RetrogeneDB ID:

retro_mdom_1721

Retrocopy
location
Organism:Opossum (Monodelphis domestica)
Coordinates:7:75675210..75677229(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMODG00000003138
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:SEC63
Ensembl ID:ENSMODG00000018012
Aliases:None
Description:SEC63 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:21082]


Retrocopy-Parental alignment summary:






>retro_mdom_1721
GTTTTTATTCCTTGCATACAAAGTTTCCAAAACAGAGAATATCAAGAATACAACCCTTATGAAGTCTTAAATTTGGATCC
TGGGGCAACAGTAACAGAGATTAAGAAACAATATCGTTTACTGTCACTTAAATACCATCCAGATAAAGGAGGAGATGAAG
TGATGTTCATGAGAATAGCAAAGGCCTATGCTGCTTTAACTGATGAAGAGTCTCGGAAAAATTGGGAAGAATATGGAAAT
CCAGATGGGCCACAAGCCACAAGTTCTGGAATTGCTTTGCCAGCTTGGATTGTGGATCAGAAGAACTCAATTTTGGTTTT
GCTTGTATATGGGTTGGCATTTATGGTTATCCTTCCAGTTGTAGTGGGCTCTTGGTGGTATAGATCAATACGCTATAGTG
GAGACCAGATCTTAATTCGCACAACTCAAATCTATACATACTTTGTGTATAAAACCCGAAACATGGATATGAAACGTCTC
ATAATGGTTTTAGCTGGGGCCTCTGAATTTGATCCTCAGTATAATAAAGATGCCACAAGCAGACCAGCTGATAATATTCA
GATACCACAGCTAATCAGAGAAATTGGCAGTATTAATTTAAAGAAGAATGAGCCTCCACTTACTTGCCCGTACAGCTTGA
AGGCCAGAGTTCTTTTACTATCTCATCTTGCTAGGATGAAAATTCCTGAAACACTTGAAGAAGATCAACAATTTGTCCTG
AAAAAATGCCCTGCCTTACTTCAAGAAATGGTTAATGTAATCTGTCAACTAATAATAATGGCTCGGAGCCGTGAAGAAAG
GGAGTTTCGTGCTCCAACTTTGGGATCCCTGGAAAACTGTATGAAGCTTTCCCAGATGTCTGTTCAAGGGCTTCAGCAAT
TTAAATCTCCCCTTCTTCAGCTCCCTCATATTGAAGAGGACAATCTTAGAAGGGTTTCTAATCATAAAAAGTTTAAAATC
AAAACTATCCAGGATTTAGTGAGTTTAAAAGAATCTGATCGCCGCAACTTACTACACTTCCTAGAAGATGAAAAATATGA
AGAAGTTATGGCTGTCCTTGGGAGTTTTCCATTTGTGACAATGGACATAAAATCACAGGTATTAGATGATGAAGATAGCA
ATAATATCACAGTAGGATCTCTTGTCACAGTATTGGTCAAATTGACAAAGCAGACAATGGCAGAAGTATTTGAAAAGGAA
CAGTCCATCTGTGCTGCAGAAGAGCAGCCAGCAGAAGATGGGCAAGGTGATGCAAACAAAAATAAGAGTAAAGGATGGCA
GCAGAAGAGTAAAGGACCTAAGAAAACTGCTAAATCAAAAAAAAAGAAACCTTTGAAAAAAAAGACAGCATCTGTTCCAT
TGCCTCAGACAAAGCAGCAGAAGCAAAAGCAGGCAAATGGGATTGTTGGGAGTGAAGCTGCCATAAAAGAAAATGAAGAT
GACATATCTGACAAAGGCAGTGACTCTGAGGAAGAAGAAACAAATAAGGACTCCCAAAGTGAAAAAGATGATGGAAGTGA
CCGAGACTCTGACAGAGAACAAGATGAAAAACAAAACAAAGATGATGAAGCAGAGTGGCAAGAATTGCAACAAAGTATAC
AGCGGAAGGAAAGAGCTCTGCTAGAAACCAAATCAAAGATAACACACCCGGTTTACAGTCTTTACTTTCCTGAGGAAAAA
CAGGAGTGGTGGTGGCTTTATATTGCTGATAGAAAGGAACAAACATTGATCTCTATGCCATATCACGTGTGCACATTAAA
AGATATGGAAGAGGTAGAACTGAAATTCCCTGCTCCAGGAAAACCTGGAAATTATCAGTATACAGTGTATCTAAGATCAG
ATTCCTATATGGGTTTGGACCAGATTAAACCATTGAAGTTGGAAGTTCATGAAGCTAAGCCAGTGCCAGAAAATCATCCA
CAATGGGATACAGCAATAGAGGGAGATGTAGACCAGGAAGATAGTGAAGGCTTTGAAGATAGTTTTGAAGAAGAAGAGGA
GGAAGAAGATGATGATGAC

