RetrogeneDB ID:

retro_mdom_1861

Retrocopy
location
Organism:Opossum (Monodelphis domestica)
Coordinates:8:126403668..126406479(+)
Located in intron of:ENSMODG00000016591
Retrocopy
information
Ensembl ID:ENSMODG00000016607
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:SMC1B
Ensembl ID:ENSMODG00000007253
Aliases:None
Description:structural maintenance of chromosomes 1B [Source:HGNC Symbol;Acc:11112]


Retrocopy-Parental alignment summary:






>retro_mdom_1861
CTTAACCAGAAGCGGCCCCAATACATTAAAGCCAAGGAAAATACTTCACACAAAATTAAGAAACTGGAAGCTGCCAAAAA
GTCTCTACAGAATGCCCAGAAACAGTATAAGAAGCGAAAAGGAGATATGGATGAACTTGAAAAAGAAATGGTATCAGTAG
AGAAGGCAAGACAAGAATTTGAAGATCGAATGGAGGAAGAGAGCCAGAGCCAGGGGCGGGACCTGACTCTGGAGGAAAAC
CAAGTAAAGAAGTACCACAGGCTGAAGGAGGAAGCCAGTAAAAGAGCAGCCACCTTGGCCCAGGAGCTAGAAAAATTCAA
TCGTGACCAGAAGGCTGACCAAGACCGACTGGACTTAGAGGAGCGAAAGAAAGTTGAGACTGAGGCCAAGATCAAACAGA
AACTGAGGGAAATTGAAGAGAATCAAAAGCGAATTGAGAAACTGGAAGAATACATCACCACCAGCAAGCAGTCTCTGGAG
GAACAGAAAAAACTAGAGGGAGAACTAACTGAGGAGGTTAAGCTGGCTAAACAGCGCATTGATGAAATCAACAAGGAGCT
GAATCAAGTGATGGAGCAACTTGGTGATGCCAGAATAGACCGACAGGAGAGCAGCAGACAGCAAAGAAAGGCAGAGATAA
TGGAGAGTATCAAACGCCTCTACCCTGGTTCTGTTTATGGCCGTCTCATTGATCTATGCCAGCCAACACAGAAGAAGTAC
CAGATTGCTGTAACTAAGGTGCTGGGCAAAAATATGGATGCCATCATTGTGGACTCTGAGAAAACTGGCCGGGACTGTAT
TCAATACATCAAGGAACAGCGTGGGGAGCCTGAGACCTTCTTACCACTTGACTACCTAGAGGTGAAACCAACAGATGAGA
AGCTTAGGGAACTGAAGGGGGCCAAGCTGGTAATTGATGTTATTCGCTATGAGCCACCACACATCAAGAAGGCTCTACAG
TATGCCTGTGGCAATGCTCTGGTATGTGACAATGTTGAAGATGCCCGCCGCATTGCTTTTGGTGGCCACCAGAGACATAA
GACAGTTGCACTAGATGGGACACTCTTCCAAAAGTCTGGTGTCATCTCTGGGGGAGCAAGTGACCTCAAAGCCAAGGCCC
GCCGATGGGATGAGAAAGCAGTTGACAAACTGAAGGAGAAGAAAGAGCGCCTCACGGAGGAGCTGAAGGAACAGATGAAA
GCTAAGAGGAAGGAGGCTGAGCTGAGGCAGGTACAGTCTCAGGCTCATGGCTTACAAATGAGGCTCAAGTACTCCCAGAG
TGACCTGGAACAGACAAAGACCCGGCACCTTGCACTTAACCTACAGGAAAAGTCCAAGCTAGAGAGTGAGCTAGCTAATT
TTGGACCCCGTATCAATGACATCAAAAGGATCATCCAGGGCCGGGAACGAGAGATGAAAGATTTGAAGGAAAAGATGAAC
CAGGTAGAAGATGAGGTATTTGAGGAGTTCTGCCGAGAAATTGGAGTTCGCAATATTCGTGAATTTGAGGAAGAGAAAGT
AAAGCGGCAAAATGAAATAGCCAAGAAACGGCTTGAGTTTGAGAACCAGAAGACTCGCCTGGGTATTCAGCTAGATTTTG
AGAAAAACCAGCTAAAAGAGGACCAGGATAAGGTTCATATGTGGGAGCAGACAGTAAAGAAGGATGAGAATGAAATTGAA
AAGCTCAAAAAGGAGGAGCAGAGACACATGAAAATAATCGATGAAACCATGGCCCAGCTACAGGACCTTAAGAACCAGCA
TCTGGCAAAGAAATCTGAAGTCAATGACAAAAACCATGAGATGGAGGAGATCCGAAAAAAGTTGGGTGGGGCCAACAAAG
AAATGACCCACTTACAAAAGGAGGTAACCGCTATTGAGACAAAGTTAGAGCAGAAGCGGAGTGACCGGCACAATCTGTTG
CAGGCCTGCAAGATGCAGGACATCAAGCTGCCCCTGGCCAAAGGCACCATGGATGACATTAGTCAAGAAGAGGGGAGCTC
CCAAGGGGAGGAGTCTGGGAGTGGCTCTCAACGAACCTCCAATATCTATGCCCGTGAGGCCTTGATTGAGATTGACTACA
GTGACCTCTGTGAGGACCTCAAAGATGCTCAGGCTGAAGAGGAGATTAAACAGGAGATGAACACATTGCAGCAAAAACTG
ACTGAACAGCAGAGTGTGCTGCAGCGCATTGCAGCACCTAACATGAAAGCCATGGAAAAACTGGAGAGTGTGCGGGACAA
GTTTCAGGAGACATCAGATGAGTTTGAGGCAGCTCGAAAGCGGGCCAAAAAAGCTAAGCATGCCTTTGAGCAGATTAAGA
AGGAACGCTTTGATCGCTTCAATGCCTGTTTTGAGTCTGTGGCTACCAACATTGATGAGATCTACAAAGCCCTGTCCCGA
AACAGCAGTGCTCAGGCCTTCTTGGGGCCTGAGAACCCAGAGGAACCCTACCTAGATGGGATCAATTACAACTGTGTAGC
CCCTGGCAAACGCTTCCGACCCATGGACAACCTGTCTGGTGGGGAAAAGACTGTAGCAGCTCTTGCTTTGCTTTTTGCCA
TCCATAGCTACAAACCAGCTCCTTTCTTTGTCCTAGACGAGATTGATGCTGCATTAGATAACACCAATATTGGCAAGGTT
GCCAACTATATAAAAGAACAGTCAACTTGCAACTTTCAAGCTATTGTCATTTCACTGAAGGAAGAATTTTATACGAAGGC
CGAGAGTCTGATTGGTGTCTATCCTGAGCAAGGGGACTGTGTTATCAGCAAGGTACTGACATTTGACCTTACCAAATACC
CAGATGCCAAC

