RetrogeneDB ID: retro_mdom_20

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 5:98051741..98055392(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000003404
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000016488
• Aliases: None
• Description: Structural maintenance of chromosomes protein [Source:UniProtKB/TrEMBL;Acc:F7D3S8]

Sequence

>retro_mdom_20
ATGATCAATAAGGAGGGCACCCCCAGGCTCATGATCTCGCACATTGTGAATCTCAACTTCAAGTCATATGCGGGCCGCAC
CCAGCTGGGGCCCTTTCACAAGCACTTCTCCTGTATCATTGGCCCGAATGGCAGTGGTAAGTCTAATGTCATCGATTCTA
TGCTCTTCGTGTTTGGCTGCCGAGCCCACAAGATCCGCTCTAAGAAGCTATCTGTGCTGATCCACCACTCAGATGACTAC
CAGGACCTGGACAGCTGCACTGTGGAGGTACACTTCCAAAAGATCATTGACAAGGAGGGCGATGACTATGAAGTGATTCC
AAACAGCTCTTTTTATGTCTCCCGGACGGCATATAAGAACAACACATCTGTATACCACATTAGTGGCAAGAAGCAAACAT
TCAGGGATGTGGGCAACCTGCTTCGAAGCCACGGGATCGACTTGGACCACAACCGCTTCCTAATCCTGCAGGGCGAAGTT
GAACAGATTGCTCTGATGAAACCAAAAGGCCAGAGTGAACATGATGAGGGTATGCTTGAATATTTAGAAGATATTATAGG
ATGTGGACGGCTAAAAGAGCCTATTGAAGTCTTGAGTCAAAGACTTGACGTATTAACTGAGGAAAGAGAAGAGAAGTTAA
ATAGAGTTAAAATAGTAGAGAAAGAAAGGAACTACTTAGAAATAGAGAAAAATCTAGCCATTGACTTCCTTACGATAGAA
AATGAAATACTCACAAAAAAGAATCATATTTGTCAGTTCTACATTTATGATTTGCACAAACGAATTGCTGAAGTGGAATA
TGAAAAAGACAAAATTCTTGAAGAAACAGAAGCTATTAAAAAGAAGACCAGTAAACTGGAAGGTGAAATGAATGCCAAGA
CTAATGCTTTAGAAGAAGCAGAAAGGAAACTCAATCAAGTTGCAACATTTATTGAGGAAAACAAAGAGAAATATACACAG
CTGGATTTGGAGGGTGTTCAAGTTAAGACGAAAATGAAATATGCTAAAACCAAAGCCAGGAAACTTGAGAAGCAGCTCCA
AAAAGACAAAGAAAAGGTTGAGGAATTTAAAGATGTACCTGCCAAGAGTGAAAAGGTAATTACTGAAACAACAACTAAAA
AAAGTACTCTAGAAGAAGAAAGAGAGAAAGAAGAGGAAAAAATGAAGCAAGTTATGGATAGTCTTAAACAGGAAACAAAG
GAACTTCAGGAAGAAAAAGAGAGCCAAGAAAAAGAACTCATGGAATTTAATAAAACTGTAAATGAAGCCCGATCCAAGAT
GGATGTTGCCCAGTCCGAACTTGATATCTACCTCAGTCACCATAATACTGCTGTGTCTCAATTAAGTGAGGCCCAAAAGG
CTTTAACTACAGCTTCTGAAACTTTGAAAGAAAGGAAAACTGCCATTAGAGATATTGAAATGAAATTGCCTCCTACTGAA
CAGGACCTAAAGGAGAAAGAAAGTGAACTTCAGAACCTCACAAAAGAAGCAAGAGATCTTGACAGTTCAATCCGAGATCT
TCTTCAAAAAGTTGAAGAAGCAAAAAGCTCTCTTGCAACAAATCAGAGCCGAGGAAAAGTTCTTAATGCATTGATTCAGC
AGAAACTATCTGGCAAAATTCAAGGAATATATGGAAGACTGGGAGATTTGGGAGCCATTGATGAAAAATACAACATTGCC
