RetrogeneDB ID:

retro_mdom_46

Retrocopy
location
Organism:Opossum (Monodelphis domestica)
Coordinates:Un:27787083..27788499(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMODG00000019213
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSMODG00000006919
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_mdom_46
CGTGGAGCCAATATGAATTGGAGTCTGGCACTTCCCAGTTCTCCAGGGTCTTCTTCTAACAAGCATGGAGACAGGTTCAT
TCCCTCCAGAGCTGGAGCCAACTGGGGCCTGTACTTCCATAAACCGACTCAACCTGAGAAATCACCCAAGCAGAAACGCA
AAGCAAAGCAAGCCACCTTAGACAGTTGTCCAGTTAACCCTTTCTATACTGCCTTGTTGAAGAACGAGCTACTAGGAGCT
GGGATCGAGAATGTCCCACATCCCAAAGGAGAGAGCCAAGGGCTGCAGTCTCCTATACCACATACAAAGAATCTCTTCTC
ATATGCTCACAACACGAAGCGCTGGAGACCTGATTCTGGTAGTGAAGTCTGTCCTTATATCTTATCTCCCATCAGCAACA
AAAGTCAGACATTACTAAAGTCCCAGCAGAAACCAATCCGAAAAATTTCTGAAAGCCCTTTCAAAATCCTCGAGGCCCCA
GAACTCCAAAATGACTTCTACTTGAACCTGGTAGACTGGTCTTGCCTAAACATCATCACTGTGGGCCTGGGCAGCCGTGC
TTACCTGTGGAATGCTGCTACATGCCAGGTGACTAAGCTGTGTGACTTGTCTAGTGATGAAGATTATGTGACTTCTGTGA
ACTGGTCTGAACAGGGGAACTTGGTAGCAGTTGGAACAGACAAAGGCCTGGTACAGGTCTGGGATGTAACTGCAGGGAAG
ATGCTGTGCAAGTTGGAGGGTCACGCAGCTCGAGTTGGCGTGCTTGCCTGGAATGCTGATCAGATTTCCTCTGGAGGCCG
GGACACGATGATCCTCCAGAGAGACATCCGGGCACCCCGCCCTCAGTCTGAGCGCTGGCTGATAGGGCACAGGCAAGAGG
TATGTGGGCTAAAGTGGTCCGTAGATCACCAGCTTCTGGCTTCAGGTGGAAATGATAATACAGTTCTGGTCTGGAGCCTC
TACAATGTTAAGCCTGTCCATAAGTACACCAAACATGTGGCTGCCGTAAAAGCGATTGCCTGGTCTCCCCATCAACACGG
CCTGTTGGCATCAGGTGGTGGAACAGCAGACCGCAACATTCGCTTCTGGAACACATTGACGGGACAGCCCGTTCAGCATA
TTGATACTGGTTCCCAAGTGTGCAATCTGGCCTGGTCCAGACATGACAACGAGCTGGTGAGCACCCATGGATATGCCGAA
AACCAGATTGCCGTCTGGAGATATCCTTCCTTGACAAAAGTAGCCAAACTCATAGGGCACTCCTACCGAGTTTTGTATCT
GGCAGTGTCTCCCGATGGACAGTCCATAGTTACAGGAGCTGGGGATGAGACACTGAGATTCTGGACTGTTTTTTATAAAA
CTCATTCTGCAAAGGAAGCTGCTTCTGCCCTCAGTCTCTTCACTAAAATTCGGTAA

ORF - retro_mdom_46 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 70.58 %
Parental protein coverage: 95.13 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalAEMRRTLTPSNSPMSSPSKHGDRFIPSRAGANWSINFHRINENEKSPSQNRKAKDATSDNGKDGLAYSAL
A.M...L....SP.SS..KHGDRFIPSRAGANW...FH.....EKSP.Q.RKAK.AT.D.......Y.AL
RetrocopyANMNWSLALPSSPGSSSNKHGDRFIPSRAGANWGLYFHKPTQPEKSPKQKRKAKQATLDSCPVNPFYTAL
ParentalLKNELLGAGIEKVQDPQTEDRRLQPSTPEKKSLFTYSLSTKRSSPDDGNEVSPYSLSPVSNKSQKLLRSP
LKNELLGAGIE.V..P..E...LQ...P..K.LF.Y...TKR..PD.G.EV.PY.LSP.SNKSQ.LL.S.
RetrocopyLKNELLGAGIENVPHPKGESQGLQSPIPHTKNLFSYAHNTKRWRPDSGSEVCPYILSPISNKSQTLLKSQ
ParentalRKPTRKISKIPFKVLDAPELQDDFYLNLVDWSSLNVLSVGLGTCVYLWSACTSQVTRLCDLSVEGDSVTS
.KP.RKIS..PFK.L.APELQ.DFYLNLVDWS.LN...VGLG...YLW.A.T.QVT.LCDLS...D.VTS
RetrocopyQKPIRKISESPFKILEAPELQNDFYLNLVDWSCLNIITVGLGSRAYLWNAATCQVTKLCDLSSDEDYVTS
ParentalVGWSERGNLVAVGTHKGFVQIWDAAAGKKLSMLEGHTARVGALAWNADQLSSGSRDRMILQRDIRTPPVQ
V.WSE.GNLVAVGT.KG.VQ.WD..AGK.L..LEGH.ARVG.LAWNADQ.SSG.RD.MILQRDIR.P..Q
RetrocopyVNWSEQGNLVAVGTDKGLVQVWDVTAGKMLCKLEGHAARVGVLAWNADQISSGGRDTMILQRDIRAPRPQ
ParentalTERRLQGHRQEVCGLKWSTDHQLLASGGNDNKLLVWNHSSLSPVQQYTEHLAAVKAIAWSPHQHGLLASG
.ER.L.GHRQEVCGLKWS.DHQLLASGGNDN..LVW......PV..YT.H.AAVKAIAWSPHQHGLLASG
RetrocopySERWLIGHRQEVCGLKWSVDHQLLASGGNDNTVLVWSLYNVKPVHKYTKHVAAVKAIAWSPHQHGLLASG
ParentalGGTADRCIRFWNTLTGQPLQCIDTGSQVCNLAWSKHANELVSTHGYSQNQILVWKYPSLTQVAKLTGHSY
GGTADR.IRFWNTLTGQP.Q.IDTGSQVCNLAWS.H.NELVSTHGY..NQI.VW.YPSLT.VAKL.GHSY
RetrocopyGGTADRNIRFWNTLTGQPVQHIDTGSQVCNLAWSRHDNELVSTHGYAENQIAVWRYPSLTKVAKLIGHSY
ParentalRVLYLAMSPDGEAIVTGAGDETLRFWNVFSKTRSTKESVSVLNLFTRIR
RVLYLA.SPDG..IVTGAGDETLRFW.VF.KT.S.KE..S.L.LFT.IR
RetrocopyRVLYLAVSPDGQSIVTGAGDETLRFWTVFYKTHSAKEAASALSLFTKIR

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_46 retrocopy.

TSS - click to see more details

Monodelphis domestica was not studied using FANTOM5 data.

Lab - click to see more details

retro_mdom_46 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 4 retrocopies.

Species Parental gene accession Retrocopies number
Monodelphis domestica ENSMODG00000006919 4 retrocopies
retro_mdom_235, retro_mdom_270, retro_mdom_296, retro_mdom_46 ,


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