RetrogeneDB ID: | retro_mmus_3515 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | X:120958193..120958881(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000083275 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Prpsap2 | ||
| Ensembl ID: | ENSMUSG00000020528 | ||
| Aliases: | Prpsap2, A230054F23Rik | ||
| Description: | phosphoribosyl pyrophosphate synthetase-associated protein 2 [Source:MGI Symbol;Acc:MGI:2384838] |
Retrocopy-Parental alignment summary:
>retro_mmus_3515
CATCTCATCACTATGGATTTACACAGGAAGGAAATCCAGGGCTTCTTCAATATTCCAGTGGATAATTTAAGAGCCTCCCC
ATTCCTGTTACAATATATTCAAGAAGAGATCCAAGATTATAGGAATGCAGTCATTGTGGCCAAGTCTCCAGCCTCAGCCA
AGAGGGCACAATCTTTTGCAACGTGTCTACGTCTGGGTATGTCAGTGATCCATGGAGAAGCACAAGATGCTGAGTCTGAC
TTGGTGGATGGCTGTCACTCCCCACCAATATTTAGGAGTGTAGCTGCCATCCACCACAGCCTGGAGATCCCAATGCTGAT
TCCTAAAGAGAAGCCCCCAATCACAGTTGTTGGTGATGTCCGAGGAAGTATTGCCGCCGCCATCATCATCATGGGTGAAA
TTATTGGATAGTTTTCTTGCTACAGCAGAGACCCTGAAGGAAAGAGGTGCATATAAAATCTTTGTGATGGCCACTCACGG
CTTGTTATCCTCTGATGCTACCAGGCTGATTGAAGAGTCTGCCATTGATGAGGTGTTGGTCACTAACACGATACCACAAG
AGATACAGAAGCTGCAGTGTCCCAAGATCAAGACTGTGGACATCAGCATGATTCTCTCAAAAGCCATCCGCCAAATTCAC
AACGGGGAGTCCATGTCCAACCTTTTCAGAAACATAGGCTTAGATGAC
ORF - retro_mmus_3515 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 86.96 % |
| Parental protein coverage: | 62.06 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | HLITMDLHQKEIQGFFNIPVDNLRASPFLLQYIQEEIPDYRNAVIVAKSPASAKRAQSFAERLRLGIAVI |
| HLITMDLH.KEIQGFFNIPVDNLRASPFLLQYIQEEI.DYRNAVIVAKSPASAKRAQSFA..LRLG..VI | |
| Retrocopy | HLITMDLHRKEIQGFFNIPVDNLRASPFLLQYIQEEIQDYRNAVIVAKSPASAKRAQSFATCLRLGMSVI |
| Parental | HGEAQDAESDLVDGRHSPPMVRSVAAIHPSLEIPMLIPKEKPPITVVGDVGGRIAIIV-DDIIDDVDSFL |
| HGEAQDAESDLVDG.HSPP..RSVAAIH.SLEIPMLIPKEKPPITVVGDV.G.IA...........DSFL | |
| Retrocopy | HGEAQDAESDLVDGCHSPPIFRSVAAIHHSLEIPMLIPKEKPPITVVGDVRGSIAAAI>SSWVKLLDSFL |
| Parental | AAAETLKERGAYKIFVMATHGLLSSDAPRLIEESAIDEVVVTNTIPHEIQKLQCPKIKTVDISMILSEAI |
| A.AETLKERGAYKIFVMATHGLLSSDA.RLIEESAIDEV.VTNTIP.EIQKLQCPKIKTVDISMILS.AI | |
| Retrocopy | ATAETLKERGAYKIFVMATHGLLSSDATRLIEESAIDEVLVTNTIPQEIQKLQCPKIKTVDISMILSKAI |
| Parental | RRIHNGESMSYLFRNIGLDD |
| R.IHNGESMS.LFRNIGLDD | |
| Retrocopy | RQIHNGESMSNLFRNIGLDD |
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 | 0 .02 RPM | 14 .88 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 11 .51 RPM |
| SRP007412_heart | 0 .00 RPM | 3 .05 RPM |
| SRP007412_kidney | 0 .02 RPM | 8 .99 RPM |
| SRP007412_liver | 0 .00 RPM | 4 .26 RPM |
| SRP007412_testis | 0 .00 RPM | 9 .15 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_3515 was not detected
No EST(s) were mapped for retro_mmus_3515 retrocopy.
No TSS is located nearby retro_mmus_3515 retrocopy 5' end.
retro_mmus_3515 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_3515 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Mus musculus | ENSMUSG00000020528 | 2 retrocopies |
retro_mmus_1937, retro_mmus_3515 ,
|
| Mus musculus | ENSMUSG00000031432 | 2 retrocopies |