RetrogeneDB ID:

retro_mdom_1114

Retrocopy
location
Organism:Opossum (Monodelphis domestica)
Coordinates:3:144668534..144671312(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMODG00000005755
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:PRPF4B
Ensembl ID:ENSMODG00000009756
Aliases:None
Description:PRP4 pre-mRNA processing factor 4 homolog B (yeast) [Source:HGNC Symbol;Acc:17346]


Retrocopy-Parental alignment summary:






>retro_mdom_1114
GAGTTTATTGATGCCTCTGACAAAGATGGGGCATCTCCACCAAAAAGAACTAAAATTGATGACTTAGCTTTGCTGGAAGA
TTTGGAGAAACAGAGAGCTTTAATTAAAGCTGAACTTGATAATGAGTTGATGGAAGGAAAAGTCCAGTCTGGAATGGGGC
TAATATTACAGGGTTATGATTCAGGATCCGAAGAAGAGGGAGAAATACATGAGAAGGTGAGAAATGGGAATAGATCAACT
GCTAGGTCATCAAATACTAAGGCAAAACTTGAACTCGTAGACAATAAAAAGCATTCAAAGAAATGAAGCAAAAGCAGATC
AAAAGAACAGAATAGACATAGATCTGATAAAACAAAAAGCAAGGGAAGCATTGAAGGAGTTAAAGAAAAAACAACCAGAA
GTAAGTCTAAGGAAAGAAAGAAGTCCAAGAGTCCATCTAAAAGAAGCAAATCCCAAGATCAAGCAAGAAAACCCAAATCC
CCAGGACTTAAAAGGCAATCTCAGGAGAAAATTGAAAAGGCCAAATCCCCTACTAAGGATAAGATTAAATTAGAAGATAA
AAGTAAATCAAAAGAAAGAAAGAAATCTCCAATTATAAATGAAAGCAAAAGTTGTGACCATGGGAAAAAATCCAAATCTC
CAATAGAACTAAGAAGCAAATCCAAAGACAGAAGGTCAAGATCCAAAGATAGAAAATCCCAAAGATCTGAGATTGACAAA
GAAAAGAAGCCAATTAAATCTCCCTCTAAAGGTGCTTCCTCTGGAAAAGAAAATAGGTCCCCAAGTAGAAGACCAGGTCG
TAGTCCTAAAGGAAAAAGTTCAACTCCAAAACAGCGTGATAAATCCAGAAGGAGTAGGTCCCCTCTACTTAATGATCAGA
GATCCAAGCTAAGTAAATCATCTCAAACTCTGCCTCCTGGTAGAAGAGCTAAGAGTCGATCAGTGGAAAGAAAACAAAGA
GAACCAGAAAGGAGAAGACTTTCTTCTACAAGAACACGTCCTAGGGATGATATTCTTAGCACACATGAGAGATCAAAAGA
TGTCAGTCCTATTAGCAGATGGTCCCCAACCAGAAGAAGATCAAGTAGGTCTCCTATCCGCAGGAGATCTTGTTCACCAC
TCAGGCAAAGCCGGTCTCCAAGGAGAAGAAGCAGGTCCCCAAGAAGAGATAGAAGTAGGCGGAGTAGATCTCGACTTCGA
TGGCGATCTCGACTTCGATGGCGATCTCGATCGAGGGGTGGTTGTAGGCGCAGAAGCAAAGTAAAGGAAGATAAATTTAC
AGGAAGCCTTTCTGAAGGGATGAAAGATGAACAGGAATCATCTGATGATAACCTAGAAGACCTTGATGTTGAAGAAGAAG
ATGAAGAAGCCCTAATAGAGAAGAGAAGACTCCAAAGGCAGGCAATTGTTCAGAAATATAAATACCTTGCTCAGGATAGC
AATATATCTATGCCATCTGAGCCAAGCAGCCCTCAGAGTAGCACTCGAACACGTTCACCGTCTCCTGATGACATTTTAGA
ATGGGTTGCTGCTGATGTTAAAGAATATGAAAGGGAAACTGTTGATACGTTTGAGGCCTCTGTAAAAGCCAAGCACAATC
TTATGACAGTTGAACAAAATGGTTCAACTCAGAAGAAACTATTGGCTCCTGACATGTTCACAGAATCAGATGATATGTTT
GCTGCATATTTTGATAGTGCTCATCTTCAGGCTGCTGGCATTGGAAAAGATTCCAAAGAAAATCCCAACCTCAGGGATAA
TTGGACTGATGCAGAAGGCTATTACCGTGTACACATAGGTGAAGTCCTAGAGAAAAGTTACACTGTGTATGGCTACACTG
GACAGGGTGTCTTCAGTAATGTAGTGAGAGCCAGAGACATGGCAAGAGCAAACCAGGAAGTGGCAGTGAAAATCATCAGG
AACAATGAGCTCATGCAAAAAACAGGGTTAAAAGAACTGGAATTTTTGAAAAAGCTTAATGATGCTGATCCTGATGACAA
ATTTCATTGTTTATGGCTCTTCAGACACTTTTACCATAAACAACATCTCTGCCTCGTGTTTGAGCCTCTAAGTATGAATT
TACGAGAGGTACTGAAAAAGTATGGAAAGGATGTCAGTCTCCATATTAAGGCTGTAAGATCCTATGGTCAGCAGTTGTTC
TTGGCATTGAAACTTCTTAAAAGGTGCAACATCCTACATGCTGATATTAAGCCAGACAATATCTTGGTTAATGAATCAAA
AACTATTCTAAAGCATTGTGACTTTGGATCAGCTTCACATGTTGCAGATAATGACATTACACCCTATCTCGTCAGTAGAT
TTTATCGTGCTCCTGAAATTATTATAGGAAAAAGCTATGACTATGGTATAGATATGTGGTCTGTAGGCTGCACATTATAT
GAACTTTATACTGGAAAAATATTATTTCCTGGTAAAACCAATAATCATATGTTGAAACTTGCTATGGACCTCAAAGGGAA
AATGCCAAATAAGATAAGAAAAGGTATGTTCAAAGAGCAGCACTTTGATCAAAATCTCAACTTCATGTACATAGAAGTAG
ATAAAGTAACAGAAAGGGAGAAAGTTACTGTCATGAGCACCATTAATCCTACCAAGGACCTGTTGGCTGATTTGATTGGG
TGCCAGAGGCTTCCTGAAGACCAACGCAAAAAAGTACACCAGCTAAAAGACTTGTTGGACCAGATCTTAATGTTGGACCC
AGCTAAACGAATTAGCACCCACCAGGCTCTACAGCATGCCTTCATCCAGGAAAAAATG

