RetrogeneDB ID:

retro_mdom_849

Retrocopy
location
Organism:Opossum (Monodelphis domestica)
Coordinates:2:190805987..190807710(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:LRP10
Ensembl ID:ENSMODG00000005233
Aliases:None
Description:low density lipoprotein receptor-related protein 10 [Source:HGNC Symbol;Acc:14553]


Retrocopy-Parental alignment summary:






>retro_mdom_849
TTTCTGCTTTCCTATATGCTAGTCGATTCATATGCCTCCTAGAAGAGTTCTGATGCCTGAACCGCAGATGTGTGCCAAAG
ATCCAGTGCTGTGATGGGATGGATAACTGTGGTGACCAATCTGATGAGACTGACTGTAGCCCAAGCCTTTTCCATAGCTT
GACTGCTGTCCCTGCCCCTGCCTGCAACCGTACCTTGGAAGACTTCTACCGGGTCTTTTCTTCCCGGAGCTATTCCCTCT
CTGCCCTATACCCAACCCCTCACTCCTGCCTCTGGCTGCTGGATCCCCATGATGGGCGAAGGCTCATCGTGCATTTTACC
ACCCTAGAGCTAAGCAAATGGGATTCAGAGCATGTGTATGACGGTCCTGGACCTCCAGATCCTTCTCACCTGCTCCGAAG
CCTTAACTATTTCAGCAATGGCAAAGCAATCATGGTGGAGACGCTCTCAGGCAAGGCTACTGTGACCTACCACATGGGGC
CGTGGAGCAAGGGTGGGTTCAATACCACCTACCATGTGAAAGGATACTGTCTGCCCTGGGACCGACCCTGTGGTGCTGGC
TCTGGAGAGGGTCCTGGGGAGGGTCCAGGAGAGGGCTGCTATAGTGAAGCCCAGCGGTGTGATGCGATCTGGGACTGTGC
CGATGGCACAGATGAAAAAGACTGCCCGGGATGCCTGTCTGGGCGCTATTCCTGTGGGGCTCCGGGAACCCCTGGTGCCA
CAGCCTGCTACCCCTCTGCCGATCGCTGCGACTACCAGACCTTTTGCGTGAACCGGGCAGATGAACAGCAGTGCCATCAC
TGCCAGCCAGGCAACTTCCGGTGCAGGGATGCTCGGTGTGTGTATGCAACTTGGGTATGTGATGGGCAGCCCGACTGCTC
TGATGGCAGCGACGAATGGGACTGTGCCTGTGCCCTGCCCCGAAAAGTCATCATGGCTGCCGCCATCGGCAGCTTGATCT
GCGGCCTGCTGCTTGTCATCGCCCTGGGATGTACCTGCAAACTCTATGCCCTCCACACGCAAGAATACAGCATCTTTGCC
CCCCTTTCAAGAGTGGAGGCCGAGATTGTACAGCAGCAAGCACCTCCATCCTATGGCCAGCTTATTGCTCACGGTGCCAT
CCCGCCTGTAGATGACTTTCCAACTGAGAACCCCAACGATAATTCAGGCCTGGGGAACCTTTGATCTCTGCTACAAATCC
TGCGCCAGGATGTGTCTTCAGGGAGTTCATCGAGTGCCTGCCGTTGCCAAGGCAGGTCTGCACAACGACTGGTCTGCCGC
CTCCGTCAGTGGGGCTTGCTTCCTGTGCATTCCCCCTGCAGGTCCCCTGACTCAGCTCAGACTGCATCTGCCCCATCTAC
TGTTGACGCCCCAGAGGGCAGTCAGGATACTCCTTTAGAAGGAGCAATGGGTGGATGAGATCCAGAGGAGGCCCCTCCAC
TGCCCATGAAGGTGCCCCTTTCTTCTACCAACTCCCCCTGCATACCCCCTGAGGACCCACCCCTCCAATCACTCCCCCTC
CACTCCCATCATCCCTGTTGTCTGGGATGGTACAGGCCCTTTGTGGCCGCCTCATGCCCAGTCTTCGGTCCCCTACTCCC
CCCCAAGCTATGCCAGACCCTCGAACAGTGCCCCCATCCCAAGAAGATGAGGATGATGTGCTGCTACTCCCTCTGGCAGA
ACCCAGGCCCTGGGTAGGGGAGGAGGATGAGCCACTGCTGACC

