RetrogeneDB ID:

retro_mdom_1892

Retrocopy
location
Organism:Opossum (Monodelphis domestica)
Coordinates:8:266278290..266280831(+)
Located in intron of:ENSMODG00000010865
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:DHX16
Ensembl ID:ENSMODG00000015890
Aliases:None
Description:DEAH (Asp-Glu-Ala-His) box polypeptide 16 [Source:HGNC Symbol;Acc:2739]


Retrocopy-Parental alignment summary:






>retro_mdom_1892
TCAGAGAACACTTTGGAGCAGCCACACAAGAAGGCCTATCAGGAGGCCCAGAAGTGCCAGAAAATGGCTGAAGACCAGAA
AGCAATGGTACCTGAGCTCAGAAAGAAATCAAGGAGGGAGTACCTTGCCAAGAGGGGGAAGGAGAAGCTGGAGGATCTAG
AAGCAGAATTGGCAGATGAGGAATTTCTTTTTGGAGATGTAGAGCTGAGCCACACTGAGCAGCAGAAACTTAAGTATAAG
AAGAGGGTACGAGATCTGGCCTGGCAGTACCAGGCAGCCAGGGAGAAAGAGAAGCTGGAGGCCACAACTCGATACCACAT
GCCAGAAGAGACTGGTGGACAGCCAACTGGTGGGGTGGAGCTGGTGGAAGAGTCGGGAGCGCCAAGAGAGGAGCAGAGGT
GCTGGGAGGAGGCCCTTTTAGGGGCAGCTGCTCTCCGGTTTGGAGCCAAGGATGCTGCTGCCTCTGAGCCTAAGTATGAA
CTGGTGTTGGAAGAGGAGGAGACCATTGAATTTATCAGAGCCACAAGGCTCCAGGGTGAGGAGGAAGCATCAGCTCCACC
CCCTTCATCCGGGGAGCAACAGAAGGAGTCCATTAGGGCTGAGAGAAGGAGCCTCCCTGTATTTCCATTCCGAAATGACC
TCCTTAATGCCATTGCTAAGCACCAGGTCCTCATCATTGAGGGTGAAACGGGGTCAGGGAAGACCACACAGATCCCCCAG
TACCTCTTGGAGGACGGTTACACACGGAAGGGAATGAAGCTTGTCTGTACCCAGCCTCGGAGAGTGGCAGCCATGAGTGT
GGCAGCCAGAGTGGCCCTCGAGATGGGGGTGAAGCTGGGGAAGGAGGTTGGCTACAGGATCCGTTTTGAGGACTGTACTT
CGGACCGGACTGTTCTCAGATACATGACGGATGGGATGCTTCTTCGAGAGTTCCTTTCCCAGCCTGACCTTGCAAGTTAC
AGTGTGGTGATGGTGGATGAAGCTCATGAACGGACTCTACACACAGACATACTGTTTGGGTTGATCAAGGACGTTGCTCG
ATTCCGCCCAGAGCTCAAGGTGCTGGTGGCTTCGGCTACCCTAGACGCTGCCCGCTTCTCAGCCTTCTTTGACGATGCCC
CTATTTTCCGGATCCCTGGCCGCAGGTTTCCCGTGGACATCTTCTATACCAAGGCTCCAGAGGCAGATTACTTGGAAGCC
TGTGTGGTGTCTGTGCTACAGATCCACATCACTCAGCCCCCTGGGGACATCCTGGTATTTCTGACGGGACAGGAAGAGAT
CGAAGCAGCTTGTGAGATGCTCCGGGATCGCTGCCGTCGCTTGGGCTCCAAGATCCGGGAGCTCCTGGTGCTGCCCATTT
ATGCCAACCTGCCTTCCCACATGCAAGCACAGATCTTCCAGCCAACACCCCCTGGGGCACGCAAGGTGGTGCTGGCGACC
AACATCGCAGAGACGTCACTGACCATTGAGGGCATCATTTATGTCCTGGACCCAGGTTTCTGCAAACAAAAGAGCTACAA
CCCCAGAACTGGCATGGAATCCCTTACTGTCACACCCTGTAGCAAGGCTTCAGCCAATCAGAGAGCTGGCAGGGCAGGTC
GGGTAGCTGCAGGGAAGTGCTTCCGCCTCTATACAGCCTGGGCTTATCAGCACGAGCTAGAGGAGACCACAGTGCCAGAG
ATCCAGAGGACCTGCCTGGGCAATGTCGTCCTGTTACTAAAGAGTCTGGGAATCCATGACTTAGTGCATTTTGACTTTCT
GGATCCTCCACCCTACGAGACCCTGATGCTGGCTCTAGAACAGTTATATGCTCTGGGAGCACTAAACCACCTGGGGGAGC
TCACCACCCTGGGCAGGAAAATGGCAGAATTGCCTGTGGACCCTATGTTATCCAAGATGATTCTGGCCTCCCAGAAGTAT
GGCTGCTCAGAGGAGATCCTCACGGTGGCAGCCATGCTCTCAGTCAACAACTCCATCTTTTACCGTCCCAAGGACAAAGC
TGTCCATGCTGATAATGCCCGTGCCAACTTCTTCTTGCCTGGTGGGGACCACCTAGTGCTACTAAATGTTTATACACAGT
GGGTTGAGAGTGGTTATTCTTCCCAGTGGTGTCATGAGAACTTTGTGCAGCTGCGCTCCTTGCGCCAAGCTCGAGATGTT
CGAGAACAGCTGGAGGGGCTCCTGGAACAGGTAGAAGTTGGGCTCAGCTCCTGCCAGGGGGACTATACTCAAGTTCGAAA
GGCCATCACTGCTGGCTACTTCTATCACACAGCACGGCTGACCCAAAGTGGGTACCGCACAGTGAAACAACAACAGACCG
TCTTCATTCACCCTGACTCCTCTCTTTTTGAGGAACAGCCACGTTGGATTCTCTACCATGAACTTGTCTGGACAACCAAG
GAGTTCATGAGACAGGTACTAGAAATTCAGAGTGGTTGGCTCCTTGAAGTAGCTCCCCACTACTACAAGGCCAGAGAGCT
AGAAGATCCTAATGCAAAGAAAATGCCCAAGAAAGTTGGCAAGACTCGGGAGGAACTGGGT