ORF - retro_mdom_1114 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 79.72 %
Parental protein coverage: 89.31 %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalEVIDASDKEGASPAKRTKIDDLALLEDLEKQRALIKAELDNELMEGKVQSGMGLILQGYESGSEEEGEIH
E.IDASDK.GASP.KRTKIDDLALLEDLEKQRALIKAELDNELMEGKVQSGMGLILQGY.SGSEEEGEIH
RetrocopyEFIDASDKDGASPPKRTKIDDLALLEDLEKQRALIKAELDNELMEGKVQSGMGLILQGYDSGSEEEGEIH
ParentalEKARNGNRSTARSSNTKGKLELVDNKNSSKKRSKSRSKERTRHRSDKKKSKGSIEGVKEKTTRSKSKERK
EK.RNGNRSTARSSNTK.KLELVDNK..SKK.SKSRSKE..RHRSDK.KSKGSIEGVKEKTTRSKSKERK
RetrocopyEKVRNGNRSTARSSNTKAKLELVDNKKHSKK*SKSRSKEQNRHRSDKTKSKGSIEGVKEKTTRSKSKERK
ParentalKSKSPSKRSKSQDQARKSKSPALKRRSQEKIGKAKSPTEDKIKLEDKSKSKDRKKSPIINESKSRDRGKK
KSKSPSKRSKSQDQARK.KSP.LKR.SQEKI.KAKSPT.DKIKLEDKSKSK.RKKSPIINESKS.D.GKK
RetrocopyKSKSPSKRSKSQDQARKPKSPGLKRQSQEKIEKAKSPTKDKIKLEDKSKSKERKKSPIINESKSCDHGKK
ParentalSKSPIELRSKSKDRRSRSKDRKSKRSEIDKEKK----PIKSPSKDASSGKENRSPSRRP-GRS--PKGKS
SKSPIELRSKSKDRRSRSKDRKS.RSEIDKEKK....P.K..S.........R.P.R.P.G.S..PK...
RetrocopySKSPIELRSKSKDRRSRSKDRKSQRSEIDKEKKPIKSPSKGASSGKENRSPSRRPGRSPKGKSSTPKQRD
ParentalLSPKQRD---KSRRSRSPLLNDRRSKQSKSPSRTLSPGRRAKSRSVERKRREPERRRLSSPRTRPRDDIL
.S...R.......RS................SR......R...R......R...R....S...R..D...
RetrocopyKSRRSRSPLLNDQRSKLSKSSQTLPPGRRAKSRSVERKQREPERRRLSSTRTRPRDDILSTHERSKD--V
ParentalSRRERSKDVSPISRWSPTRRRSSRSPIRRRSRSPLRRSRSPRRRSRSPRRRDRGRRSRSRLRRRSRSRGG
S...R.......S..SP.RRRS..SP.R..SRSP.RRSRSPR.R.RS.RR................SRGG
RetrocopySPISRWSPTRRRSSRSPIRRRSC-SPLRQ-SRSPRRRSRSPR-RDRS-RRSXXXXXXXXXXXXXXXSRGG
ParentalRRRRSRSKVKEDKFKGSLSEGMKVEQESSSDDNLEDFDVEEEDEEALIEQRRIQRQAIVQKYKYLAEDSN
.RRRS..KVKEDKF.GSLSEGMK.EQESS.DDN....................QRQAIVQKYKYLA.DSN
RetrocopyCRRRS--KVKEDKFTGSLSEGMKDEQESS-DDNXXXXXXXXXXXXXXXXXXXLQRQAIVQKYKYLAQDSN
ParentalMSMPSEPSSPQSSTRTRSPSPDDILERVAADVKEYERENVDTFEASVKAKHNLMTVEQNNGSTQKKLLAP
.SMPSEPSSPQSSTRTRSPSPDDILE.VAADVKEYERE.VDTFEASVKAKHNLMTVEQN.GSTQKKLLAP
RetrocopyISMPSEPSSPQSSTRTRSPSPDDILEWVAADVKEYERETVDTFEASVKAKHNLMTVEQN-GSTQKKLLAP
