RetrogeneDB ID: | retro_mmus_3643 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | X:77290246..77290815(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000084202 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Ctsh | ||
| Ensembl ID: | ENSMUSG00000032359 | ||
| Aliases: | Ctsh, AL022844 | ||
| Description: | cathepsin H [Source:MGI Symbol;Acc:MGI:107285] |
Retrocopy-Parental alignment summary:
>retro_mmus_3643
ATGTGCGCTGCGCTGCCACCACTCTGGACAGGGCCTGGCTGCTGAGAATGCAGGCCAACGCTGAGCTGACAGTCAACGCC
ACAGAAAAATTTCACTTTAAGTCATGGACAAAACAGCATCAAAAGACGTACAGCTTAGAGGAGTAAAACCATAGGCTGCA
GATGTTTGCCAACAACTGGAGGAAGATTCATGACCACAACCAGAGGAACCACACATTTAAATTTGTGTTGAACCAGTTTT
CAGATATGAGCTTTGCTGAAATAAAACACAAATATTTCTGGTCAGAGCCTCAGAACTGCTCAGCCACCAAAAGTAACTGT
CTCCGTGGTACTGGCCCCTACCCTGCCTCCGTGGAATGTCTGAAGAAAGGAAGTGTTGTTTTAGCAGGGAAAAATCAGGG
GGCCTGTGGCAGTTTCTGGACTTTCTCCATCACGGAGGCCCTAGGGTCGGCTGTGGCTATTGCCAGTGGGAAAATGCTGT
CTTTGGCTGAACAGCAGCTGGTGGATTGTGCCCAGGACAATCATGGCAGCGAAGGAGGTCTCCCCAGCCAGACCTTCGAG
TACATCCTG
ORF - retro_mmus_3643 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 79.27 % |
| Parental protein coverage: | 57.66 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MWAALPLLCAG-AWLLSTGATAELTVNAIEKFHFKSWMKQHQKTYSSVEYNHRLQMFANNWRKIQAHNQR |
| M.AALP.L..G.AWLL...A.AELTVNA.EKFHFKSW.KQHQKTYS..E.NHRLQMFANNWRKI..HNQR | |
| Retrocopy | MCAALPPLWTG<AWLLRMQANAELTVNATEKFHFKSWTKQHQKTYSLEE*NHRLQMFANNWRKIHDHNQR |
| Parental | NHTFKMALNQFSDMSFAEIKHKFLWSEPQNCSATKSNYLRGTGPYPSSMDWRKKGNVVSPVKNQGACGSC |
| NHTFK..LNQFSDMSFAEIKHK..WSEPQNCSATKSN.LRGTGPYP.S....KKG.VV...KNQGACGS. | |
| Retrocopy | NHTFKFVLNQFSDMSFAEIKHKYFWSEPQNCSATKSNCLRGTGPYPASVECLKKGSVVLAGKNQGACGSF |
| Parental | WTFSTTGALESAVAIASGKMLSLAEQQLVDCAQAFNNHGCKGGLPSQAFEYIL |
| WTFS.T.AL.SAVAIASGKMLSLAEQQLVDCAQ...NHG..GGLPSQ.FEYIL | |
| Retrocopy | WTFSITEALGSAVAIASGKMLSLAEQQLVDCAQ--DNHGSEGGLPSQTFEYIL |
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 .23 RPM | 8 .50 RPM |
| SRP007412_cerebellum | 0 .13 RPM | 6 .51 RPM |
| SRP007412_heart | 0 .00 RPM | 26 .90 RPM |
| SRP007412_kidney | 0 .02 RPM | 102 .99 RPM |
| SRP007412_liver | 0 .00 RPM | 200 .50 RPM |
| SRP007412_testis | 0 .09 RPM | 5 .21 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_3643 was not detected
No EST(s) were mapped for retro_mmus_3643 retrocopy.
No TSS is located nearby retro_mmus_3643 retrocopy 5' end.
retro_mmus_3643 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_3643 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 | ENSMUSG00000021939 | 1 retrocopy | |
| Mus musculus | ENSMUSG00000032359 | 1 retrocopy |
retro_mmus_3643 ,
|