ORF - retro_mdom_1861 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 53.2 %
Parental protein coverage: 72.88 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalLNQKRPQYIKAKENTSHHLKKLETAKKAIRVSEKQCTKQEDDIQALEKELWDLDRTWRNFEKQVEEERLR
LNQKRPQYIKAKENTSH..KKLE.AKK......KQ..K...D...LEKE..........FE...EEE...
RetrocopyLNQKRPQYIKAKENTSHKIKKLEAAKKSLQNAQKQYKKRKGDMDELEKEMVSVEKARQEFEDRMEEESQS
ParentalRGRDIELEASQLDQYKELKEQVIKKVATMTQQLEKLQWEQRADEERLAFGDRRRAEVQGNLKQVKEQVED
.GRD..LE..Q...Y..LKE...K..AT..Q.LEK....Q.AD..RL....R...E.....KQ.....E.
RetrocopyQGRDLTLEENQVKKYHRLKEEASKRAATLAQELEKFNRDQKADQDRLDLEERKKVETEAKIKQKLREIEE
ParentalHNKRIEKLEEYTSTCIDCLKEKTQQEEALSEELEQSRVRMAEVNSELSRIGGELQNAHIDHHEGKRQQKK
..KRIEKLEEY..T....L.E....E..L.EE......R..E.N.EL......L..A.ID..E..RQQ.K
RetrocopyNQKRIEKLEEYITTSKQSLEEQKKLEGELTEEVKLAKQRIDEINKELNQVMEQLGDARIDRQESSRQQRK
ParentalAEVLEFLKRLYPESVYGRLLDLCHPIHKKYQLAVTKLFGRYMVAIVVVSEKVARDCIRFLKEERAEPETF
AE..E..KRLYP.SVYGRL.DLC.P..KKYQ.AVTK..G..M.AI.V.SEK..RDCI...KE.R.EPETF
RetrocopyAEIMESIKRLYPGSVYGRLIDLCQPTQKKYQIAVTKVLGKNMDAIIVDSEKTGRDCIQYIKEQRGEPETF
ParentalLALDYLDIKPINERLREMKGSKMVIDVVQTQLPQLKKVIQFVCGNGLVCETVEEARHMAFDGPERLKTVA
L.LDYL..KP..E.LRE.KG.K.VIDV.....P..KK..Q..CGN.LVC..VE.AR..AF.G..R.KTVA
RetrocopyLPLDYLEVKPTDEKLRELKGAKLVIDVIRYEPPHIKKALQYACGNALVCDNVEDARRIAFGGHQRHKTVA
ParentalLDGTLFLKSGVISGGSSDLKLKARCWDEKEINKLKERRDQLIRELKDLMKIRRKETDLKQIQALVQGTHT
LDGTLF.KSGVISGG.SDLK.KAR.WDEK...KLKE....L..ELK..MK..RKE..L.Q.Q....G...
RetrocopyLDGTLFQKSGVISGGASDLKAKARRWDEKAVDKLKEKKERLTEELKEQMKAKRKEAELRQVQSQAHGLQM
ParentalRLKYSQNELETIKKKHLARFNKEQSQLQSELLNIESQYVMLSDGIEKRIRQITDFQEKIDKVEDEIFHDF
RLKYSQ..LE..K..HLA....E.S.L.SEL.N...........I..R.R...D..EK...VEDE.F..F
RetrocopyRLKYSQSDLEQTKTRHLALNLQEKSKLESELANFGPRINDIKRIIQGREREMKDLKEKMNQVEDEVFEEF
ParentalCEEIGVENIREYENQQVKQQQEIDKKRLEFEKLKTRLNIQLEYSHNQLKKKTNKVTTLKEAIVKDTEDLE
C.EIGV.NIRE.E...VK.Q.EI.KKRLEFE..KTRL.IQL....NQLK....KV........KD....E
RetrocopyCREIGVRNIREFEEEKVKRQNEIAKKRLEFENQKTRLGIQLDFEKNQLKEDQDKVHMWEQTVKKDENEIE
ParentalSLKKVEENCLQVVDDLMTKRQQLKDVCVAQNVSIEKAQGQVEEARKKFLISNREVGKMQKEMAAVQTALE
