RetrogeneDB ID:

retro_mdom_279

Retrocopy
location
Organism:Opossum (Monodelphis domestica)
Coordinates:1:576318899..576320768(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMODG00000010492
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSMODG00000008679
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_mdom_279
ATGGCGTCCACGGACTATAGTACCTACAGTCAAGCTGCAGCCCAGCAGGACTACAGTGCTTATGCAGCCCAGCCAGCTCA
AGGATATGCACAGACCACCCAGGCATGTGGGCAACAAAGTTATGGAGACTATGAGCAGCCTACTGATGTCAGCTATACAC
AGGCTCAAACAACTGCGATGTATGGGCAGACTGCGTATGCAACCTCTTATGGACAGCCTCCAACAGGTTATACTACACCA
ACCTCACCTCAGGCTTACAGTCAGCCTGTCCAAGAATATGGCCCGGGGGCCTACGATACCACCACTGCTACAGTTACGAC
CACCCAAGCATCCTATGCAGCCCAATCTGCATATGGCACCCAGCCTGCTTACCCAACCTATGGGCAGCAGCCAGCAAGAC
CCCAGGATGGTAGCAAGCCCGCTGAGACTAGTCAGCCTCAATCTAGTACAGCAGGCTACAGCCAACCCAGCCTAGGATAC
GGGCAGAGCAACTACAGTTACCCACAGGGGCCCGGCAGCGACCCCAGGCAGCCAGTCACCGCACCTCCTTCCTATCCTCC
AACCAGCTATTCCTCTACGCAGCCGACTAGTTACGATGAGAGCAGTTACTCCCAGCAGAATACCTATGGGCAGCAGAGCA
TTTATGGACAGCAGAGTGGCTATGGTCAACAGCCCCCCACGAGTGGGCCCCCCCAAACTGGATCCTACAGCCAGGCTCCA
AGTCAATCTAGCCAACAGAGCAGCAGCTACGGGCAGCAGAGTGCCTTCCAGCAGGACCATCCCAGTAGCATGGGTGTATA
TGGGCAGGAGTCTGGAGGCTTTTCCGGATCTGGAGAAAACCAGAGCATGAGTGGCCCTGATGACCCGGGCAGGGGAAGAG
GGGGATTTGATTGTGGAGGCATGAGCAGAGGTGGGCGGGGAGGAGGGGGAGGAGGACACGGTGGAATGGGCAGCGCTGGA
GAGCGAGGTGGCTTCAGTAAGCCTGGTGGACCTATGGAAGAAGCACCAGACCTTGACTTGGGCCCACCTGTAGATCCAGA
TGAAGACCCTGAAAACAGTGCAATTTATGTACAGGGCCTGAACGAAAGCGTGACTGCTGATGAGCTGGCAGACTTTTTCA
AACAGTGTGGGGTTGTCAAGATGAACAAAAGGACTGGGCAGCCGGTGATTAACATTTACTTAGACAAGGAAACCGGGAAA
CCCAAAGGAGATGCCACCGTGTCCTATGATGACCCACCTACTGCAAAGGCTGCAGTAGAATGGTTTGATGGGAAAGATTT
CCAAGGGAGCAAACTCAAAGTGTCTCTTGCTCGAGGTGGTATGCCACCCCGTGAAGGCAGAGGGATGCCTCCCCCTCTCC
GAGGAGGTCCTGAAGGACCAGGGGGGCCAGGAGGTCCCATGGGTCGAATGGGAGGCAGAGGAGGAGACAGGGAAGGTTTT
CCACCAAGAGGACCCAGGGGTTCCCGTGGAAACCCCTCAGGAGGAGAAAATGTCCAGCACAGAGCAGGGGATTGGCAGTG
CCCTAATCCAGGCTGCGGAAACCAGAATTTTGCCTGGAGAACAGAGTGTAATCAATGCAAGGCCCCTAAGCCAGAGGGCA
GAGGTGGCCCCGGTGGCATGAGGAGTGGCAGAGGTGGGCTCATGGACCATGGTGGGCCTGGCGGTATGTTCCGAGGAGGC
CGAGGTGGAGACAGAGGCGACTTTCGGGGAGGTCGAGGCATGGACCAAGGGGACTTTGGTGGAGGAAGAAGAAGAGGCCC
TGGGGGTCCTCCCAGACCTCTCATGGAGCAAATGGGTGGCAGAAGAGGAGGGCATGGCAGGCCTGGAAAAGGTGAGCGTC
GCCAGGAGCGCAGAGACCGGCCCTACTAG

