RetrogeneDB ID:

retro_mmus_1501

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:16:23014210..23016588(-)
Located in intron of:ENSMUSG00000060459
Retrocopy
information
Ensembl ID:ENSMUSG00000090021
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:Tnpo1
Ensembl ID:ENSMUSG00000009470
Aliases:Tnpo1, AU021749, D13Ertd688e, IPO2, Kpnb2, MIP, MIP1, TRN
Description:transportin 1 [Source:MGI Symbol;Acc:MGI:2681523]


Retrocopy-Parental alignment summary:






>retro_mmus_1501
AGTGAATGTCTAAATAACATTGGGGACTCCTCTCCGTTGATCAGAGCCACTGTCGGTATTTTAATTACAACCATAGCCTC
CAAGGGAGAGCTGCAGAATTGGCCTGATCTCTTACCAAACCTCTGTAGCCTGCTGGATTCCGAAGACTACAACACTTGTG
AGGGAGCCTTCGGTGCCCTTCAGAAGATATGTGAGGACTCTGCAGAGATTTTAGACAGTGATGTCTTAGATCGCCCTCTC
AACATCATGATCCCCAAGTTTTTACAGTTTTTCAAGCACAGGAGTCCCAAAATAAGGTCTCGTGCTGTTGCATGTGTCAA
TCAGTTCATCATCAGCCGGACCCAGGCGCTCATGCTGCACATGGATTCCTTCATTGAGAACCTCTTTGCACTGGCTGGCG
ACGAGGAAGCAGAGGTGCGGAAGAACGTGTGCCGGGCGCTTGTGATGTTGCTTGAAGCCCGGATGGACCGCCTGCTTCCT
CATATGCACAACATAGTCGAGTACATGCTGCAGAGAACCCAAGACCAAGATGAGAATGTAGCTCTGGAGGCCTGTGAATT
CTGGCTGACTTTGGCTGAACAGCCAATATGCAAAGATGTACTTGTAAGGCATCTACCAAAGTTGATTCCTGTGTTAGTGA
ATGGCATGAAGTACTCAGATATAGATATTATCCTGCTTAAGGGTGATGTTGAGGAAGAGACCATCCCGGATAGTGAGCAG
GATATACGGCCACGGTTTCATCGCTCGAGGACAGTGGCTCAGCAGCATGAGGAGGATGGGATTGAGGAGGAAGAAGATGA
TGATGATGACACGATTTCTGACTGGAACCTGAGAAAATGTTCTGCTGCTGCTCTCTCGATGTTCTCGCAAATGTTTATCG
TGATGAGCTTTTGCCGCACATTTTGCCACTTTTGAAAGAATTGCTTTTCCATCATGAATGGGTTGTGAAAGAATCTGGCA
TCTTGGTTTTAGGAGCAATTGCTGAAGGTTGTATGCAAGGCATGATTCCATACCTGCCCGAGCTCATTCCTCACCTTATT
CAGTGCCTTTCTGATAAAAAGGCTCTTGTACGTTCCATCACCTGCTGGACTCTCAGCCGCTATGCACACTGGGTAGTCAG
CCAGCCACCAGATACGTACCTGAAGCCATTAATGACAGAACTGCTGAAGTGTATCCTGGATAGCAACAAGAGAAGACAAG
AAGCTGCTTGCAGTGCCTTCGCTACATTAGAAGAGGAGGCTTGTACAGAGCTCGTCCCTTACCTTGCTTATATACTCGAT
ACCCTCGTCTTCGCCTTCAGTAAATACCAGCATAAGAACCTGCTCATTCTGTACGACGCCCTAGGGACGCTGGCAGATTC
AGTGGGACAGCATTTAAACAAGCCAGAATATATTCAGATGCTAATGCCTCCTTTGATCCAGAAATGGAACATGCTGAAGG
ATGAAGACAAGGATCTTTTCCCTTTGCTTGAGTGTCTCTCGTCTGTTGCCACAGCCTTGCAGTCTGGCTTCCGTCCACAT
TGTGAACCTGTAGATCAGCGTTGCGTAAACCTAGTTCAGAAGACTCTAGCACAAGCCATGCTAAACAATGCTCAACCAGA
ACAGTATGAAGCTCCAGATAAAGGTTTTATGATTGTGGCTCTTGACTTACTCAGTGGCCTGGCTGAGGGCCTGGGAGGCA
ACATTGCGCAGCTGGTGGCCCGCAGTAACATCCTAACGCTGATGTATCGGTGCATGCAGGATAAAATGCCAGAGGTTCGG
CAGAGTTCTTTTGCGTTGCTAGGTGACCTGACTAAAGCGTGCTTCCAGCATGTTAAGCCTTGTATAGCTGATTTCATGCC
AATATTGGGAACCAATCTAAATCCAGAGTTTATTTCAGTCTGCAACAATGCCACCTGGGCGATTGGGGAAATATCAATTC
AAATGGGTATAGAGATGCAGCCCTACATCCCTATGGTGTTGCACCAGCTTCTGGAAATCATTAACAGACCCAACACCCCA
AAGACGCTGTTGGAGAACACAGCAATAACAATTGGTCGTCTTGGTTAAGTTTGTCCTCAAGAGGTGGCCCCCATGCTACA
GCAGTTTATAAGACCCTGGTGTACCTCTCTGAGAAACATAAGAGACAATGAAGAAAAAGATTCAGCATTCCGGGGGATTT
GTACCATGATCAGTGTGAATCCCAGTGGCGTAATCCAAGATTTTATATTTTTTTGTGATGCTGTTGCATCATGGATTAAC
CCAAAAGGTGATCTCAGAGACATGTTCTGTAAGATCCTTCATGGATTTAAAAACCAAGTTGGGGATGAAAATTGGAGGCG
ATTCTCTGACCAGTTTCCTCTTCCCTTAAAAGAACGTCTTGCAGCTTTTTATGGTGTT

