RetrogeneDB ID:

retro_mdom_1776

Retrocopy
location
Organism:Opossum (Monodelphis domestica)
Coordinates:7:56836162..56837749(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMODG00000025293
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSMODG00000014364
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_mdom_1776
ATGGCAGACAAACTCCCTTCAGAATTTGATGTGATCGTGATAGGGACTGGTTTGCCTGAGTCCATCACTGCAGCTGCTTG
CTCAAGAAGTGGCCAGAGTGTTCTACATCTTGATTCAAGAAGCTATTATGGAGGAAACTGGGCTAGTTTCAGCTTTTCAG
GACTATTGTCCTGGATAAAGGAATATCAGGAACAGAGTGATATTGGAGAAGAATGGACAGCATGGAAAGAGCTAATACTA
GAAACAGAAGAAGGCATTGCTCTTAGAAAGAAGGATCAGACCATCCAACATGTAGAAGTCATCTGTTATGCCAGTCAGGA
TTCAGATGATCATGCTGAAGAGATTGGTGCTTTGCAGAAGAATCCTGCCTCTCTGACTTCTGCTGGCACAAATCACCCTC
CAGACTCAATGGATACAGCTTCCTCAGATACATCTAAATTATTAGCACCATTAAGTGAACCAGAGACTGCACTGGTGGTA
CCTGAAGTAGATATGACATTGGAGAAAGAAAATGATGGTAGTTACACAGATTGTAGCCAGTTAGATTTGGAACCAAAAAA
AACTGAAAACATTCTAATCACAGAAGATGTTGCTGATGCACCCAAGAAGAGTGGGATCACTTACTCCCAGATTGTTAAAG
AAGGCCGGAGATTTAATATTGATTTGACCTCAAAGCTTCTTTATTCTCGAGGATTGCTAATTGACCTTCTAATCAAATCA
AATGTTAGCCGATATGCAGAATTCAAAAATGTCACCAGGATTCTTGGGTTTCAAGAAGGGAGCGTGCTACAGGTGCCTTG
TTCCAGAGCAGATGTTTTTAATAGCAAGAAACTCACTATGGTAGAAAAGAGAATGCTGATGAAATTTCTGACATTTTGCT
TAGATTATGAGCAGCACCCTAATGAATACAAAGCTTATGAGGAAAGTACCTTTTCAGAATACTTGAAAACTCAAAAACTG
ACACCCATCTTGAGACACTTTGTCCTTCATTCCATTGCAATGGCATCAGAGACATCTACCAGCACCTTAGATGGCCTCAG
AGGAACGAAAAACTTTCTTCAGTGTCTTGGGCGGTATGGCAATACTCCCTTTTTGTTCCCCTTGTATGGCCAAGGAGAAA
TACCCCAGTGTTTCTGCAGAATGTGTGCAGTATTTGGTGGAACCTATTGTCTTAACCATGCAGTACAGTGCCTTGTAGTG
GACAAAGAATCTGGAAAATGTAAGGCAATCATCGATCATTTTGGTCAGAGGATAAATGCTAAGTATTTTATTGTAGAAGA
TAGTTACCTTTCTGAGAAAACGTGTTCAAATGTGACCTATACCCAGATATCAAGGGGAGTGCTGATCACAGATCGATCTA
TACTGAAGACAGATTCTGATCAGCATATCTCTGTTCTGACAGTACCACCAGTGGAGCCAGGATCTGCTGCCGTCCGGGTC
ATTGAATTGTCTTCTTCTACCATGACATGTATGAAAGGTACATATCTTGTCCATTTAACTTGTACATCCTCAAAAAATAC
AGCAAGAGAAGATTTAGAATTAGTTGTGCAGAAATTATTCACCCCCTATGCTGAAGTGGAGCTGGAA