ORF - retro_mdom_1892 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 90.46 %
Parental protein coverage: 95.07 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalTRNILERSDKKAYEEAQKRLKMAEEDQKAMVPELRKKSRREYLAKREREKLEDLEAELADEEFLFGDVEL
..N.LE...KKAY.EAQK..KMAE.DQKAMVPELRKKSRREYLAKR..EKLEDLEAELADEEFLFGDVEL
RetrocopySENTLEQPHKKAYQEAQKCQKMAE-DQKAMVPELRKKSRREYLAKRGKEKLEDLEAELADEEFLFGDVEL
ParentalSHTERQELKYKKRVRDLAREYRAAGEQEKLEATTRYHMPEETRGQPARGVELVEEESGAPGEEQRRWEEA
SHTE.Q.LKYKKRVRDLA..Y.AA.E.EKLEATTRYHMPEET.GQP..GVELVEE.SGAP.EEQR.WEEA
RetrocopySHTEQQKLKYKKRVRDLAWQYQAAREKEKLEATTRYHMPEETGGQPTGGVELVEE-SGAPREEQRCWEEA
ParentalRLGAAALRFGAKDAAPSEPKYQLVLEEEETIEFVRATRLQGDEEPSAPPPSSGDQQKESIRAVRRSLPVF
.LGAAALRFGAKDAA.SEPKY.LVLEEEETIEF.RATRLQG.EE.SAPPPSSG.QQKESIRA.RRSLPVF
RetrocopyLLGAAALRFGAKDAAASEPKYELVLEEEETIEFIRATRLQGEEEASAPPPSSGEQQKESIRAERRSLPVF
ParentalPFRNDLLDAIANHQVLIIEGETGSGKTTQIPQYLFEEGYTQKGMKIACTQPRRVAAMSVAARVAREMGVK
PFRNDLL.AIA.HQVLIIEGETGSGKTTQIPQYL.E.GYT.KGMK..CTQP............A.EMGVK
RetrocopyPFRNDLLNAIAKHQVLIIEGETGSGKTTQIPQYLLEDGYTRKGMKLVCTQPXXXXXXXXXXXXALEMGVK
ParentalLGNEVGYSIRFEDCTSERTVLRYMTDGMLLREFLSEPDLGSYSVVMVDEAHERTLHTDILFGLIKDVARF
LG.EVGY.IRFEDCTS.RTVLRYMTDGMLLREFLS.PDL.SYSVVMVDEAHERTLHTDILFGLIKDVARF
RetrocopyLGKEVGYRIRFEDCTSDRTVLRYMTDGMLLREFLSQPDLASYSVVMVDEAHERTLHTDILFGLIKDVARF
ParentalRPELKVLVASATLDTARFSAFFDDAPVFRIPGRRFPVDIFYTKAPEADYLEACVVSVLQIHVTQPPGDIL
RPELKVLVASATLD.ARFSAFFDDAP.FRIPGRRFPVDIFYTKAPEADYLEACVVSVLQIH.TQPPGDIL
RetrocopyRPELKVLVASATLDAARFSAFFDDAPIFRIPGRRFPVDIFYTKAPEADYLEACVVSVLQIHITQPPGDIL
ParentalVFLTGQEEIEAACEMLQDRCRRLGSKIRELLVLPIYANLPSDMQARIFQPTPPGARKVVVATNIAETSLT
VFLTGQEEIEAACEML.DRCRRLGSKIRELLVLPIYANLPS.MQA.IFQPTPPGARKVV.ATNIAETSLT
RetrocopyVFLTGQEEIEAACEMLRDRCRRLGSKIRELLVLPIYANLPSHMQAQIFQPTPPGARKVVLATNIAETSLT
