RetrogeneDB ID: | retro_mmus_1918 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 2:52619753..52620182(+) | ||
| Located in intron of: | ENSMUSG00000017412 | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000025201 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Bloc1s2a | ||
| Ensembl ID: | ENSMUSG00000057506 | ||
| Aliases: | Bloc1s2, 2410089B13Rik, BLOS2, Bloc1s2a | ||
| Description: | biogenesis of lysosome-related organelles complex-1, subunit 2A [Source:MGI Symbol;Acc:MGI:1920939] |
Retrocopy-Parental alignment summary:
>retro_mmus_1918
ATGGCGGCGGCTGCGGAGGGCGTCCCGGCGACGCGACGGGAGGAGCAGCCACCTCGAGATGATGCTGCGGTGGAGACAGC
CGAGGAAGCAAAGGAGCCTGCCGAAGCTGACATCAATGAGCTCTGCAGGGACATGTTCTCCAAAATGGCCACATATTTGA
CTGGGGAACTGACAGCCACCAGTGAAGACTACAAACTCCTGGAAAATATGAATAAGCTAACAAGCTTGAAGTACCTTGAA
ATGAAAGATATTGCTATCAACATCAGCAGAAACCTGAAGGACTTAAACCAGAAATATGCTGAACTACAGCCATATCTGGA
CCAGATCAACATGATTGAGGAGCAGGTGGCAGCTCTGGAGCAGGCAGCCTACAAGCTCGATGCTTATTCAAAAAAACTGG
AAGCCAAGTACAAGAAGTTGGAGAAGCGA
ORF - retro_mmus_1918 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 | MAAAAEGVPATRREEQPPRDDAAVETAEEAKEPAEADINELCRDMFSKMATYLTGELTATSEDYKLLENM |
| MAAAAEGVPATRREEQPPRDDAAVETAEEAKEPAEADINELCRDMFSKMATYLTGELTATSEDYKLLENM | |
| Retrocopy | MAAAAEGVPATRREEQPPRDDAAVETAEEAKEPAEADINELCRDMFSKMATYLTGELTATSEDYKLLENM |
| Parental | NKLTSLKYLEMKDIAINISRNLKDLNQKYAELQPYLDQINMIEEQVAALEQAAYKLDAYSKKLEAKYKKL |
| NKLTSLKYLEMKDIAINISRNLKDLNQKYAELQPYLDQINMIEEQVAALEQAAYKLDAYSKKLEAKYKKL | |
| Retrocopy | NKLTSLKYLEMKDIAINISRNLKDLNQKYAELQPYLDQINMIEEQVAALEQAAYKLDAYSKKLEAKYKKL |
| Parental | EKR |
| EKR | |
| Retrocopy | EKR |
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 .12 RPM | 6 .03 RPM |
| SRP007412_cerebellum | 0 .04 RPM | 5 .17 RPM |
| SRP007412_heart | 0 .06 RPM | 3 .30 RPM |
| SRP007412_kidney | 0 .00 RPM | 4 .04 RPM |
| SRP007412_liver | 0 .00 RPM | 3 .11 RPM |
| SRP007412_testis | 0 .09 RPM | 8 .92 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_1918 was not detected
No EST(s) were mapped for retro_mmus_1918 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_87539 | 421 libraries | 318 libraries | 329 libraries | 4 libraries | 0 libraries |
The graphical summary, for retro_mmus_1918 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_1918 was not experimentally validated.