RetrogeneDB ID:

retro_mdom_143

Retrocopy
location
Organism:Opossum (Monodelphis domestica)
Coordinates:1:294954738..294956670(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMODG00000023896
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSMODG00000017949
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_mdom_143
ATGGGGCGGAGATCTACATCATCCACCAAGAGTGGGAAGTTCATGAACCCCACTGACCAGGCTCAAAAAGAAGCCCGGAA
GAGGGAATTAAAAAAGAATAAGAAACAACGAATGATGGTACGAGCTGCAGTACTAAAGATGAAGGATCCCAAACAAATTA
TCCGGGACATGGAGAAATTAGATGAGATGGAGTTCAATCCAGTACAGCAACCACAACTAAATGAGAAGGTGCTAAAAGAT
AAACGAAAAAAGCTTCGTGAAACTTTTGAGCGCATTCTCCGACTCTATGAAAAGGAAAATCCAGATATCTACAAAGAACT
TAGAAAGTTAGAGGTAGAATATGAGCAGAAAAGGGCCCAACTCAGTCAATACTTTGATGCAGTAAAGAATGCTCAACATG
TTGAAGTGGAAAGCATCCCATTGCCAGATATGCCTCATGCTCCTTCTAACATCTTGATCCAAGACATCCCATTGCCTGGT
GCACAGCCACCCTCTATTCTCAAAAAAACCTCTGCCTATGGACCTCCCACCAGGGCAATTTCTATACTTCCTCTTCTTGG
ACATGGTGTCCCTCGTTTGCCTCCTGGCAGAAAGCCTCCTGGGCCACCTCCTGGACCACCTCCTCCCCAAGTTCTGCAGA
TGTATGGTCGTAAAGTGGGCTTTGCCCTAGAACTTGCCCCTCCGCGGCGAGAGGAGGACATTTTATATAGTCCAGACCCT
GCTCATCGAAGTCATGATGATGATGCTTCCAGCACGAGTGAAGATGAAGGTTATCCTGAAGACATGGATCAAGATAAGCA
TGATGACAGCAGTGATGACAGTGACACTGATAGGTCAGATGCCGACAGTGAAGGAGAGGAGTTCATGCATCGTGATGAAG
AAGAGAGAGAGACTAATGAGGACAAAAAGTCAGGTCTGAGTGTACAATTTGCTGATGTTCCTGGAAAATCACGAAAGAAA
AAGAAAAACATGAAGGAATTAACACCTCTTCAAGCTATGATGCTTAGAATGGCAGGTCAAGAAATTCCTGAAGAGGGCCG
AGAAGTGGAAGAATTTTCAGAGGATGATGATGAGGAGGATTCTGATGACTCGGAGTCAGAGGACACAGCACAGCAGCAGC
ACAAAGAAGACTCTCTTCCTGATGGGGCAGCATCATCTCCTGCTTCCCAACAACAGCAGCCACCTCCACAATCTGTTCCT
CCTGCTCAAATACAGGCACCTCCCATGCCAGGACCACCCCCTCTTGGACCACCACCTGCTCCACCATTACGACCACCTGG
ACCACCCACTGGCCTTCCTCCTGGTCCACCTCCAGGAGCTCCTCCATTTTTAAGACCACCTGGAATGCCAGGGCTTCGAG
GGCCTTTACCCCGGCTTCTACCTCCTGGTCCTCCACCAGGCAGGCCTCCTGGTCCACCACCAGGCCCACCTCCTGGTCTT
CCTCCTGGTCCTCCTCCACGAGGACCACCTCCAAGGTTACCTCCCCCAGCACCTCCAGGCATCCCTCCACCTAGTCCTGG
TATGATGCGCCCACCTTTGGTGCCTCCTCTTGGACCTGCTCCACCTGGGCTTTTTCCACCAGCTCCCTTACCGAATCCAG
GGGTTTTAAGTGCCCCACCCAATTTGATTCAGAGACCCAAAGTGGATAATACCAGTGCAGCCACTATTGAGAAGAAAGCC
ACAGCAACCATCAGTGCCAAGCCACAAATCACTAATCCCAAGGCAGAAATTACCAGGTTTGTGCCCACTGCACTGAGAGT
TCGACGAGAGAACAAAGGAGCTACTGCTGCTCCCCAAAGAAAATCAGAAGAGGATTCTACTATACCCCTTGCCAAAGCAG
TCCCCAAATCTGGCCCCTCTGCTCCTGTTTCAGTACAAACCAAGGATGATGTGTATGAAGCCTTCATGAAAGAGATGGAG
GGGCTACTGTGA