ORF - retro_mdom_1776 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 81.7 %
Parental protein coverage: 99.81 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalMADKLPSEFDVVVIGTGLPESIVAAACSRSGQCVLHVDSRSYYGGNWASFSFSGLLSWIKEYQEKRD-KE
MADKLPSEFDV.VIGTGLPESI.AAACSRSGQ.VLH.DSRSYYGGNWASFSFSGLLSWIKEYQE..D..E
RetrocopyMADKLPSEFDVIVIGTGLPESITAAACSRSGQSVLHLDSRSYYGGNWASFSFSGLLSWIKEYQEQSDIGE
ParentalEWATWQELILETEEAIALRKKDQTIQHVEVICYASQESDEHVEELGVVQKNPTSVTSASSNDPLDSMGTA
EW..W.ELILETEE.IALRKKDQTIQHVEVICYASQ.SD.H.EE.G..QKNP.S.TSA..N.P.DSM.TA
RetrocopyEWTAWKELILETEEGIALRKKDQTIQHVEVICYASQDSDDHAEEIGALQKNPASLTSAGTNHPPDSMDTA
ParentalCSDTSELTAQLSEPDTAQEVPKGDMPLGNENCGGDAECSQSPLEQEKAENVPV-EDV-DSTKKNRITYSQ
.SDTS.L.A.LSEP.TA..VP..DM.L..EN.G....CSQ..LE....EN....EDV.D..KK..ITYSQ
RetrocopySSDTSKLLAPLSEPETALVVPEVDMTLEKENDGSYTDCSQLDLEXXXXENILITEDVADAPKKSGITYSQ
ParentalIVKEGRRFNIDLTSKLLYSRGLLIDLLIKSNVSRYAEFKSVTRILGYQEGNVLQVVPCSRADVFNSKKLS
IVKEGRRFNIDLTSKLLYSRGLLIDLLIKSNVSRYAEFK.VTRILG.QEG.VLQV.PCSRADVFNSKKL.
RetrocopyIVKEGRRFNIDLTSKLLYSRGLLIDLLIKSNVSRYAEFKNVTRILGFQEGSVLQV-PCSRADVFNSKKLT
ParentalMVEKRMLMKFLTFCLDYEQHHDDYKAYEDCTFSEYLKTQRLTPNLQHFVLHSIAMVSETSTSTLDGLRET
MVEKRMLMKFLTFCLDYEQH...YKAYE..TFSEYLKTQ.LTP.L.HFVLHSIAM.SETSTSTLDGLR.T
RetrocopyMVEKRMLMKFLTFCLDYEQHPNEYKAYEESTFSEYLKTQKLTPILRHFVLHSIAMASETSTSTLDGLRGT
ParentalRNFLQCLGRYGNTPFLFPLYGQGEMPQCFCRMCAVFGGTYCLNHAVQCLVVDKGSGKCKAIIDQCGQRIS
.NFLQCLGRYGNTPFLFPLYGQGE.PQCFCRMCAVFGGTYCLNHAVQCLVVDK.SGKCKAIID..GQRI.
RetrocopyKNFLQCLGRYGNTPFLFPLYGQGEIPQCFCRMCAVFGGTYCLNHAVQCLVVDKESGKCKAIIDHFGQRIN
ParentalAKHFIVEDSCLSEQTCSNVTYRQILRAVLITDRSVLKADSDQQISVLTVPPQEPGSAAIQVIELCSSTMT
AK.FIVEDS.LSE.TCSNVTY.QI.R.VLITDRS.LK.DSDQ.ISVLTVPP.EPGSAA..VIEL.SSTMT
RetrocopyAKYFIVEDSYLSEKTCSNVTYTQISRGVLITDRSILKTDSDQHISVLTVPPVEPGSAAVRVIELSSSTMT
ParentalCMKGTYLIHLTCPSSKKTAREDLELVVRKLFTPYDEAELE
CMKGTYL.HLTC.SSK.TAREDLELVV.KLFTPY.E.ELE
RetrocopyCMKGTYLVHLTCTSSKNTAREDLELVVQKLFTPYAEVELE

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_1776 retrocopy.

TSS - click to see more details

Monodelphis domestica was not studied using FANTOM5 data.

Lab - click to see more details

retro_mdom_1776 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 21 parental genes, and 21 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000101901 retrocopy
retro_amel_733,
Bos taurus ENSBTAG000000095981 retrocopy
retro_btau_227,
Canis familiaris ENSCAFG000000174061 retrocopy
retro_cfam_1873,
Equus caballus ENSECAG000000192011 retrocopy
retro_ecab_36,
Felis catus ENSFCAG000000306521 retrocopy
retro_fcat_1744,
Homo sapiens ENSG000001884191 retrocopy
retro_hsap_56,
Gorilla gorilla ENSGGOG000000229121 retrocopy
retro_ggor_488,
Loxodonta africana ENSLAFG000000005231 retrocopy
retro_lafr_441,
Myotis lucifugus ENSMLUG000000112861 retrocopy
retro_mluc_138,
Macaca mulatta ENSMMUG000000167761 retrocopy
retro_mmul_460,
Monodelphis domestica ENSMODG00000014364 1 retrocopy
retro_mdom_1776 ,
Mustela putorius furoENSMPUG000000011941 retrocopy
retro_mputfur_831,
Mus musculus ENSMUSG000000255311 retrocopy
retro_mmus_284,
Nomascus leucogenys ENSNLEG000000027621 retrocopy
retro_nleu_120,
Oryctolagus cuniculus ENSOCUG000000128191 retrocopy
retro_ocun_893,
Pongo abelii ENSPPYG000000205201 retrocopy
retro_pabe_215,
Pan troglodytes ENSPTRG000000220711 retrocopy
retro_ptro_400,
Rattus norvegicus ENSRNOG000000001611 retrocopy
retro_rnor_981,
Sarcophilus harrisii ENSSHAG000000175681 retrocopy
retro_shar_127,
Ictidomys tridecemlineatus ENSSTOG000000221111 retrocopy
retro_itri_870,
Vicugna pacos ENSVPAG000000019631 retrocopy
retro_vpac_231,


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