RetrogeneDB ID: | retro_mmus_278 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 13:21495305..21495695(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000078139 | |
| Aliases: | None | ||
| Status: | KNOWN_PROTEIN_CODING | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Isca1 | ||
| Ensembl ID: | ENSMUSG00000044792 | ||
| Aliases: | Isca1, 1810010A06Rik, Hbld2 | ||
| Description: | iron-sulfur cluster assembly 1 homolog (S. cerevisiae) [Source:MGI Symbol;Acc:MGI:1916296] |
Retrocopy-Parental alignment summary:
>retro_mmus_278
ATGTCGGCGTCGTTGGTCCGCGCCACCGTGTGGGCCGTGAGCAAGAGAAAACTGCAGCCCACGCGGGCGGCCCTCACACT
GACCCCCTCTGCTGTAAACAAGATAAAACAACTTCTTAAAGACAAACCTGAGCATGTGGGTCTGAAAGTTGGCGTGCGAA
CCAGGGGCTGTAATGGCCTCTCTTACAGCCTGGAGTACACAAAGACAAAAGGAGATTCTGATGAAGAAGTTATTCAAGAT
GGAGTCCGAGTGTTCATCGAGAAGAAAGCACAGCTAACCCTGTTAGGAACAGAGATGGACTATGTGGAAGACAAACTGTC
CAGTGAGTTTGTGTTCAATAACCCCAACATCAAGGGAACCTGTGGCTGCGGTGAGAGCTTTCACGTGTGA
ORF - retro_mmus_278 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 99.22 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MSASLVRATVRAVSKRKLQPTRAALTLTPSAVNKIKQLLKDKPEHVGLKVGVRTRGCNGLSYSLEYTKTK |
| MSASLVRATV.AVSKRKLQPTRAALTLTPSAVNKIKQLLKDKPEHVGLKVGVRTRGCNGLSYSLEYTKTK | |
| Retrocopy | MSASLVRATVWAVSKRKLQPTRAALTLTPSAVNKIKQLLKDKPEHVGLKVGVRTRGCNGLSYSLEYTKTK |
| Parental | GDSDEEVIQDGVRVFIEKKAQLTLLGTEMDYVEDKLSSEFVFNNPNIKGTCGCGESFHV |
| GDSDEEVIQDGVRVFIEKKAQLTLLGTEMDYVEDKLSSEFVFNNPNIKGTCGCGESFHV | |
| Retrocopy | GDSDEEVIQDGVRVFIEKKAQLTLLGTEMDYVEDKLSSEFVFNNPNIKGTCGCGESFHV |
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 .23 RPM | 46 .45 RPM |
| SRP007412_cerebellum | 0 .96 RPM | 26 .49 RPM |
| SRP007412_heart | 0 .31 RPM | 64 .50 RPM |
| SRP007412_kidney | 0 .98 RPM | 29 .74 RPM |
| SRP007412_liver | 0 .41 RPM | 13 .98 RPM |
| SRP007412_testis | 2 .70 RPM | 31 .38 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_278 was not detected
No EST(s) were mapped for retro_mmus_278 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_27726 | 333 libraries | 145 libraries | 426 libraries | 137 libraries | 31 libraries |
| TSS #2 | TSS_27727 | 528 libraries | 480 libraries | 59 libraries | 3 libraries | 2 libraries |
The graphical summary, for retro_mmus_278 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_278 was not experimentally validated.