RetrogeneDB ID: | retro_mmus_1542 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 17:8260659..8261294(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Ppcs | ||
| Ensembl ID: | ENSMUSG00000028636 | ||
| Aliases: | Ppcs, 6330579B17Rik, AI413471, AI790434 | ||
| Description: | phosphopantothenoylcysteine synthetase [Source:MGI Symbol;Acc:MGI:1915237] |
Retrocopy-Parental alignment summary:
>retro_mmus_1542
ATGGCGGAAATGGACCTGGTGGCTGAGTTGCCGCGTCCCCCGGGTGCTGCGCGCTGGGCCGAGGTTATGGCTCGCTTTGC
GGCCAGGCTGGGCGAGCAGGGCCGGCGGGTGGTGCTGATCACATCTGGAGGCACCAAGGTCCCACTGGAAGCGTGCGCTT
TCTGGACAACTTCAGTAACGGGCAACAGGGAGCCGCGTCGGCGGAGGTCTTCCTGGCTGCCGGCTATGGAGTCCTGTTCT
TGTTCGGAGGGCACTCAGCCTTCCCCTATACCCATCGCTTCCCGCCCCAGGCCTGGCTGCCAGCCCTCCGGCCTTCTGGC
CCAGCCCAGTCGGGCAAGCTGAGTCTGGAGGCCTAAGAGAATGCGCTCCCGGGCTTTGCTACAGCATTGCAGAGCTTCCA
AGAGACTGGTACCTTCCTGGCTGTAGAGTTTACCACTTTGGCGGATTACCTGCATCTGCTGCAGGCTGCTGCCTTGGCTC
TCGGTCCATTAGGCTCTTCTGCGATGTTTTACCTGGCCGCCGCAGTGTCAGATTTCTATATTCCTGTCTCCGAAATGCCT
GAACACAAGATCCACTCATCTGGTGGCCCACTGCAGGTGATGGACTCTTCTCTTCCAGAGATCTGACCCCCTCTA
ORF - retro_mmus_1542 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 83.49 % |
| Parental protein coverage: | 69.77 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MAEMDLVAELPRPAGAARWAEVMARFAARLGEQGRRVVLITSGGTKVPLEARAVRFLDNFSSGRR-GAAS |
| MAEMDLVAELPRP.GAARWAEVMARFAARLGEQGRRVVLITSGGTKVPLEA.A..F......G.R.GAAS | |
| Retrocopy | MAEMDLVAELPRPPGAARWAEVMARFAARLGEQGRRVVLITSGGTKVPLEACA--FWTTSVTGNR<GAAS |
| Parental | AEVFLAAGYGVLFLYRARSAFPYAHRFPPQAWLSALRPSGPAQSGKLSLEAEENALPGFAAALQSYQEAA |
| AEVFLAAGYGVLFL....SAFPY.HRFPPQAWL.ALRPSGPAQSGKLSLEA.ENALPGFA.ALQS.QE.. | |
| Retrocopy | AEVFLAAGYGVLFLFGGHSAFPYTHRFPPQAWLPALRPSGPAQSGKLSLEA*ENALPGFATALQSFQE-- |
| Parental | AAGTFLAVEFTTLADYLHLLQAAALALSPLGSSAMFYLAAAVSDFYIPVSEMPEHKIHSSGGPLQITMKM |
| ..GTFLAVEFTTLADYLHLLQAAALAL.PLGSSAMFYLAAAVSDFYIPVSEMPEHKIHSSGGPLQ..... | |
| Retrocopy | -TGTFLAVEFTTLADYLHLLQAAALALGPLGSSAMFYLAAAVSDFYIPVSEMPEHKIHSSGGPLQVMDSS |
| Parental | VPKMLSPL |
| .P....PL | |
| Retrocopy | LPEI*PPL |
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 | 2 .59 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 2 .61 RPM |
| SRP007412_heart | 0 .00 RPM | 5 .17 RPM |
| SRP007412_kidney | 0 .04 RPM | 11 .09 RPM |
| SRP007412_liver | 0 .00 RPM | 9 .01 RPM |
| SRP007412_testis | 0 .05 RPM | 2 .15 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_1542 was not detected
No EST(s) were mapped for retro_mmus_1542 retrocopy.
No TSS is located nearby retro_mmus_1542 retrocopy 5' end.
retro_mmus_1542 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_1542 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 | ENSMUSG00000028636 | 1 retrocopy |
retro_mmus_1542 ,
|
| Otolemur garnettii | ENSOGAG00000031647 | 1 retrocopy |