RetrogeneDB ID:

retro_mdom_1090

Retrocopy
location
Organism:Opossum (Monodelphis domestica)
Coordinates:3:56444981..56446433(-)
Located in intron of:ENSMODG00000015728
Retrocopy
information
Ensembl ID:ENSMODG00000015734
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSMODG00000017657
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_mdom_1090
ATGAACACTGCTGCCAGCAGTTACCCCATGGCCTCCCTATATGTCGGTGACTTGCACTCAGATGTCACCGAAGCCATGCT
GTACGAGAAGTTCAGCCCTGCTGGACCCGTGCTGTCCATTCGGGTCTGCAGGGACATGATTACCAGGCGCTCCCTGGGAT
ATGCCTATGTCAACTTTCAGCAACCAGCTGATGCTGAAAGGGCCCTGGATACCATGAACTTTGATGTCATTAAAGGCAAA
CCAATCCGTATCATGTGGTCTCAACGGGATCCCTCCTTGAGGAAATCAGGAGTTGGGAATGTTTTCATTAAAAACCTGGA
TAAGTCCATAGACAACAAGGCACTTTATGACACCTTTTCAGCATTTGGGAACATCTTGTCCTGCAAGGTGGTGTGTGATG
AAAATGGTTCTAAAGGCTACGCATTTGTGCACTTTGAGACCCAGGATGCTGCAGATAGGGCCATCGAGAAGATGAACGGC
ATGCTTCTCAACGACCGAAAAGTGTTTGTTGGTAGATTCAAGTCAAGGAAAGAACGGGAAGCAGAGCTGGGAGCCAAAGC
TAAGGAATTCACCAATGTGTACATCAAAAACTTTGGTGATGATATGGATGATGGAAGACTGAAGGAGCTTTTCAGCAAAT
ATGGTAAAACTCTTAGTGTCAAAGTGATGACTGATCCTAGTGGAAAATCCAAAGGCTTTGGCTTTGTGAGTTTTGAGAAG
CATGAAGATGCCAATAAGGCAGTTGAAGAAATGAATGGAAAAGACATCAATGGAAAGATGGTATTTGTAGGCCGGGCACA
GAAAAAAGTTGAACGCCAGGCTGAATTAAAACGGAAATTTGAGCAGCTAAAACAAGAGAGAATCAGCCGCTACCAGGGGG
TGAATCTCTATATTAAGAACTTGGATGACACCATTGATGATGAAAAATTAAGGAAGGAATTTTCTCCTTTTGGATCAATT
ACCAGTGCCAAGGTGATGCTCGAGGATGGGAGAAGTAAAGGCTTTGGCTTTGTCTGCTTCTCTTCGCCTGATGAGGCAAC
CAAAGCAGTAACAGAAATGAATGGGCGCATTGTGGGCTCAAAGCCCTTGTATGTTGCACTTGCACAGAGGAAAGAAGAAA
GGAAAGCTCACCTAACCAATCAGTATATGCAGCGTATTGCAGGAATGAGAGCCCTACCTGCCAACACTATCATCAATCAG
TTTCAGCCAACTCCTGGGGGCTACTTCATGCCAGCAGTGCCCCAGGCTCAGAATAGACCTCCTTATTATGCTCCCAATCA
GATAGCCCAGATGAGACCCAATCCCCGATGGCAACAAGGTGGAAGACCTCAAGGCTTTCAAGGAGTACCAAACACCATTC
GTCAGTCTGGGCCATGCCCTGCTCTTCGACACCTGACTCCAGCCAGTAATACCCAGGCTTCTCGAGGGCTCCCTACTACT
CCTCAGAGAGTG

