RetrogeneDB ID: | retro_mmus_3489 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | X:94789716..94790346(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000082964 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Rpl13 | ||
| Ensembl ID: | ENSMUSG00000000740 | ||
| Aliases: | Rpl13, A52, L13 | ||
| Description: | ribosomal protein L13 [Source:MGI Symbol;Acc:MGI:105922] |
Retrocopy-Parental alignment summary:
>retro_mmus_3489
ATGGCACCCAGCCGGAATGGCATGATCATGAAGCCCCACTTCCACAAGCATTGGCAGCAGCGAGTGTACACTTGGTTCAA
CCAGCTACCATGCAAGACCTGCAGACTCAAGGCTCGGCAGGAGAAAGCACACAGCATTCCCCCTCGTCCCGCGTCCGGCC
CCATCAGGCCCACTGTGAGGTCCCCTACAGTAAGATACCACACCAAGGTCCGGGCTGTCAGGGGCTTCAGCCTAGAGGAA
CTCAGGGTGGCTGGGATCCACATGAAAATGGTTTGCACCATCAGCATCTCTGTGGACCCAAGGAGGCAAAACAAATCCAC
TGAACCGCTGCAGGCCACCGTGCAGCGCCTGAAGGAGTACTGCTCCAAGCTCATACTTTCCCCCAGGAAGCCTTCTGCTC
CAAAGAAGGGAGACAGTTCTGCTGAAGAACTTAAACTGGCCACCCAGCTGACAGGACCTGTGATGCCCATCTGGAATGTA
TACAAAAAGGAAAAGGCCAGCGTCGTCACAGAAGAAGAAAACTCTAAGGCTTTTGCCAGTCTTCACTTGGCCCATGCCAA
TGCCTGGCTCTTTGGCATCCGAGCAAAAAGCGCGAAGGAAGCTTCGGAGCAAGACGTTGAAGAGAAAAAG
ORF - retro_mmus_3489 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 81.99 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MAPSRNGMILKPHFHKDWQQRVDTWFNQPARKIRRRKARQAKARRIAPRPASGPIRPIVRCPTVRYHTKV |
| MAPSRNGMI.KPHFHK.WQQRV.TWFNQ...K..R.KARQ.KA..I.PRPASGPIRP.VR.PTVRYHTKV | |
| Retrocopy | MAPSRNGMIMKPHFHKHWQQRVYTWFNQLPCKTCRLKARQEKAHSIPPRPASGPIRPTVRSPTVRYHTKV |
| Parental | RAGRGFSLEELRVAGIHKKVARTIGISVDPRRRNKSTESLQANVQRLKEYRSKLILFPRKPSAPKKGDSS |
| RA.RGFSLEELRVAGIH.K...TI.ISVDPRR.NKSTE.LQA.VQRLKEY.SKLIL.PRKPSAPKKGDSS | |
| Retrocopy | RAVRGFSLEELRVAGIHMKMVCTISISVDPRRQNKSTEPLQATVQRLKEYCSKLILSPRKPSAPKKGDSS |
| Parental | AEELKLATQLTGPVMPIRNVYKKEKARVITEEEKNFKAFASLRMARANARLFGIRAKRAKEAAEQDVEKK |
| AEELKLATQLTGPVMPI.NVYKKEKA.V.TEEE.N.KAFASL..A.ANA.LFGIRAK.AKEA.EQDVE.K | |
| Retrocopy | AEELKLATQLTGPVMPIWNVYKKEKASVVTEEE-NSKAFASLHLAHANAWLFGIRAKSAKEASEQDVEEK |
| Parental | K |
| K | |
| Retrocopy | K |
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 .16 RPM | 36 .87 RPM |
| SRP007412_cerebellum | 0 .04 RPM | 16 .93 RPM |
| SRP007412_heart | 0 .03 RPM | 41 .50 RPM |
| SRP007412_kidney | 0 .12 RPM | 25 .02 RPM |
| SRP007412_liver | 0 .05 RPM | 22 .80 RPM |
| SRP007412_testis | 0 .00 RPM | 37 .64 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_3489 was not detected
No EST(s) were mapped for retro_mmus_3489 retrocopy.
| TSS No. | TSS Name | TSS expression level (Expr) in TPM range: | ||||
|---|---|---|---|---|---|---|
| no expression | 0 < Expr ≤ 1 | 1 < Expr ≤ 5 | 5 < Expr ≤ 10 | Expr > 10 | ||
| TSS #1 | TSS_158569 | 338 libraries | 478 libraries | 249 libraries | 4 libraries | 3 libraries |
The graphical summary, for retro_mmus_3489 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)
retro_mmus_3489 was not experimentally validated.