RetrogeneDB ID: | retro_pabe_3593 | ||
Retrocopy location | Organism: | Orangutan (Pongo abelii) | |
| Coordinates: | Un:41604789..41606614(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | DLGAP4 | ||
| Ensembl ID: | ENSPPYG00000010970 | ||
| Aliases: | None | ||
| Description: | disks large-associated protein 4 [Source:RefSeq peptide;Acc:NP_001127321] |
Retrocopy-Parental alignment summary:
>retro_pabe_3593
ATGAAAGGCCTCAGTGACAGCCGCCCCCACCACCTCTCTAGGGACAGCCTAGACCCACCCCACGAGCCCGATTGCAGGGA
CCGACCACAACTCCTACCTGCTGTCGCCCACGGAGGCCTTCGCTGGCAAGGCCCGCTTCCCTGGGCAGGACACCCTGCTG
GGGGATGGCCCCTTTCCCCACAACAACCTGCTGCCCCCGCCCAGCAGCACCTTTCCCTGCATCCACGACAACTCCCACTT
CGAGGTGCCAGAGGAGATCCCCTTCCCCAGCCATGCCCAGGCCACCAAGATCAACCGGCTGCCCACCAACCTACTGGTCC
AGTTTGAGAAGCAGCTGCCCGTCCACCGTGGTGGCTTCAGCACCCTCCAATTCCCCCGTGGTGAGACCAAGGCCCATGGC
GAGAGCCCTGGCCGCATCCACCACCTGGTCCACTCAGTCCAGCGGCTTTTCTTCACCAAGGCACCCTCACTGGATGGCAC
AGTGGGCAAGGTCGGTGGCAATGGCAGCAAGAAGGGTGGCATTGAGGACTGGCAAGGGCCAGAGGGCCAAAAGCAAGGAG
CGGGCCAAGGTTGGGGAGCCCAAAGGGTGCAGCTGCTCCAACATCTCAGGCTGGTGGAGCGCCGATGACAACTTGGATGG
CGAGGCCAGCACCTTCCGCAGCAGTGGCCCAGCCTCCGGGCTGATGACACTAGGCTGCCAGGCAGAACGCAGCCAGCCAC
GCTACTTCATGCACGCCTACAACACCCTCAGTGGGCACATGCTCAAAACCACCAAGAAAACACCACCTAGCTGACCGTCC
CACCACCCCCTCCTGCACCCCAAGCCACCTGCCCCAGCCTTGGGGTGGGCACTGACACCAACTACGTCAAACGGGGCTCC
TGGTTCACTCTGACCCTCAGCCACACCCACGAAGTCTGCCAGAAGACCTCGGCCACCTTTGATAAGAGCGTGCTCAAGCC
CAAATCCTGCCACCAGGGTCCAGCCTACCATTACCCGCAGGTGCCTGGCGGTGGCGAGTGCAGCACCACGATGCTGTCCC
CACGTGAGATGGATGCCACAGCCGACGGCCCCAGCCCATTCCGGCTCATGCGCAGCAGCAGCTACATCAAGGCCATGGGC
AACAAGGACAGCGACGAGTCCGGCCGCAGCTCCGAGCCCTCACCCAAGACTGCAGCGCGGCGCCAGAGCTATCTGCGGGT
CACGCAGCCATCACTGGGAGAGCAGAGCAACCCCCACAGGAGTCTGGACTGCCTGGAGTCAGTGGACATGCTGCTGCCCT
CCAAGTGTCCGGGCTGGGAAGAGGACTACATGCCCATCAGTGACAGCCTCAACGACTCCAGCTGCATCAGCCAGATTTTT
GGACAGGCCTCCCTGATCCCCCAGTTGTTTGGCCATGAGCAGCAGGTACAGGAGGCAGAGCCGAGTGAACAGGATGAGGC
GGCCTGCAAGTCAGCCTGCAGTGAAGCGGAGTCCACAGTGGCAGAAATGCTTGATTTGCCACTGCCTAGCTGCTTCCGCT
CCCGCAGCCCCAGCTACCTGCGTGCCATCCAGGCAGGCTGCTTGCAGGAGGAGGACAGTGTCTCCCTGCAGTCCCTCTCC
CCACCACCCGGTACCAGCAGCCTCAGCAATAGTCGCAGCCTTCCGAGTTCATCATGCCTAGTGGCGTATAAGAAGACCCT
GCCACCGGTCCCTCCATGCACCACTTCAAAGCCGTTCATCTCAGTCACAGTCCAGAGCGGTACTGAGTCTGCCCAGGATA
CCTACCTGGATAGCCAGGACCACAAGAGCGAGGTGACTAGCCAGTTGGGTCTGAGCAACCCATCA
ORF - retro_pabe_3593 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 84.67 % |
| Parental protein coverage: | 61.39 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | MKGLGDSRPRHLS-DSLDPPHE-PLFAGTDRNPYLLSPTEAFAREARFPGQNTLPGDGLFPLNNQLPPPS |
| MKGL.DSRP.HLS.DSLDPPHE.P..AGTD.N.YLLSPTEAFA..ARFPGQ.TL.GDG.FP.NN.LPPPS | |