ORF - retro_mdom_849 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 87.59 %
Parental protein coverage: 81.41 %
Number of stop codons detected: 3
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalFLLSYML-DRFICLREEFRCLNRRCVPRIQRCDGIDNCGDQSDETDCSPSLFHSLTAVPTPACNRTLEDF
FLLSYML..RFICL.EEF.CLNRRCVP.IQ.CDG.DNCGDQSDETDCSPSLFHSLTAVP.PACNRTLEDF
RetrocopyFLLSYML<SRFICLLEEF*CLNRRCVPKIQCCDGMDNCGDQSDETDCSPSLFHSLTAVPAPACNRTLEDF
ParentalYGVFSSPSYSLSALYPSPHSCLWLLDPHDGRRLIVRFTTLELGKWDSVHVYDGPGPPDPSRLLRSLNYFS
Y.VFSS.SYSLSALYP.PHSCLWLLDPHDGRRLIV.FTTLEL.KWDS.HVYDGPGPPDPS.LLRSLNYFS
RetrocopyYRVFSSRSYSLSALYPTPHSCLWLLDPHDGRRLIVHFTTLELSKWDSEHVYDGPGPPDPSHLLRSLNYFS
ParentalNGKAIMVETLSGKATVTYHMGPWSKGGFNATYHVKGYCLPWDRPCGAGSGEGPGEGPGEGCYSEAQRCDG
NGKAIMVETLSGKATVTYHMGPWSKGGFN.TYHVKGYCLPWDRPCGAG............CYSEAQRCD.
RetrocopyNGKAIMVETLSGKATVTYHMGPWSKGGFNTTYHVKGYCLPWDRPCGAGXXXXXXXXXXXXCYSEAQRCDA
ParentalIWDCADGTDEKDCPGCLPGRYPCGAPGTPGATACYPSADRCNYQTFCVNGADEQQCRHCQPGNFRCRDDR
IWDCADGTDEKDCPGCL.GRY.CGAPGTPGATACYPSADRC.YQTFCVN.ADEQQC.HCQPGNFRCRD.R
RetrocopyIWDCADGTDEKDCPGCLSGRYSCGAPGTPGATACYPSADRCDYQTFCVNRADEQQCHHCQPGNFRCRDAR
ParentalCVYETWVCDGQPDCSDGSDEWDCAYALPRKVITAAVIGSLICGLLLVIALGCTCKLYAIRTQEYSIFAPL
CVY.TWVCDGQPDCSDGSDEWDCA.ALPRKVI.AA.IGSLICGLLLVIALGCTCKLYA..TQEYSIFAPL
RetrocopyCVYATWVCDGQPDCSDGSDEWDCACALPRKVIMAAAIGSLICGLLLVIALGCTCKLYALHTQEYSIFAPL
ParentalSRVEAEIVQQQAPPSYGQLIAQGAIPPVDDFPTENPNDNSVLGNLRSLLQILRQDVSSGGSSSARRRQRG
SRVEAEIVQQQAPPSYGQLIA.GAIPPVDDFPTENPNDNS.LGNL.SLLQILRQDVSSG.SSSA.R.Q.G
RetrocopySRVEAEIVQQQAPPSYGQLIAHGAIPPVDDFPTENPNDNSGLGNL*SLLQILRQDVSSGSSSSACRCQ-G
ParentalRSARRLVRRLRRWGLLPRANPPSRAPDSSLQTASTPSTTDTPEGSQGTPLEGAMGGRDPEEAPPLPVKVP
RSA.RLV.RLR.WGLLP....P.R.PDS..QTAS.PST.D.PEGSQ.TPLEGAMGG.DPEEAPPLP.KVP
RetrocopyRSAQRLVCRLRQWGLLP-VHSPCRSPDSA-QTASAPSTVDAPEGSQDTPLEGAMGG*DPEEAPPLPMKVP
ParentalLSSTNSPCIPPEDPP-PPITPPPPPSSLLSGVVQALRGRLMPSLRSPTPPQAIPDPRTVPPSQEEEDDVL
LSSTNSPCIPPEDPP.PPITPPP.PSSLLSG.VQAL.GRLMPSLRSPTPPQA.PDPRTVPPSQE.EDDVL
RetrocopyLSSTNSPCIPPEDPP<PPITPPPLPSSLLSGMVQALCGRLMPSLRSPTPPQAMPDPRTVPPSQEDEDDVL
ParentalLLPLAEPGPWVGEEDEPLLT
LLPLAEP.PWVGEEDEPLLT
RetrocopyLLPLAEPRPWVGEEDEPLLT

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 161 .15 RPM
SRP007412_cerebellum 0 .00 RPM 183 .79 RPM
SRP007412_heart 0 .00 RPM 444 .75 RPM
SRP007412_kidney 0 .00 RPM 1062 .68 RPM
SRP007412_liver 0 .00 RPM 509 .03 RPM
SRP007412_testis 0 .00 RPM 165 .20 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_849 retrocopy.

TSS - click to see more details

Monodelphis domestica was not studied using FANTOM5 data.

Lab - click to see more details

retro_mdom_849 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 ENSMODG00000005233 1 retrocopy
retro_mdom_849 ,


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