RetrogeneDB ID: | retro_mmus_54 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 19:23675847..23676480(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000051255 | |
| Aliases: | None | ||
| Status: | KNOWN_PROTEIN_CODING | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Sarnp | ||
| Ensembl ID: | ENSMUSG00000078427 | ||
| Aliases: | Sarnp, 1110005A23Rik, Cip29 | ||
| Description: | SAP domain containing ribonucleoprotein [Source:MGI Symbol;Acc:MGI:1913368] |
Retrocopy-Parental alignment summary:
>retro_mmus_54
ATGGCGGCCGAGACGGTGGAGCTCCACAAGCTGAAGCTTGCTGAACTAAAGCAAGAATGTCTTGCTCGTGGTTTAGAGAC
CAAGGGAATAAAACAAGATCTTATAAATAGGCTGCAGGCCTATCTTGAAGACCATGCAGAAGAAGAAGCAAATGAAGAAG
ATGTACTGGGAGATGAAACTGAGGAAGAAGAACCAAAGCCCATAGAACTGCCTGTTAAAGAGGAAGAACCTCCTGAAAAG
GCTGTTGATATGGCATCGGAAAAGAAGGTGGTAAAGATTACATCTGGAATACCTCAGACTGAAAGAATGCAGAAGAGGGC
TGAACGATTCAATGTACCTGTAAGCCTGGAGAGTAAGAAGGCTGCCCGGGCGGCTAGGTTTGGAATTTCTTCAGTTCCAA
CAAAAGGTTTATCATCTGACACCAAGCCTATGGTTAACCTGGATAAACTAAAGGAAAGAGCACAGAGATTTGGTTTGAAT
GTCTCTTCCATCTCTAGAAAGTCTGAGGATGATGAGAAGCTGAAGAAACGGAAGGAGAGATTTGGGATTGTGACAAGTTC
AGCTGGAACTGGAACCACAGAGGATACAGAGGCAAAGAAAAGAAAAAGAGCAGAGCGTTTTGGAATTGCATAA
ORF - retro_mmus_54 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 100.0 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MAAETVELHKLKLAELKQECLARGLETKGIKQDLINRLQAYLEDHAEEEANEEDVLGDETEEEEPKPIEL |
| MAAETVELHKLKLAELKQECLARGLETKGIKQDLINRLQAYLEDHAEEEANEEDVLGDETEEEEPKPIEL | |
| Retrocopy | MAAETVELHKLKLAELKQECLARGLETKGIKQDLINRLQAYLEDHAEEEANEEDVLGDETEEEEPKPIEL |
| Parental | PVKEEEPPEKAVDMASEKKVVKITSGIPQTERMQKRAERFNVPVSLESKKAARAARFGISSVPTKGLSSD |
| PVKEEEPPEKAVDMASEKKVVKITSGIPQTERMQKRAERFNVPVSLESKKAARAARFGISSVPTKGLSSD | |
| Retrocopy | PVKEEEPPEKAVDMASEKKVVKITSGIPQTERMQKRAERFNVPVSLESKKAARAARFGISSVPTKGLSSD |
| Parental | TKPMVNLDKLKERAQRFGLNVSSISRKSEDDEKLKKRKERFGIVTSSAGTGTTEDTEAKKRKRAERFGIA |
| TKPMVNLDKLKERAQRFGLNVSSISRKSEDDEKLKKRKERFGIVTSSAGTGTTEDTEAKKRKRAERFGIA | |
| Retrocopy | TKPMVNLDKLKERAQRFGLNVSSISRKSEDDEKLKKRKERFGIVTSSAGTGTTEDTEAKKRKRAERFGIA |
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 .49 RPM | 7 .45 RPM |
| SRP007412_cerebellum | 0 .52 RPM | 7 .47 RPM |
| SRP007412_heart | 0 .56 RPM | 5 .88 RPM |
| SRP007412_kidney | 0 .65 RPM | 6 .68 RPM |
| SRP007412_liver | 0 .36 RPM | 4 .62 RPM |
| SRP007412_testis | 0 .50 RPM | 7 .78 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_54 was not detected
| 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_63145 | 178 libraries | 287 libraries | 572 libraries | 28 libraries | 7 libraries |
The graphical summary, for retro_mmus_54 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_54 was not experimentally validated.