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]


Retrocopy-Parental alignment summary:






>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. %
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 ENSMICG000000176401 retrocopy
retro_mmur_1261,
Myotis lucifugus ENSMLUG000000073791 retrocopy
retro_mluc_171,
Mus musculus ENSMUSG000000197152 retrocopies
retro_mmus_3505, retro_mmus_460,
Rattus norvegicus ENSRNOG00000015237 1 retrocopy
retro_rnor_2323 ,


Copyright © RetrogeneDB 2014-2017