RetrogeneDB ID:

retro_mdom_8

Retrocopy
location
Organism:Opossum (Monodelphis domestica)
Coordinates:Un:19004539..19006090(-)
Located in intron of:ENSMODG00000027637
Retrocopy
information
Ensembl ID:ENSMODG00000022806
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:TBL1XR1
Ensembl ID:ENSMODG00000021312
Aliases:None
Description:F-box-like/WD repeat-containing protein TBL1XR1 [Source:RefSeq peptide;Acc:NP_001239539]


Retrocopy-Parental alignment summary:






>retro_mdom_8
AAGATGAGTATAAGCAGTGATGAGGTCAACTTCTTGGTATATAGATACTTGCAAGAGTCAGGGTTTTCTCATTCAGCATT
TACCTTTGGTATAGAAAGCCATATCAGCCAGTCTAATATCAATGGTGCCCTGGTTCCACCCGCTGCTCTGATTTCTATCA
TCCAGAAAGGCCTGCAGTATGTAGAGGCAGAAGTCAGTATTAATGAGGACGGTACCTTGTTTGATGGAAGACCTATAGAA
TCTTTGTCACTGATCGATGCCGTGATGCCTGACGTGGTTCAAACCAGACAGCAAGCCTACAGAGATAAACTTGCCCAACA
ACAGGCCGCAGCAGCTGCTGCCACTGCCGCTGCCACAACCAACCAACAGGGCTCCGCGAAAAATGGAGAAAATACTGCAA
ATGGAGAAGAAAATGGAGCCCATAGTATAGCAAATAACCATACGGATATGATGGAAGTGGATGGCGATGTTGAAATCCCC
CCAAACAAAGCTGTGGTATTACGGGGTCATGAGTCAGAAGTATTCATCTGTGCCTGGAATCCCGTCAGTGACCTTCTGGC
CTCAGGATCTGGTGACTCAACAGCGAGAATATGGAATCTGAGTGAGAACAGCACAAGCGGTTCGACCCAGTTAGTCCTCC
GCCATTGCATAAGGGAAGGCGGGCAGGACGTGCCCAGCAACAAAGACGTGACGTCCCTCGACTGGAATAGTGAAGGCACA
CTTCTCGCCACTGGGTCATATGATGGATTTGCCAGAATATGGACTAAAGATGGTAATCTTGCTAGCACCTTGGGACAACA
TAAAGGTCCTATTTTTGCATTAAAATGGAACAAGAAAGGAAATTTCATACTGAGTGCAGGAGTAGACAAGACCACGATTA
TCTGGGATGCACATACTGGTGAAGCCAAACAGCAGTTCCCTTTTCATTCAGCACCGGCACTGGACGTGGATTGGCAGAGC
AACAATACCTTTGCCTCTTGCAGCACCGATATGTGCATTCATGTCTGTAAATTGGGACAAGATAGACCTATCAAGACATT
CCAGGGACACACAAACAAAGTAAATGCTATCAAATGGGACCCAACTGGTAACCTTCTGGCCTCCTGTTCTGATGACATGA
CTTTAAAGATATGGAGTATGAAGCAAGAGAGTTGTGTCCATGATTTGCAAGCACATAATAAAGAAATTTATACTATCAAA
TGGAGTCCAACAGGACCAGGAACAAACAATCCAAACGCCAACCTCATGCTAGCCAGCGCATCCTTTGACTCCACCGTTCG
GTTATGGGATGTGGACCGGGGCATCTGCATCCACACTTTGACGAAGCACCAAGAGCCTGTGTACAGTGTGGCATTCAGTC
CTGACGGCAGGTACCTGGCCAGCGGCTCCTTTGACAAGTGTGTGCATATCTGGAACACGCAGATGGGTGCCCTAGTTCAT
AGCTATAGGGGAACAGGCGGAATATTTGAGGTTTGCTGGAACGCGGCCGGAGACAAAGTTGGAGCCAGTGCGTCAGATGG
TTCAGTTTGTGTACTAGACCTACGGAAATAG

