RetrogeneDB ID: | retro_pabe_3751 | ||
Retrocopy location | Organism: | Orangutan (Pongo abelii) | |
| Coordinates: | X:48061618..48062100(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | NICN1 | ||
| Ensembl ID: | ENSPPYG00000029914 | ||
| Aliases: | None | ||
| Description: | nicolin 1 [Source:HGNC Symbol;Acc:18317] |
Retrocopy-Parental alignment summary:
>retro_pabe_3751
TACTACACAGCTTTTTTGAGCATCCGTGTCTGTCAGCACACCTCAGCACACACACTGGCCAAGTGGGTGACCTGCCTGTG
GGACTACTGTCTGATGCCCGACCCACACAGTGAGGAAGGAGCCAGGAGTATGTGTCGCTGTTCAAGCAACAGATACTGTG
TGACATGGCCAGAGTATCGGAGCTACACCTGATTCTGCGGCAGCCATAACCACTGTGGCTGTCTTTCACAGTGGAGGAGC
TGCAGATCTATCAGCAGGGACCAAAGAGCCCCTCCATGATCTTCCCCAAGTGGCTCTCCCACCCAGTGCCCTGTGAGCAA
CCTGCACCCCTCCACGAGGGTTTCCCAGACCCCAGCAGGGTATCCTCTGAGGTGCAGCAGATGTGGGCACTGATAGAGAT
GATCCGGGCCAGTCACACCTCCGCGAGGATCGGCCACTTTTATGTAGATGGCTGTTATGACCTGAACTTGCTCTCCTACA
CT
ORF - retro_pabe_3751 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 88.89 % |
| Parental protein coverage: | 75.59 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | YYTAFLSIRVRQHTSAHTPAKWVTCLRDYCLMPDPHSEEGA-QEYVSLFKHQMLCDMARISELRLILRQP |
| YYTAFLSIRV.QHTSAHT.AKWVTCL.DYCLMPDPHSEEGA.QEYVSLFK.Q.LCDMAR.SEL.LILRQP | |
| Retrocopy | YYTAFLSIRVCQHTSAHTLAKWVTCLWDYCLMPDPHSEEGA<QEYVSLFKQQILCDMARVSELHLILRQP |
| Parental | SPLWLSFTVEELQIYQQGPKSPSVTFPKWLSHPVPCEQPALLREGLPDPSRVSSEVQQMWALTEMIRASH |
| .PLWLSFTVEELQIYQQGPKSPS..FPKWLSHPVPCEQPA.L.EG.PDPSRVSSEVQQMWAL.EMIRASH | |
| Retrocopy | *PLWLSFTVEELQIYQQGPKSPSMIFPKWLSHPVPCEQPAPLHEGFPDPSRVSSEVQQMWALIEMIRASH |
| Parental | TSTRIGRFDVDGCYDLNLLSYT |
| TS.RIG.F.VDGCYDLNLLSYT | |
| Retrocopy | TSARIGHFYVDGCYDLNLLSYT |
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 | 18 .47 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 10 .58 RPM |
| SRP007412_heart | 0 .00 RPM | 5 .30 RPM |
| SRP007412_kidney | 0 .00 RPM | 11 .97 RPM |
| SRP007412_liver | 0 .00 RPM | 4 .74 RPM |
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_3751 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_3751 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_pabe_3751 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 4 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Homo sapiens | ENSG00000145029 | 1 retrocopy | |
| Nomascus leucogenys | ENSNLEG00000006851 | 1 retrocopy | |
| Pongo abelii | ENSPPYG00000029914 | 1 retrocopy |
retro_pabe_3751 ,
|
| Pan troglodytes | ENSPTRG00000032494 | 1 retrocopy |