RetrogeneDB ID: | retro_mmus_2929 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 7:45324964..45325450(+) | ||
| Located in intron of: | ENSMUSG00000038260 | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000046721 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Rpl14 | ||
| Ensembl ID: | ENSMUSG00000025794 | ||
| Aliases: | Rpl14, 3100001N19Rik, AA407502, AL022816, CAG-ISL-7, CTG-B33, L14 | ||
| Description: | ribosomal protein L14 [Source:MGI Symbol;Acc:MGI:1914365] |
Retrocopy-Parental alignment summary:
>retro_mmus_2929
ATGGTGTTCAGGCGTTACGTGGAGGTTGGCCGGGTGGCCTACATTTCCTTCGGGCCCCATGCTGGAAAGCTGGTCGCAAT
TGTAGATGTCATTGATCAGAACAGGGCTTTAGTGGATGGACCCTGTACTCGGGTGAGGAGGCAGGCCATGCCCTTCAAAT
GCATGCAGCTCACTGACTTCATCCTCAAGTTCCCACACAGTGCCCGCCAGAAGTATGTCCGAAAAGCTTGGGAGAAGGCG
GATATCAATACGAAATGGGCAGCCACAAGATGGGCCAAGAAAATTGATGCCAGAGAAAGGAAAGCCAAGATGACAGACTT
TGATCGTTTCAAGGTCATGAAGGCAAAGAAAATGAGGAACAGAATAATCAAGACTGAAGTAAAGAAACTTCAAAGAGCTG
CTATCCTGAAAGCTTCTCCTAAGAAAGCAGCTGTGGCCAAAGCTGCCATTGCGGCTGCAGCTGCTGCTGCTGCTAAAGCT
AAAGTC
ORF - retro_mmus_2929 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 99.39 % |
| Parental protein coverage: | 75.12 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MVFRRYVEVGRVAYISFGPHAGKLVAIVDVIDQNRALVDGPCTRVRRQAMPFKCMQLTDFILKFPHSARQ |
| MVFRRYVEVGRVAYISFGPHAGKLVAIVDVIDQNRALVDGPCTRVRRQAMPFKCMQLTDFILKFPHSARQ | |
| Retrocopy | MVFRRYVEVGRVAYISFGPHAGKLVAIVDVIDQNRALVDGPCTRVRRQAMPFKCMQLTDFILKFPHSARQ |
| Parental | KYVRKAWEKADINTKWAATRWAKKIDARERKAKMTDFDRFKVMKAKKMRNRIIKTEVKKLQRAAILKASP |
| KYVRKAWEKADINTKWAATRWAKKIDARERKAKMTDFDRFKVMKAKKMRNRIIKTEVKKLQRAAILKASP | |
| Retrocopy | KYVRKAWEKADINTKWAATRWAKKIDARERKAKMTDFDRFKVMKAKKMRNRIIKTEVKKLQRAAILKASP |
| Parental | KKAAVAKAAIAAAAAAAAAKAKV |
| KKAAVAKAAIAAAAAAAA.KAKV | |
| Retrocopy | KKAAVAKAAIAAAAAAAA-KAKV |
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 .61 RPM | 77 .31 RPM |
| SRP007412_cerebellum | 0 .78 RPM | 57 .84 RPM |
| SRP007412_heart | 1 .49 RPM | 77 .27 RPM |
| SRP007412_kidney | 1 .54 RPM | 91 .22 RPM |
| SRP007412_liver | 0 .82 RPM | 78 .51 RPM |
| SRP007412_testis | 0 .27 RPM | 31 .74 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_2929 was not detected
No EST(s) were mapped for retro_mmus_2929 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_135578 | 4 libraries | 0 libraries | 2 libraries | 4 libraries | 1062 libraries |
| TSS #2 | TSS_135579 | 236 libraries | 546 libraries | 282 libraries | 5 libraries | 3 libraries |
The graphical summary, for retro_mmus_2929 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_2929 was not experimentally validated.