RetrogeneDB ID: | retro_mmus_249 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 3:85915782..85916070(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000044330 | |
| Aliases: | None | ||
| Status: | KNOWN_PROTEIN_CODING | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Higd1a | ||
| Ensembl ID: | ENSMUSG00000038412 | ||
| Aliases: | Higd1a, 2210020B17Rik, 7420700H20Rik, AI303276, AW049839, HIMP1, Hig1 | ||
| Description: | HIG1 domain family, member 1A [Source:MGI Symbol;Acc:MGI:1930666] |
Retrocopy-Parental alignment summary:
>retro_mmus_249
ATGTCAACCAACACAGACCTTTCTCTCTCTTCATACGATGAAGGTCAGGGTTCTAAGTTTATTCGGAAAGCTAAGGAGAC
ACTGTTTGTCCCCATTGGAATGGCGGGCTTTGCAGCGATTGTTGCCTATGGGTTGTACAAGCTGAAGAGCAGAGGAAATA
CAAAGATGTCCATTCACTTGATCCACATGCGTGTAGCAGCCCAGGGCTTTGTTGTGGGGGCCATGACTCTTGGTATGGGC
TACTCCATGTATCAGGAATTCTGGGCCAACCCTAAGCCTAAGCCTTAG
ORF - retro_mmus_249 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 98.95 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MSTNTDLSLSSYDEGQGSKFIRKAKETPFVPIGMAGFAAIVAYGLYKLKSRGNTKMSIHLIHMRVAAQGF |
| MSTNTDLSLSSYDEGQGSKFIRKAKET.FVPIGMAGFAAIVAYGLYKLKSRGNTKMSIHLIHMRVAAQGF | |
| Retrocopy | MSTNTDLSLSSYDEGQGSKFIRKAKETLFVPIGMAGFAAIVAYGLYKLKSRGNTKMSIHLIHMRVAAQGF |
| Parental | VVGAMTLGMGYSMYQEFWANPKPKP |
| VVGAMTLGMGYSMYQEFWANPKPKP | |
| Retrocopy | VVGAMTLGMGYSMYQEFWANPKPKP |
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 .02 RPM | 45 .74 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 45 .16 RPM |
| SRP007412_heart | 0 .31 RPM | 45 .33 RPM |
| SRP007412_kidney | 0 .10 RPM | 27 .20 RPM |
| SRP007412_liver | 0 .08 RPM | 20 .02 RPM |
| SRP007412_testis | 0 .09 RPM | 25 .80 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_249 was not detected
No EST(s) were mapped for retro_mmus_249 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_96446 | 223 libraries | 343 libraries | 422 libraries | 70 libraries | 14 libraries |
The graphical summary, for retro_mmus_249 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_249 was not experimentally validated.