RetrogeneDB ID: | retro_pabe_3555 | ||
Retrocopy location | Organism: | Orangutan (Pongo abelii) | |
| Coordinates: | Un:65635888..65637713(+) | ||
| 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_3555
ATGAAAGGCCTCGGTGACAGCCGCCCCCACCACCTCTCTAGGGACAGCCTAGACCCACCCCACGAGCCCGTTTGCAGGGA
CCGACCGCAACTCCTACCTGCTGTCGCCCACGGAGGCCTTCGCCGGCAAGGCCCGCTTCCCTGGGCAGGACACCCTGCCG
GGGGATGGCCTCTTTCCCCACAACAACCAGCTGCCCCCGCCCAGCAGCACCTTTCCCTGCATCCACGACAACTCCCACTT
CGAGGTGCCAGAGGAGAGCCCCTTCCCCAGCCATGCCCAGGCCACCAAGATCAACCGGCTGCCCACCAACCTCCTGGTCC
AGTTTGAGAAGCAGCTGCCCGTCCACCGTGGTGGCTTCAGCACCCTCCAGTTCCCCCGTGGTGAGACCAAGGCCCGTGGC
GAGAGCCCTGGCCGCATCCGCCACCTGGTCCACTCAGTCCAGCGGCTTTTCTTCACCAAGGCACCCTCACTGGATGGCAC
AGTGGGCAAGGTCGGTGGCAATGGCAGCAAGAAGGGTGGCATGGAGGACTGGCAAGGGCCAGAGGGCCAAAAGCAAGGAG
CGGGCCAAGGTTGGGGAGCCCAAAGGGCGCAGCCGCTCCAACATCTCAGGCTGGTGGAGCGCCGATGACAACTTGGATGG
CGAGGCCGGCACCTTCCGCAGCAGTGGCCCAGCCTCCGGGCTGATGACACTAGGCCGCCAGGCAGAACGCAGCCAGCCAC
GCTACTTCATGCACGCCTACAACACCCTCAGTGGGCACATGCTCAAAGCCACCAAGAACACACCACCCAGCTGACCGCCC
CACCACCTCCGCCTGCACCCCCAGCCACCTGCCCCAGCCTTGGGGTGGGCACTGACACCAACTACGTCAAACGGGGCTCC
TGGTCCACTCTGACCATCAGCCACGCCCACGAGGTCTGCCAGAAGACCTCGGCCACCTTTGATAAGAGCGTGCTCAAGCC
CAAATCCTGCCACCAGGGTCTAGCCTACCATTACCCGCAGGTGCCTGGCGGCGGCGAGTGCAGCACAACGATGCTGTCCC
CACGCGAGACAGATGCCGCAGCCAAGGGCCCCAGCCCGTTCCGGCTCATGCGCAGCAGCAGCTACATCAAGGCCATGGGC
GACAAGGACAGCGACGAGTCCGGCCGCAGCCCCGAGCCCTCACCCAAGACCGCAGCGCGGCGCCAGAGCTATCTGAAGGT
CACGCAGCCGTCACTGGGAGAGCAGAGCAACCCCCACAGGAGTCTGGACCGCCTGGATTCAGTGGACATGCTGCTGCCCT
CCAAGTGTCCGGGCTGGGAAGAGGACTACATGCCCGTCAGTGACAGCCTCAACGACTCCAGCTGCATCAGCCAGATTTTT
GGACAGGCCTCCCTGATCCCCTAGTTGTTTGGCCACGAGCAGCAGGTACGGGAGGCAGAGCCCAGTGAACCGGATGAGGC
GGCCTGCGAGTCAGCCTGCAGTGAAGCGGAGTCCACAGCGGCGGAGATGCTTGATTTGCCACTGCCCAGCTGCTTCCGCT
CCCGCAGCCCCAGCTACCTGCGTGCCATCCAGGCAGGCTGCTCGCAGGAAGAGGACAGTGTCTCCCTGCAGTCCCTCTCC
CCACCACCCGGTACCAGCAGCCTCAGCAATAGTTGCAGCCTTCCGAGTTCATCATGCCTAGTGGCGTATAAGAAGACCCT
GCCACCAGTCCCTCCATGCACCACTTCAAAGCCGTTCATCTCAGTCACAGTCCAGAGCGGTACTGAGTCTGCCCAGGATA
CCTACCTGGACAGCCAGGACCACAAGAGCGAGGTGACTAGCCAGTTGGGCCTGAGCAACTCATCA
ORF - retro_pabe_3555 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 88.42 % |
| Parental protein coverage: | 61.39 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | MKGLGDSRPRHLS-DSLDP-PHEPLFAGTDRNPYLLSPTEAFAREARFPGQNTLPGDGLFPLNNQLPPPS |
| MKGLGDSRP.HLS.DSLDP.P..P.FAGTDRN.YLLSPTEAFA..ARFPGQ.TLPGDGLFP.NNQLPPPS | |
