RetrogeneDB ID: | retro_mmus_731 | ||
Retrocopylocation | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 11:83800607..83801021(+) | ||
| Located in intron of: | None | ||
Retrocopyinformation | Ensembl ID: | ENSMUSG00000081342 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental geneinformation | Parental gene summary: | ||
| Parental gene symbol: | Commd9 | ||
| Ensembl ID: | ENSMUSG00000027163 | ||
| Aliases: | Commd9, 1810029F08Rik, AA409293 | ||
| Description: | COMM domain containing 9 [Source:MGI Symbol;Acc:MGI:1923751] |
Retrocopy-Parental alignment summary:
>retro_mmus_731
CTCCTAGATAATACATGTTCCAGCTTGTCTGTGACCCAGGAGGCAGAGCAACTGCTCCAGGCTCTGCACCACTTCACTAG
GCTGGTGGCCTTCCGTGACCTGACCTCTGCTGAGGCGATTCTGTCTCTCTTTCCAGAAAAGTTCCACCAAAATCTCAAAA
ACCTGCTGACAAAAATCATCCTAGGGCACATATCGACTTGGAGAGCTGAAGCCCAAGCAAACCAGATCTCTCTGCCACAC
CTGGTGGACCTGGACTGGAGAGTGGATATCAAAACCTCCTCCGACAACATCAGCCGCAAGGTTGTCCCCGCCTGCCTGCT
CCAGATGAAGATCCAGGAGGATCCTAGTCTGTGTGGAGAGAAACCCTCCATCTCGGCTATGACCATGGAGCTGAGCAAAG
AGACACTGGACACC
CTCCTAGATAATACATGTTCCAGCTTGTCTGTGACCCAGGAGGCAGAGCAACTGCTCCAGGCTCTGCACCACTTCACTAG
GCTGGTGGCCTTCCGTGACCTGACCTCTGCTGAGGCGATTCTGTCTCTCTTTCCAGAAAAGTTCCACCAAAATCTCAAAA
ACCTGCTGACAAAAATCATCCTAGGGCACATATCGACTTGGAGAGCTGAAGCCCAAGCAAACCAGATCTCTCTGCCACAC
CTGGTGGACCTGGACTGGAGAGTGGATATCAAAACCTCCTCCGACAACATCAGCCGCAAGGTTGTCCCCGCCTGCCTGCT
CCAGATGAAGATCCAGGAGGATCCTAGTCTGTGTGGAGAGAAACCCTCCATCTCGGCTATGACCATGGAGCTGAGCAAAG
AGACACTGGACACC
ORF - retro_mmus_731 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 89.93 % |
| Parental protein coverage: | 70.2 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | LLDKTCSSLSVPQGEAAQLLQALHHFTRLVAFRDLSSAEAILALFPENFHQNLKNLLTKIIVEHISTWRA |
| LLD.TCSSLSV.Q.EA.QLLQALHHFTRLVAFRDL.SAEAIL.LFPE.FHQNLKNLLTKII..HISTWRA | |
| Retrocopy | LLDNTCSSLSVTQ-EAEQLLQALHHFTRLVAFRDLTSAEAILSLFPEKFHQNLKNLLTKIILGHISTWRA |
| Parental | EAQANQISLPRLVDLDWRVDIKTSSDNISRMAVPTCLLQMKIQEDPSLCGEKPSISAVTMELSKETLDT |
| EAQANQISLP.LVDLDWRVDIKTSSDNISR..VP.CLLQMKIQEDPSLCGEKPSISA.TMELSKETLDT | |
| Retrocopy | EAQANQISLPHLVDLDWRVDIKTSSDNISRKVVPACLLQMKIQEDPSLCGEKPSISAMTMELSKETLDT |
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 .09 RPM | 12 .06 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 13 .03 RPM |
| SRP007412_heart | 0 .00 RPM | 11 .11 RPM |
| SRP007412_kidney | 0 .10 RPM | 16 .30 RPM |
| SRP007412_liver | 0 .00 RPM | 8 .85 RPM |
| SRP007412_testis | 0 .05 RPM | 12 .49 RPM |
RNA Polymerase II actvity near the 5' end of retro_mmus_731 was not detected
No EST(s) were mapped for retro_mmus_731 retrocopy.
No TSS is located nearby retro_mmus_731 retrocopy 5' end.
retro_mmus_731 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_731 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 | ENSMUSG00000027163 | 2 retrocopies |
retro_mmus_3347, retro_mmus_731 ,
|
| Ochotona princeps | ENSOPRG00000010271 | 2 retrocopies |