RetrogeneDB ID:

retro_mdom_1805

Retrocopy
location
Organism:Opossum (Monodelphis domestica)
Coordinates:7:171450532..171451951(-)
Located in intron of:ENSMODG00000015097
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSMODG00000017657
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_mdom_1805
GCTGCCAGCAGTTACCCATGACCTCCCTATATGTCGGTGATTTGCACTCAGGTGGCACCAAAGCCATGCCGTACAAGAAG
TTCAGCCCTGCTGGACCTGTGCTGTCCATCCAGGTCTGCAGGGACATAATAACCAGATGCTCCCTGGGGTATCCTATGTC
AACTTTCAGCAGCCAGCTGATGGCAGAATGTGCCCTGGATACCATGAACTTTGATATAAGTAAAGGCAAACCAATTTGTG
TCATGTGGTCTCAACAGGATCCCATATTGAGGAAATCAGGAGTTGAGAATGTTTTCAATAAAACCTGGATAAGTGCATAG
ACAACAAGGCGCTTTACAATGCCTTTTCAGCATTTGGGAACATCTTGTCCTGCAAGGTGGTGTGTGATGAAAATAGTTCT
AAAGGCTAAGTATTTGTGCACTTTGAGACCCAGGATGCTGCAGATAGGGCCATCAAGAAAATGAATGGCATGCTTCTCAA
CCACTGAAAAGTGTTTGTTGGTAGATTCAAGTCAAGGAAGGAGGGAGAAGCAGAGCTGGGAGCCAAAGCCTTGGAATTCA
CCAATGTGTCCATCAAAAACTTGGTGATGGTATGGATGATGGAAGACTGAAGGGAGCTTTTCAGCAAATATGGTAAAACT
GAGTGTGAAAGCGAAGAAGGATCCTAGTGGAAAATCCAAAGACTTTGGCTTTGTGAGTTTTGAGAAACATGAAGATACCA
ATAAGGCAAGTGAAGAAAAGAATGGAAAAGACATCAATGGAAAATGGTATTTGTAGGCTGGGCACAGAAAAAAGTTGAAC
TCCAGGCTGAATTAAAACAGAAATTCAAACAGAAGAGAATCAGCCACTACCAGGAGGTAAATCTCTATATTAAGAACTTG
GATGACACCACTGATGATGAAAAATTAAGGAAGGAATTTTCTCCTTTTGGATCAATTACCAGCGCCAAGGTGATGCTCGA
GGACAGGAGAAGTAAAGACTTTGGCTTTGTCTGCTTCTCTTCACCTGATGAGGAGACCAAAGCAGTGACATAAATGAATG
GGTGTATTTTGGACTCAAAGCCCCCCATATGTTGCACTTGCACAGAGGAAAGAAAACAAAAAGCCCACCTAACCAATCAA
TATATGCAGAGTATTACAGGAATGAGAGTCCTCCCTGCCAACACTATCATCAACAGTTTCAGCCAACTCCTGGGGGCTAT
TTCATGCCAGCAATGCCCCAGGCTCAGAATATACCTTATTATTGCTGCCAATCAAATAGCCCAGATAAGACTTAATCCCC
ATGGCAACAAGTTGGAAGACCTCAAGGCTTCCAAGGAGTACCAAACACCATTCATCAATCTGGGCCATGCTGGGCTCTTC
AACACCTGACTCCAGCCAGTAACACCCAGGCTTCTCGGGGGCTCCCTACTACACCTCAG

ORF - retro_mdom_1805 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 80.69 %
Parental protein coverage: 73.17 %
Number of stop codons detected: 3
Number of frameshifts detected: 12


Retrocopy - Parental Gene Alignment:

