RetrogeneDB ID: | retro_mmus_2703 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 5:142852677..142853199(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000082308 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Mrpl12 | ||
| Ensembl ID: | ENSMUSG00000039640 | ||
| Aliases: | None | ||
| Description: | mitochondrial ribosomal protein L12 [Source:MGI Symbol;Acc:MGI:1926273] |
Retrocopy-Parental alignment summary:
>retro_mmus_2703
GTGGCGGCTAGCCGCTGTCTGTGGAGGCCACGGCTTGGACTAGGGGGGGCAGCGCTCCGCCTTGCCAGGCAACAGATGCC
CAGCGTCTGTGCAGCGCAGCAGTTGAGAAGCAGCAGCCACCGAAGGAGTGAAGCACTCGCCGGCGCACCTCTGGATAATG
TTCCCAAAGTATACCCCCCCAAGACCCAGCAGCTGGTCCAAGACATTGCCAGCCTTATGCTCCTGGAGATCTCAGACCTC
AACGGACTCCTGAAGAAAACATTGAAGATCCAGGATGTCAGCCTTATGCCAATGGGTGGCATGGTGCCTGGTCTCGTCTC
TGCTGCAGCACCGGCCTCTGAGGCGGCCGAGGAAGAAGACGTCCCCAAACAGAAAGAGCGGACACACTTCACCGTCCGCC
TGACAGAGGCAAAGCCTGTGGACAAAGTGAAGCTGATCAAGAAGATCAAGAACTATGTCCAGGGCATCAACCTCGTCCAG
GCCAAGAAGCTGGTGGAGTCCCTGCCCCAGGTAATCAAAGCC
ORF - retro_mmus_2703 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 93.1 % |
| Parental protein coverage: | 86.57 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | VAASRCLWGPRLGLRGAALRLARQQMPSVCAARQLRSSSHRRSEALAGAPLDNAPKEYPPKIQQLVQDIA |
| VAASRCLW.PRLGL.GAALRLARQQMPSVCAA.QLRSSSHRRSEALAGAPLDN.PK.YPPK.QQLVQDIA | |
| Retrocopy | VAASRCLWRPRLGLGGAALRLARQQMPSVCAAQQLRSSSHRRSEALAGAPLDNVPKVYPPKTQQLVQDIA |
| Parental | SLTLLEISDLNELLKKTLKIQDVGLMPMGGMVPGPVSAAAPASEAAEEEDVPKQKERTHFTVRLTEAKPV |
| SL.LLEISDLN.LLKKTLKIQDV.LMPMGGMVPG.VSAAAPASEAAEEEDVPKQKERTHFTVRLTEAKPV | |
| Retrocopy | SLMLLEISDLNGLLKKTLKIQDVSLMPMGGMVPGLVSAAAPASEAAEEEDVPKQKERTHFTVRLTEAKPV |
| Parental | DKVKLIKEIKNYVQGINLVQAKKLVESLPQEIKA |
| DKVKLIK.IKNYVQGINLVQAKKLVESLPQ.IKA | |
| Retrocopy | DKVKLIKKIKNYVQGINLVQAKKLVESLPQVIKA |
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 .05 RPM | 18 .01 RPM |
| SRP007412_cerebellum | 0 .04 RPM | 17 .33 RPM |
| SRP007412_heart | 0 .03 RPM | 73 .06 RPM |
| SRP007412_kidney | 0 .00 RPM | 57 .23 RPM |
| SRP007412_liver | 0 .03 RPM | 45 .25 RPM |
| SRP007412_testis | 0 .00 RPM | 22 .78 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_2703 was not detected
No EST(s) were mapped for retro_mmus_2703 retrocopy.
No TSS is located nearby retro_mmus_2703 retrocopy 5' end.
retro_mmus_2703 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_2703 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 | |
|---|---|---|---|
| Mus musculus | ENSMUSG00000039640 | 1 retrocopy |
retro_mmus_2703 ,
|
| Tarsius syrichta | ENSTSYG00000009746 | 1 retrocopy |