RetrogeneDB ID:

retro_mdom_39

Retrocopy
location
Organism:Opossum (Monodelphis domestica)
Coordinates:X:23545514..23547266(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMODG00000020561
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSMODG00000007003
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_mdom_39
ATGACAGCAGATTCCGCTACAAAGATGAGCAATGATTCCACCAACGCGGCGGCAGCCAAAGCTCCTGAAGGTGTAGCCGG
GGCACCTAATGAGGCTGCCCTGTTGGCTCTCATGGAGCGCACGGGCTACAGTATGACACAGGAAAACGGTCAGCGCAAGT
ATGGTGGTCCTCCCCCTGGATGGGAAGGGCTGCACCCCCCGCGTGGCTGTGAGGTCTTCGTGGGTAAAATTCCCCGAGAC
GTGTATGAAGACGAGCTGGTTCCAGTGTTTGAGTCCGTGGGGCGTATCTACCAGATGCGACTGATGATGGACTTTGATGG
GAAGAACCGCGGCTACGCTTTTGTCATGTATACTCACAAGCGCGAAGCCAAGCGGGCCGTGAGGGAACTGGACAATCATG
AAATCAGACCGGGTCGACCTCTGGGAGTCTGTTGCAGTGTGGATAACTGCCGACTCTTCATCGGTGGCATCCCTAAGATG
AAAAAGAGAGACGAGATCCTGGAAGAGATCTCTAAGGTGACCGAAGGGGTTCTAGACGTTATCGTGTACGCAAGTGCCAC
GGATAAGACGAAGAACAGAGGGTTTGCCTTCATAGAGTACGAGAGCCACCGGGCAGCGGCCATGGCCAGGAGAAAGCTCA
TGCCTGGAAGGATCCAGCTGTGGGGACAGCAGATCGCGGTGGACTGGGCAGAGCCAGAGATGGATGTCGACGAAGATGTC
ATGGAAACCGTTAAGATCCTGTACGTGAGAAATCTGATGATCAAAACCAGCGAGGAGACGATCAGAAAGACCTTCAGCCA
GTTTGGCTGTGTGGAACGAGTCAAAAAGATCCGCGATTACGCATTTGTTCACTTCACCAGCCGGGAAGATGCCATCCGTG
CTATGAACAGCCTCAATGGCACCGAGCTCGAAGGCTCGTGTCTTGGAGTTACTTTGGCCAAACCAGTAGACAAAGAGCAA
TACGCACGCTATCGGAAGGCAGTCAAAGGAAGTGTGACAGCAGAAGTCCAGCAGCTCAACTATGTTTACTCGTGCGATCC
CTATACTTTGGCCTACTACAGCTATCCCTACAGTGCTCTCTTTGGGCCCAACAGAGATTATTTTGTGAAGGCAGAGAGCG
TGAGAGGCCGAGGGCAAGACACAGCTGGCAGCAGAGCCCCGGGCCCCAGGGGATCCTACTTCGGGGGGTACTCTGCAGGC
CGTGGCATCTATAGCCGATATCATGAGGGGAAAGGAAAGTGGCGAGAAAGAGGATATGAGTTTGTACCGAACTTGGAATT
ATCTGCCGCCAATCCAGTTCCTATTAAACCCGGTACAGTGGCAATCCCTGCTCTTGGCGCCCAGTATTCCATGTTTCAGG
CTGGCCCTGCTCCCAAGTTGCTGGAAGATGGCAAAATGCATGCAATGGAACACATGATCAACCCCATAGCAGTACAAGCA
GACCCAGCCGGTGCCTCTGCTGCCGCCGCCGCTGCCACCATACCTGCTGGTTCCACCCCTCCACCTTTCCAGGCACGCCC
GATAACTCCAGTATTCACAGGGGCTCCAAACGTCCAGAGAATTCCCGCGGCTGGGCTCTACGGTGCCGGTTACATCCCCT
TTGCTGCTCCTGCCTCAGCCACATCAGCCACAGTACAGAAGAGCGCCGCAGCCACAGCTCCCGTTTATGGAGGTTATGGT
GGCTATATTCCTCAGCCATTCCCTTCGGCTACCATTCAGCCTCCCATACACGAAGACTACCAGACATACTGA

