Prot;Acc:Q4KLN4]

Parental	WETLRALRNSSKGRLRYDREWLLRYEDVLEECMSLPKLSSYSGWVVDHILPNTSHHTQENAPS-SDNSPS
	WETLR......KG.L......L.R....LE.C.S.P.LS.YSGWVVDHI.P.TSHH....AP...DNSPS
Retrocopy	WETLRV--SLTKGLLHCEQKGLMRLHDLECISFPTLSCYSGWVVDHIPPTTSHHKPDMAPA<LDNSPS

Parental	SGSASGLYQSTL-KSPVRSSPQSP-SPSTPSGTQSAHESPFTEPIALQSSRAIKVEGCIRMYELAHRMRG
	S.SA.G..QS.L.KSP..S..QSP.SPST..GT.S.HES.FT.P.ALQ.SRAI.VEGCI..Y.LA.R.R.
Retrocopy	SRSAAGQNQSSLLKSPGTSTLQSP<SPSTANGTHSTHESLFTDPMALQCSRAIRVEGCI*NYKLASRRRA

Parental	TEGLRQWQEEQERKVQALSEMASEQLKRFDELKELKLHKEFRDLQEVMEKSTREALGHQEKLKAEHRHRA
	.EGLR..QEEQERKV.ALSEMA..QL.RFD.L.E.KL.K.FR..Q..MEK..REAL..Q.KLKAEH..RA
Retrocopy	AEGLRLQQEEQERKVGALSEMACQQLERFDQLREQKLQKDFRGFQGRMEKGRREALDRQKKLKAEHGLRA

Parental	KILNLKLREA-EQQRVKQAEQEQLRKEEGQIRLRSLYTLQEEVLQL-NQQLDASSQHKDLLNVDLAAFQT
	K.L.LKL.EA..QQ..KQAE.E.L..EEGQI..RSLY.LQEEVL....Q......QH.DLLNVDL.AFQ.
Retrocopy	KLLTLKLGEAKQQQHKKQAE*ERLPEEEGQICVRSLYPLQEEVLSQ>QQLEASFQQHRDLLNVDLSAFQS

Parental	RGNQLCGLISGIIRTTLESGYPTAENQAEAERVLQEMRDLLSNLEQEITRASEMKKKDEEEARVKLQESQ
	RG.QLCG.ISG...TTL..GYPTAEN.AEAE..LQEMRDLL..LEQEI.RA..................Q
Retrocopy	RGKQLCGFISGLLPTTLDTGYPTAENHAEAEGALQEMRDLLIHLEQEISRAT*VXXXXXXXXXXXCIKQQ

Parental	VQQGP---GAPTKTSAPSPSLVGTQS-EDLQVKVQDSTMQWYQQLQDASAKCVLAFEDLTSSKDSQIKKI
	..QGP....AP..TSA.SPS..GTQ...DLQV..QD.TM.WYQQLQDASAKC.LAFEDL.SSKDSQ...I
Retrocopy	ESQGPQRPRAPAQTSATSPSPAGTQAKKDLQVQFQDGTMHWYQQLQDASAKCELAFEDLSSSKDSQDRRI

Parental	KMDLQKAATIPVSQISTIAGSKLKEVFDKIHSLLSGKPVQSGGRSVCVTLNPQGLDFVQYKLAEKFVKQG
	KMDLQKAATIPVSQIS..AGSKLKEVFDK.HSLLSG.PVQSGG....VTLNPQGLD.VQYK.AEKF.KQG
Retrocopy	KMDLQKAATIPVSQISSSAGSKLKEVFDKLHSLLSGQPVQSGGPPMSVTLNPQGLDLVQYKVAEKFDKQG

Parental	E-EEVASHHEAAFPIAVVASGIWMLHPKVGDLILAHLHKKCPYSVPFYPAFKEGMPL-EDYQRMLGYQVT
	E..EVASH..A.FPIA.VASGIWMLHP.VGDLIL..LH...PYSV..YPAFKE.M.L..DY...L.Y..T
Retrocopy	E<VEVASHPKAPFPIAAVASGIWMLHPRVGDLILDQLHRQHPYSVSLYPAFKEAMGL<DDY*WKLAYKLT

Parental	DSKVEQQDNFLKRMSGMIRLYAAIIQLQWPYGSRQEAHPHGLNHGWRWLAQILNMEPLSDVTATLLFDFL
	.SKVEQ.DN.LK.M.GMI.L.A.II..Q.P..SR.E.H.HGL...W..LA..LN.EP..DV.ATLLFD.L
Retrocopy	YSKVEQHDNILKQMAGMIHLSATIIPFQRPDKSRSEPHTHGLHYDWWSLA*ALNLEPFLDVIATLLFDVL

Parental	EVCGNALMKQYQVQF-WKMILLIKEDYFPRIEAITSSGQMGSFIRLKQFLEKCLQRRE-IPVPKGFLTPS
	EVCG.AL.KQYQV...WKM.L...EDY.PR..AI.SSG.MGS...L.QFL.KCLQ.RE..PVP.GFL..S
Retrocopy	EVCGTALVKQYQVRY<WKMVLVTREDYLPRVKAILSSG*MGSLMHLQQFLDKCLQHRE<VPVPRGFLKSS

Parental	FWRS
	FW.S
Retrocopy	FWSS

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

RetrogeneDB ID:

retro_rnor_2323