RetrogeneDB ID: | retro_mdom_682 | ||
Retrocopy location | Organism: | Opossum (Monodelphis domestica) | |
| Coordinates: | 2:88377907..88380168(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | ATP1A1 | ||
| Ensembl ID: | ENSMODG00000005035 | ||
| Aliases: | None | ||
| Description: | ATPase, Na+/K+ transporting, alpha 1 polypeptide [Source:HGNC Symbol;Acc:799] |
Retrocopy-Parental alignment summary:
>retro_mdom_682
GATGAAGGATGACTCCAAAAGCAAAGAAAGAAGGAGCACCAGAAAGAACTCAAGAAAGTGGATGACCACAAACTCACCCC
TAAGAAATTAGAATAAAAGCATGAAACAAACATCATCCAAGATCTCACTAGCACATAAGCTGCAGAGGTCTTGACTTTGA
TGGCCCCAATGTCCTCACTCCATTCAAAGACACTCCAGAAATCATCAAATTCCTCAAACAAATGGTTGGTGGATTCTCTA
GCTTCTTGTGGGTAGGAGCTATCCTATGTTTCATTGCCTATGTGATTGAATTTACAAAGAAAAATTCTACTTCCATGGAC
AATCTCTTTTTAGGTATTGTGCTTGTCCTGGTGGTCATCCTCACTGGAATATTTGTTTATTACCAAGAGGCAAAAAGCAC
CAACATCATTGGGAGCATCAGCAAAATGATTCCTAGGAAAGTCTTTGTCATCAGAGATGGAGAAAAGTTAGAGATTCCTG
CAAAGGAGCTTGTTGTTAGAGATATTGGAGAGATTAAAGGTGGAGACCAGATTCCTGCTGATATCAGGATCCTAGACTCC
CAAAGATATAAGGTAAATAATTTATCTCTTACTGAGGAATCAGAGGCTCAGTCTTGTTCTTGTCATTTTAGCCATAAGAA
CACTTTGGAGACAAAGAACATTGGATTTTTCTCTACAATTTGTCTGGAACTGCAACTGGCATAGTTATCAACATGGGTGA
CCATACCATCATTGGAAGAATTGCCTCACTGGATTCATCAGTTGGGCATGAGAAGACACCAATTGCCATAGAAATTGAGC
CCTTTGTCCATATTGTGGCTGGGGTGGCTGTTTCCTTTGGTATCGGGTTCTTCATCATTGCAATATTCATGAAATACTGG
GTCTTGGATGTTGTCATTTTCCTGATTGGCATAATTTTGGCCAATGTGCCAGAGGGCCTGGTGGCTGCTGTTACTATGAG
TCTGACTTTGACAGCAAAAGGGATGGCCAAGAAGAACTGTCTGGTGAAGAACCTGGAAGCGGTGGAAACTCTGCACTCTA
CTTCCATCATCTGCTCTGATAAGACTGGGACCTTAACCCAAAACAGAATTACTGTGACCCATCTGTGGTTTGACAACCAG
ATCTATCAGGCTGATACAAGTGAAGATCAGAAAGTCCAGAACTTTGATCAAAGTACTGCAACCTGGGCCTCCTTATTCAA
GACATAACACTGTGCAACTGAGCTTAGTTCAGGCCAGGACAGGAAAATGTCTCCGTCATGAAGACAATTGTGATGGGAGA
TACCTCAGAAACTGCCCTCCTGAAGTTTTCAGAATTCATTATGGGAGATGTGATAGAAAGAAGAAAAAGAAACAAAAAAG
TGGCTGAAATCCCTTTTAACTCCCTAAATAAATCCCAGCTCTCCATACATGAGACAGATGACCCTGATGACGAAAGCTTC
CTCTTGGTGATGAAAGGAGATCTTGAGACAATCCTATAGAAATGTAGCACCATTATAATCAATGGCCAGGAGCAGCCTCT
TGATGAAAGTGGAAGAGAAGTCTTCCAAACTGCTTACAGATTGCTGGGAGGCTTAGAGGAGAGAGTATTGGTTTCTGCCA
