RetrogeneDB ID:

retro_mdom_1412

Retrocopy
location
Organism:Opossum (Monodelphis domestica)
Coordinates:4:347632472..347634150(-)
Located in intron of:ENSMODG00000007901
Retrocopy
information
Ensembl ID:ENSMODG00000007885
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:EFR3A
Ensembl ID:ENSMODG00000001307
Aliases:None
Description:EFR3 homolog A (S. cerevisiae) [Source:HGNC Symbol;Acc:28970]


Retrocopy-Parental alignment summary:






>retro_mdom_1412
CACTTAGATCATCACCACCTATGGGATCCCAATGAATTTGCAGTCCATTGCTTTAAAGTTATAATGTATTCCATTCAGAC
ACAGTATTCTCACCACGTGATCCAAGAGACCCTTGTACATCTTGATGTTCGAAAAAAAGACTCTCCACGTGTTCGGGCCG
GGATTATCCAGGTTCTGTTAGAAGCAGTGGCCATTGCTGCTAAAGGATCTATAGGCCCCACAGTACTGGAAGTATTCAAT
ACCATACTGAAGCATTTACGTCTCAGTGTTGAATTTGAGGCTGATGAAAGATGGGGCTCCATGGGTAGTGTCAATGTAAG
CACAAGCACCAAAGATAATTATGAGAGGATTGTCCAGAATGCTATTATTCAAACAATAGGTTTTTTTTGGAAGTAATTTA
CCAGATTATCAGAGATCAGAAATTATGATGTTTATCATGGGAAAAGTACCTGTTTTCCGAACTACCACACATACATTGGA
TACCAGTCAGCTAGGGGATTTGGGGACCAGACGGATTCAAATAATGTTGCTGAGATCTTTACTTATGGCAACATCTGGAT
ACAAAGCTAAGACTATTGTTACTGCATTACCTGCCCCATTTCTTGATCCTATATTATCTCCATCTCTAATGGAAGACTAT
GAATTGAGACAACTGGTCCTGGAAATTATGCATAACCTCACTGATCGACATGACAGTTGGGCAAAACTACGAGGAATCAG
AATCATACCAGATGTAGCTGACCTTAAGATAAAAAGAGAGAAAATTTCCAAGCAATATGCAAGTTTTATGAAAAAGAATG
GTCAGCAGTTATACCGGCACATTTATTTGGGCTGTAAGGAAGATGACAACATTCAAAAAAACTTTGAATTACTCTATACT
TCACTTGCTCTGATAACTATTGAACTGGCCAATGAAGAAGTAGTTATTGATCTTATACGAGTAGCCATTGCTTTACAGGA
TAATGCCATCATTAATGAGGATAATTTGCCCATGTTTCATCATTGTGCTATGATGGCATTAGTTGCAGCATATCTCAACT
TTTTAAGTCAGATGATAGCAGTTCCTGCTTTTTGCCAGCATGTCAGCAAGGTTATTGAAATAAGAACAATGGAAGCACCC
TATTTTCTACCAGAACATATTTTCAGAGATAAGTGCATGCTTCCAAAGTCTCTAGAGAAATATGAAAAAAATTTGTATTT
CTTGACTAACAAGATAGCAGAATCATTAGGGGGCAGTGGATATAATGTTGAAAAACTAACAGTGCCATATGTGCCACAAG
TAACAGATGAAGATCGACTTTCCAGACGGAAGAGCATTGTAGACACTGTATCCATTCAGGTGGATATTTTACCAGGCAGC
AACCCTATTGATAATATGGTCAGTACTACCACTGAAGAAATAACCTTTGAAGCATTGAAAAAAGCAATTGATACCAATGG
AATGGAAGAACAAGAAAAAGAGAAGAGGCGCCTTGTGATAGAGAAATTTCAGAAAGCACCTTTTGAAGAAATTGCAGCTC
AATGTGAAACTAAAGCAAATTTTCTTCATGACAGACTTGCACAAATACTGGAGCTCACCATACATCCTCCCCGGAGTCCA
TCAGGAACATTAACCATTACATCTGGACATGCCCAGTACCAGTCTGTCCCAGTTTATGAGATGAAGTTTCCAGATCTC

