RetrogeneDB ID: | retro_pabe_1279 | ||
Retrocopy location | Organism: | Orangutan (Pongo abelii) | |
| Coordinates: | 15:28262417..28263879(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | HCN1 | ||
| Ensembl ID: | ENSPPYG00000015446 | ||
| Aliases: | None | ||
| Description: | hyperpolarization activated cyclic nucleotide-gated potassium channel 1 [Source:HGNC Symbol;Acc:4845] |
Retrocopy-Parental alignment summary:
>retro_pabe_1279
TACAGAGACTTCACCATGCTGCTGTTCATGGTGGGAAACCTCATCATCCCAGTGGGCATCACCTTCTTCAAGGACGAGAC
CACCGCCCTGTGGATCGTGTTCAACGTGGTCTCGGACACCTTCTTCCTCATGGACCCGGTGTTGAACTTCCACACCGGCA
TTGTGATCGAGGACAACACGGAGATCATCCTGGACCCCAAGAAGATCAAGAAGAAGTACCTGCGCAAGTGGTTCGTGGTG
GACTTCGTGTCCTCCATCCCCGTGGACTACATCTTTCTCATCGTGGAGAAGGGCATGGACTCCGAGGTCTACAAGACGGC
GTGCGCCCTGCGCATCGTGAGCTTCACCAAGATCCTCAACCTCCGGTGGCTGCTGGGCCTCTCGCACCTGATCCGATACA
TCCACCAGTGGGAGATCTTCCACATGACCTATGACCTGGCCAGCGCGGTGATGCGGATCTGCAACCTCATCAGTATGATG
CTGCTGCTCTGCCACTGGGATGGCTGCCTGCAGTTCCTGGTGGCCATGCTGCAGGACTTCCCGTGCAACTGCTGGGTGTC
CATCAATGGCATGGTGAACCACTAGTGTAGCCAACTGTATTCCTTCGCACTCTTCACGGCCATGAGCCACATGCTGTGCA
TTGGGTACGGCCGGCAGGCGCCCCAGAGCATGACGGACATCTGGCTGACCATGCTCAGCATGATTGTGGATGCCACCTGT
TACGCCATGTTCATCGGCTACGCCACTGCCCTCATCCAGTCGCTGGACTCCTCGCGGCGCCAGTACCAGGAGAAGTACGA
GCAGGTGGAGCAGTACATGTCCTTCCACAAGCTACCGGCCGACTTCCGCCAGAAGATCCACGACTACTACGAGCACCGTT
ACCAGGGCAAGATGTTCGACGAGGACAGCGTCCTGGGCGAGCTCAACAGGCCCCTGCAGGAGGAGATCGTCAACTTCAAC
TGCCGGAAGCTGGTGGCCTCCATGCCGCTGTTCGCCAGTGCTGACCCCAACTTCGTCACGGCCATGCTGACCAAGCTCAA
GTTCGAGGTCTTCCAGCCGGGTGACTACCTCATCCGCTAAGGCACCACGGGGAAGATGTACTTCATCCAGCACGGCGTGG
TCAGCGTGCTCGCTAAGGGCAACAAGGAGATGAAGCTGTTTGATGGCTCCTACTTCGGGGAGATCTGCCTGCTCACCCGG
GGCCACGCACGGTGAGCGTGCGGGCCAAACCTACTGCCGCCTCTATTCGCTGAGCGTGGACAACTTCAACGAGGTGCTGG
AGGAGTACCCCATGATGCGGCGCGCCTTCAAGACGGTGGCCATCCACCGCCTGGACCGCTTCCGCAAGAAGAATTCCATC
CTCCTGCACAAGGTGCAGCATGACCTCAACTCGGGCATATTCAACAACCAGGAGAACGCCATCATCCAGGAGATCGTCAA
GTACCACCGCGAGATGGTGCAG
ORF - retro_pabe_1279 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 78.09 % |
| Parental protein coverage: | 55.61 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | YWDLIMLIMMVGNLVIIPVGITFFTEQTTTPWIIFNVASDTVFLLDLIMNFRTGTVNEDSSEIILDPKVI |
| Y.D..ML..MVGNL.IIPVGITFF...TT..WI.FNV.SDT.FL.D...NF.TG.V.ED..EIILDPK.I | |