ORF - retro_mdom_39 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 86.66 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMTAEDSTTTMSNDSTNVSAAKVPEGIAGAPNEAALLALMERTGYSMIQENGQRKYGGPPPGWEGLHPPRG
MTA.DS.T.MSNDSTN..AAK.PEG.AGAPNEAALLALMERTGYSM.QENGQRKYGGPPPGWEGLHPPRG
RetrocopyMTA-DSATKMSNDSTNAAAAKAPEGVAGAPNEAALLALMERTGYSMTQENGQRKYGGPPPGWEGLHPPRG
ParentalCEVFVGKIPRDVYEDELVPVFESVGRIYEMRLMMDFDGKNRGYAFVMYTHKHEAKRAVRELNNYEIRPGR
CEVFVGKIPRDVYEDELVPVFESVGRIY.MRLMMDFDGKNRGYAFVMYTHK.EAKRAVREL.N.EIRPGR
RetrocopyCEVFVGKIPRDVYEDELVPVFESVGRIYQMRLMMDFDGKNRGYAFVMYTHKREAKRAVRELDNHEIRPGR
ParentalLLGVCCSVDNCRLFIGGIPKMKKREEILEEISKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMA
.LGVCCSVDNCRLFIGGIPKMKKR.EILEEISKVTEGVLDVIVYASA.DK.KNRGFAF.EYESHRAAAMA
RetrocopyPLGVCCSVDNCRLFIGGIPKMKKRDEILEEISKVTEGVLDVIVYASATDKTKNRGFAFIEYESHRAAAMA
ParentalRRKLMPGRIQLWGHQIAVDWAEPEIDVDEDVMETVKILYVRNLMIETTEETIKKSFGQFNPGCVERVKKI
RRKLMPGRIQLWG.QIAVDWAEPE.DVDEDVMETVKILYVRNLMI.T.EETI.K.F.QF..GCVERVKKI
RetrocopyRRKLMPGRIQLWGQQIAVDWAEPEMDVDEDVMETVKILYVRNLMIKTSEETIRKTFSQF--GCVERVKKI
ParentalRDYAFVHFTSREDAVHAMNSLNGTELEGSCLEVTLAKPVDKEQYTRYQKAAKGSATAEVTPQQPNYVYSC
RDYAFVHFTSREDA..AMNSLNGTELEGSCL.VTLAKPVDKEQY.RY.KA.KGS.TAEV..QQ.NYVYSC
RetrocopyRDYAFVHFTSREDAIRAMNSLNGTELEGSCLGVTLAKPVDKEQYARYRKAVKGSVTAEV--QQLNYVYSC
ParentalDPYTLAYYSYPYNALIGPNRDYFVKAGSVRGRGRGAAGNRAPGPRGSYLGGYSAGRGIYSRYHEGKGKQQ
DPYTLAYYSYPY.AL.GPNRDYFVKA.SVRGRG...AG.RAPGPRGSY.GGYSAGRGIYSRYHEGKGK..
RetrocopyDPYTLAYYSYPYSALFGPNRDYFVKAESVRGRGQDTAGSRAPGPRGSYFGGYSAGRGIYSRYHEGKGKWR
ParentalEKGYELVPNLELSAVNPVPIKPGTVAIPAIGAQYSMFQTAPAPKMLEDGKIHTMEHMINPIAVQPDPASA
E.GYE.VPNLELSA.NPVPIKPGTVAIPA.GAQYSMFQ..PAPK.LEDGK.H.MEHMINPIAVQ.DPA.A
RetrocopyERGYEFVPNLELSAANPVPIKPGTVAIPALGAQYSMFQAGPAPKLLEDGKMHAMEHMINPIAVQADPAGA
ParentalAAAAAAAAAAAVMPAVSTPPPFQGRPITPVYTVAPNVQRIPAAGIYGASYVPFAAPASATLATIQKSAAA
.AAAAAA......PA.STPPPFQ.RPITPV.T.APNVQRIPAAG.YGA.Y.PFAAPASAT.AT.QKSAAA
RetrocopySAAAAAA----TIPAGSTPPPFQARPITPVFTGAPNVQRIPAAGLYGAGYIPFAAPASATSATVQKSAAA
ParentalAAAVYGGYGGYIPQPFPTATIQVPIHDVYQTY
.A.VYGGYGGYIPQPFP.ATIQ.PIH..YQTY
RetrocopyTAPVYGGYGGYIPQPFPSATIQPPIHEDYQTY

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_39 retrocopy.

TSS - click to see more details

Monodelphis domestica was not studied using FANTOM5 data.

Lab - click to see more details

retro_mdom_39 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
Monodelphis domestica ENSMODG00000007003 1 retrocopy
retro_mdom_39 ,
Monodelphis domestica ENSMODG000000161441 retrocopy
retro_mdom_240,
Otolemur garnettii ENSOGAG000000293671 retrocopy
retro_ogar_273,


Copyright © RetrogeneDB 2014-2017