ORF - retro_mdom_279 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 72.44 %
Parental protein coverage: 67.32 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalTTTQASYAAQSAYGTQPAYPTYGQQPATAAPARPQDGSKPAETSQPQSSTAGYSQPSLGYGQSNYSYPQV
TTT......Q..Y..Q.A...YG.QP..A.P...Q....P...S.P.......S....GY.Q....Y.Q.
RetrocopyTTTATVTTTQASYAAQSA---YGTQP--AYPTYGQQPARPQDGSKPAETSQPQSSTA-GYSQPSLGYGQS
ParentalPGSYPMQPVTAP--PSYPPTSYSSTQPTSYDQSSYSQQNTYGQQSSYGQQSSYGQQSSYGQQPPTSYPPQ
..SYP..P...P..P...P.SY..T...S....SY.....Y.QQ..YGQQS.YGQQS.YGQQPPTS.PPQ
RetrocopyNYSYPQGPGSDPRQPVTAPPSYPPTSYSSTQPTSYDE-SSYSQQNTYGQQSIYGQQSGYGQQPPTSGPPQ
ParentalTGSYSQAPSQYSQQSSSYGQQSAFRQDHPSSMGVYGQESGGFSGPGENRSMSGPDNRGRGRGGFDRGGMS
TGSYSQAPSQ.SQQSSSYGQQSAF.QDHPSSMGVYGQESGGFSG.GEN.SMSGPD..GRGRGGFD.GGMS
RetrocopyTGSYSQAPSQSSQQSSSYGQQSAFQQDHPSSMGVYGQESGGFSGSGENQSMSGPDDPGRGRGGFDCGGMS
ParentalRGGRGGGGGGRGGMG-AGERGGFNKPGGPMEEGPDLDLGSPVDPDEDSENSAIYVQGLNESVTADELADF
RGGRGGGGGG.GGMG.AGERGGF.KPGGPMEE.PDLDLG.PVDPDED.ENSAIYVQGLNESVTADELADF
RetrocopyRGGRGGGGGGHGGMGSAGERGGFSKPGGPMEEAPDLDLGPPVDPDEDPENSAIYVQGLNESVTADELADF
ParentalFKQCGVVKMNKRTGQPMINIYLDKETGKPKGDATVSYDDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPP
FKQCGVVKMNKRTGQP.INIYLDKETGKPKGDATVSYDDPPTAKAAVEWFDGKDFQGSKLKVSLAR...P
RetrocopyFKQCGVVKMNKRTGQPVINIYLDKETGKPKGDATVSYDDPPTAKAAVEWFDGKDFQGSKLKVSLARGGMP
ParentalMNSMRGGMPPREGRGMPPPLRGGPGGPGGPGGPMGRMGGRGGDRGGFPPRGPRGSRGNPSGGGNVQHRAG
....RG..PP..G....P...GGPGGP.G....MG..GG...DR.GFPPRGPRGSRGNPSGG.NVQHRAG
RetrocopyPREGRGMPPPLRGGPEGP---GGPGGPMG---RMGGRGG---DREGFPPRGPRGSRGNPSGGENVQHRAG
ParentalDWQCPNPGCGNQNFAWRTECNQCKAPKPEG
DWQCPNPGCGNQNFAWRTECNQCKAPKPEG
RetrocopyDWQCPNPGCGNQNFAWRTECNQCKAPKPEG

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 7 .03 RPM 0 .00 RPM
SRP007412_cerebellum 9 .14 RPM 0 .00 RPM
SRP007412_heart 5 .18 RPM 0 .00 RPM
SRP007412_kidney 0 .00 RPM 0 .00 RPM
SRP007412_liver 4 .53 RPM 0 .00 RPM
SRP007412_testis 11 .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_279 retrocopy.

TSS - click to see more details

Monodelphis domestica was not studied using FANTOM5 data.

Lab - click to see more details

retro_mdom_279 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 17 parental genes, and 30 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000082982 retrocopies
retro_amel_191, retro_amel_959,
Canis familiaris ENSCAFG000000121608 retrocopies
retro_cfam_1142, retro_cfam_1183, retro_cfam_1225, retro_cfam_133, retro_cfam_1397, retro_cfam_1736, retro_cfam_1889, retro_cfam_560,
Callithrix jacchus ENSCJAG000000199874 retrocopies
retro_cjac_1716, retro_cjac_2022, retro_cjac_2813, retro_cjac_2911,
Cavia porcellus ENSCPOG000000095021 retrocopy
retro_cpor_1353,
Felis catus ENSFCAG000000042431 retrocopy
retro_fcat_519,
Homo sapiens ENSG000001829441 retrocopy
retro_hsap_463,
Gorilla gorilla ENSGGOG000000122121 retrocopy
retro_ggor_444,
Macropus eugenii ENSMEUG000000087031 retrocopy
retro_meug_1424,
Myotis lucifugus ENSMLUG000000120581 retrocopy
retro_mluc_328,
Monodelphis domestica ENSMODG00000008679 1 retrocopy
retro_mdom_279 ,
Mustela putorius furoENSMPUG000000134322 retrocopies
retro_mputfur_56, retro_mputfur_572,
Mus musculus ENSMUSG000000090791 retrocopy
retro_mmus_1379,
Oryctolagus cuniculus ENSOCUG000000044322 retrocopies
retro_ocun_1346, retro_ocun_242,
Pongo abelii ENSPPYG000000116841 retrocopy
retro_pabe_1769,
Pan troglodytes ENSPTRG000000142181 retrocopy
retro_ptro_350,
Ictidomys tridecemlineatus ENSSTOG000000231771 retrocopy
retro_itri_1892,
Tursiops truncatus ENSTTRG000000118811 retrocopy
retro_ttru_1366,


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