RetrogeneDB ID:

retro_mdom_1916

Retrocopy
location
Organism:Opossum (Monodelphis domestica)
Coordinates:8:113931388..113933245(-)
Located in intron of:ENSMODG00000018283
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSMODG00000012887
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_mdom_1916
AATAACCTGGTAAAAGAATGGATACGGGAAATCAGTGAAAGCAAGAATCTTCCATAGTCTGTAATTGAAAATGTTGGAGG
AAAAATTTTTACATTTGGATCCTACAGATTAGGAGTTCATACAAAAAGGTGCTGATATTGATGCATTGTGTTTTGCACCA
AGACATGTTGACCGCAGTGACTTTTTCACCTCATTCTATGAAAAATTGAAGTTACAGGAAGAAGGAAAAGATTTGAGAGC
TATTGAAGAGGCATTTGTACCAGTTATCAAGCTATGTTTTGATGGTATTGAGATTGATATTTTGTTTGCAAGATTAGCAC
TGCAGACTATTCCTGAAAATTTGGACCTTCGTGATGACAGTCTACTAAAAAATTTAGATATTAGATGCATAAGAAATCTT
TATGGTTGCAGGGTAACCGATGAAATTTTACATCTAGTATCAAACATTGACAACTTCAGGTTAACTCTGAGAGCTTTCAA
ACTTTGGGCCAAACGCCACAACATCTATTCCAATATATTAGGTTTCCTCAGTGGTGTTCCCTAGTAGCAAGAACTTGCCA
GCTTTATCCAAATGCAATAGCATCAACTCTTGAACATAAATTTTTCTTGGTATTTTCTAAATGGGAATGGCCAAATCCAG
TGCTATTGAAACAACCTGAAGAATGCAATTTTAATTTGCCTGTGTGGGACCCAAGGGTAAACCCCAGTGATAGGTACCAT
CTTATTCCTATAATTACACCAGCATACCCATAACAGAATTCTACATACAATGTGTTCATTTCTACATGGAATGTCATGGT
TGAGGAGTATAATAAACAAGGTCTTGCTATCACAGATGAAATTTTGCTGAGTAAGGCAGAGTGGTCCAAACTTTTTGAAG
CTCCCAACTACTTTCAAAAGTACAAGCATTATATTGTACTTTTAGCAAGTGCACCAACAGAAAAGCAGTGACTAGAATGG
GTGGGCTTGATGGAATCAAAAATCCGAATCCTGGTTGGAAATTTGGAGAAGAATGAATTTATTACACTGGCTCATGTGAA
TCCTCAGTCATTTCCAGCACCGAAAGAAAATCCTGACAAGGAAGAATTTCCTACAATGTGGGTGATTGGATTAGTGTTTG
AAAAAACAGAAAACTCTGAAAACCTCAGTGTTGACCTTACATATGACATTCAGTCTTTTACAGATACAGTTTATAGGCAA
GCAATAAACAGCAAGATGTTTGAGATGGATATGAAAATTGCTGCAATGCATGTAAAAAGAAGACAACTTCATCAACTCCT
ACCTAATCACGTGCTTCAGAAAAAGAAAAAGCATTCATCAGAAGTTCAATTGACAGCTCTAAATGTCAGCAGTCTAGATT
TGTCTATGGATAGTGACAACAGCATGTCTGTGCCTTCTCCTACCAGTGCTATGAAGACCAGTCCATTGAATAGTTCTGGC
AGCTCGCAGGGCAGAAACAATCCTGCTCCAGCTGTAACAGCAGCATCTTTGACCAACATCCAGGCAACTGAGGTTTCTGT
GCCACAAGTAAATTCCAGTGAAAGCTCAAGGGGTACTTCAAGTGAAAGCATTCCTCAAACTGCCACTCAGCCAGCCATTT
CTCCACCACCAAAGCCTACAGTCTCCAGAGTTGTTTCCTCAACATGTCTGGTAAACCAACCACCAAGACCTTCAGGAAAC
ACAGCAACAAAAGTTCCTAATCCTATAGTAGGAGTCAAAAGGACGTCTTCACCTCATAAAGAAGAGAGTCCCAAGAAAAC
CAAAACAGAGGAGGATGAGACAAGTGAAGATGTCAACTGTCTTGATTTGATTGAACATGATAAACGGGAAACTAAGAAAA
AACATCCAGTACAGACC