ORF - retro_mdom_143 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 99.07 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalMGRRSTSSTKSGKFMNPTDQARKEARKRELKKNKKQRMMVRAAVLKMKDPKQIIRDMEKLDEMEFNPVQQ
MGRRSTSSTKSGKFMNPTDQA.KEARKRELKKNKKQRMMVRAAVLKMKDPKQIIRDMEKLDEMEFNPVQQ
RetrocopyMGRRSTSSTKSGKFMNPTDQAQKEARKRELKKNKKQRMMVRAAVLKMKDPKQIIRDMEKLDEMEFNPVQQ
ParentalPQLNEKVLKDKRKKLRETFERILRLYEKENPDIYKELRKLEVEYEQKRAQLSQYFDAVKNAQHVEVESIP
PQLNEKVLKDKRKKLRETFERILRLYEKENPDIYKELRKLEVEYEQKRAQLSQYFDAVKNAQHVEVESIP
RetrocopyPQLNEKVLKDKRKKLRETFERILRLYEKENPDIYKELRKLEVEYEQKRAQLSQYFDAVKNAQHVEVESIP
ParentalLPDMPHAPSNILIQDIPLPGAQPPSILKKTSAYGPPTRAISILPLLGHGVPRLPPGRKPPGPPPGPPPPQ
LPDMPHAPSNILIQDIPLPGAQPPSILKKTSAYGPPTRAISILPLLGHGVPRLPPGRKPPGPPPGPPPPQ
RetrocopyLPDMPHAPSNILIQDIPLPGAQPPSILKKTSAYGPPTRAISILPLLGHGVPRLPPGRKPPGPPPGPPPPQ
ParentalVLQMYGRKVGFALELAPRRREEDILYSPDLAHRSHDDDASSTSEDEGYPEDMDQDKHDDSSDDSDTDRSD
VLQMYGRKVGFALELAP.RREEDILYSPD.AHRSHDDDASSTSEDEGYPEDMDQDKHDDSSDDSDTDRSD
RetrocopyVLQMYGRKVGFALELAPPRREEDILYSPDPAHRSHDDDASSTSEDEGYPEDMDQDKHDDSSDDSDTDRSD
ParentalADSEGEEFMHRDEEERETNEDKKSGLSVRFADVPGKSRKKKKNMKELTPLQAMMLRMAGQEIPEEGREVE
ADSEGEEFMHRDEEERETNEDKKSGLSV.FADVPGKSRKKKKNMKELTPLQAMMLRMAGQEIPEEGREVE
RetrocopyADSEGEEFMHRDEEERETNEDKKSGLSVQFADVPGKSRKKKKNMKELTPLQAMMLRMAGQEIPEEGREVE
ParentalEFSEDDDEEDSDDSESEDTAQQQHKEDSLPDGAASSPASQQQQPPPQSVPPAQIQAPPMPGPPPLGPPPA
EFSEDDDEEDSDDSESEDTAQQQHKEDSLPDGAASSPASQQQQPPPQSVPPAQIQAPPMPGPPPLGPPPA
RetrocopyEFSEDDDEEDSDDSESEDTAQQQHKEDSLPDGAASSPASQQQQPPPQSVPPAQIQAPPMPGPPPLGPPPA
ParentalPPLRPPGPPTGLPPGPPPGAPPFLRPPGMPGLRGPLPRLLPPGPPPGRPPGPPPGPPPGLPPGPPPRGPP
PPLRPPGPPTGLPPGPPPGAPPFLRPPGMPGLRGPLPRLLPPGPPPGRPPGPPPGPPPGLPPGPPPRGPP
RetrocopyPPLRPPGPPTGLPPGPPPGAPPFLRPPGMPGLRGPLPRLLPPGPPPGRPPGPPPGPPPGLPPGPPPRGPP
ParentalPRLPPPAPPGIPPPRPGMMRPPLVPPLGPAPPGLFPPAPLPNPGVLSAPPNLIQRPKVDDTSAATIEKKA
PRLPPPAPPGIPPP.PGMMRPPLVPPLGPAPPGLFPPAPLPNPGVLSAPPNLIQRPKVD.TSAATIEKKA
RetrocopyPRLPPPAPPGIPPPSPGMMRPPLVPPLGPAPPGLFPPAPLPNPGVLSAPPNLIQRPKVDNTSAATIEKKA
ParentalTATISAKPQITNPKAEITRFVPTALRVRRENKGATAAPQRKSEEDSTIPLAKAVPKSGPSAPVSVQTKDD
TATISAKPQITNPKAEITRFVPTALRVRRENKGATAAPQRKSEEDSTIPLAKAVPKSGPSAPVSVQTKDD
RetrocopyTATISAKPQITNPKAEITRFVPTALRVRRENKGATAAPQRKSEEDSTIPLAKAVPKSGPSAPVSVQTKDD
ParentalVYEAFMKEMEGLL
VYEAFMKEMEGLL
RetrocopyVYEAFMKEMEGLL