TCTGTACCTGCCAGAAGATGAGTTTCCAGATACCTACTCCTTTGATACAGAGACTATGAACTTTCCCACCTCTGACCTCT
GCTTTGTAGGGCTAATATCATTGATTGATCCCCCTCAATCCACTGTCCCTGATGCAATCATCAAATGCTGCAGTGCTGGT
ATCAAGGTCATCATGATGACTAGTGATCATCCAATCACAAACAAAGCTATTGCCAGAAGCTTGGGCATCATTTCAGCCAA
CAGTGAGACTGTGGAAGACATAGCAAAACCTCTTAAAATTCCTGTGGAACAGGTTAACCAAAGGGAGGCAAAAGCAGCTG
TGGTAAGTGGAATGGAGATGAAGAAGATGAGCCCAGAGCAGCTGGATGAGCTCCTGAAAAACCACAGTGAGATTGTCTTT
GTAAGGACATCTCCCCAGCAAGAGCTGGTAATTGTGGAGGGCTGTCAGAGACAGGATGATATTGTTGCAGTGACAGGAGA
TGGTGTTAATGATTCTCCAGCCCTAAAGAAGGCTGATATTGGGATTGCCATGGGCTTTGCAGGCTCTGATGCAGCAAAAA
TTGCAGCAGAAATGGTCTTACTAGATGACAACTTTGCCTCTATTGTGACAGGAATAGAGGGAGGTCGTCTAATCTTTGAC
AATTTGAAGAAAATCATTGCA
ORF - retro_mdom_682 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 59.37 % |
| Parental protein coverage: | 74.34 % |
| Number of stop codons detected: | 6 |
| Number of frameshifts detected: | 4 |
Retrocopy - Parental Gene Alignment:
| Parental | EQGDKKKAKKEKDMDELKKEVSMDDHKLSLDELHRKYGTDLSRGLTSARAAEILAR-DGPNALTPPPTTP |
| ..G...K..K.....ELKK....DDHKL....L..K..T.....LTS..AAE.L...DGPN.LTP...TP | |
| Retrocopy | DEG*LQKQRKKEHQKELKK---VDDHKLTPKKLE*KHETNIIQDLTST*AAEVLTL<DGPNVLTPFKDTP |
| Parental | EWIKFCRQLFGGFSMLLWIGAVLCFLAYGIQAATEDEPQNDNLYLGVVLSAVVIITGCFSYYQEAKSSKI |
| E.IKF..Q..GGFS..LW.GA.LCF.AY.I..........DNL.LG.VL..VVI.TG.F.YYQEAKS..I | |
| Retrocopy | EIIKFLKQMVGGFSSFLWVGAILCFIAYVIEFTKKNSTSMDNLFLGIVLVLVVILTGIFVYYQEAKSTNI |
| Parental | MESFKNMVPQQALVIRNGEKMSINAEDVVVGDLVEVKGGDRIPADLRIISANGCKVDNSSLTGESEPQTR |
| ..S...M.P....VIR.GEK..I.A...VV.D..E.KGGD.IPAD.RI......KV.N.SLT.ESE.Q.. | |
| Retrocopy | IGSISKMIPRKVFVIRDGEKLEIPAKELVVRDIGEIKGGDQIPADIRILDSQRYKVNNLSLTEESEAQSC |
| Parental | SPDFTNENPLETRNIAF-FSTNCVEGTARGIVVYTGDRTVMGRIATLASGLEGGQTPIAAEIEHFIHLIT |
| S..F...N.LET.NI.F.F..N...GTA.GIV...GD.T..GRIA.L.S......TPIA.EIE.F.H... | |
| Retrocopy | SCHFSHKNTLETKNIGF<FLYN-LSGTATGIVINMGDHTIIGRIASLDSSVGHEKTPIAIEIEPFVHIVA |
| Parental | GVAVFLGVTFFILSLILEYTWLEAVIFLIGIIVANVPEGLLATVTVCLTLTAKRMARKNCLVKNLEAVET |