ORF - retro_mdom_1916 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 92.31 %
Parental protein coverage: 84.15 %
Number of stop codons detected: 3
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalNNLVKEWIREISESKNLPQSVIENVGGKIFTFGSYRLGVHTK-GADIDALCVAPRHVDRSDFFTSFYEKL
NNLVKEWIREISESKNLP.SVIENVGGKIFTFGSYRLGVHTK.GADIDALC.APRHVDRSDFFTSFYEKL
RetrocopyNNLVKEWIREISESKNLP*SVIENVGGKIFTFGSYRLGVHTK>GADIDALCFAPRHVDRSDFFTSFYEKL
ParentalKLQEEVKDLRAVEEAFVPVIKLCFDGIEIDILFARLALQTIPEDLDLRDDSLLKNLDIRCIRSLNGCRVT
KLQEE.KDLRA.EEAFVPVIKLCFDGIEIDILFARLALQTIPE.LDLRDDSLLKNLDIRCIR.L.GCRVT
RetrocopyKLQEEGKDLRAIEEAFVPVIKLCFDGIEIDILFARLALQTIPENLDLRDDSLLKNLDIRCIRNLYGCRVT
ParentalDEILHLVPNIDNFRLTLRAIKLWAKRHNIYSNILGFLGGVS-WAMLVARTCQLYPNAIASTLVHKFFLVF
DEILHLV.NIDNFRLTLRA.KLWAKRHNIYSNI...LG..S.W..LVARTCQLYPNAIASTL.HKFFLVF
RetrocopyDEILHLVSNIDNFRLTLRAFKLWAKRHNIYSNI---LGFLS<WCSLVARTCQLYPNAIASTLEHKFFLVF
ParentalSKWEWPNPVLLKQPEECNLNLPVWDPRVNPSDRYHLMPIITPAYPQQNSTYNVSVSTRMVMVEEF-KQGL
SKWEWPNPVLLKQPEECN.NLPVWDPRVNPSDRYHL.PIITPAYP.QNSTYNV..ST..VMVEE..KQGL
RetrocopySKWEWPNPVLLKQPEECNFNLPVWDPRVNPSDRYHLIPIITPAYP*QNSTYNVFISTWNVMVEEYNKQGL
ParentalAITDEILLSKAEWSKLFEAPNFFQKYKHYIVLLASAPTEKQRLEWVGLVESKIRILVGSLEKNEFITLAH
AITDEILLSKAEWSKLFEAPN.FQKYKHYIVLLASAPTEKQ.LEWVGL.ESKIRILVG.LEKNEFITLAH
RetrocopyAITDEILLSKAEWSKLFEAPNYFQKYKHYIVLLASAPTEKQ*LEWVGLMESKIRILVGNLEKNEFITLAH
ParentalVNPQSFPAPKENPDKEEFRTMWVIGLVFKKTENSENLSVDLTYDIQSFTDTVYRQAINSKMFEMDMKIAA
VNPQSFPAPKENPDKEEF.TMWVIGLVF.KTENSENLSVDLTYDIQSFTDTVYRQAINSKMFEMDMKIAA
RetrocopyVNPQSFPAPKENPDKEEFPTMWVIGLVFEKTENSENLSVDLTYDIQSFTDTVYRQAINSKMFEMDMKIAA
ParentalMHVKRRQLHQLLPNHVLQKKKKHSSEVRLTALNDSSLDLSMDSDNSMSVPSPTSAMKTSPLNSSGSSQGR
MHVKRRQLHQLLPNHVLQKKKKHSSEV.LTALN.SSLDLSMDSDNSMSVPSPTSAMKTSPLNSSGSSQGR
RetrocopyMHVKRRQLHQLLPNHVLQKKKKHSSEVQLTALNVSSLDLSMDSDNSMSVPSPTSAMKTSPLNSSGSSQGR
ParentalNSPAPAVTAASVTNIQATEVSVPQVNSSESSGGTSSESIPQTATQPAISPPPKPTVSRVVSSTRLVNQPP
N.PAPAVTAAS.TNIQATEVSVPQVNSSESS.GTSSESIPQTATQPAISPPPKPTVSRVVSST.LVNQPP
RetrocopyNNPAPAVTAASLTNIQATEVSVPQVNSSESSRGTSSESIPQTATQPAISPPPKPTVSRVVSSTCLVNQPP
ParentalRPSGNTATKVPNPIVGVKRTSSPHKEESPKKTKTEEDETSEDANCLDLIEHDKQETKEQLDTET
RPSGNTATKVPNPIVGVKRTSSPHKEESPKKTKTEEDETSED.NCLDLIEHDK.ETK......T
RetrocopyRPSGNTATKVPNPIVGVKRTSSPHKEESPKKTKTEEDETSEDVNCLDLIEHDKRETKKKHPVQT