ATTTCATCTTGCTGTAGTGCCCTGGACTACATTGTTGTTAACACTATTGATACAGCCCAAGTATGTGTGAACTTCCTGAA
GAAACAAAATATAGGAGTGGCAACATTTATTGGGTTAGATAAGATTAAAGTTTTAGAAAAAAATATGAACCCACTGCAAA
CCCCAGAAAATATCCCTCGGTTATTTGATTTAGTCAAAGCAAAAGATGAGAATATTCGCCGAGCCTTTTACTTTGCTTTA
CGTGATACTTTAGTAGCTGACAACCTGGACCAGGCAACAAGAGTGGCTTTTCAGAAAGATAAAAGGTGGAGAGTTGTGAC
ATTACAGGGACAAATCATTGAGCAATCTGGGACAATGACTGGTGGTGGAAGCAAACCAATGAAAGGTAGAATGGGTTCCT
CACTTGTTATGGAAGTTTCTGAAGAAGAGGTAGCCAATATGGAATCCATATTGCGAAGGGACTCCCAAAGAGCTATTGAG
GTCCAAGAACGCAAAGCACAGCTTGAAGAGGCCATGATCAAACTGCGTCACAGTGTGCAAGACATGAGGAACACATTGGA
AAAGTTTACTGTGAGCATCCAGAGTTTATCAGAACAAGAAGCATACTTGAATGCACAAGTTAAAGAACTCAAAGCCAATG
TCTGTGATACTGTCCCTGACAAAAACAAGCAGAAATTTCTAGAAACACAAATAAATACCTTCAAGAAAGAGTATGAATGT
GTTGCTTTGAAGGCTGGCAAGGTCGAAGCTGAAGTCAAAAGACTACACAATTTAATTATGGAGATAAATAATCATAAGCT
GAAATCCCAGCAAGACAAGCTTGACAAGATAAATAAACAGCTCGACCAATGTGCATCTTCCATCACAAAAGCTCAAGTAG
GAGTAAGGACAGCAAACAGAAATCTTAAAAAAGCACAAGATTCTGTCCTTCGCACAGAGAAAGAAATAACTGATAATGAC
AAGGAAATGGAAGACTTCACCCAAGAACTCGAAGATCTCGAGGAGAAGGCAACTGAAATCATGAAGAATTCCAAAGAAGC
TGGGGAATCCTTGCCTGAGATCCAGAGGGAGCATAATAACCTGGTGAAAGAAATGAAAGTAATTAAAGAAAATGAATGCA
GCCTACAAAATGATGCACTTAGTAATAAGTTAAAACTGGAACAGGTAGATAGTTACATTGCTGAACAGCATTCTAAAGTC
AGATTTTGGGAGAAAGAGATGTCAAGAATAGCATTGCATCCAATAGAAAATAATCAAGCTGAACAGATTTCTCTTCTAAG
CCAAGAGGATCTTGAAGAGATAGGAAATCCTAATTTTCTGAATAATCAGATTGAACTTCTGGAATCTCAGTGCAATGCAA
TGAACCCAAATCTTGATTCCATCGAAGAGTATAAAAAGAAGAATCAACAATATTTACATCGAGTGGCAGAATTGGAAAAA
ATTACCATTGAGAGAGATCGCTACAGACGGGCTTATAAAGATCTTCGGGAACGAAGACTCAATGAATTTATGGCAGGTTT
CACTATAATAACAAATAAACTGAAGGAAAACTACCAGATGCTTACTTTGGGAGGTGATGCAGAATTGGAACTGATTGACA
GCTTGGATCCTTTCTCTGAAGGCATCATGTTCTCTGTTCGTCCACCCCAAAAAAGCTGGAAGAAGATCTTTAATCTTTCA
GGAGGAGAGAAGACACTCAGTTCACTGGCTCTGGTTTTCGCCCTCCACGATTATAAGCCCACACCCCTCTACTTCATGGA
TGAAATCGATGCAGCTCTGGATTTTAAGAATGTGTTCATTGTGGCATACTACATCTACAAACAAAAAAAAGACGCACAGT
TTATAATAATTTCACTTCGAAATAACATGTTCGAGATCGCAGATAGGCTCATTGGAATTTACAAGACTAACAACGTAACC
AAAAGTGTCACAATAAATCCAAAAGCCATCGCAGCTAAAGGAGTGTGCTGA

