RetrogeneDB ID: | retro_mmus_2990 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 7:10656484..10656820(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000093826 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Eif1 | ||
| Ensembl ID: | ENSMUSG00000035530 | ||
| Aliases: | Eif1, Sui1-rs1 | ||
| Description: | eukaryotic translation initiation factor 1 [Source:MGI Symbol;Acc:MGI:105125] |
Retrocopy-Parental alignment summary:
>retro_mmus_2990
ATGTCCGCTATCCAGAACCTCCACTCTTTCGACCCCTTTGCTGATGCAAGTAAGGGTGATGACCTGCTTCCTGCTGGCAC
TGAGGATTATATCCATATAAGAATTCAACAGAGAAACGGCAGGAAGACCCTTACTACTGTCCAAGGGATCGCTGATGATT
ACGATAAAAAGAAACTAGTGAAGGCGTTGAAAAAGAAATTTGCCTGCAATGGTACTGTAATTGAGCATCCAGAATATGGA
GAAGTAATTCAGCTACAGGGTGACCAGCGCGAGAACATATGCCAGTTCCTGATAGAGACTGGGCTGGCTAAGGACGATCA
GCTGAAGGCTCATGGG
ORF - retro_mmus_2990 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 96.43 % |
| Parental protein coverage: | 99.12 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MSAIQNLHSFDPFADASKGDDLLPAGTEDYIHIRIQQRNGRKTLTTVQGIADDYDKKKLVKAFKKKFACN |
| MSAIQNLHSFDPFADASKGDDLLPAGTEDYIHIRIQQRNGRKTLTTVQGIADDYDKKKLVKA.KKKFACN | |
| Retrocopy | MSAIQNLHSFDPFADASKGDDLLPAGTEDYIHIRIQQRNGRKTLTTVQGIADDYDKKKLVKALKKKFACN |
| Parental | GTVIEHPEYGEVIQLQGDQRKNICQFLIEIGLAKDDQLKVHG |
| GTVIEHPEYGEVIQLQGDQR.NICQFLIE.GLAKDDQLK.HG | |
| Retrocopy | GTVIEHPEYGEVIQLQGDQRENICQFLIETGLAKDDQLKAHG |
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 .05 RPM | 129 .24 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 91 .10 RPM |
| SRP007412_heart | 0 .09 RPM | 194 .38 RPM |
| SRP007412_kidney | 0 .08 RPM | 123 .04 RPM |
| SRP007412_liver | 0 .00 RPM | 113 .49 RPM |
| SRP007412_testis | 0 .05 RPM | 149 .52 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_2990 was not detected
No EST(s) were mapped for retro_mmus_2990 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_127333 | 135 libraries | 386 libraries | 535 libraries | 11 libraries | 5 libraries |
The graphical summary, for retro_mmus_2990 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_2990 was not experimentally validated.