RetrogeneDB ID: | retro_mmus_2388 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 4:115480967..115481273(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000086724 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Prkrip1 | ||
| Ensembl ID: | ENSMUSG00000039737 | ||
| Aliases: | None | ||
| Description: | Prkr interacting protein 1 (IL11 inducible) [Source:MGI Symbol;Acc:MGI:1914051] |
Retrocopy-Parental alignment summary:
>retro_mmus_2388
ATGTATAGGCACCTACGGTGGAGAGAGTACCAGCGGCAGGACTACATGGATGCCATGGCTGAGAAGCAAAAACTGAGTGC
AGAGTTTCAGAAGAGACTAGAAAAGAGTAAAATTGCTGCAGAGGAGCAGATTGCAAAGCACCGGAAAAAGCGCCAGAAGT
TAAAAGAGAAGTTACTGGCAAAGAAGATGAAACTTGAGCAGAAGAAACAGAAGGAAGAACCCTGTCAGGGCCAGGAACTG
CATGCCAGCAGCTCTGAAGAGGCATCTGAAACATAGGAGGAAGAGGAGCCCAGCGTTGTCATCATG
ORF - retro_mmus_2388 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 87.5 % |
| Parental protein coverage: | 55.91 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | VYRHLRRREYQRQDYMDAMAEKQKLDAEFQKRLEKNKIAAEEQTAKRRKKRQKLKEKKLLAKKMKLEQKK |
| .YRHLR.REYQRQDYMDAMAEKQKL.AEFQKRLEK.KIAAEEQ.AK.RKKRQKLKE.KLLAKKMKLEQKK | |
| Retrocopy | MYRHLRWREYQRQDYMDAMAEKQKLSAEFQKRLEKSKIAAEEQIAKHRKKRQKLKE-KLLAKKMKLEQKK |
| Parental | QKEEPSQCQEQHASSSDEASETEEEEEEPSVVIM |
| QKEEP.Q.QE.HASSS.EASET..EEEEPSVVIM | |
| Retrocopy | QKEEPCQGQELHASSSEEASET-*EEEEPSVVIM |
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 | 15 .61 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 16 .07 RPM |
| SRP007412_heart | 0 .00 RPM | 7 .10 RPM |
| SRP007412_kidney | 0 .04 RPM | 10 .34 RPM |
| SRP007412_liver | 0 .00 RPM | 5 .84 RPM |
| SRP007412_testis | 0 .00 RPM | 24 .29 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_2388 was not detected
No EST(s) were mapped for retro_mmus_2388 retrocopy.
No TSS is located nearby retro_mmus_2388 retrocopy 5' end.
retro_mmus_2388 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_2388 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Bos taurus | ENSBTAG00000004106 | 1 retrocopy | |
| Mus musculus | ENSMUSG00000039737 | 1 retrocopy |
retro_mmus_2388 ,
|