RetrogeneDB ID:

retro_mmus_3683

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:X:106281914..106284638(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMUSG00000081289
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:Ipo5
Ensembl ID:ENSMUSG00000030662
Aliases:Ipo5, 1110011C18Rik, 5730478E03Rik, AA409333, C76941, IMB3, Kpnb3, Ranbp5
Description:importin 5 [Source:MGI Symbol;Acc:MGI:1917822]


Retrocopy-Parental alignment summary:






>retro_mmus_3683
CATATTTTGATCAGGACACTGTCTGCCAGAGCTACTGCTGCCTTCATACTTGCCAATGAGCATAATGGTGCTCTGTTCAT
TCACTTCGCAGACTTGCTGCCTGGATTCTTACAGGCTGTCAATGACTCATGTTACCAGAATGATGATTCTGTCCTAAAAT
TCCTTGTTGAGATTGCTGATACTGTTCCAAAGTATTTGCACCCTCACTTAGAAGCAACTCTGCAGTTAAGTCTAAAGTTG
TGTGGAGACGCTAACCTCAATAATATGCAATGCCAGCTTGTCCTTGAAGTGATTGTGACACTGTCAGAGACTGCAGCTGC
TATGTTAAGAAAGCACACCAATATCATCGCACAGACTATTCCTCAGATGTTGGCAATGATGGTTGACCTAGAAGAAGATG
AGGACTGGGCAAATGCTGATGAGCTAGAAGATGATGATTTCAATAGCAATGCAGTTGTTAGTGAAAGTGCATTAGACGAA
ATGGCCTGTGGACTTGGTGGAAAACTCGTTCTGCCCATGATCAAGGAACACATTATGTAAATGCCTCAAAACCCTGATTG
GAAATACAGGCATGCAGGATTAATGGCCCTATCTGCCATTGACAAAGGATGCCACCAGCAGATGGAAGGAACTCTAAGTG
AGATTGTAAATTTTGTCTTGCTTTTCCTCCAGGATCCTCATCCGAGAGTCCGGTATGCAGCCTGCAATGTCAGATGGCTA
CAGATTTTGCACCTGGTTTTCAAAAGAAATTTCATGAGAAGGTGATTGCAGCTTTGCTTCAGACCATGGAAGACCAAGGC
AACCAGCGGGTGCAGGCCCATGCAGTAGCTGCCCTTATTAACTTCACTGAAGATTGTCCCAAGTCACTGCTTAGTCTGTA
CTTGGATAACTTGGTGAAGTACCTGCACTCCATCATGGTGCTCAAGATCCAGGAGATGATTCAGAAAGGCACCAAGTTAG
TTTTGCAACAAGTTGTGACAGCCATTGCATCAGTTGCAGATACTGCAGAGGAAAAGTTTGTCCCCTACTATGACTTGTTT
ATGCCATCACTGAAGCACATTGTCGAGAACACAGTCCAGGAGCTGAAGCTGCTGCAACGGAAGACCATCGAGTGCACCAG
CCTCATCGGTCTGGTAGTCGGGAAGGAGAAATTCATGCAGGATGCTTCAGATGTGATGCAGCTATTGTTGAAGACACAGA
CAGACTTCAATGATATGGAATATGACGACCCTCAGATTTCTTACATGATCTCAGCATGAGCTAGGATGTGCAAAATCCTT
GGGAAAGAATTCCAGCAGTACCTTCCCGTGGTTATGGGGCCCCTGATGAAGACTGCTTCAATTAAGCCTGAAGTGGCCCT
TCTAGATACCTAGGACATGGGGAATATGAGTGATGATGACGGTTGGGAATTTGTGAACCTCAGAGATCAGCAAAGTTTTG
GTATTAAAACTGTAGGACTGGAAGAAAAGTCAATGGCTTGCCAGATGTTGGTTTGCTATGCTAAGGAATTAAAGGGAGGT
TTTTGTGGAATACACTGAACAAGTTGTCAAACTGATGGTCCCACTGCTGAAATTTTATTTCCATGATGGGGTCTGAGTGG
CAGCAGCAGAGTCCATGCCTCTTCTCCTCGAGTGTACGAGAGTCTGGGGTCCCGAGTACCTTACGCAGATGTGGCACTTC
ATGTGTGACGCTCTCATCAAGGCCATCAGCACAGAGCCCGACTTAGACGTCCTCTCAGAGATCATGCACTCCTTCACAAA
GTACATTGAAGTAATGGGAGACAGGTGCCTCAACAATGAACACTTTGAGAAGCTTGGAGGTATCCTGAAGGTGAAGCTTG
AAGAACATTTCAAAAATCAAGAGTTGCGGCACGTTAAAAGACAAGATGAAGACTATGACGAACAGGTTGAAGAGTCACTA
TAAGATGAGGATGATAATGATGTTTATGTACTGACTAAAGTATCAGATATTTTACACTCAATATTCAGTAGCTACAAAGA
AAAGGTGTTGCTGTGGTTTGAACAGCTGCTCCCATTAATTGTCAACCTGATTTGTCTGCAAAGACCATGGCCAGACAGAC
AATGGGGGATTGTGCATCTTCGATGGTATCATAGAACACTGTAGTCCAGCTTCATTTAAGTATGCAGAATATTTCTTAAG
GCCAATGCTCCAGGAGGTGTGTGACAACAGCCCAGAAGTCAGGCAAGCTGTGGTGTATGGCCTAGGCGTCATGGCACAGT
TTGCTTGCGATAACTACCGCCCTTTCTGTACCGAAGCACTCCCGCTGCTTGTAAGAGTTATTCAGGCTGCAGAGTCTAAG
ACCAAAGAAAATGTCAATGCCATCGAGAACTGCATCTCAGCAGTGGGAAAGATCATGAAGTTTAAGCCCGACTGTGTGAA
TGTGGAGGAGGTCTTACCACACTGGATGTCCTGGCTCCCCCTACACGAAGATAAAGAAGCTGTCCAGACCTTCAGTTACC
TGTGCAACCTGATTGAAAGTAATCACCCAATTGTTCTTGCCCAAACAATACCAATCTACCGAAAATATTCAGTATAATTG
CAGAAGGAGAAATGCATGAGGCCATTAAACATGAAGACCCCTGTGCCAAACACATGGCCAATGTAGTTCGCCAAGTACAG
ACTTCTGGAGGATTGTGGACTGAATGCATAGCTCGACTCAGTCTGGAGCAGCAGGAAGCCATCAAGAAGCTCCTGAACTC
TGCC

