RetrogeneDB ID: | retro_mmus_101 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 9:72174578..72174959(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000061390 | |
| Aliases: | None | ||
| Status: | KNOWN_PROTEIN_CODING | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Uba52 | ||
| Ensembl ID: | ENSMUSG00000090137 | ||
| Aliases: | Uba52, D8Ertd21e, Gm1863, Rps27a, Ubb, Ubc | ||
| Description: | ubiquitin A-52 residue ribosomal protein fusion product 1 [Source:MGI Symbol;Acc:MGI:98887] |
Retrocopy-Parental alignment summary:
>retro_mmus_101
GTGCAGATCTTCGTGAAGACCCTGACGGGCAAGACCATCACTCTTGAGGTCGAGCCCAGTGACACCATCAAGAATGTCAA
GGCCAAGATCCAAGACAAGGAAGGCATCCCACCTGACCAGCAGAGGCTGATATTCGCGGGCAAACAGCTGGAGGATGGCC
GCACCCTGTCCGACTACAACATCCAGAAAGAGTCCACCTTGCACCTGGTGCTGCGTCTGCGCGGTGGCATCATTGAGCCA
TCCCTTCGTCAGCTTGCCCAGAAGTACAACTGTGACAAGATGATCTGCCGCAAGTGCTACGCACGCCTGCACCCTCATGC
AGTCAACTGCCGCAAGAAGTGCGACCATACCAACAACCTGCGCCCCAAGAAGGTCAAATAA
ORF - retro_mmus_101 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 96.0 % |
| Parental protein coverage: | 97.66 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLV |
| .QIFVKTLTGKTITLEVEPSDTI.NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLV | |
| Retrocopy | VQIFVKTLTGKTITLEVEPSDTIKNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLV |
| Parental | LRLRGGIIEPSLRQLAQKYNCDKMICRKCYARLHPRAVNCRKKKCGHTNNLRPKK |
| LRLRGGIIEPSLRQLAQKYNCDKMICRKCYARLHP.AVNCR.KKC.HTNNLRPKK | |
| Retrocopy | LRLRGGIIEPSLRQLAQKYNCDKMICRKCYARLHPHAVNCR-KKCDHTNNLRPKK |
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 | 2 .48 RPM |
| SRP007412_cerebellum | 0 .04 RPM | 2 .17 RPM |
| SRP007412_heart | 0 .06 RPM | 4 .39 RPM |
| SRP007412_kidney | 0 .15 RPM | 2 .18 RPM |
| SRP007412_liver | 0 .05 RPM | 2 .92 RPM |
| SRP007412_testis | 0 .09 RPM | 5 .12 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_101 was not detected
No EST(s) were mapped for retro_mmus_101 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_152869 | 137 libraries | 347 libraries | 538 libraries | 44 libraries | 6 libraries |
The graphical summary, for retro_mmus_101 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_101 was not experimentally validated.