RetrogeneDB ID: | retro_mmus_2246 | ||
Retrocopylocation | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 3:45775935..45776192(-) | ||
| Located in intron of: | None | ||
Retrocopyinformation | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental geneinformation | Parental gene summary: | ||
| Parental gene symbol: | Ufm1 | ||
| Ensembl ID: | ENSMUSG00000027746 | ||
| Aliases: | None | ||
| Description: | ubiquitin-fold modifier 1 [Source:MGI Symbol;Acc:MGI:1915140] |
Retrocopy-Parental alignment summary:
>retro_mmus_2246
GTGTCGAAGGTGTCCTTTAAAATCACGTTTTAAAAAAAAGACCTGCGGCTGCCATACAAAGTTCTCAGTGTTCCTGAAAG
TACGCCGTTCACAGCAGGCTAAAGTTTGCAGCAGAAGAATTTAAAGTTCCTGCAGCTACAAGCACGATTATTACTAATGA
TGGAATAGGAATGAATCCTGCACGGACTGCTGGGAACGTTTTCCTGAAGCACGGCTCAGAACTGAGAATCCTTCCTAGAG
ACCGAGTTGGAAGCTGC
GTGTCGAAGGTGTCCTTTAAAATCACGTTTTAAAAAAAAGACCTGCGGCTGCCATACAAAGTTCTCAGTGTTCCTGAAAG
TACGCCGTTCACAGCAGGCTAAAGTTTGCAGCAGAAGAATTTAAAGTTCCTGCAGCTACAAGCACGATTATTACTAATGA
TGGAATAGGAATGAATCCTGCACGGACTGCTGGGAACGTTTTCCTGAAGCACGGCTCAGAACTGAGAATCCTTCCTAGAG
ACCGAGTTGGAAGCTGC
ORF - retro_mmus_2246 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 86.21 % |
| Parental protein coverage: | 100. % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MSKVSFKITLTS-DPRLPYKVLSVPESTPFTAV-LKFAAEEFKVPAATSAIITNDGIGINPAQTAGNVFL |
| .SKVSFKIT....D.RLPYKVLSVPESTPFTA..LKFAAEEFKVPAATS.IITNDGIG.NPA.TAGNVFL | |
| Retrocopy | VSKVSFKITFXXXDLRLPYKVLSVPESTPFTAG<LKFAAEEFKVPAATSTIITNDGIGMNPARTAGNVFL |
| Parental | KHGSELRIIPRDRVGSC |
| KHGSELRI.PRDRVGSC | |
| Retrocopy | KHGSELRILPRDRVGSC |
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 .00 RPM | 32 .89 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 34 .95 RPM |
| SRP007412_heart | 0 .00 RPM | 20 .51 RPM |
| SRP007412_kidney | 0 .00 RPM | 47 .87 RPM |
| SRP007412_liver | 0 .03 RPM | 33 .86 RPM |
| SRP007412_testis | 0 .00 RPM | 9 .83 RPM |
RNA Polymerase II actvity near the 5' end of retro_mmus_2246 was not detected
No EST(s) were mapped for retro_mmus_2246 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_94790 | 87 libraries | 33 libraries | 587 libraries | 317 libraries | 48 libraries |
The graphical summary, for retro_mmus_2246 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_2246 was not experimentally validated.