RetrogeneDB ID:

retro_mdom_169

Retrocopy
location
Organism:Opossum (Monodelphis domestica)
Coordinates:3:144717556..144719449(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMODG00000025020
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSMODG00000008490
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_mdom_169
ACGGATGACCCCAGCGTGGGTCCCAAGATTCCACAGGCTTTAGAGAAGATTCTTCAGCTGAAGGAAATTCGCCAAGAAGA
GCTGATATCAGTACATGAAGTAGAGGACATGGAGACAGACACAAAGTCATCCTTGGGGGTTGCTGCGTCTGAGACTGAAG
AAGACACAGGATCTTTTTCTAAAGAGGAGAAAAACCGAAAGAGACGGAACCGCAAGAAGAAGAAGAAGCCCCAACATGTG
GCAGCGGGACTTGGTGCCCCCTCTGGGGGCTGTGAGAAAGAGACTCCATGCCCCAGTGGCACAGACTCTCCGACTGCCAC
GGTAGAGATCGAGTATGTAACTGAGGAACCTGAACCCTATGAACCAAACTTTATTTTTTTTAAGAGGATTTTCCAAGCTT
TCAAGCTAACTTATAATGTGAAGAAAGAGAAGGAGCCAGAGAAACTGGACAAGTTGGAGAACTCCACAGCTCCCAAGAAG
GGCTTCGAGGATGAGCACAAAGACAATGATGACGATAGTGATGATGAGCAGGAGAAGAAACCCGAGGCTCCGAAACGATC
TAAAAAAAAGCTACGGAGGATGAACCGTTTTACTGTGGATGAGCTGAAGCAGCTGGTGGCCCGGCCAGATGTGGTGGAGA
TGCATGATGTGACAGCCCAGGACCCCAAGCTATTGGTGCACCTAAAGGCCACCAGGAACTCGGTGCCAGTGCCACGCCAC
TGGTGCTTTAAGCACAAATACCTGCAGGGCAAGCGAGGCATTGAGAAGCCCCCTTTTGAATTGCCCGATTTCATTAAACG
AACCGGAATTCAGGAGATGCGAGAGGCTTTCCAGGAGCAGGAAGAACAGAAGACCATGAAGTCAAAAATGAGAGAAAAGG
TTAGACCCAAGATGGGGAAGATTGACATTGACTACCAGAAACTCCATGATGCCTTCTTCAAGTGGCAGACCAAGCCAAAA
TTGACGATTCATGGGGACCTTTACTATGAGGGGAAAGAGTTTGAGACTAGGTTGAAGGAGAAGAAGCCGGGAGATTTGTC
AGATGAATTGAGGATTTCATTGGGGATGCCAGTTGGACCAAATGCCCACAAAGTTCCTCCTCCATGGCTAATTGCTATGC
AGCGATATGGACCTCCCCCTTCATACCCCAACCTGAAGATCCTTGGACTGAATTCTCCCATCCCTGAGAGCTGTTCCTTT
GGTTACCATGCTGGGGGCTGGGGCAAACCTCCTGTGGACGAGACTGGGAAACCGCTATACGGAGATGTATTTGGAACCAA
TGCAGTGGAATTCCAGACCAAGACAGAGGAAGAAGAGATTGACCCGACTCTTTGGGGGGAGCTGGAGCCTTCTAATGAGA
AATCCTCGGAGGAGGAAGAAGAGAGTGATGAAGATAAACTTAATGAAGCAGGCTTCATTACCCCTGCAGACAGTGGTCTT
ATCACCCCTAGGGGCTTCTCTTCAGTGCCAGCTGGGATGGAGATACCTGAACTGATTGAACTCCGAAAAAAGAAGATTAA
AGAGGCTATGAATGGCAGTGAGACACCCCAGCTGTTCACTGTGCTTCCTGAGAAGAGGACGGCCACCGTTGGTGGAGCCA
TGATGGGTTCCACCCATATTTATGACATGTCTACGGTGATGAGCCGGAAGGGCCCAGCCCCTAAACTACAAGGGGTGGAA
GTGGCCTTGGCCCCCGAGGAGTTGGAGCTGGATCCCATGGCAATGACCCAGAAATATGAGGAACACATGCTCGAACAACA
GGCCCAGGTGGAGAAGGAGGACTTCAGTGACATGGTGGCTGATCATGCTGCCAAGCAGAAGCAAAAGAAGCAGAAGGCTC
AGCCCCAGGAGAGCAGAGGGGGAAGTAAGAAGTACAAAGAATTCAAGTTTTAA