ORF - retro_mmus_3683 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 88.65 %
Parental protein coverage: 83.14 %
Number of stop codons detected: 5
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalHPSIRTLSARATAAFILANEHNVALFKHFADLLPGFLQAVNDSCYQNDDSVLKSLVEIADTVPKYLRPHL
H..IRTLSARATAAFILANEHN.ALF.HFADLLPGFLQAVNDSCYQNDDSVLK.LVEIADTVPKYL.PHL
RetrocopyHILIRTLSARATAAFILANEHNGALFIHFADLLPGFLQAVNDSCYQNDDSVLKFLVEIADTVPKYLHPHL
ParentalEATLQLSLKLCGDTNLNNMQRQLALEVIVTLSETAAAMLRKHTSLIAQTIPQMLAMMVDLEEDEDWANAD
EATLQLSLKLCGD.NLNNMQ.QL.LEVIVTLSETAAAMLRKHT..IAQTIPQMLAMMVDLEEDEDWANAD
RetrocopyEATLQLSLKLCGDANLNNMQCQLVLEVIVTLSETAAAMLRKHTNIIAQTIPQMLAMMVDLEEDEDWANAD
ParentalELEDDDFDSNAVAGESALDRMACGLGGKLVLPMIKEHIMQMLQNPDWKYRHAGLMALSAIGEGCHQQMEG
ELEDDDF.SNAV..ESALD.MACGLGGKLVLPMIKEHIM.M.QNPDWKYRHAGLMALSAI..GCHQQMEG
RetrocopyELEDDDFNSNAVVSESALDEMACGLGGKLVLPMIKEHIM*MPQNPDWKYRHAGLMALSAIDKGCHQQMEG
ParentalILNEIVN-FVLLFLQDPHPRVRYAACNAVGQMATDFAPGFQKKFHEKVIAALLQTMEDQGNQRVQAHAAA
.L.EIVN.F.L.F...P........C....QMATDFAPGFQKKFHEKVIAALLQTMEDQGNQRVQAHA.A
RetrocopyTLSEIVN<FCLAF--PPGSSSESPVCSLQCQMATDFAPGFQKKFHEKVIAALLQTMEDQGNQRVQAHAVA
ParentalALINFTEDCPKSLLIPYLDNLVKHLHSIMVLKLQELIQKGTKLVLEQVVTSIASVADTAEEKFVPYYDLF
ALINFTEDCPKSLL..YLDNLVK.LHSIMVLK.QE.IQKGTKLVL.QVVT.IASVADTAEEKFVPYYDLF
RetrocopyALINFTEDCPKSLLSLYLDNLVKYLHSIMVLKIQEMIQKGTKLVLQQVVTAIASVADTAEEKFVPYYDLF
ParentalMPSLKHIVENAVQKELRLLRGKTIECISLIGLAVGKEKFMQDASDVMQLLLKTQTDFNDMEDDDPQISYM
MPSLKHIVEN.VQ.EL.LL..KTIEC.SLIGL.VGKEKFMQDASDVMQLLLKTQTDFNDME.DDPQISYM
RetrocopyMPSLKHIVENTVQ-ELKLLQRKTIECTSLIGLVVGKEKFMQDASDVMQLLLKTQTDFNDMEYDDPQISYM