| Retrocopy | YRDFTMLLFMVGNL-IIPVGITFFKDETTALWIVFNVVSDTFFLMDPVLNFHTGIVIEDNTEIILDPKKI |
| Parental | KMNYLKSWFVVDFISSIPVDYIFLIVEKGMDSEVYKTARALRIVRFTKILSLLRLLRLSRLIRYIHQWEE |
| K..YL..WFVVDF.SSIPVDYIFLIVEKGMDSEVYKTA.ALRIV.FTKIL.L..LL.LS.LIRYIHQWE. | |
| Retrocopy | KKKYLRKWFVVDFVSSIPVDYIFLIVEKGMDSEVYKTACALRIVSFTKILNLRWLLGLSHLIRYIHQWE- |
| Parental | IFHMTYDLASAVVRIFNLIGMMLLLCHWDGCLQFLVPLLQDFPPDCWVSLNEMVNDSWGKQYSYALFKAM |
| IFHMTYDLASAV.RI.NLI.MMLLLCHWDGCLQFLV..LQDFP..CWVS.N.MVN......YS.ALF.AM | |
| Retrocopy | IFHMTYDLASAVMRICNLISMMLLLCHWDGCLQFLVAMLQDFPCNCWVSINGMVNH*CSQLYSFALFTAM |
| Parental | SHMLCIGYGAQAPVSMSDLWITMLSMIVGATCYAMFVGHATALIQSLDSSRRQYQEKYKQVEQYMSFHKL |
| SHMLCIGYG.QAP.SM.D.W.TMLSMIV.ATCYAMF.G.ATALIQSLDSSRRQYQEKY.QVEQYMSFHKL | |
| Retrocopy | SHMLCIGYGRQAPQSMTDIWLTMLSMIVDATCYAMFIGYATALIQSLDSSRRQYQEKYEQVEQYMSFHKL |
| Parental | PADMRQKIHDYYEHRYQGKIFDEENILNELNDPLREEIVNFNCRKLVATMPLFANADPNFVTAMLSKLRF |
| PAD.RQKIHDYYEHRYQGK.FDE...L.ELN.PL.EEIVNFNCRKLVA.MPLFA.ADPNFVTAML.KL.F | |
| Retrocopy | PADFRQKIHDYYEHRYQGKMFDEDSVLGELNRPLQEEIVNFNCRKLVASMPLFASADPNFVTAMLTKLKF |
| Parental | EVFQPGDYIIREGAVGKKMYFIQHGVAGVITKSSKEMKLTDGSYFGEICLLTKGR-RTASVRA-DTYCRL |
| EVFQPGDY.IR.G..G.KMYFIQHGV..V..K..KEMKL.DGSYFGEICLLT.G..RT.SVRA..TYCRL | |
| Retrocopy | EVFQPGDYLIR*GTTG-KMYFIQHGVVSVLAKGNKEMKLFDGSYFGEICLLTRGH<RTVSVRA<QTYCRL |
| Parental | YSLSVDNFNEVLEEYPMMRRAFETVAIDRLDRIGKKNSILLQKFQKDLNTGVFNNQENEILKQIVKHDRE |
| YSLSVDNFNEVLEEYPMMRRAF.TVAI.RLDR..KKNSILL.K.Q.DLN.G.FNNQEN.I...IVK..RE | |
| Retrocopy | YSLSVDNFNEVLEEYPMMRRAFKTVAIHRLDRFRKKNSILLHKVQHDLNSGIFNNQENAIIQEIVKYHRE |
| Parental | MVQ |
| MVQ | |
| Retrocopy | MVQ |
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 | 22 .95 RPM | 51 .09 RPM |
| SRP007412_cerebellum | 9 .12 RPM | 34 .53 RPM |
| SRP007412_heart | 0 .78 RPM | 0 .09 RPM |
| SRP007412_kidney | 0 .30 RPM | 0 .00 RPM |
| SRP007412_liver | 0 .18 RPM | 0 .28 RPM |
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_1279 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_1279 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_pabe_1279 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Pongo abelii | ENSPPYG00000015446 | 1 retrocopy |
retro_pabe_1279 ,
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