RetrogeneDB ID: | retro_mmus_2340 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 4:34485831..34486290(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000095588 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Chchd2 | ||
| Ensembl ID: | ENSMUSG00000070493 | ||
| Aliases: | Chchd2, AL033347, Etohi6 | ||
| Description: | coiled-coil-helix-coiled-coil-helix domain containing 2 [Source:MGI Symbol;Acc:MGI:1261428] |
Retrocopy-Parental alignment summary:
>retro_mmus_2340
ATGCCGCGTGGAAGCCGAAGCCGCACTTCCCGGGTGACTCCTCCGGTCAGCCGGGCCCCTCAGATGAGGGCTGCTCCCCA
AAGAGCACCTGCAGCTCAGCCTCCAGCAGCAGCTGCAACATCTGCAGTTGGCTCACCTGCCGCTGCGCCCCGGCAGCCAG
GCCTGATGGCCCAGATGGCTACCACCGCGGCCGGTGTGGCTGTGGGCTCTGCAGTGGGGCACACCCTGGGTCACGCCATC
ACTGGGGGCTTCAGCGGAGGTGGCAGTGCTGAGCCCGCAAAGCCCGACATCACTTACCAGGAGCCTCAGGGAGCCCAGCT
GCAGAACCAGCAGTCTTTTGGACCTTGCTCTCTAGAGATCAAGCAGTTTCTGGAGTGTGCTCAGAACCAGAGCGATGTCA
AGCTCTGTGAGGGCTTCAACGAGGTGCTGCGGCAGTGCAGGATTGCAAATGGTTTAATG
ORF - retro_mmus_2340 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 98.04 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MPRGSRSRTSRVTPPASRAPQMRAAPRRAPAAQPPAAAAPSAVGSPAAAPRQPGLMAQMATTAAGVAVGS |
| MPRGSRSRTSRVTPP.SRAPQMRAAP.RAPAAQPPAAAA.SAVGSPAAAPRQPGLMAQMATTAAGVAVGS | |
| Retrocopy | MPRGSRSRTSRVTPPVSRAPQMRAAPQRAPAAQPPAAAATSAVGSPAAAPRQPGLMAQMATTAAGVAVGS |
| Parental | AVGHTLGHAITGGFSGGGSAEPAKPDITYQEPQGAQLQNQQSFGPCSLEIKQFLECAQNQSDVKLCEGFN |
| AVGHTLGHAITGGFSGGGSAEPAKPDITYQEPQGAQLQNQQSFGPCSLEIKQFLECAQNQSDVKLCEGFN | |
| Retrocopy | AVGHTLGHAITGGFSGGGSAEPAKPDITYQEPQGAQLQNQQSFGPCSLEIKQFLECAQNQSDVKLCEGFN |
| Parental | EVLRQCRIANGLM |
| EVLRQCRIANGLM | |
| Retrocopy | EVLRQCRIANGLM |
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 .07 RPM | 64 .25 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 52 .97 RPM |
| SRP007412_heart | 0 .22 RPM | 153 .19 RPM |
| SRP007412_kidney | 0 .17 RPM | 152 .73 RPM |
| SRP007412_liver | 0 .05 RPM | 123 .02 RPM |
| SRP007412_testis | 0 .18 RPM | 32 .75 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_2340 was not detected
No EST(s) were mapped for retro_mmus_2340 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_104411 | 372 libraries | 58 libraries | 136 libraries | 217 libraries | 289 libraries |
| TSS #2 | TSS_104412 | 602 libraries | 329 libraries | 137 libraries | 2 libraries | 2 libraries |
| TSS #3 | TSS_104413 | 122 libraries | 283 libraries | 224 libraries | 130 libraries | 313 libraries |
The graphical summary, for retro_mmus_2340 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_2340 was not experimentally validated.