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 209 .67 RPM
SRP007412_cerebellum 0 .00 RPM 192 .93 RPM
SRP007412_heart 0 .00 RPM 156 .29 RPM
SRP007412_kidney 0 .00 RPM 273 .90 RPM
SRP007412_liver 0 .00 RPM 159 .10 RPM
SRP007412_testis 0 .00 RPM 460 .05 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_1916 retrocopy.

TSS - click to see more details

Monodelphis domestica was not studied using FANTOM5 data.

Lab - click to see more details

retro_mdom_1916 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 20 parental genes, and 22 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000141421 retrocopy
retro_amel_517,
Bos taurus ENSBTAG000000040541 retrocopy
retro_btau_1078,
Canis familiaris ENSCAFG000000177831 retrocopy
retro_cfam_1783,
Callithrix jacchus ENSCJAG000000065122 retrocopies
retro_cjac_1763, retro_cjac_543,
Homo sapiens ENSG000000900601 retrocopy
retro_hsap_30,
Gorilla gorilla ENSGGOG000000062871 retrocopy
retro_ggor_202,
Loxodonta africana ENSLAFG000000009461 retrocopy
retro_lafr_895,
Myotis lucifugus ENSMLUG000000109221 retrocopy
retro_mluc_1396,
Macaca mulatta ENSMMUG000000186101 retrocopy
retro_mmul_1675,
Monodelphis domestica ENSMODG00000012887 2 retrocopies
retro_mdom_1714, retro_mdom_1916 ,
Mustela putorius furoENSMPUG000000030541 retrocopy
retro_mputfur_1375,
Mus musculus ENSMUSG000000211111 retrocopy
retro_mmus_37,
Nomascus leucogenys ENSNLEG000000006251 retrocopy
retro_nleu_2771,
Otolemur garnettii ENSOGAG000000046111 retrocopy
retro_ogar_987,
Procavia capensis ENSPCAG000000041991 retrocopy
retro_pcap_91,
Pongo abelii ENSPPYG000000061281 retrocopy
retro_pabe_3113,
Pan troglodytes ENSPTRG000000067041 retrocopy
retro_ptro_2595,
Pteropus vampyrus ENSPVAG000000139251 retrocopy
retro_pvam_360,
Rattus norvegicus ENSRNOG000000048271 retrocopy
retro_rnor_863,
Vicugna pacos ENSVPAG000000064641 retrocopy
retro_vpac_378,


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