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 symbol: ATP1A1
• Ensembl ID: ENSMODG00000005035
• Aliases: None
• Description: ATPase, Na+/K+ transporting, alpha 1 polypeptide [Source:HGNC Symbol;Acc:799]

Sequence

>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

Alignment

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

Expression

RNA-Seq

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

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_682 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_682 was not experimentally validated.

Homology

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.

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Myotis lucifugus	ENSMLUG00000005048	1 retrocopy	retro_mluc_1196,
Monodelphis domestica	ENSMODG00000005035	1 retrocopy	retro_mdom_682 ,