Alignment

ORF - retro_mdom_20 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.91 %
• Parental protein coverage: 94.54 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MTNEAGAPRLMITHIVNLNFKSYAGRKLLGPFPR-FSCII-PNGSGKSNVIDSMLFVFGYRAQKIRSKKL
          M.N..G.PRLMI.HIVNLNFKSYAGR..LGPF...FSCII.PNGSGKSNVIDSMLFVFG.RA.KIRSKKL
Retrocopy MINKEGTPRLMISHIVNLNFKSYAGRTQLGPFHKHFSCIIGPNGSGKSNVIDSMLFVFGCRAHKIRSKKL

Parental  SVLIHNSDEHQDLDSCTVEVHFQKIIDKEDDDYQVIPNSTFSVSRTGYRDNTSVYHISGKKKTFKEVGKL
          SVLIH.SD..QDLDSCTVEVHFQKIIDKE.DDY.VIPNS.F.VSRT.Y..NTSVYHISGKK.TF..VG.L
Retrocopy SVLIHHSDDYQDLDSCTVEVHFQKIIDKEGDDYEVIPNSSFYVSRTAYKNNTSVYHISGKKQTFRDVGNL

Parental  VGSHGIDLDHNRFLILQGEVEQIAMMKPKGQTEHDEGMLEYLEDIIGCGRLKEPIQVLCRRVEILNEQRG
          ..SHGIDLDHNRFLILQGEVEQIA.MKPKGQ.EHDEGMLEYLEDIIGCGRLKEPI.VL..R...L.E.R.
Retrocopy LRSHGIDLDHNRFLILQGEVEQIALMKPKGQSEHDEGMLEYLEDIIGCGRLKEPIEVLSQRLDVLTEERE

Parental  EKLNRVKMVEKEKDALEGEKNIAIEFLTLENEVFKKKNHVCQYYIYDLQKRIAEMETQKEKIHEDTKDIN
          EKLNRVK.VEKE...LE.EKN.AI.FLT.ENE...KKNH.CQ.YIYDL.KRIAE.E..K.KI.E.T..I.
Retrocopy EKLNRVKIVEKERNYLEIEKNLAIDFLTIENEILTKKNHICQFYIYDLHKRIAEVEYEKDKILEETEAIK

Parental  KKSSELADQMKAKTKALKDIEKKLNKVTKFIEENKEKFTQLDLEDVQVREKMKHAKNKAKKLEKQLQKDK
          KK.S.L...M.AKT.AL...E.KLN.V..FIEENKEK.TQLDLE.VQV..KMK.AK.KA.KLEKQLQKDK
Retrocopy KKTSKLEGEMNAKTNALEEAERKLNQVATFIEENKEKYTQLDLEGVQVKTKMKYAKTKARKLEKQLQKDK

Parental  EKVEEFKGVPASSEKVITETTARKSTLEKEKEKEEEKLKQVMDSLKQETKELQEEKESQEKELMEFSKTV
          EKVEEFK.VPA.SEKVITETT..KSTLE.E.EKEEEK.KQVMDSLKQETKELQEEKESQEKELMEF.KTV
Retrocopy EKVEEFKDVPAKSEKVITETTTKKSTLEEEREKEEEKMKQVMDSLKQETKELQEEKESQEKELMEFNKTV

Parental  NEARSKMDVAQSELDIYLSHHNTAVSQLSEAKKALTTASETLKERKTAIRNLEIKLPPTEQDLKQKESEL
          NEARSKMDVAQSELDIYLSHHNTAVSQLSEA.KALTTASETLKERKTAIR..E.KLPPTEQDLK.KESEL
Retrocopy NEARSKMDVAQSELDIYLSHHNTAVSQLSEAQKALTTASETLKERKTAIRDIEMKLPPTEQDLKEKESEL

Parental  QNLTKEAIDLDSSVRDLLQKVEEAKSSLATNHSRGKVLNALIQQKKSGKIPGIYGRLGDLGAIDEKYDIA
          QNLTKEA.DLDSS.RDLLQKVEEAKSSLATN.SRGKVLNALIQQK.SGKI.GIYGRLGDLGAIDEKY.IA
Retrocopy QNLTKEARDLDSSIRDLLQKVEEAKSSLATNQSRGKVLNALIQQKLSGKIQGIYGRLGDLGAIDEKYNIA

Parental  ISSCCGALDYIVVDTIDTAQICVNFLKKQNIGVATFIGLDKIKVLEKHMNPLQTPENTPRLFDLVKVKDE
          ISSCC.ALDYIVV.TIDTAQ.CVNFLKKQNIGVATFIGLDKIKVLEK.MNPLQTPEN.PRLFDLVK.KDE
Retrocopy ISSCCSALDYIVVNTIDTAQVCVNFLKKQNIGVATFIGLDKIKVLEKNMNPLQTPENIPRLFDLVKAKDE