ParentalISAWARMCKILGKEFQQYLPVVMGPLMKTASIKPEVALLDTQDMENMSDDDGWEFVNLGDQQSFGIKTAG
ISA.ARMCKILGKEFQQYLPVVMGPLMKTASIKPEVALLDT.DM.NMSDDDGWEFVNL.DQQSFGIKT.G
RetrocopyISA*ARMCKILGKEFQQYLPVVMGPLMKTASIKPEVALLDT*DMGNMSDDDGWEFVNLRDQQSFGIKTVG
ParentalLEEKSTACQMLVCYAKELKEG-FVEYTEQVVKLMVPLLKFYFHDGVRVAAAESMPLLLECARVRGPEYLT
LEEKS.ACQMLVCYAKELK.G.FVEYTEQVVKLMVPLLKFYFHDGV.VAAAESMPLLLEC.RV.GPEYLT
RetrocopyLEEKSMACQMLVCYAKELKGG>FVEYTEQVVKLMVPLLKFYFHDGV*VAAAESMPLLLECTRVWGPEYLT
ParentalQMWHFMCDALIKAIGTEPDSDVLSEIMHSFAKCIEVMGDGCLNNEHFEELGGILKAKLEEHFKNQELRQV
QMWHFMCDALIKAI.TEPD.DVLSEIMHSF.K.IEVMGD.CLNNEHFE.LGGILK.KLEEHFKNQELR.V
RetrocopyQMWHFMCDALIKAISTEPDLDVLSEIMHSFTKYIEVMGDRCLNNEHFEKLGGILKVKLEEHFKNQELRHV
ParentalKRQDEDYDEQVEESLQDEDDNDVYILTKVSDILHSIFSSYKEKVLPWFEQLLPLIVNLICPQRPWPDRQW
KRQDEDYDEQVEESL.DEDDNDVY.LTKVSDILHSIFSSYKEKVL.WFEQLLPLIVNLIC.QRPWPDRQW
RetrocopyKRQDEDYDEQVEESL*DEDDNDVYVLTKVSDILHSIFSSYKEKVLLWFEQLLPLIVNLICLQRPWPDRQW
Parental-GLCIFDDIVEHCSPASFKYAEYFISPMLQYVCDNSPEVRQAAAYGLGVMAQFGGDNYRPFCTDALPLLV
.GLCIFD.I.EHCSPASFKYAEYF..PMLQ.VCDNSPEVRQA..YGLGVMAQF..DNYRPFCT.ALPLLV
Retrocopy>GLCIFDGIIEHCSPASFKYAEYFLRPMLQEVCDNSPEVRQAVVYGLGVMAQFACDNYRPFCTEALPLLV
ParentalRVIQAPEAKTKENVNATENCISAVGKIMKFKPDCVNVEEVLPHWLSWLPLHEDKEEAVQTFSYLCDLIES
RVIQA.E.KTKENVNA.ENCISAVGKIMKFKPDCVNVEEVLPHW.SWLPLHEDK.EAVQTFSYLC.LIES
RetrocopyRVIQAAESKTKENVNAIENCISAVGKIMKFKPDCVNVEEVLPHWMSWLPLHEDK-EAVQTFSYLCNLIES
ParentalNHPIVLG-PNNTNLPKIFSIIAEGEMHEAIKHEDPCAKRLANVVRQVQTSGGLWTECIAQLSPEQQAAIQ
NHPIVL..PNNTNLPKIFSIIAEGEMHEAIKHEDPCAK..ANVVRQVQTSGGLWTECIA.LS.EQQ.AI.
RetrocopyNHPIVLA<PNNTNLPKIFSIIAEGEMHEAIKHEDPCAKHMANVVRQVQTSGGLWTECIARLSLEQQEAIK
ParentalELLNSA
.LLNSA
RetrocopyKLLNSA