ParentalAASSYP-MASLYVGDLHSDVTEAMLYEKFSPAGPVLSIRVCRDMITRRSLGY-AYVNFQQPAD-AERALD
AASSYP.M.SLYVGDLHS..T.AM.Y.KFSPAGPVLSI.VCRD.ITR.SLGY..YVNFQQPAD.AE.ALD
RetrocopyAASSYP<MTSLYVGDLHSGGTKAMPYKKFSPAGPVLSIQVCRDIITRCSLGY<SYVNFQQPAD>AECALD
ParentalTMNFDVIKGKPIRIMWSQRDPSLRKSGVGNVFIK-NLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKG
TMNFD..KGKPI..MWSQ.DP.LRKSGV.NVF.K.NLDK.IDNKALY..FSAFGNILSCKVVCDEN.SKG
RetrocopyTMNFDISKGKPICVMWSQQDPILRKSGVENVFNK<NLDKCIDNKALYNAFSAFGNILSCKVVCDENSSKG
ParentalYAFVHFETQDAADRAIEKMNGMLLNDRKVFVGRFKSRKEREAELGAKAKEFTNVYIKNF-GDDMDDGRLK
..FVHFETQDAADRAI.KMNGMLLN..KVFVGRFKSRKE.EAELGAKA.EFTNV.IKN..GD.MDDGRLK
Retrocopy*VFVHFETQDAADRAIKKMNGMLLNH*KVFVGRFKSRKEGEAELGAKALEFTNVSIKNL<GDGMDDGRLK
ParentalELF-SKYGKTLSVKVMTDPSGKSKGFGFVSFEKHEDANKAVEEMNGKDINGK-MVFVGRAQKKVERQAEL
..F.S.....LSVK...DPSGKSK.FGFVSFEKHED.NKA.EE.NGKDINGK.MVFVG.AQKKVE.QAEL
RetrocopyGAF<SANMVKLSVKAKKDPSGKSKDFGFVSFEKHEDTNKASEEKNGKDINGK<MVFVGWAQKKVELQAEL
ParentalKRKFEQLKQERISRYQGVNLYIKNLDDTIDDEKLRKEFSPFGSITSAKVVMLEDGRSKGFGFVCFSSPDE
K.KF...KQ.RIS.YQ.VNLYIKNLDDT.DDEKLRKEFSPFGSITSAKV.MLED.RSK.FGFVCFSSPDE
RetrocopyKQKF---KQKRISHYQEVNLYIKNLDDTTDDEKLRKEFSPFGSITSAKV-MLEDRRSKDFGFVCFSSPDE
ParentalATKAVTEMNGRIVGSK-PLYVALAQRKE-ERKAHLTNQYMQRIAGMRALPANTIIN-QFQPTPGGYFMPA
.TKAVT.MNG.I..SK.P.YVALAQRKE...KAHLTNQYMQ.I.GMR.LPANTIIN.QFQPTPGGYFMPA
RetrocopyETKAVT*MNGCILDSK>PPYVALAQRKE<KQKAHLTNQYMQSITGMRVLPANTIIN<QFQPTPGGYFMPA
ParentalVPQAQNRPPYY-APNQIAQMRPNPR-WQQGGRPQGFQGVPNTIRQSGPRPALRHLTPASNTQASRGLPTT
.PQAQN..PYY.A.NQIAQ.R.NP..WQQ.GRPQGFQGVPNTI.QSGP..AL.HLTPASNTQASRGLPTT
RetrocopyMPQAQN-IPYY>AANQIAQIRLNPH<WQQVGRPQGFQGVPNTIHQSGPCWALQHLTPASNTQASRGLPTT
ParentalPQ
PQ
RetrocopyPQ

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_1805 retrocopy.

TSS - click to see more details

Monodelphis domestica was not studied using FANTOM5 data.

Lab - click to see more details

retro_mdom_1805 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
retro_amel_107, retro_amel_676,
Bos taurus ENSBTAG000000171253 retrocopies
retro_btau_1492, retro_btau_28, retro_btau_656,
Canis familiaris ENSCAFG000000030812 retrocopies
retro_cfam_45, retro_cfam_837,
Choloepus hoffmanni ENSCHOG000000053273 retrocopies
retro_chof_1150, retro_chof_1182, retro_chof_1274,
Callithrix jacchus ENSCJAG000000025123 retrocopies
retro_cjac_214, retro_cjac_2722, retro_cjac_284,
Cavia porcellus ENSCPOG000000095522 retrocopies
retro_cpor_1330, retro_cpor_77,
Equus caballus ENSECAG000000093962 retrocopies
retro_ecab_2, retro_ecab_502,
Felis catus ENSFCAG000000152542 retrocopies
retro_fcat_116, retro_fcat_545,
Homo sapiens ENSG000000906212 retrocopies
retro_hsap_109, retro_hsap_74,
Gorilla gorilla ENSGGOG000000040023 retrocopies
retro_ggor_2127, retro_ggor_87, retro_ggor_916,
Loxodonta africana ENSLAFG000000001513 retrocopies
retro_lafr_1144, retro_lafr_390, retro_lafr_597,
Microcebus murinus ENSMICG000000166331 retrocopy
retro_mmur_675,
Myotis lucifugus ENSMLUG000000120682 retrocopies
retro_mluc_228, retro_mluc_397,
Macaca mulatta ENSMMUG000000074971 retrocopy
retro_mmul_178,
Monodelphis domestica ENSMODG000000062224 retrocopies
retro_mdom_123, retro_mdom_1867, retro_mdom_216, retro_mdom_43,
Monodelphis domestica ENSMODG00000017657 2 retrocopies
retro_mdom_1090, retro_mdom_1805 ,
Mustela putorius furoENSMPUG000000144142 retrocopies
retro_mputfur_152, retro_mputfur_546,
Mus musculus ENSMUSG000000112577 retrocopies
retro_mmus_2006, retro_mmus_2326, retro_mmus_2327, retro_mmus_798, retro_mmus_801, retro_mmus_803, retro_mmus_805,
Nomascus leucogenys ENSNLEG000000119282 retrocopies
retro_nleu_1517, retro_nleu_62,
Oryctolagus cuniculus ENSOCUG000000005622 retrocopies
retro_ocun_153, retro_ocun_792,
Otolemur garnettii ENSOGAG000000040671 retrocopy
retro_ogar_71,
Ochotona princeps ENSOPRG000000119841 retrocopy
retro_opri_1133,
Pongo abelii ENSPPYG000000015062 retrocopies
retro_pabe_190, retro_pabe_2563,
Pan troglodytes ENSPTRG000000005733 retrocopies
retro_ptro_101, retro_ptro_2093, retro_ptro_8,
Rattus norvegicus ENSRNOG000000156422 retrocopies
retro_rnor_175, retro_rnor_92,
Sarcophilus harrisii ENSSHAG000000181391 retrocopy
retro_shar_823,
Sus scrofa ENSSSCG000000036603 retrocopies
retro_sscr_1210, retro_sscr_974, retro_sscr_975,
Tursiops truncatus ENSTTRG000000143402 retrocopies
retro_ttru_1117, retro_ttru_246,


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