RetrogeneDB ID: | retro_mmus_2926 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 7:42879395..42880002(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000092191 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Ppm1a | ||
| Ensembl ID: | ENSMUSG00000021096 | ||
| Aliases: | Ppm1a, 2310003C21Rik, 2900017D14Rik, AI427932, AU017636, MMPa-2, MPPa-1 | ||
| Description: | protein phosphatase 1A, magnesium dependent, alpha isoform [Source:MGI Symbol;Acc:MGI:99878] |
Retrocopy-Parental alignment summary:
>retro_mmus_2926
ATTCAGAATGCAGGGGGCTCGATGATGATTCAGCGTGTCAATGGCTCTCTGGCTGGGGATTTCGATTACAAATGTGTCCA
TCGCAAAGGTCCCACAGAGCAGCCTGTCTCACCAAGCCCGAAGTCCATGATATTGAAAGGTCTGAAGAAGAATATCAGTT
GATCATTCTTGCATATGATGGTATCTGGGACGTCACTGGAAACGAAGAGCTCTGTGACTTTGTGAGATCCAGACTTGAAG
TCACTTATGACCATGAGGAAGTTTGTGATGAAGCAGTAGACACCTGTTTGTATAAGGAAAGTCGAGACACCGTAAGTGCG
ATTTTGATCTGTTTTCCAAATGCACCTAAAGCCTCAGCAGAAGCGGGGAAGAAGGAGGCGGGGCTGAGCGAGTACCTGGA
AAGCAGAGGAGAAGAAATCATAAGAAGCAGGGGGAAGGCGTCCCTGATTTAGTCCACGTGATGTGCACGGTAGCCATTGA
GCACATCCGCAGCCTCCCACCAGGGGGTGAATTGGCAAGCAAGCAGAAAGTAATTGAAGCCATTTACAATAGACTAAATA
CTTACAAAAATGACGACAATGATTCTACATCAACTGATGACATGTGG
ORF - retro_mmus_2926 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 75.12 % |
| Parental protein coverage: | 52.09 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | IQRVNGSLAVSRA----LGDFDYKCVHGKGPTEQLVSP-EPEVHDIERSEEDDQFIILACDGIWDVMGNE |
| IQ...GS....R......GDFDYKCVH.KGPTEQ.VSP..PEVHDIERSEE..Q.IILA.DGIWDV.GNE | |
| Retrocopy | IQNAGGSMMIQRVNGSLAGDFDYKCVHRKGPTEQPVSP<KPEVHDIERSEEEYQLIILAYDGIWDVTGNE |
| Parental | ELCDFVRSRLEVTDDLEKVCNEVVDTCLYKGSRDNMSVILICFPSAPKVSAEAVKKEAELDKYLESRVEE |
| ELCDFVRSRLEVT.D.E.VC.E.VDTCLYK.SRD..S.ILICFP.APK.SAEA.KKEA.L..YLESR.EE | |
| Retrocopy | ELCDFVRSRLEVTYDHEEVCDEAVDTCLYKESRDTVSAILICFPNAPKASAEAGKKEAGLSEYLESRGEE |
| Parental | II-KKQVEGVPDLVHVMRTLASENIPSLPPGGELASKRNVIEAVYNRLNPYKNDDTDSASTDDMW |
| II.KKQ.EGVPDLVHVM.T.A.E.I.SLPPGGELASK..VIEA.YNRLN.YKNDD.DS.STDDMW | |
| Retrocopy | II<KKQGEGVPDLVHVMCTVAIEHIRSLPPGGELASKQKVIEAIYNRLNTYKNDDNDSTSTDDMW |
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 .00 RPM | 146 .81 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 124 .75 RPM |
| SRP007412_heart | 0 .00 RPM | 115 .21 RPM |
| SRP007412_kidney | 0 .00 RPM | 104 .35 RPM |
| SRP007412_liver | 0 .00 RPM | 126 .41 RPM |
| SRP007412_testis | 0 .59 RPM | 332 .16 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_2926 was not detected
No EST(s) were mapped for retro_mmus_2926 retrocopy.
No TSS is located nearby retro_mmus_2926 retrocopy 5' end.
retro_mmus_2926 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_2926 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 5 parental genes, and 6 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Mus musculus | ENSMUSG00000021096 | 2 retrocopies |
retro_mmus_2925, retro_mmus_2926 ,
|
| Mus musculus | ENSMUSG00000061130 | 1 retrocopy | |
| Otolemur garnettii | ENSOGAG00000003689 | 1 retrocopy | |
| Drosophila melanogaster | FBgn0035425 | 1 retrocopy | |
| Drosophila melanogaster | FBgn0086361 | 1 retrocopy |