| GVAV..G..FFI......Y..L..VIFLIGII.ANVPEGL.A.VT..LTLTAK.MA.KNCLVKNLEAVET | |
| Retrocopy | GVAVSFGIGFFIIAIFMKYWVLDVVIFLIGIILANVPEGLVAAVTMSLTLTAKGMAKKNCLVKNLEAVET |
| Parental | LGSTSTICSDKTGTLTQNRMTVAHMWFDNQIHEADTTENQSGVSFDKSSATWLALSRI-AGLCNRAVFQA |
| L.STS.ICSDKTGTLTQNR.TV.H.WFDNQI..ADT.E.Q....FD.S.ATW..L......LCN.A.F.. | |
| Retrocopy | LHSTSIICSDKTGTLTQNRITVTHLWFDNQIYQADTSEDQKVQNFDQSTATWASLFKT<ITLCN*A*FRP |
| Parental | NQENLPILKRAVAGDASESALLKCIELCCGSVKEMRDRYAKIVEIPFNSTNKYQLSIHKNPNTSEPRHLL |
| .QEN....K..V.GD.SE.ALLK..E...G.V...........EIPFNS.NK.QLSIH..........LL | |
| Retrocopy | GQENVSVMKTIVMGDTSETALLKFSEFIMGDVXXXXXXXXXVAEIPFNSLNKSQLSIHETDDPDDESFLL |
| Parental | VMKGAPERILDRCSSILIHGKEQQLDEELKDAFQNAYLELGGLGERVL-GFCHLLLPDEQFPEGFQFDTD |
| VMKG..E.IL..CS.I.I.G.EQ.LDE.....FQ.AY..LGGL.ERVL.GFCHL.LP...FP....FDT. | |
| Retrocopy | VMKGDLETIL*KCSTIIINGQEQPLDESGREVFQTAYRLLGGLEERVL<GFCHLYLPEDEFPDTYSFDTE |
| Parental | EVNFPVDNLCFVGLISMIDPPRAAVPDAVGKCRSAGIKVIMVTGDHPITAKAIAKGVGIISEGNETVEDI |
| ..NFP...LCFVGLIS.IDPP...VPDA..KC.SAGIKVIM.T.DHPIT.KAIA...GIIS...ETVEDI | |
| Retrocopy | TMNFPTSDLCFVGLISLIDPPQSTVPDAIIKCCSAGIKVIMMTSDHPITNKAIARSLGIISANSETVEDI |
| Parental | AARLNIPVSQVNARDAKACVVHGSDLKDMTSEQLDDILKHHTEIVFARTSPQQKLIIVEGCQRQGAIVAV |
| A..L.IPV.QVN.R.AKA.VV.G...K.M..EQLD..LK.H.EIVF.RTSPQQ.L.IVEGCQRQ..IVAV | |
| Retrocopy | AKPLKIPVEQVNQREAKAAVVSGMEMKKMSPEQLDELLKNHSEIVFVRTSPQQELVIVEGCQRQDDIVAV |
| Parental | TGDGVNDSPALKKADIGVAMGISGSDVSKQAADMILLDDNFASIVTGVEEGRLIFDNLKKSIA |
| TGDGVNDSPALKKADIG.AMG..GSD..K.AA.M.LLDDNFASIVTG.E.GRLIFDNLKK.IA | |
| Retrocopy | TGDGVNDSPALKKADIGIAMGFAGSDAAKIAAEMVLLDDNFASIVTGIEGGRLIFDNLKKIIA |
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_682 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_682 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 | |
|---|---|---|---|
| Myotis lucifugus | ENSMLUG00000005048 | 1 retrocopy | |
| Monodelphis domestica | ENSMODG00000005035 | 1 retrocopy |
retro_mdom_682 ,
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