RetrogeneDB ID: | retro_mmus_31 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 9:19927895..19928282(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000091460 | |
| 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_31
ATGCAGATCTTCGTGAAGACCCTGACGGGCAAGACCATCACTCTTGAGGTCGAGCCCAGTGACACCATCGAGAATGTCAA
GGCCAAGATCCAAGACAAGGAAGGCATCCCACCTGACCAGCAGAGGCTGATATTCGCGGGCAAACAGCTGGAGGATGGCC
TCACCCTGTCCGACTACAACATCCAGAAAGAGTCCACCTTGCACCTGGTGCTGCGTCTGCATGGTGGCATCATTGAGCCA
TCCCTTCGTCAGCTTGCCCAGAAGTACAATTGTGACAAGATGATCTGCCGCAAGTGCTACGCACGCCTGCACCCTCGTGC
AGTCAACTGCCGCAAGAAGAAGTGCGGCCATACCAACAACCTGCGCCCCAAGAAGAAGGTCAAATAA
ORF - retro_mmus_31 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 98.44 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLV |
| MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDG.TLSDYNIQKESTLHLV | |
| Retrocopy | MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGLTLSDYNIQKESTLHLV |
| Parental | LRLRGGIIEPSLRQLAQKYNCDKMICRKCYARLHPRAVNCRKKKCGHTNNLRPKKKVK |
| LRL.GGIIEPSLRQLAQKYNCDKMICRKCYARLHPRAVNCRKKKCGHTNNLRPKKKVK | |
| Retrocopy | LRLHGGIIEPSLRQLAQKYNCDKMICRKCYARLHPRAVNCRKKKCGHTNNLRPKKKVK |
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 .19 RPM | 2 .48 RPM |
| SRP007412_cerebellum | 0 .04 RPM | 2 .17 RPM |
| SRP007412_heart | 0 .28 RPM | 4 .39 RPM |
| SRP007412_kidney | 0 .17 RPM | 2 .18 RPM |
| SRP007412_liver | 0 .14 RPM | 2 .92 RPM |
| SRP007412_testis | 0 .05 RPM | 5 .12 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_31 was not detected
No EST(s) were mapped for retro_mmus_31 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_148436 | 9 libraries | 0 libraries | 10 libraries | 52 libraries | 1001 libraries |
The graphical summary, for retro_mmus_31 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_31 was not experimentally validated.