ORF - retro_mdom_8 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 99.61 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMSISSDEVNFLVYRYLQESGFSHSAFTFGIESHISQSNINGALVPPAALISIIQKGLQYVEAEVSINEDG
MSISSDEVNFLVYRYLQESGFSHSAFTFGIESHISQSNINGALVPPAALISIIQKGLQYVEAEVSINEDG
RetrocopyMSISSDEVNFLVYRYLQESGFSHSAFTFGIESHISQSNINGALVPPAALISIIQKGLQYVEAEVSINEDG
ParentalTLFDGRPIESLSLIDAVMPDVVQTRQQAYRDKLAQQQAAAAAATAAATTNQQGSAKNGENTANGEENGAH
TLFDGRPIESLSLIDAVMPDVVQTRQQAYRDKLAQQQAAAAAATAAATTNQQGSAKNGENTANGEENGAH
RetrocopyTLFDGRPIESLSLIDAVMPDVVQTRQQAYRDKLAQQQAAAAAATAAATTNQQGSAKNGENTANGEENGAH
ParentalSIANNHTDMMEVDGDVEIPPNKAVVLRGHESEVFICAWNPVSDLLASGSGDSTARIWNLSENSTSGSTQL
SIANNHTDMMEVDGDVEIPPNKAVVLRGHESEVFICAWNPVSDLLASGSGDSTARIWNLSENSTSGSTQL
RetrocopySIANNHTDMMEVDGDVEIPPNKAVVLRGHESEVFICAWNPVSDLLASGSGDSTARIWNLSENSTSGSTQL
ParentalVLRHCIREGGQDVPSNKDVTSLDWNSEGTLLATGSYDGFARIWTKDGNLASTLGQHKGPIFALKWNKKGN
VLRHCIREGGQDVPSNKDVTSLDWNSEGTLLATGSYDGFARIWTKDGNLASTLGQHKGPIFALKWNKKGN
RetrocopyVLRHCIREGGQDVPSNKDVTSLDWNSEGTLLATGSYDGFARIWTKDGNLASTLGQHKGPIFALKWNKKGN
ParentalFILSAGVDKTTIIWDAHTGEAKQQFPFHSAPALDVDWQSNNTFASCSTDMCIHVCKLGQDRPIKTFQGHT
FILSAGVDKTTIIWDAHTGEAKQQFPFHSAPALDVDWQSNNTFASCSTDMCIHVCKLGQDRPIKTFQGHT
RetrocopyFILSAGVDKTTIIWDAHTGEAKQQFPFHSAPALDVDWQSNNTFASCSTDMCIHVCKLGQDRPIKTFQGHT
ParentalNEVNAIKWDPTGNLLASCSDDMTLKIWSMKQESCVHDLQAHNKEIYTIKWSPTGPGTNNPNANLMLASAS
N.VNAIKWDPTGNLLASCSDDMTLKIWSMKQESCVHDLQAHNKEIYTIKWSPTGPGTNNPNANLMLASAS
RetrocopyNKVNAIKWDPTGNLLASCSDDMTLKIWSMKQESCVHDLQAHNKEIYTIKWSPTGPGTNNPNANLMLASAS
ParentalFDSTVRLWDVDRGICIHTLTKHQEPVYSVAFSPDGRYLASGSFDKCVHIWNTQTGALVHSYRGTGGIFEV
FDSTVRLWDVDRGICIHTLTKHQEPVYSVAFSPDGRYLASGSFDKCVHIWNTQ.GALVHSYRGTGGIFEV
RetrocopyFDSTVRLWDVDRGICIHTLTKHQEPVYSVAFSPDGRYLASGSFDKCVHIWNTQMGALVHSYRGTGGIFEV
ParentalCWNAAGDKVGASASDGSVCVLDLRK
CWNAAGDKVGASASDGSVCVLDLRK
RetrocopyCWNAAGDKVGASASDGSVCVLDLRK

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_8 retrocopy.

TSS - click to see more details

Monodelphis domestica was not studied using FANTOM5 data.

Lab - click to see more details

retro_mdom_8 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 2 parental genes, and 2 retrocopies.

Species Parental gene accession Retrocopies number
Dasypus novemcinctus ENSDNOG000000023171 retrocopy
retro_dnov_1938,
Monodelphis domestica ENSMODG00000021312 1 retrocopy
retro_mdom_8 ,


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