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 .07 RPM 164 .99 RPM
SRP007412_cerebellum 0 .04 RPM 119 .06 RPM
SRP007412_heart 0 .22 RPM 209 .91 RPM
SRP007412_kidney 0 .02 RPM 124 .58 RPM
SRP007412_liver 0 .03 RPM 73 .05 RPM
SRP007412_testis 0 .73 RPM 1253 .84 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_mmus_3683 was not detected

EST - click to see more details

No EST(s) were mapped for retro_mmus_3683 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_mmus_3683 retrocopy 5' end.

Lab - click to see more details

retro_mmus_3683 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_3683 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 21 parental genes, and 25 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000037841 retrocopy
retro_amel_3,
Bos taurus ENSBTAG000000393741 retrocopy
retro_btau_104,
Canis familiaris ENSCAFG000000055611 retrocopy
retro_cfam_452,
Choloepus hoffmanni ENSCHOG000000060611 retrocopy
retro_chof_11,
Cavia porcellus ENSCPOG000000048272 retrocopies
retro_cpor_265, retro_cpor_57,
Equus caballus ENSECAG000000148081 retrocopy
retro_ecab_37,
Felis catus ENSFCAG000000256571 retrocopy
retro_fcat_24,
Homo sapiens ENSG000000651501 retrocopy
retro_hsap_57,
Gorilla gorilla ENSGGOG000000087421 retrocopy
retro_ggor_47,
Loxodonta africana ENSLAFG000000161901 retrocopy
retro_lafr_22,
Myotis lucifugus ENSMLUG000000065001 retrocopy
retro_mluc_295,
Mus musculus ENSMUSG00000030662 2 retrocopies
retro_mmus_251, retro_mmus_3683 ,
Nomascus leucogenys ENSNLEG000000078312 retrocopies
retro_nleu_1610, retro_nleu_2482,
Oryctolagus cuniculus ENSOCUG000000038981 retrocopy
retro_ocun_143,
Otolemur garnettii ENSOGAG000000075701 retrocopy
retro_ogar_169,
Pongo abelii ENSPPYG000000054581 retrocopy
retro_pabe_172,
Pan troglodytes ENSPTRG000000059842 retrocopies
retro_ptro_49, retro_ptro_745,
Pteropus vampyrus ENSPVAG000000045161 retrocopy
retro_pvam_8,
Rattus norvegicus ENSRNOG000000109891 retrocopy
retro_rnor_240,
Sus scrofa ENSSSCG000000095091 retrocopy
retro_sscr_24,
Ictidomys tridecemlineatus ENSSTOG000000111641 retrocopy
retro_itri_32,




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