RetrogeneDB ID: | retro_hsap_2099 | ||
Retrocopy location | Organism: | Human (Homo sapiens) | |
| Coordinates: | 2:44497759..44498041(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSG00000226972 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | RPL12 | ||
| Ensembl ID: | ENSG00000197958 | ||
| Aliases: | RPL12, L12 | ||
| Description: | ribosomal protein L12 [Source:HGNC Symbol;Acc:10302] |
Retrocopy-Parental alignment summary:
>retro_hsap_2099
ATGCCGCCGAAGTTCCACCCCAATGAGATCAAAGTCGTATACTTCACGTGCACTGGAGTTGAAGTCGGTGCCACTTCTGC
TCTGGCCCCCAAGATTGGCCCCGCGGGTCTGTCTCCAAAAGAGGTTGGTGATGACATTGCCAAGGTAACGGGTGACTGGA
AGGGCCTGAGGATTACAGTGAAACTGACCATTCAGAACAGACAGGCCCAGATTGAAGTGGTACCTTCTGCCTCCGCCCTG
ATCATCAAAAGGAACTACCAAGAGACAGAAAGAAACAGAAAA
ORF - retro_hsap_2099 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 85.11 % |
| Parental protein coverage: | 56.36 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MPPKFDPNEIKVVYLRCTGGEVGATSALAPKIGPLGLSPKKVGDDIAKATGDWKGLRITVKLTIQNRQAQ |
| MPPKF.PNEIKVVY..CTG.EVGATSALAPKIGP.GLSPK.VGDDIAK.TGDWKGLRITVKLTIQNRQAQ | |
| Retrocopy | MPPKFHPNEIKVVYFTCTGVEVGATSALAPKIGPAGLSPKEVGDDIAKVTGDWKGLRITVKLTIQNRQAQ |
| Parental | IEVVPSASALIIKA-LKEPPRDRK |
| IEVVPSASALIIK....E..R.RK | |
| Retrocopy | IEVVPSASALIIKRNYQETERNRK |
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 |
|---|---|---|
| bodymap2_adipose | 0 .00 RPM | 334 .37 RPM |
| bodymap2_adrenal | 0 .04 RPM | 375 .59 RPM |
| bodymap2_brain | 0 .02 RPM | 87 .48 RPM |
| bodymap2_breast | 0 .00 RPM | 274 .19 RPM |
| bodymap2_colon | 0 .00 RPM | 494 .79 RPM |
| bodymap2_heart | 0 .00 RPM | 91 .33 RPM |
| bodymap2_kidney | 0 .00 RPM | 286 .03 RPM |
| bodymap2_liver | 0 .00 RPM | 146 .20 RPM |
| bodymap2_lung | 0 .02 RPM | 420 .61 RPM |
| bodymap2_lymph_node | 0 .00 RPM | 493 .85 RPM |
| bodymap2_ovary | 0 .00 RPM | 470 .84 RPM |
| bodymap2_prostate | 0 .00 RPM | 765 .31 RPM |
| bodymap2_skeletal_muscle | 0 .00 RPM | 532 .70 RPM |
| bodymap2_testis | 0 .02 RPM | 314 .22 RPM |
| bodymap2_thyroid | 0 .00 RPM | 203 .98 RPM |
| bodymap2_white_blood_cells | 0 .00 RPM | 691 .71 RPM |
RNA Polymerase II activity near the 5' end of retro_hsap_2099 was not detected
No EST(s) were mapped for retro_hsap_2099 retrocopy.
| TSS No. | TSS Name | TSS expression level (Expr) in TPM range: | ||||
|---|---|---|---|---|---|---|
| no expression | 0 < Expr ≤ 1 | 1 < Expr ≤ 5 | 5 < Expr ≤ 10 | Expr > 10 | ||
| TSS #1 | TSS_123035 | 966 libraries | 70 libraries | 482 libraries | 248 libraries | 63 libraries |
The graphical summary, for retro_hsap_2099 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1829 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)
retro_hsap_2099 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_hsap_2099 has 1 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Pongo abelii | retro_pabe_2000 |