RetrogeneDB ID: | retro_mmus_1139 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 13:100946407..100946815(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000096789 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | H3f3a | ||
| Ensembl ID: | ENSMUSG00000060743 | ||
| Aliases: | H3f3a, H3.3A | ||
| Description: | H3 histone, family 3A [Source:MGI Symbol;Acc:MGI:1097686] |
Retrocopy-Parental alignment summary:
>retro_mmus_1139
ATGGCTCGTACAAAGCAGACTGCCCGCAAATCCACCGGTGGTAAAGCACCCAGGAAACAACTGGCTACAAAAGCCGCTCG
CAAGAGTGTGCCCTCTACTGGAGGGGTGAAGAAACCTCATCGTTACAGGCCTGGTACTGTGGCACTCCGTGAAATCAGAC
GCTATCAGAAGTCCACTGAACTTCTGATCCGCAAGCTCCCCTTTCAGGGTCTGGTGCGAGAAATTGCTCAGGACTTCAAA
ACAGATCTGCGCTTCCAGAGTGCAGCTATTGGTGCTTTGCAGGAGGCAAGTGAGGCCTATCTGGTTGGCCTTTTTGAAGA
TACCAATCTGTGTGCTATCCATGCCAAACGTGTAACAATTATGCCAAAAGATATCCAGCTAGCACGCCGCATATGCGGAG
AACGTGCT
ORF - retro_mmus_1139 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 97.79 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MARTKQTARKSTGGKAPRKQLATKAARKSAPSTGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQR |
| MARTKQTARKSTGGKAPRKQLATKAARKS.PSTGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQ. | |
| Retrocopy | MARTKQTARKSTGGKAPRKQLATKAARKSVPSTGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQG |
| Parental | LVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA |
| LVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRI.GERA | |
| Retrocopy | LVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRICGERA |
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 .05 RPM | 12 .50 RPM |
| SRP007412_cerebellum | 0 .04 RPM | 12 .64 RPM |
| SRP007412_heart | 0 .03 RPM | 12 .70 RPM |
| SRP007412_kidney | 0 .00 RPM | 15 .34 RPM |
| SRP007412_liver | 0 .03 RPM | 8 .74 RPM |
| SRP007412_testis | 0 .00 RPM | 30 .87 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_1139 was not detected
No EST(s) were mapped for retro_mmus_1139 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_26182 | 181 libraries | 342 libraries | 494 libraries | 55 libraries | 0 libraries |
The graphical summary, for retro_mmus_1139 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_1139 was not experimentally validated.