RetrogeneDB ID: | retro_mmus_3660 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | X:90744665..90745062(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000084289 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Fth1 | ||
| Ensembl ID: | ENSMUSG00000024661 | ||
| Aliases: | Fth1, FHC, Fth, HFt, MFH | ||
| Description: | ferritin heavy chain 1 [Source:MGI Symbol;Acc:MGI:95588] |
Retrocopy-Parental alignment summary:
>retro_mmus_3660
ATGACCACCATGTCTCCCTCGCAATTGTTCCAGAACTACCACCAGAACGCAAAGGCTGCCATCAACCTGCCAGATCAACC
TGGAGTTGTATGCCTCCTACATCTGTCTGTCTATGTCTTGCTATTTTGACAGAGATGATGTGGCTCTGAAGAACTTTCCA
AAATACTTTCTCCACCAATCTCATGAGGAGAGGGAGCATGATGAGAAACTGATAAAGCTGCAGAACCAACAAGGTGGCCA
AATCTTCCTGCAGGATATAAAGAAACCAGACCGTGATGACTGGGATAGCAGGCTGAATGCAATGGAGTGTGCACTGCACT
TGGAAAAGAGTGTGAATCAGTCACTACTGGAACTGCACAAACTGGCTACTGACAAGAATGATCCCCACTTATGTGAC
ORF - retro_mmus_3660 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 87.97 % |
| Parental protein coverage: | 72.53 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MTTASPSQVRQNYHQDAEAAINR-QINLELYASYVYLSMSCYFDRDDVALKNFAKYFLHQSHEEREHAEK |
| MTT.SPSQ..QNYHQ.A.AAIN..QINLELYASY..LSMSCYFDRDDVALKNF.KYFLHQSHEEREH.EK | |
| Retrocopy | MTTMSPSQLFQNYHQNAKAAINL>QINLELYASYICLSMSCYFDRDDVALKNFPKYFLHQSHEEREHDEK |
| Parental | LMKLQNQRGGRIFLQDIKKPDRDDWESGLNAMECALHLEKSVNQSLLELHKLATDKNDPHLCD |
| L.KLQNQ.GG.IFLQDIKKPDRDDW.S.LNAMECALHLEKSVNQSLLELHKLATDKNDPHLCD | |
| Retrocopy | LIKLQNQQGGQIFLQDIKKPDRDDWDSRLNAMECALHLEKSVNQSLLELHKLATDKNDPHLCD |
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 | 1 .03 RPM | 1220 .31 RPM |
| SRP007412_cerebellum | 1 .09 RPM | 1340 .29 RPM |
| SRP007412_heart | 1 .06 RPM | 1076 .05 RPM |
| SRP007412_kidney | 2 .62 RPM | 2397 .51 RPM |
| SRP007412_liver | 0 .71 RPM | 1186 .06 RPM |
| SRP007412_testis | 0 .09 RPM | 144 .99 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_3660 was not detected
No EST(s) were mapped for retro_mmus_3660 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_158397 | 242 libraries | 374 libraries | 205 libraries | 101 libraries | 150 libraries |
| TSS #2 | TSS_158398 | 286 libraries | 383 libraries | 192 libraries | 103 libraries | 108 libraries |
The graphical summary, for retro_mmus_3660 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_3660 was not experimentally validated.