Parental  KIRRAFYFALHDTLVANNLDQATRVAFQKDKRWRVVTLQGQIIEQSGTMTGGGSKPMKGRMGSSFVVEVS
          .IRRAFYFAL.DTLVA.NLDQATRVAFQKDKRWRVVTLQGQIIEQSGTMTGGGSKPMKGRMGSS.V.EVS
Retrocopy NIRRAFYFALRDTLVADNLDQATRVAFQKDKRWRVVTLQGQIIEQSGTMTGGGSKPMKGRMGSSLVMEVS

Parental  EEEVAKMESKLQKDSQRAVQVQERKAQLEETVIKLRHSVQDMRNTLEKFTASIQSLSEQEAYLDIQVKEL
          EEEVA.MES.L..DSQRA..VQERKAQLEE..IKLRHSVQDMRNTLEKFT.SIQSLSEQEAYL..QVKEL
Retrocopy EEEVANMESILRRDSQRAIEVQERKAQLEEAMIKLRHSVQDMRNTLEKFTVSIQSLSEQEAYLNAQVKEL

Parental  EANVRDTAPDKKKQKLLETNINIFKKEYECVAAKAGKVEAEVKRLHNLIVEINNHKLKAQQDKLDKINQQ
          .ANV.DT.PDK.KQK.LET.IN.FKKEYECVA.KAGKVEAEVKRLHNLI.EINNHKLK.QQDKLDKIN.Q
Retrocopy KANVCDTVPDKNKQKFLETQINTFKKEYECVALKAGKVEAEVKRLHNLIMEINNHKLKSQQDKLDKINKQ

Parental  LDQCASAITKAQVAVKTADRNLKKAQDSVLPPEKEIKDNGKEVENLPHELQNLEEKATEVMKNSQKTGES
          LDQCAS.ITKAQV.V.TA.RNLKKAQDSVL..EKEI.DN.KE.E....EL..LEEKATE.MKNS...GES
Retrocopy LDQCASSITKAQVGVRTANRNLKKAQDSVLRTEKEITDNDKEMEDFTQELEDLEEKATEIMKNSKEAGES

Parental  LPGIPKELLNLLPEMKGI-ENGPALQNDALSIKLKLEQLDSHISEHHSKVKYWEKEISRISLHPIEDNPV
          LP.I..E..NL..EMK.I.EN...LQNDALS.KLKLEQ.DS.I.E.HSKV..WEKE.SRI.LHPIE.N..
Retrocopy LPEIQREHNNLVKEMKVIKENECSLQNDALSNKLKLEQVDSYIAEQHSKVRFWEKEMSRIALHPIENNQA

Parental  EEISVLSQEDLEAIKSPDSLTNQIALLEAQCHEMKPNLGSIAEYKKKEELYLHRVAELDKITTERERFRN
          E.IS.LSQEDLE.I..P..L.NQI.LLE.QC..M.PNL.SI.EYKKK...YLHRVAEL.KIT.ER.R.R.
Retrocopy EQISLLSQEDLEEIGNPNFLNNQIELLESQCNAMNPNLDSIEEYKKKNQQYLHRVAELEKITIERDRYRR

Parental  AYEDLRKQRLNEFMAGFNIITNKLKENYQMLTLGGDAELELVDSLDPFSEGIMFSVRPPKKSWKKIFNLS
          AY.DLR..RLNEFMAGF.IITNKLKENYQMLTLGGDAELEL.DSLDPFSEGIMFSVRPP.KSWKKIFNLS
Retrocopy AYKDLRERRLNEFMAGFTIITNKLKENYQMLTLGGDAELELIDSLDPFSEGIMFSVRPPQKSWKKIFNLS

Parental  GGEKTLSSLALVFALHHYKPTPLYFMDEIDAALDFKNVSIVAFYIYEQTKNAQFIIISLRNNMFEIADRL
          GGEKTLSSLALVFALH.YKPTPLYFMDEIDAALDFKNV.IVA.YIY.Q.K.AQFIIISLRNNMFEIADRL
Retrocopy GGEKTLSSLALVFALHDYKPTPLYFMDEIDAALDFKNVFIVAYYIYKQKKDAQFIIISLRNNMFEIADRL

Parental  IGIYKTHNITKSVAINPKVIASKGLC
          IGIYKT.N.TKSV.INPK.IA.KG.C
Retrocopy IGIYKTNNVTKSVTINPKAIAAKGVC

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_20 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_20 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000016488	1 retrocopy	retro_mdom_20 ,