ORF - retro_mmus_1501 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 96.38 %
Parental protein coverage: 89.66 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalSECLNNIGDSSPLIRATVGILITTIASKGELQNWPDLLPKLCSLLDSEDYNTCEGAFGALQKICEDSAEI
SECLNNIGDSSPLIRATVGILITTIASKGELQNWPDLLP.LCSLLDSEDYNTCEGAFGALQKICEDSAEI
RetrocopySECLNNIGDSSPLIRATVGILITTIASKGELQNWPDLLPNLCSLLDSEDYNTCEGAFGALQKICEDSAEI
ParentalLDSDVLDRPLNIMIPKFLQFFKHSSPKIRSHAVACVNQFIISRTQALMLHIDSFIENLFALAGDEEAEVR
LDSDVLDRPLNIMIPKFLQFFKH.SPKIRS.AVACVNQFIISRTQALMLH.DSFIENLFALAGDEEAEVR
RetrocopyLDSDVLDRPLNIMIPKFLQFFKHRSPKIRSRAVACVNQFIISRTQALMLHMDSFIENLFALAGDEEAEVR
ParentalKNVCRALVMLLEVRMDRLLPHMHNIVEYMLQRTQDQDENVALEACEFWLTLAEQPICKDVLVRHLPKLIP
KNVCRALVMLLE.RMDRLLPHMHNIVEYMLQRTQDQDENVALEACEFWLTLAEQPICKDVLVRHLPKLIP
RetrocopyKNVCRALVMLLEARMDRLLPHMHNIVEYMLQRTQDQDENVALEACEFWLTLAEQPICKDVLVRHLPKLIP
ParentalVLVNGMKYSDIDIILLKGDVEEDETIPDSEQDIRPRFHRSRTVAQQHEEDGIEEEDDDDDEIDDDDTISD
VLVNGMKYSDIDIILLKGDVEE.ETIPDSEQDIRPRFHRSRTVAQQHEEDGI.EE..D....DDDDTISD
RetrocopyVLVNGMKYSDIDIILLKGDVEE-ETIPDSEQDIRPRFHRSRTVAQQHEEDGI-EEEED----DDDDTISD
ParentalWNLRKCS-AA-ALDVLANVYRDELLPHILPLLKELLFHHEWVVKESGILVLGAIAEGCMQGMIPYLPELI
WNLRKCS.AA..LDVLANVYRDELLPHILPLLKELLFHHEWVVKESGILVLGAIAEGCMQGMIPYLPELI
RetrocopyWNLRKCSAAA<SLDVLANVYRDELLPHILPLLKELLFHHEWVVKESGILVLGAIAEGCMQGMIPYLPELI
ParentalPHLIQCLSDKKALVRSITCWTLSRYAHWVVSQPPDTYLKPLMTELLKRILDSNKRVQEAACSAFATLEEE
PHLIQCLSDKKALVRSITCWTLSRYAHWVVSQPPDTYLKPLMTELLK.ILDSNKR.QEAACSAFATLEEE
RetrocopyPHLIQCLSDKKALVRSITCWTLSRYAHWVVSQPPDTYLKPLMTELLKCILDSNKRRQEAACSAFATLEEE
ParentalACTELVPYLAYILDTLVFAFSKYQHKNLLILYDAIGTLADSVGHHLNKPEYIQMLMPPLIQKWNMLKDED
ACTELVPYLAYILDTLVFAFSKYQHKNLLILYDA.GTLADSVG.HLNKPEYIQMLMPPLIQKWNMLKDED
RetrocopyACTELVPYLAYILDTLVFAFSKYQHKNLLILYDALGTLADSVGQHLNKPEYIQMLMPPLIQKWNMLKDED
ParentalKDLFPLLECLSSVATALQSGFLPYCEPVYQRCVNLVQKTLAQAMLNNAQPEQYEAPDKDFMIVALDLLSG
KDLFPLLECLSSVATALQSGF.P.CEPV.QRCVNLVQKTLAQAMLNNAQPEQYEAPDK.FMIVALDLLSG