ParentalDMFTESDDMFAAYFDSARLRAAGIGKDFKENPNLRDNWTDAEGYYRVNIGEVLDKRYNVYGYTGQGVFSN
DMFTESDDMFAAYFDSA.L.AAGIGKD.KENPNLRDNWTDAEGYYRV.IGEVL.K.Y.VYGYTGQGVFSN
RetrocopyDMFTESDDMFAAYFDSAHLQAAGIGKDSKENPNLRDNWTDAEGYYRVHIGEVLEKSYTVYGYTGQGVFSN
ParentalVVRARDMARANQEVAVKIIRNNELMQKTGLKELEFLKKLNDADPDDKFHCLRLFRHFYHKQHLCLVFEPL
VVRARDMARANQEVAVKIIRNNELMQKTGLKELEFLKKLNDADPDDKFHCL.LFRHFYHKQHLCLVFEPL
RetrocopyVVRARDMARANQEVAVKIIRNNELMQKTGLKELEFLKKLNDADPDDKFHCLWLFRHFYHKQHLCLVFEPL
ParentalSMNLREVLKKYGKDVGLHIKAVRSYSQQLFLALKLLKRCNILHADIKPDNILVNESKTILKLCDFGSASH
SMNLREVLKKYGKDV.LHIKAVRSY.QQLFLALKLLKRCNILHADIKPDNILVNESKTILK.CDFGSASH
RetrocopySMNLREVLKKYGKDVSLHIKAVRSYGQQLFLALKLLKRCNILHADIKPDNILVNESKTILKHCDFGSASH
ParentalVADNDITPYLVSRFYRAPEIIIGKSYDYGIDMWSVGCTLYELYTGKILFPGKTNNHMLKLAMDLKGKMPN
VADNDITPYLVSRFYRAPEIIIGKSYDYGIDMWSVGCTLYELYTGKILFPGKTNNHMLKLAMDLKGKMPN
RetrocopyVADNDITPYLVSRFYRAPEIIIGKSYDYGIDMWSVGCTLYELYTGKILFPGKTNNHMLKLAMDLKGKMPN
ParentalKMIRKGVFKDQHFDQNLNFMYIEVDKVTEREKVTVMSTINPTKDLLADLIGCQRLPEDQRKKVHQLKDLL
K.IRKG.FK.QHFDQNLNFMYIEVDKVTEREKVTVMSTINPTKDLLADLIGCQRLPEDQRKKVHQLKDLL
RetrocopyK-IRKGMFKEQHFDQNLNFMYIEVDKVTEREKVTVMSTINPTKDLLADLIGCQRLPEDQRKKVHQLKDLL
ParentalDQILMLDPAKRISINQALQHAFIQEKI
DQILMLDPAKRIS..QALQHAFIQEK.
RetrocopyDQILMLDPAKRISTHQALQHAFIQEKM

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_1114 retrocopy.

TSS - click to see more details

Monodelphis domestica was not studied using FANTOM5 data.

Lab - click to see more details

retro_mdom_1114 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 6 parental genes, and 6 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG000001127391 retrocopy
retro_hsap_4212,
Gorilla gorilla ENSGGOG000000064221 retrocopy
retro_ggor_2821,
Myotis lucifugus ENSMLUG000000059011 retrocopy
retro_mluc_259,
Monodelphis domestica ENSMODG00000009756 1 retrocopy
retro_mdom_1114 ,
Nomascus leucogenys ENSNLEG000000112911 retrocopy
retro_nleu_1453,
Pan troglodytes ENSPTRG000000176831 retrocopy
retro_ptro_2859,




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