ORF - retro_mdom_1721 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 96.29 %
Parental protein coverage: 88.67 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalLFLAYKVSKTDREYQEYNPYEVLNLDPGATVTEIKKQYRLLSLKYHPDKGGDEVMFMRIAKAYAALTDEE
.F.....S...REYQEYNPYEVLNLDPGATVTEIKKQYRLLSLKYHPDKGGDEVMFMRIAKAYAALTDEE
RetrocopyVFIPCIQSFQNREYQEYNPYEVLNLDPGATVTEIKKQYRLLSLKYHPDKGGDEVMFMRIAKAYAALTDEE
ParentalSRKNWEEYGNPDGPQATSFGIALPAWIVDQKNSILVLLVYGLAFMVILPVVVGSWWYRSIRYSGDQILIR
SRKNWEEYGNPDGPQATS.GIALPAWIVDQKNSILVLLVYGLAFMVILPVVVGSWWYRSIRYSGDQILIR
RetrocopySRKNWEEYGNPDGPQATSSGIALPAWIVDQKNSILVLLVYGLAFMVILPVVVGSWWYRSIRYSGDQILIR
ParentalTTQIYTYFVYKTRNMDMKRLIMVLAGASEFDPQYNKDATSRPADNIQIPQLIREIGSINLKKNEPPLTCP
TTQIYTYFVYKTRNMDMKRLIMVLAGASEFDPQYNKDATSRPADNIQIPQLIREIGSINLKKNEPPLTCP
RetrocopyTTQIYTYFVYKTRNMDMKRLIMVLAGASEFDPQYNKDATSRPADNIQIPQLIREIGSINLKKNEPPLTCP
ParentalYSLKARVLLLSHLARMKIPETLEEDQQFVLKKCPALLQEMVNVICQLIIMARSREEREFRAPTLGSLENC
YSLKARVLLLSHLARMKIPETLEEDQQFVLKKCPALLQEMVNVICQLIIMARSREEREFRAPTLGSLENC
RetrocopyYSLKARVLLLSHLARMKIPETLEEDQQFVLKKCPALLQEMVNVICQLIIMARSREEREFRAPTLGSLENC
ParentalMKLSQMSVQGLQQFKSPLLQLPHIEEDNLRRVSNHKKFKIKTIQDLVSLKESDRRNLLHFLEDEKYEEVM
MKLSQMSVQGLQQFKSPLLQLPHIEEDNLRRVSNHKKFKIKTIQDLVSLKESDRRNLLHFLEDEKYEEVM
RetrocopyMKLSQMSVQGLQQFKSPLLQLPHIEEDNLRRVSNHKKFKIKTIQDLVSLKESDRRNLLHFLEDEKYEEVM
ParentalAVLGSFPFVTMDIKSQVLDDEDSNNITVGSLVTVLVKLTRQTMAEVFEKEQSICAAEEQPAEDGASDANK
AVLGSFPFVTMDIKSQVLDDEDSNNITVGSLVTVLVKLT.QTMAEVFEKEQSICAAEEQPAEDG..DANK
RetrocopyAVLGSFPFVTMDIKSQVLDDEDSNNITVGSLVTVLVKLTKQTMAEVFEKEQSICAAEEQPAEDGQGDANK
ParentalNKSKGWQQKSKGPKKTAKSKKKKPLKKKTASVPLPQTKQQKQKQANGIVGSEAAIKEDEDDISDKGSDSE
NKSKGWQQKSKGPKKTAK..........TASVPLPQTKQQKQKQANGIVGSEAAIKE.EDDISDKGSDSE
RetrocopyNKSKGWQQKSKGPKKTAKXXXXXXXXXXTASVPLPQTKQQKQKQANGIVGSEAAIKENEDDISDKGSDSE
ParentalEEETNKDSQSEKDDGSDRDSDREQDEKQNKDDEAEWQELQQSIQRKERALLETKSKITHPVYSLYFPEEK
EEETNKDSQSEKDDGSDRDSDREQDEKQNKDDEAEWQELQQSIQRKERALLETKSKITHPVYSLYFPEEK
RetrocopyEEETNKDSQSEKDDGSDRDSDREQDEKQNKDDEAEWQELQQSIQRKERALLETKSKITHPVYSLYFPEEK
ParentalQEWWWLYIADRKEQTLISMPYHVCTLKDMEEVELKFPAPGKPGNYQYTVYLRSDSYMGLDQIKPLKLEVH
QEWWWLYIADRKEQTLISMPYHVCTLKDMEEVELKFPAPGKPGNYQYTVYLRSDSYMGLDQIKPLKLEVH
RetrocopyQEWWWLYIADRKEQTLISMPYHVCTLKDMEEVELKFPAPGKPGNYQYTVYLRSDSYMGLDQIKPLKLEVH
ParentalEAKPVPENHPQWDTAIEGDEDQEDSEGFEDSFEEEEEEEDDDD
EAKPVPENHPQWDTAIEGD.DQEDSEGFEDSFEEEEEEEDDDD
RetrocopyEAKPVPENHPQWDTAIEGDVDQEDSEGFEDSFEEEEEEEDDDD

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_1721 retrocopy.

TSS - click to see more details

Monodelphis domestica was not studied using FANTOM5 data.

Lab - click to see more details

retro_mdom_1721 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 ENSMODG00000018012 1 retrocopy
retro_mdom_1721 ,


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