| Retrocopy | MKGLSDSRPHHLSRDSLDPPHE>PI-AGTDHNSYLLSPTEAFAGKARFPGQDTLLGDGPFPHNNLLPPPS |
| Parental | STFPRIHYNSHFEVPEESPFPSHAQATKINRLPANLLDQFEKQLPIHRDGFSTLQFPRGEAKARGESPGR |
| STFP.IH.NSHFEVPEE.PFPSHAQATKINRLP.NLL.QFEKQLP.HR.GFSTLQFPRGE.KA.GESPGR | |
| Retrocopy | STFPCIHDNSHFEVPEEIPFPSHAQATKINRLPTNLLVQFEKQLPVHRGGFSTLQFPRGETKAHGESPGR |
| Parental | IRHLVHSVQRLFFTKAPSLEGTAGKVGGNGSKKGGIEE-GKGRSAKSKERAKAGEPKRRSRSNISGWWSS |
| I.HLVHSVQRLFFTKAPSL.GT.GKVGGNGSKKGGIE..GKG..AKSKERAK.GEPK..S.SNISGWWS. | |
| Retrocopy | IHHLVHSVQRLFFTKAPSLDGTVGKVGGNGSKKGGIED>GKGQRAKSKERAKVGEPKGCSCSNISGWWSA |
| Parental | DDNLDGEAGAFRSSGPASGLMTLGRQAERSQPRYFMHAYNTISGHMLKATKN-NTTELTAPPPPPAPPAT |
| DDNLDGEA..FRSSGPASGLMTLG.QAERSQPRYFMHAYNT.SGHMLK.TK..NTT.LT.PPPPPAP.AT | |
| Retrocopy | DDNLDGEASTFRSSGPASGLMTLGCQAERSQPRYFMHAYNTLSGHMLKTTKK<NTT*LTVPPPPPAPQAT |
| Parental | CPSLGVGTDTNYVKRGSWSTLTLSHAHEVCQKTSATLDKSLLKSKSCHQGLAYHYLQVPGGGGEWSTTLL |
| CPSLGVGTDTNYVKRGSW.TLTLSH.HEVCQKTSAT.DKS.LK.KSCHQG.AYHY.QVPGGG.E.STT.L | |
| Retrocopy | CPSLGVGTDTNYVKRGSWFTLTLSHTHEVCQKTSATFDKSVLKPKSCHQGPAYHYPQVPGGG-ECSTTML |
| Parental | SPRETDAAAEGPIPCRRMRSGSYIKAMGDEDSDESGGSPKPSPKTAARRQSYLRATQQSLGEQSNPRRSL |
| SPRE.DA.A.GP.P.R.MRS.SYIKAMG..DSDESG.S..PSPKTAARRQSYLR.TQ.SLGEQSNP.RSL | |
| Retrocopy | SPREMDATADGPSPFRLMRSSSYIKAMGNKDSDESGRSSEPSPKTAARRQSYLRVTQPSLGEQSNPHRSL |
| Parental | DRLDSVDMLLPSKCPSWEEDYTPVSDSLNDSSCISQIFGQASLIPQLFGHEQQVREAELSDQYEAACESA |
| D.L.SVDMLLPSKCP.WEEDY.P.SDSLNDSSCISQIFGQASLIPQLFGHEQQV.EAE.S.Q.EAAC.SA | |
| Retrocopy | DCLESVDMLLPSKCPGWEEDYMPISDSLNDSSCISQIFGQASLIPQLFGHEQQVQEAEPSEQDEAACKSA |
| Parental | CSEAESTAAETLDLPLPSYFRSRSHSYLRAIQAGCSQEEDSVSLQSLSPPPSTGSLSNSRTLPSSSCLVA |
| CSEAEST.AE.LDLPLPS.FRSRS.SYLRAIQAGC.QEEDSVSLQSLSPPP.T.SLSNSR.LPSSSCLVA | |
| Retrocopy | CSEAESTVAEMLDLPLPSCFRSRSPSYLRAIQAGCLQEEDSVSLQSLSPPPGTSSLSNSRSLPSSSCLVA |
| Parental | YKKTPPPVPPRTTSKPFISVTVQSSTESAQDTYLDSQDHKSEVTSQSGLSNSS |
| YKKT.PPVPP.TTSKPFISVTVQS.TESAQDTYLDSQDHKSEVTSQ.GLSN.S | |
| Retrocopy | YKKTLPPVPPCTTSKPFISVTVQSGTESAQDTYLDSQDHKSEVTSQLGLSNPS |
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_prefrontal_cortex | 0 .00 RPM | 74 .31 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 16 .05 RPM |
| SRP007412_heart | 0 .00 RPM | 5 .75 RPM |
| SRP007412_kidney | 0 .00 RPM | 16 .77 RPM |
| SRP007412_liver | 0 .00 RPM | 4 .90 RPM |
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_3593 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_3593 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_pabe_3593 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Pongo abelii | ENSPPYG00000010970 | 2 retrocopies |
retro_pabe_3555, retro_pabe_3593 ,
|