RetrogeneDB ID: | retro_mmus_2981 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 7:139774744..139775179(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Rpl24 | ||
| Ensembl ID: | ENSMUSG00000022601 | ||
| Aliases: | Zbtb11, 9230110G02Rik, ZNF-U69274 | ||
| Description: | ribosomal protein L24 [Source:MGI Symbol;Acc:MGI:1915443] |
Retrocopy-Parental alignment summary:
>retro_mmus_2981
AAGATCTACCCGGGACATGGGCGGCACTATGCCAGCACCTACGAGAAGATTTTCCAGTTTCTTAATGCAAAATGTGAGTC
CGCATTCCTTTCCAAAAGGAATCCTAGGCAAATAAACTGGACTGTCCTCTACAGAAGAAAACACAAGAAAGGGCAGTTGG
AAGAAATTCAAAAGAAAAGAACCTGCCGTGCAGTCAAATTCCAACAAGCCATCATTGGTGCATCTCTTGCTGATATAATG
GCCAAGAGGAATCAGAAACCAGAGGTTAAGAAAGCCCAGTGAGAGCAGGCTATCAGGGCTGCCAAGGAAGCAAAAGAGGC
TAAGCAGGCATCAAAGAAGACAGCAATGGCTGCTGCCAAGGCCCCCACAAAGGCAGCACCTAAACAAAAGATTGTGAAGC
CTGTGAAGGTCTCTGCCCCCAGAGTTGGTGGGAAA
ORF - retro_mmus_2981 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 91.72 % |
| Parental protein coverage: | 92.36 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | KIYPGHGRRYARTDGKVFQFLNAKCESAFLSKRNPRQINWTVLYRRKHKKGQSEEIQKKRTRRAVKFQRA |
| KIYPGHGR.YA.T..K.FQFLNAKCESAFLSKRNPRQINWTVLYRRKHKKGQ.EEIQKKRT.RAVKFQ.A | |
| Retrocopy | KIYPGHGRHYASTYEKIFQFLNAKCESAFLSKRNPRQINWTVLYRRKHKKGQLEEIQKKRTCRAVKFQQA |
| Parental | ITGASLADIMAKRNQKPEVRKAQREQAIRAAKEAKKAKQASKKTAMAAAKAPTKAAPKQKIVKPVKVSAP |
| I.GASLADIMAKRNQKPEV.KAQ.EQAIRAAKEAK.AKQASKKTAMAAAKAPTKAAPKQKIVKPVKVSAP | |
| Retrocopy | IIGASLADIMAKRNQKPEVKKAQ*EQAIRAAKEAKEAKQASKKTAMAAAKAPTKAAPKQKIVKPVKVSAP |
| Parental | RVGGK |
| RVGGK | |
| Retrocopy | RVGGK |
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 .02 RPM | 83 .94 RPM |
| SRP007412_cerebellum | 0 .09 RPM | 81 .85 RPM |
| SRP007412_heart | 0 .00 RPM | 59 .33 RPM |
| SRP007412_kidney | 0 .02 RPM | 59 .77 RPM |
| SRP007412_liver | 0 .00 RPM | 60 .76 RPM |
| SRP007412_testis | 0 .00 RPM | 67 .05 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_2981 was not detected
No EST(s) were mapped for retro_mmus_2981 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_130242 | 78 libraries | 108 libraries | 660 libraries | 148 libraries | 78 libraries |
The graphical summary, for retro_mmus_2981 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_2981 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_2981 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 13 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Mus musculus | ENSMUSG00000022601 | 13 retrocopies |