| Retrocopy | MKGLGDSRPHHLSRDSLDP>PTSP-FAGTDRNSYLLSPTEAFAGKARFPGQDTLPGDGLFPHNNQLPPPS |
| Parental | STFPRIHYNSHFEVPEESPFPSHAQATKINRLPANLLDQFEKQLPIHRDGFSTLQFPRGEAKARGESPGR |
| STFP.IH.NSHFEVPEESPFPSHAQATKINRLP.NLL.QFEKQLP.HR.GFSTLQFPRGE.KARGESPGR | |
| Retrocopy | STFPCIHDNSHFEVPEESPFPSHAQATKINRLPTNLLVQFEKQLPVHRGGFSTLQFPRGETKARGESPGR |
| Parental | IRHLVHSVQRLFFTKAPSLEGTAGKVGGNGSKKGGIEE-GKGRSAKSKERAKAGEPKRRSRSNISGWWSS |
| IRHLVHSVQRLFFTKAPSL.GT.GKVGGNGSKKGG.E..GKG..AKSKERAK.GEPK.RSRSNISGWWS. | |
| Retrocopy | IRHLVHSVQRLFFTKAPSLDGTVGKVGGNGSKKGGMED>GKGQRAKSKERAKVGEPKGRSRSNISGWWSA |
| Parental | DDNLDGEAGAFRSSGPASGLMTLGRQAERSQPRYFMHAYNTISGHMLKATKN-NTTELTAPPPPPAPPAT |
| DDNLDGEAG.FRSSGPASGLMTLGRQAERSQPRYFMHAYNT.SGHMLKATKN..TT.LTAPPPPPAPPAT | |
| Retrocopy | DDNLDGEAGTFRSSGPASGLMTLGRQAERSQPRYFMHAYNTLSGHMLKATKN<HTTQLTAPPPPPAPPAT |
| Parental | CPSLGVGTDTNYVKRGSWSTLTLSHAHEVCQKTSATLDKSLLKSKSCHQGLAYHYLQVPGGGGEWSTTLL |
| CPSLGVGTDTNYVKRGSWSTLT.SHAHEVCQKTSAT.DKS.LK.KSCHQGLAYHY.QVPGGG.E.STT.L | |
| Retrocopy | CPSLGVGTDTNYVKRGSWSTLTISHAHEVCQKTSATFDKSVLKPKSCHQGLAYHYPQVPGGG-ECSTTML |
| Parental | SPRETDAAAEGPIPCRRMRSGSYIKAMGDEDSDESGGSPKPSPKTAARRQSYLRATQQSLGEQSNPRRSL |
| SPRETDAAA.GP.P.R.MRS.SYIKAMGD.DSDESG.SP.PSPKTAARRQSYL..TQ.SLGEQSNP.RSL | |
| Retrocopy | SPRETDAAAKGPSPFRLMRSSSYIKAMGDKDSDESGRSPEPSPKTAARRQSYLKVTQPSLGEQSNPHRSL |
| Parental | DRLDSVDMLLPSKCPSWEEDYTPVSDSLNDSSCISQIFGQASLIPQLFGHEQQVREAELSDQYEAACESA |
| DRLDSVDMLLPSKCP.WEEDY.PVSDSLNDSSCISQIFGQASLIP.LFGHEQQVREAE.S...EAACESA | |
| Retrocopy | DRLDSVDMLLPSKCPGWEEDYMPVSDSLNDSSCISQIFGQASLIP*LFGHEQQVREAEPSEPDEAACESA |
| Parental | CSEAESTAAETLDLPLPSYFRSRSHSYLRAIQAGCSQEEDSVSLQSLSPPPSTGSLSNSRTLPSSSCLVA |
| CSEAESTAAE.LDLPLPS.FRSRS.SYLRAIQAGCSQEEDSVSLQSLSPPP.T.SLSNS..LPSSSCLVA | |
| Retrocopy | CSEAESTAAEMLDLPLPSCFRSRSPSYLRAIQAGCSQEEDSVSLQSLSPPPGTSSLSNSCSLPSSSCLVA |
| Parental | YKKTPPPVPPRTTSKPFISVTVQSSTESAQDTYLDSQDHKSEVTSQSGLSNSS |
| YKKT.PPVPP.TTSKPFISVTVQS.TESAQDTYLDSQDHKSEVTSQ.GLSNSS | |
| Retrocopy | YKKTLPPVPPCTTSKPFISVTVQSGTESAQDTYLDSQDHKSEVTSQLGLSNSS |
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 .50 RPM | 74 .31 RPM |
| SRP007412_cerebellum | 0 .12 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_3555 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_3555 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_pabe_3555 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,
|