ORF - retro_mdom_169 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 91.24 %
Parental protein coverage: 78.31 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalTDDPSVGPKIPQALEKILQLKEIRQEELISVHDEEDMETDTRSSLGVSASETEEDTLSFSKKEKNRKRRN
TDDPSVGPKIPQALEKILQLKEIRQEELISVH..EDMETDT.SSLGV.ASETEEDT.SFSK.EKNRKRRN
RetrocopyTDDPSVGPKIPQALEKILQLKEIRQEELISVHEVEDMETDTKSSLGVAASETEEDTGSFSKEEKNRKRRN
ParentalRKKKKKPQRAAAGRGASSGSPGGREKEAPRPRGTDSPAAAVEIEYVTEEPEIYEPNFIFFKRIFEAFKLT
RKKKKKPQ..AAG.GA.S...GG.EKE.P.P.GTDSP.A.VEIEYVTEEPE.YEPNFIFFKRIF.AFKLT
RetrocopyRKKKKKPQHVAAGLGAPS---GGCEKETPCPSGTDSPTATVEIEYVTEEPEPYEPNFIFFKRIFQAFKLT
ParentalDDVKKEKEKEPEKLDKLENSTAPKKKGFEEERKDSDDDSSDDEQEKKPEAPKLSKKKLRRMNRFTVAELK
..VKKEKE..PEKLDKLENSTAPKK.GFE.E.KD.DDDS.DDEQEKKPEAPK.SKKKLRRMNRFTV.ELK
RetrocopyYNVKKEKE--PEKLDKLENSTAPKK-GFEDEHKDNDDDS-DDEQEKKPEAPKRSKKKLRRMNRFTVDELK
ParentalQLVARPDVVEMHDVTAQDPKLLVHLKATRNSVPVPRHWCFKRKYLQGKRGIEKPPFELPDFIKRTGIQEM
QLVARPDVVEMHDVTAQDPKLLVHLKATRNSVPVPRHWCFK.KYLQGKRGIEKPPFELPDFIKRTGIQEM
RetrocopyQLVARPDVVEMHDVTAQDPKLLVHLKATRNSVPVPRHWCFKHKYLQGKRGIEKPPFELPDFIKRTGIQEM
ParentalREALQEKEEQKTMKSKMREKVRPKMGKIDIDYQKLHDAFFKWQTKPKLTIHGDLYYEGKEFETRLKEKKP
REA.QE.EEQKTMKSKMREKVRPKMGKIDIDYQKLHDAFFKWQTKPKLTIHGDLYYEGKEFETRLKEKKP
RetrocopyREAFQEQEEQKTMKSKMREKVRPKMGKIDIDYQKLHDAFFKWQTKPKLTIHGDLYYEGKEFETRLKEKKP
ParentalGDLSDELRISLGMPVGPNAHKVPPPWLIAMQRYGPPPSYPNLKIPGLNSPIPESCSFGYHAGGWGKPPVD
GDLSDELRISLGMPVGPNAHKVPPPWLIAMQRYGPPPSYPNLKI.GLNSPIPESCSFGYHAGGWGKPPVD
RetrocopyGDLSDELRISLGMPVGPNAHKVPPPWLIAMQRYGPPPSYPNLKILGLNSPIPESCSFGYHAGGWGKPPVD
ParentalETGKPLYGDVFGTNAAEFQTKTEEEEIDRTPWGELEPSDEESSEEEEEEESDEDKPDETGFITPADSGLI
ETGKPLYGDVFGTNA.EFQTKTEEEEID.T.WGELEPS.E.SS..EEEEESDEDK..E.GFITPADSGLI
RetrocopyETGKPLYGDVFGTNAVEFQTKTEEEEIDPTLWGELEPSNEKSS--EEEEESDEDKLNEAGFITPADSGLI
ParentalTPGGFSSVPAGMETPELIELRKKKIEEAMDGSETPQLFTVLPEKRTATVGGAMMGSTHIYDMSTVMSRKG
TP.GFSSVPAGME.PELIELRKKKI.EAM.GSETPQLFTVLPEKRTATVGGAMMGSTHIYDMSTVMSRKG
RetrocopyTPRGFSSVPAGMEIPELIELRKKKIKEAMNGSETPQLFTVLPEKRTATVGGAMMGSTHIYDMSTVMSRKG
ParentalPAPELQGVEVALAPEELELDPMAMTQKYEEHVREQQAQVEKEDFSDMVAEHAAKQKQKKRKAQPQDSRGG
PAP.LQGVEVALAPEELELDPMAMTQKYEEH..EQQAQVEKEDFSDMVA.HAAKQKQKK.KAQPQ.SRGG
RetrocopyPAPKLQGVEVALAPEELELDPMAMTQKYEEHMLEQQAQVEKEDFSDMVADHAAKQKQKKQKAQPQESRGG
ParentalSKKYKEFKF
SKKYKEFKF
RetrocopySKKYKEFKF

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_169 retrocopy.

TSS - click to see more details

Monodelphis domestica was not studied using FANTOM5 data.

Lab - click to see more details

retro_mdom_169 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 3 parental genes, and 3 retrocopies.

Species Parental gene accession Retrocopies number
Microcebus murinus ENSMICG000000085651 retrocopy
retro_mmur_730,
Myotis lucifugus ENSMLUG000000111361 retrocopy
retro_mluc_936,
Monodelphis domestica ENSMODG00000008490 1 retrocopy
retro_mdom_169 ,


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