RetrogeneDB ID: | retro_pabe_908 | ||
Retrocopy location | Organism: | Orangutan (Pongo abelii) | |
| Coordinates: | 12:19075909..19076239(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | NDFIP1 | ||
| Ensembl ID: | ENSPPYG00000015896 | ||
| Aliases: | None | ||
| Description: | Nedd4 family interacting protein 1 [Source:HGNC Symbol;Acc:17592] |
Retrocopy-Parental alignment summary:
>retro_pabe_908
TTGGCATTAGTGGCACCAGTGGCAGTTGAGCTGGTCTGCAGCAGCAAGTACCAACATTTATAGGATGAGGAAGAGCCTGA
GGAACCTGAGAAGGCTTCAGGTGAGGTTCCTCCACCTTATGGCGTCAACTCTGCAGAGAGTATGGTATATTTGACTACAC
AGATGAGTCTAATTTTCCAAAGCCCCCATTTTACAATGTGGTTGCAAACATTACCAATTTATAATAAAGTCATGAGAATC
AAGGCTGAAGCTCTTTCTTTGGTTCCTGGAAGAGATGAGGATTTTGTGGGACAGGATGATTTTGATGATGCTGACCAGTT
GAGGATAGGA
ORF - retro_pabe_908 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 66.37 % |
| Parental protein coverage: | 50.23 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | LALAALAAVEPACGSRYQQLQNEEESGEPEQAAGDAPPPYSSISAESAAY-FDYKDESGFPKPPSYNVAT |
| LAL.A..AVE..C.S.YQ.L..EEE..EPE.A.G..PPPY...SAES..Y.FDY.DES.FPKPP.YNV.. | |
| Retrocopy | LALVAPVAVELVCSSKYQHL*DEEEPEEPEKASGEVPPPYGVNSAESMVY<FDYTDESNFPKPPFYNVVA |
| Parental | -TLPSYDEAERTKAEATIPLVPGRDEDFVGRDDFDDADQLRIG |
| .TLP.Y....R.KAEA...LVPGRDEDFVG.DDFDDADQLRIG | |
| Retrocopy | >TLPIYNKVMRIKAEA-LSLVPGRDEDFVGQDDFDDADQLRIG |
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 | 236 .87 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 179 .60 RPM |
| SRP007412_heart | 0 .00 RPM | 40 .16 RPM |
| SRP007412_kidney | 0 .00 RPM | 94 .07 RPM |
| SRP007412_liver | 0 .00 RPM | 66 .34 RPM |
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_908 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_908 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_pabe_908 has 5 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Homo sapiens | retro_hsap_1091 |
| Pan troglodytes | retro_ptro_743 |
| Gorilla gorilla | retro_ggor_859 |
| Macaca mulatta | retro_mmul_846 |
| Callithrix jacchus | retro_cjac_3175 |
Parental genes homology:
Parental genes homology involve 11 parental genes, and 11 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Bos taurus | ENSBTAG00000047747 | 1 retrocopy | |
| Callithrix jacchus | ENSCJAG00000018271 | 1 retrocopy | |
| Equus caballus | ENSECAG00000021907 | 1 retrocopy | |
| Homo sapiens | ENSG00000131507 | 1 retrocopy | |
| Gorilla gorilla | ENSGGOG00000004879 | 1 retrocopy | |
| Macaca mulatta | ENSMMUG00000016787 | 1 retrocopy | |
| Pongo abelii | ENSPPYG00000015896 | 1 retrocopy |
retro_pabe_908 ,
|
| Pan troglodytes | ENSPTRG00000017358 | 1 retrocopy | |
| Sarcophilus harrisii | ENSSHAG00000002466 | 1 retrocopy | |
| Sus scrofa | ENSSSCG00000025295 | 1 retrocopy | |
| Ictidomys tridecemlineatus | ENSSTOG00000005153 | 1 retrocopy |