RetrogeneDB ID: | retro_mmus_131 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 16:76403250..76403652(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000050299 | |
| Aliases: | None | ||
| Status: | KNOWN_PROTEIN_CODING | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Fau | ||
| Ensembl ID: | ENSMUSG00000038274 | ||
| Aliases: | Fau, MNSFbeta | ||
| Description: | Finkel-Biskis-Reilly murine sarcoma virus (FBR-MuSV) ubiquitously expressed (fox derived) [Source:MGI Symbol;Acc:MGI:102547] |
Retrocopy-Parental alignment summary:
>retro_mmus_131
ATGCAGCTCTTTGTCCGCGCCCAGGAACTACACACCCTCGAGGTGACCGGCCAGGAGACGGTCGCCCAGATCAAAGATCA
TGTGGCCTCCCTGGAAGGCATTGCCCCCGAAGATCAAGTCGTGCTTCTGGCAGGCTCGCCGCTGGAGGATGAGGCCACCC
TAGGCCAGTGTGGCGTAGAGGCCCTGACCACTCTGGAAGTAGCAGGCCGCATGCTGGGAGGTAAAGTTCACGGTTCCCTG
GCTCGGGCTGGAAAAGTGAGAGGTCAGACTCCCAAGGTGGCCAAACAGGAAAAGAAGAAGAAGAAGACAGGCCGGGCCAA
GAGGCGAATGCAGTACAACCGGCGCTTTGTCAATGTTGTGCCCACCTTTGGGAAGAAGAAGGGCCCCAATGCCAATTCCT
AA
ORF - retro_mmus_131 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 | MQLFVRAQELHTLEVTGQETVAQIKDHVASLEGIAPEDQVVLLAGSPLEDEATLGQCGVEALTTLEVAGR |
| MQLFVRAQELHTLEVTGQETVAQIKDHVASLEGIAPEDQVVLLAGSPLEDEATLGQCGVEALTTLEVAGR | |
| Retrocopy | MQLFVRAQELHTLEVTGQETVAQIKDHVASLEGIAPEDQVVLLAGSPLEDEATLGQCGVEALTTLEVAGR |
| Parental | MLGGKVHGSLARAGKVRGQTPKVAKQEKKKKKTGRAKRRMQYNRRFVNVVPTFGKKKGPNANS |
| MLGGKVHGSLARAGKVRGQTPKVAKQEKKKKKTGRAKRRMQYNRRFVNVVPTFGKKKGPNANS | |
| Retrocopy | MLGGKVHGSLARAGKVRGQTPKVAKQEKKKKKTGRAKRRMQYNRRFVNVVPTFGKKKGPNANS |
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 .65 RPM | 30 .68 RPM |
| SRP007412_cerebellum | 0 .26 RPM | 25 .27 RPM |
| SRP007412_heart | 0 .59 RPM | 44 .89 RPM |
| SRP007412_kidney | 1 .10 RPM | 49 .72 RPM |
| SRP007412_liver | 0 .71 RPM | 61 .80 RPM |
| SRP007412_testis | 0 .55 RPM | 53 .38 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_131 was not detected
No EST(s) were mapped for retro_mmus_131 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_48881 | 7 libraries | 0 libraries | 1 library | 14 libraries | 1050 libraries |
The graphical summary, for retro_mmus_131 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_131 was not experimentally validated.