RetrocopyKDLFPLLECLSSVATALQSGFRPHCEPVDQRCVNLVQKTLAQAMLNNAQPEQYEAPDKGFMIVALDLLSG
ParentalLAEGLGGNIEQLVARSNILTLMYQCMQDKMPEVRQSSFALLGDLTKACFQHVKPCIADFMPILGTNLNPE
LAEGLGGNI.QLVARSNILTLMY.CMQDKMPEVRQSSFALLGDLTKACFQHVKPCIADFMPILGTNLNPE
RetrocopyLAEGLGGNIAQLVARSNILTLMYRCMQDKMPEVRQSSFALLGDLTKACFQHVKPCIADFMPILGTNLNPE
ParentalFISVCNNATWAIGEISIQMGIEMQPYIPMVLHQLVEIINRPNTPKTLLENTAITIGRLGYVCPQEVAPML
FISVCNNATWAIGEISIQMGIEMQPYIPMVLHQL.EIINRPNTPKTLLENTAITIGRLG.VCPQEVAPML
RetrocopyFISVCNNATWAIGEISIQMGIEMQPYIPMVLHQLLEIINRPNTPKTLLENTAITIGRLG*VCPQEVAPML
ParentalQQFIRPWCTSLRNIRDNEEKDSAFRGICTMISVNPSGVIQDFIFFCDAVASWINPKDDLRDMFCKILHGF
QQFIRPWCTSLRNIRDNEEKDSAFRGICTMISVNPSGVIQDFIFFCDAVASWINPK.DLRDMFCKILHGF
RetrocopyQQFIRPWCTSLRNIRDNEEKDSAFRGICTMISVNPSGVIQDFIFFCDAVASWINPKGDLRDMFCKILHGF
ParentalKNQVGDENWRRFSDQFPLPLKERLAAFYGV
KNQVGDENWRRFSDQFPLPLKERLAAFYGV
RetrocopyKNQVGDENWRRFSDQFPLPLKERLAAFYGV

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 .05 RPM 79 .34 RPM
SRP007412_cerebellum 0 .17 RPM 86 .19 RPM
SRP007412_heart 0 .16 RPM 74 .49 RPM
SRP007412_kidney 1 .06 RPM 144 .80 RPM
SRP007412_liver 0 .36 RPM 82 .47 RPM
SRP007412_testis 0 .27 RPM 100 .85 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_mmus_1501 was not detected

EST - click to see more details

No EST(s) were mapped for retro_mmus_1501 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_mmus_1501 retrocopy 5' end.

Lab - click to see more details

retro_mmus_1501 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_1501 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 5 parental genes, and 7 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG000000833122 retrocopies
retro_hsap_1724, retro_hsap_1813,
Mus musculus ENSMUSG00000009470 1 retrocopy
retro_mmus_1501 ,
Pongo abelii ENSPPYG000000155451 retrocopy
retro_pabe_1528,
Pan troglodytes ENSPTRG000000169722 retrocopies
retro_ptro_1176, retro_ptro_3060,
Tursiops truncatus ENSTTRG000000002091 retrocopy
retro_ttru_1345,


Copyright © RetrogeneDB 2014-2017