.LKK.E.......D..M...Q.LK....A............EE.RKK....N.E....QKE..A..T.LE
RetrocopyKLKKEEQRHMKIIDETMAQLQDLKNQHLAKKSEVNDKNHEMEEIRKKLGGANKEMTHLQKEVTAIETKLE
ParentalQQRLEKHNILLSCKVQDIEVALVAGSLDETIQQSEGRGLGEQAESTQSTVAAMYEREGALQIDYSSLAED
Q.R...HN.L..CK.QDI...L..G..D..I.Q.EG...GE...S........Y.RE....IDYS.L.ED
RetrocopyQKRSDRHNLLQACKMQDIKLPLAKGTMDD-ISQEEGSSQGEESGSGSQRTSNIYAREALIEIDYSDLCED
ParentalLKDLQSDKEIKAQLGLLEQQLATHEDILLKTTAPNLRALQNLQNVRDKFQESIDAFEASRKEARVCRQEF
LKD.Q...EIK.....L.Q.L......L....APN..A...L..VRDKFQE..D.FEA.RK.A......F
RetrocopyLKDAQAEEEIKQEMNTLQQKLTEQQSVLQRIAAPNMKAMEKLESVRDKFQETSDEFEAARKRAKKAKHAF
ParentalEQVKKKRYDLFSQCFEHVSVSIDQIYKKLCRNNSAQAFLSPENPEEPYLEGISYNCVAPGKRFMPMDNLS
EQ.KK.R.D.F..CFE.V...ID.IYK.L.RN.SAQAFL.PENPEEPYL.GI.YNCVAPGKRF.PMDNLS
RetrocopyEQIKKERFDRFNACFESVATNIDEIYKALSRNSSAQAFLGPENPEEPYLDGINYNCVAPGKRFRPMDNLS
ParentalGGEKCVAALALLFAVHSFRPAPFFVLDEVDAALDNTNIGKVSSYIREQTREQFQMIIISLKEEFYSKADA
GGEK.VAALALLFA.HS..PAPFFVLDE.DAALDNTNIGKV..YI.EQ....FQ.I.ISLKEEFY.KA..
RetrocopyGGEKTVAALALLFAIHSYKPAPFFVLDEIDAALDNTNIGKVANYIKEQSTCNFQAIVISLKEEFYTKAES
ParentalLVGIYPEQGDCMFSRVLTLDLSLYPDSD
L.G.YPEQGDC..S.VLT.DL..YPD..
RetrocopyLIGVYPEQGDCVISKVLTFDLTKYPDAN

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 0 .00 RPM
SRP007412_cerebellum 0 .00 RPM 0 .00 RPM
SRP007412_heart 0 .00 RPM 0 .00 RPM
SRP007412_kidney 0 .00 RPM 0 .00 RPM
SRP007412_liver 0 .00 RPM 0 .00 RPM
SRP007412_testis 0 .00 RPM 0 .00 RPM

ChIP-Seq - click to see more details

Monodelphis domestica was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_mdom_1861 retrocopy.

TSS - click to see more details

Monodelphis domestica was not studied using FANTOM5 data.

Lab - click to see more details

retro_mdom_1861 was not experimentally validated.

Retrocopy orthology:
Monodelphis domestica 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 1 parental gene, and 1 retrocopy.

Species Parental gene accession Retrocopies number
Monodelphis domestica ENSMODG00000007253 1 retrocopy
retro_mdom_1861 ,


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