ORF - retro_mdom_1090 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 99.59 %
Parental protein coverage: 73.93 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMNTAASSYPMASLYVGDLHSDVTEAMLYEKFSPAGPVLSIRVCRDMITRRSLGYAYVNFQQPADAERALD
MNTAASSYPMASLYVGDLHSDVTEAMLYEKFSPAGPVLSIRVCRDMITRRSLGYAYVNFQQPADAERALD
RetrocopyMNTAASSYPMASLYVGDLHSDVTEAMLYEKFSPAGPVLSIRVCRDMITRRSLGYAYVNFQQPADAERALD
ParentalTMNFDVIKGKPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGY
TMNFDVIKGKPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGY
RetrocopyTMNFDVIKGKPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGY
ParentalAFVHFETQDAADRAIEKMNGMLLNDRKVFVGRFKSRKEREAELGAKAKEFTNVYIKNFGDDMDDGRLKEL
AFVHFETQDAADRAIEKMNGMLLNDRKVFVGRFKSRKEREAELGAKAKEFTNVYIKNFGDDMDDGRLKEL
RetrocopyAFVHFETQDAADRAIEKMNGMLLNDRKVFVGRFKSRKEREAELGAKAKEFTNVYIKNFGDDMDDGRLKEL
ParentalFSKYGKTLSVKVMTDPSGKSKGFGFVSFEKHEDANKAVEEMNGKDINGKMVFVGRAQKKVERQAELKRKF
FSKYGKTLSVKVMTDPSGKSKGFGFVSFEKHEDANKAVEEMNGKDINGKMVFVGRAQKKVERQAELKRKF
RetrocopyFSKYGKTLSVKVMTDPSGKSKGFGFVSFEKHEDANKAVEEMNGKDINGKMVFVGRAQKKVERQAELKRKF
ParentalEQLKQERISRYQGVNLYIKNLDDTIDDEKLRKEFSPFGSITSAKVVMLEDGRSKGFGFVCFSSPDEATKA
EQLKQERISRYQGVNLYIKNLDDTIDDEKLRKEFSPFGSITSAKV.MLEDGRSKGFGFVCFSSPDEATKA
RetrocopyEQLKQERISRYQGVNLYIKNLDDTIDDEKLRKEFSPFGSITSAKV-MLEDGRSKGFGFVCFSSPDEATKA
ParentalVTEMNGRIVGSKPLYVALAQRKEERKAHLTNQYMQRIAGMRALPANTIINQFQPTPGGYFMPAVPQAQNR
VTEMNGRIVGSKPLYVALAQRKEERKAHLTNQYMQRIAGMRALPANTIINQFQPTPGGYFMPAVPQAQNR
RetrocopyVTEMNGRIVGSKPLYVALAQRKEERKAHLTNQYMQRIAGMRALPANTIINQFQPTPGGYFMPAVPQAQNR
ParentalPPYYAPNQIAQMRPNPRWQQGGRPQGFQGVPNTIRQSGPRPALRHLTPASNTQASRGLPTTPQRV
PPYYAPNQIAQMRPNPRWQQGGRPQGFQGVPNTIRQSGP.PALRHLTPASNTQASRGLPTTPQRV
RetrocopyPPYYAPNQIAQMRPNPRWQQGGRPQGFQGVPNTIRQSGPCPALRHLTPASNTQASRGLPTTPQRV

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






(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
Monodelphis domestica was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_mdom_1090 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_1090 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 28 parental genes, and 65 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000115352 retrocopies
Bos taurus ENSBTAG000000171253 retrocopies
Canis familiaris ENSCAFG000000030812 retrocopies
Choloepus hoffmanni ENSCHOG000000053273 retrocopies
Callithrix jacchus ENSCJAG000000025123 retrocopies
Cavia porcellus ENSCPOG000000095522 retrocopies
Equus caballus ENSECAG000000093962 retrocopies
Felis catus ENSFCAG000000152542 retrocopies
Homo sapiens ENSG000000906212 retrocopies
Gorilla gorilla ENSGGOG000000040023 retrocopies
Loxodonta africana ENSLAFG000000001513 retrocopies
Microcebus murinus ENSMICG000000166331 retrocopy
Myotis lucifugus ENSMLUG000000120682 retrocopies
Macaca mulatta ENSMMUG000000074971 retrocopy
Monodelphis domestica ENSMODG000000062224 retrocopies
Monodelphis domestica ENSMODG00000017657 2 retrocopies
retro_mdom_1090 , retro_mdom_1805,
Mustela putorius furoENSMPUG000000144142 retrocopies
Mus musculus ENSMUSG000000112577 retrocopies
Nomascus leucogenys ENSNLEG000000119282 retrocopies
Oryctolagus cuniculus ENSOCUG000000005622 retrocopies
Otolemur garnettii ENSOGAG000000040671 retrocopy
Ochotona princeps ENSOPRG000000119841 retrocopy
Pongo abelii ENSPPYG000000015062 retrocopies
Pan troglodytes ENSPTRG000000005733 retrocopies
Rattus norvegicus ENSRNOG000000156422 retrocopies
Sarcophilus harrisii ENSSHAG000000181391 retrocopy
Sus scrofa ENSSSCG000000036603 retrocopies
Tursiops truncatus ENSTTRG000000143402 retrocopies



Copyright © RetrogeneDB 2014-2017