ParentalIEGIIYVLDPGFCKQKSYNPRTGMESLTVTPCSKASANQRAGRAGRVAAGKCFRLYTAWAYQHELEETTV
IEGIIYVLDPGFCKQKSYNPRTGMESLTVTPCSKASANQRAGRAGRVAAGKCFRLYTAWAYQHELEETTV
RetrocopyIEGIIYVLDPGFCKQKSYNPRTGMESLTVTPCSKASANQRAGRAGRVAAGKCFRLYTAWAYQHELEETTV
ParentalPEIQRTSLGNVVLLLKSLGIHDLMHFDFLDPPPYETLLLALEQLYALGALNHLGELTTPGRKMAELPVDP
PEIQRT.LGNVVLLLKSLGIHDL.HFDFLDPPPYETL.LALEQLYALGALNHLGELTT.GRKMAELPVDP
RetrocopyPEIQRTCLGNVVLLLKSLGIHDLVHFDFLDPPPYETLMLALEQLYALGALNHLGELTTLGRKMAELPVDP
ParentalMLSKMILASEKYGCSEEILTVAAMLSVNNSIFYRPKDKVVHADNARVNFFLPGGDHLVLLNVYTQWVESG
MLSKMILAS.KYGCSEEILTVAAMLSVNNSIFYRPKDK.VHADNAR.NFFLPGGDHLVLLNVYTQWVESG
RetrocopyMLSKMILASQKYGCSEEILTVAAMLSVNNSIFYRPKDKAVHADNARANFFLPGGDHLVLLNVYTQWVESG
ParentalYSSQWCYENFVQLRSLRRARDVREQLEGLLERVEVGLSSCQGDYTRVRKAITAGYFYHTARLTRSGYRTV
YSSQWC.ENFVQLRSLR.ARDVREQLEGLLE.VEVGLSSCQGDYT.VRKAITAGYFYHTARLT.SGYRTV
RetrocopyYSSQWCHENFVQLRSLRQARDVREQLEGLLEQVEVGLSSCQGDYTQVRKAITAGYFYHTARLTQSGYRTV
ParentalKQQQTVFIHPNSSLFEEQPRWLLYHELVLTTKEFMRQVLEIESGWLLEVAPHYYKARELEDPNAKKMPKK
KQQQTVFIHP.SSLFEEQPRW.LYHELV.TTKEFMRQVLEI.SGWLLEVAPHYYKARELEDPNAKKMPKK
RetrocopyKQQQTVFIHPDSSLFEEQPRWILYHELVWTTKEFMRQVLEIQSGWLLEVAPHYYKARELEDPNAKKMPKK
ParentalVGKTREELG
VGKTREELG
RetrocopyVGKTREELG

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_1892 retrocopy.

TSS - click to see more details

Monodelphis domestica was not studied using FANTOM5 data.

Lab - click to see more details

retro_mdom_1892 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 2 parental genes, and 3 retrocopies.

Species Parental gene accession Retrocopies number
Myotis lucifugus ENSMLUG000000089322 retrocopies
retro_mluc_434, retro_mluc_651,
Monodelphis domestica ENSMODG00000015890 1 retrocopy
retro_mdom_1892 ,




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