ORF - retro_mdom_1412 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 96.43 %
Parental protein coverage: 68.42 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalHLDHHHLWDPNEFAVHCFKVIMYSIQAQYSHHVIQETLAHLDVRKKDSPRVRAGIIQVLLEAVAIAAKGS
HLDHHHLWDPNEFAVHCFKVIMYSIQ.QYSHHVIQETL.HLDVRKKDSPRVRAGIIQVLLEAVAIAAKGS
RetrocopyHLDHHHLWDPNEFAVHCFKVIMYSIQTQYSHHVIQETLVHLDVRKKDSPRVRAGIIQVLLEAVAIAAKGS
ParentalIGPTVLEVFNTLLKHLRLSVEFEAGERRGSMGSVNVSTSTKDNDERIVQNAIIQTIGFF-GSNLPDYQRS
IGPTVLEVFNT.LKHLRLSVEFEA.ER.GSMGSVNVSTSTKDN.ERIVQNAIIQTI....GSNLPDYQRS
RetrocopyIGPTVLEVFNTILKHLRLSVEFEADERWGSMGSVNVSTSTKDNYERIVQNAIIQTIXXX>GSNLPDYQRS
ParentalEIMMFIMGKVPVFGTTTHTLDTSQLGDLGTRRIQIMLLRSLLMVTSGYKAKTIVTALPAPFLDPILSPSL
EIMMFIMGKVPVF.TTTHTLDTSQLGDLGTRRIQIMLLRSLLM.TSGYKAKTIVTALPAPFLDPILSPSL
RetrocopyEIMMFIMGKVPVFRTTTHTLDTSQLGDLGTRRIQIMLLRSLLMATSGYKAKTIVTALPAPFLDPILSPSL
ParentalMEDYELRQLVLEIMHNLTDRHDNRAKLRGIRIIPDVADLKIKREKISKQDASFMKKNGQQLYRHIYLGCK
MEDYELRQLVLEIMHNLTDRHD..AKLRGIRIIPDVADLKIKREKISKQ.ASFMKKNGQQLYRHIYLGCK
RetrocopyMEDYELRQLVLEIMHNLTDRHDSWAKLRGIRIIPDVADLKIKREKISKQYASFMKKNGQQLYRHIYLGCK
ParentalEDDNVQKNFELLYTSLALITIELANEEVVIDLIRVAIALQDNAIINEDNLPMFHRCAMMALVAAYLNFLS
EDDN.QKNFELLYTSLALITIELANEEVVIDLIRVAIALQDNAIINEDNLPMFH.CAMMALVAAYLNFLS
RetrocopyEDDNIQKNFELLYTSLALITIELANEEVVIDLIRVAIALQDNAIINEDNLPMFHHCAMMALVAAYLNFLS
ParentalQMIAVPAFCQHVSKVIEIRTMEAPYFLPEHIFRDKCMLPKSLEKHEKNLYFLTNKIAESLGGSGYNVEKL
QMIAVPAFCQHVSKVIEIRTMEAPYFLPEHIFRDKCMLPKSLEK.EKNLYFLTNKIAESLGGSGYNVEKL
RetrocopyQMIAVPAFCQHVSKVIEIRTMEAPYFLPEHIFRDKCMLPKSLEKYEKNLYFLTNKIAESLGGSGYNVEKL
ParentalTVPYVPQVTDEDRLSRRKSIVDTVSIQVDILPGSNPIDNMVSTTTEEITFEALKKAIDTNGMEEQEKEKR
TVPYVPQVTDEDRLSRRKSIVDTVSIQVDILPGSNPIDNMVSTTTEEITFEALKKAIDTNGMEEQEKEKR
RetrocopyTVPYVPQVTDEDRLSRRKSIVDTVSIQVDILPGSNPIDNMVSTTTEEITFEALKKAIDTNGMEEQEKEKR
ParentalRLVIEKFQKAPFEEIAAQCETKANFLHDRLAQILELTIRPPPSPSGTLTITSGHAQYQSVPVYEMKFPDL
RLVIEKFQKAPFEEIAAQCETKANFLHDRLAQILELTI.PP.SPSGTLTITSGHAQYQSVPVYEMKFPDL
RetrocopyRLVIEKFQKAPFEEIAAQCETKANFLHDRLAQILELTIHPPRSPSGTLTITSGHAQYQSVPVYEMKFPDL

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_1412 retrocopy.

TSS - click to see more details

Monodelphis domestica was not studied using FANTOM5 data.

Lab - click to see more details

retro_mdom_1412 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 1 parental gene, and 1 retrocopy.

Species Parental gene accession Retrocopies number
Monodelphis domestica ENSMODG00000001307 1 retrocopy
retro_mdom_1412 ,




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