RetrogeneDB ID: | retro_mmus_2780 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 6:116173736..116174120(+) | ||
| Located in intron of: | ENSMUSG00000030126 | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000060214 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | H2afz | ||
| Ensembl ID: | ENSMUSG00000037894 | ||
| Aliases: | H2afz, H2A.Z, H2a.z-1 | ||
| Description: | H2A histone family, member Z [Source:MGI Symbol;Acc:MGI:1888388] |
Retrocopy-Parental alignment summary:
>retro_mmus_2780
ATGGCTGGCGGTAAGGCTGGAAAGGACTCCGGAAAGGCCAAGACAAAGGCGGTTTCCCGCTCGCAGCGAGCCGGCTTGCA
GTTCCCTGTGGGCCGTATTCATCGACACCTGAAATCTAGGACAACCAGCCACGGACGTGTGGGCGCGACCGCCGCTGTGT
ACAGCGCAGCCATCCTGGAGTACCTCACCGCAGAGGTACTTGAGTTGGCAGGAAATGCGTCAAAAGACTTAAAGGTAAAG
CGTATCACCCCTCGTCACTTGCAGCTTGCTATACGTGGAGATGAAGAATTGGATTCTCTGATCAAAGCTACCATTGCTGG
TGGTGGTGTCATCCCACACATCCACAAATCGCTGATCGGGAAGAAAGGACAACAGAAGACTGTT
ORF - retro_mmus_2780 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 100.0 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MAGGKAGKDSGKAKTKAVSRSQRAGLQFPVGRIHRHLKSRTTSHGRVGATAAVYSAAILEYLTAEVLELA |
| MAGGKAGKDSGKAKTKAVSRSQRAGLQFPVGRIHRHLKSRTTSHGRVGATAAVYSAAILEYLTAEVLELA | |
| Retrocopy | MAGGKAGKDSGKAKTKAVSRSQRAGLQFPVGRIHRHLKSRTTSHGRVGATAAVYSAAILEYLTAEVLELA |
| Parental | GNASKDLKVKRITPRHLQLAIRGDEELDSLIKATIAGGGVIPHIHKSLIGKKGQQKTV |
| GNASKDLKVKRITPRHLQLAIRGDEELDSLIKATIAGGGVIPHIHKSLIGKKGQQKTV | |
| Retrocopy | GNASKDLKVKRITPRHLQLAIRGDEELDSLIKATIAGGGVIPHIHKSLIGKKGQQKTV |
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 .16 RPM | 23 .71 RPM |
| SRP007412_cerebellum | 0 .13 RPM | 27 .96 RPM |
| SRP007412_heart | 0 .09 RPM | 17 .09 RPM |
| SRP007412_kidney | 0 .19 RPM | 21 .10 RPM |
| SRP007412_liver | 0 .05 RPM | 15 .54 RPM |
| SRP007412_testis | 0 .46 RPM | 73 .59 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_2780 was not detected
No EST(s) were mapped for retro_mmus_2780 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_117449 | 202 libraries | 398 libraries | 428 libraries | 37 libraries | 7 libraries |
| TSS #2 | TSS_117450 | 434 libraries | 488 libraries | 144 libraries | 4 libraries | 2 libraries |
The graphical summary, for retro_mmus_2780 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_2780 was not experimentally validated.