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 6 .08 RPM 0 .00 RPM
SRP007412_cerebellum 5 .22 RPM 0 .00 RPM
SRP007412_heart 4 .39 RPM 0 .00 RPM
SRP007412_kidney 23 .70 RPM 0 .00 RPM
SRP007412_liver 8 .56 RPM 0 .00 RPM
SRP007412_testis 3 .93 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_143 retrocopy.

TSS - click to see more details

Monodelphis domestica was not studied using FANTOM5 data.

Lab - click to see more details

retro_mdom_143 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 22 parental genes, and 34 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000147591 retrocopy
retro_btau_20,
Canis familiaris ENSCAFG000000129262 retrocopies
retro_cfam_1369, retro_cfam_1911,
Callithrix jacchus ENSCJAG000000216111 retrocopy
retro_cjac_1737,
Homo sapiens ENSG000000844632 retrocopies
retro_hsap_1878, retro_hsap_4719,
Gorilla gorilla ENSGGOG000000044483 retrocopies
retro_ggor_1375, retro_ggor_1711, retro_ggor_2932,
Macropus eugenii ENSMEUG000000139711 retrocopy
retro_meug_1952,
Myotis lucifugus ENSMLUG000000152161 retrocopy
retro_mluc_1074,
Macaca mulatta ENSMMUG000000192991 retrocopy
retro_mmul_1329,
Monodelphis domestica ENSMODG00000017949 1 retrocopy
retro_mdom_143 ,
Mustela putorius furoENSMPUG000000116191 retrocopy
retro_mputfur_280,
Mus musculus ENSMUSG000000302161 retrocopy
retro_mmus_2740,
Nomascus leucogenys ENSNLEG000000039261 retrocopy
retro_nleu_2651,
Oryctolagus cuniculus ENSOCUG000000171771 retrocopy
retro_ocun_974,
Otolemur garnettii ENSOGAG000000105181 retrocopy
retro_ogar_207,
Ochotona princeps ENSOPRG000000150083 retrocopies
retro_opri_107, retro_opri_1159, retro_opri_678,
Pongo abelii ENSPPYG000000043233 retrocopies
retro_pabe_1558, retro_pabe_2099, retro_pabe_3663,
Pan troglodytes ENSPTRG000000047243 retrocopies
retro_ptro_1260, retro_ptro_1637, retro_ptro_3136,
Rattus norvegicus ENSRNOG000000055053 retrocopies
retro_rnor_1287, retro_rnor_2726, retro_rnor_741,
Rattus norvegicus ENSRNOG000000495931 retrocopy
retro_rnor_740,
Sorex araneus ENSSARG000000070851 retrocopy
retro_sara_753,
Sarcophilus harrisii ENSSHAG000000166491 retrocopy
retro_shar_81,
Tupaia belangeri ENSTBEG000000033941 retrocopy
retro_tbel_2213,


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