RetrogeneDB ID: | retro_shar_608 | ||
Retrocopy location | Organism: | Tasmanian devil (Sarcophilus harrisii) | |
| Coordinates: | GL856749.1:4284039..4285214(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | MBD4 | ||
| Ensembl ID: | ENSSHAG00000012953 | ||
| Aliases: | None | ||
| Description: | methyl-CpG binding domain protein 4 [Source:HGNC Symbol;Acc:6919] |
Retrocopy-Parental alignment summary:
>retro_shar_608
GAAGAAATTGAAATCCCAGGAGTTGAAAAAAAAAAGGGAGATGACAAGATAAAGTGACTGAAAGAAGAGAAGAAATAGCT
TTCCAGTTACAGGAACCGAATGTCAGCACTCAGTGCAATGGTGCTGCTCTCATCAAGAACTCTTAAGTCTATCCCTTGTG
AATAAGGAAGAATTGTAAAACAAAGATTACCAAGAAAAGCTGCTGGAAAATATCATGTCTATTTTATGAGTCTTGAAGGA
ATGAAACTCGAGGCCAAAAGTTTACTTGCATGTTACCTTTACAAAAATGGAGAGGCTTTTTTTAAGCTAGAAGATTCTGA
CTTCAGGGCTCCTCCCAAGAATAATACTCCATCAAATTACTCATATCACAGTGAGAAAACTCTGGTAGTACAGTTTCAGG
TGGAACAGAGCTTCCTGAGCCTCAACCAAAAGCTTAGGACCCCTTAAAGGAAAGAGAAAGGTAGGATTCCTCTGCCTTGA
AGGTTTCACGGGTGCAGGACCAGAATAGTGAACTCCTTTGCTTTCAGCCACAGGGGCCAGAAGGATGCTGATGTTCTTGA
CTCTCAAAATCACAAAAAGCCCATTAGAAAGGTAATAACTGAAAAAAGAAATCATATTGAAGTAGTTAAGAAAAAGAATA
GGAAAAGTCATTCTGGTTGCATTCAGAGACAAAAAGGTCAGCCTCTAGTAAAGAAGCTCCTATAGCTATTTCCATTGCAT
AAGATAATCATCTTTAGAGACCCCTGTGCTGTTCTGATGAGTGAAAGAGGAACAAGAATATAGCAGTGACAGATGAAGAA
AAAAAGAACTGATAAATAAAATATTTGCTTTAAGTTCATGCTCCCAAATGCATCCTGTGCAAGTAAGTTCTTGCAGAGAA
AAAACATTCTGTGCCAATAAAATTTCAGAATATAAAGAGAAGTATGGATATCCTGTAGGATCTGAAAGTATCTTTGTAGG
AACTGGGGAAAAGAGGGAGCATTGCAAATGCTGACATTTTAAAATGTAATTCTGAAATAGACAGCAGTAGCTCCCAGGAT
GAACAAAATTTGACTTTTGTGGTAACATTTCAAGAAAAAACCATCTGACAAACACAAGTGGAGAGAAAGAAAACCAGCAA
GTATTTCTCCAACAAATGCAACAAAGGCTTAGTCTACCCTGATAGAAACTGTTTA
ORF - retro_shar_608 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 57.46 % |
| Parental protein coverage: | 69.2 % |
| Number of stop codons detected: | 6 |
| Number of frameshifts detected: | 7 |
Retrocopy - Parental Gene Alignment:
| Parental | EEVEFPGVEKMGDDER-KLVTEEREEITPQLQELNASIHCDGGTIMEHS-KSVPCGWERIVKQRLSGKTA |
| EE.E.PGV.....D.....VTE.REEI..QLQE.N.S..C.G......S.KS.PC...RIVKQRL..K.A | |
| Retrocopy | EEIEIPGVXXXXGDDK<DKVTERREEIAFQLQEPNVSTQCNGAALIKNS>KSIPCE*GRIVKQRLPRKAA |
| Parental | GKYDVYFISPEGVKLRSKSLLACYLHKSGETSLKPEDFDFRAPPKSDTPSGLPHASKEALAAQFQGEQSC |
| GKY.VYF.S.EG.KL..KSLLACYL.K.GE...K.ED.DFRAPPK..TPS.....S...L..QFQ.EQS. | |
| Retrocopy | GKYHVYFMSLEGMKLEAKSLLACYLYKNGEAFFKLEDSDFRAPPKNNTPSNYSYHSEKTLVVQFQVEQSF |
| Parental | LSPKQKLRTPHRKEKDALPLP-CKVSQVQDQNSELSRFTSKPRLQKG-ADVSDSQNLKTPTGKATATKGS |
| LS..QKLRTP.RKEK...PLP..KVS.VQDQNSEL..F...P....G.ADV.DSQN.K.P..K....K.. | |
| Retrocopy | LSLNQKLRTP*RKEKGRIPLP<LKVSRVQDQNSELLCF--QPQGPEG>ADVLDSQNHKKPIRKVITEKRN |
| Parental | HMKEAKKRARKGHSGCSQRQ-KRAASGKGA---ISIAQDKHLEKPLCCSDDRMSNMNIKTTEEE-EKELI |
| H....KK..RK.HSGC.QRQ.KR.AS.K.A...ISIA.D.HL..PLCCSD....N.NI..T.EE..KELI | |
| Retrocopy | HIEVVKKKNRKSHSGCIQRQ<KRSASSKEAPIAISIA*DNHL*RPLCCSDE*KRNKNIAVTDEE<KKELI |
| Parental | NKIYASGSHAQMHTAH-GTCTENALGASEVSEYKEKSGRTSGGSEKTFIETGEKKEH-LHADILKCNSEI |
| NKI.A..S..QMH......C.E....A...SEYKEK.G....GSE..F..TGEK.EH...ADILKCNSEI | |
| Retrocopy | NKIFALSSCSQMHPVQVSSCREKTFCANKISEYKEKYGYPV-GSESIFVGTGEKREH>ANADILKCNSEI |
| Parental | DSSSSQDEKDLTFVPTFQENIIQRPQVERRKTSQYFSNKYNQEALSPPRRKL |
| DSSSSQDE..LTFV.TFQE..I...QVER.KTS.YFSNK.N.....P.R..L | |
| Retrocopy | DSSSSQDEQNLTFVVTFQEKTI*QTQVERKKTSKYFSNKCNKGLVYPDRNCL |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
Sarcophilus harrisii was not studied using RNA-Seq expression data.
Sarcophilus harrisii was not studied using ChIP-Seq data.
Sarcophilus harrisii was not studied using EST data.
Sarcophilus harrisii was not studied using FANTOM5 data.
retro_shar_608 was not experimentally validated.
Retrocopy orthology:
Sarcophilus harrisii 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 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Sarcophilus harrisii | ENSSHAG00000012953 | 1 retrocopy |
retro_shar_608 ,
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