RetrogeneDB ID: | retro_mmus_3713 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | X:151413670..151414451(-) | ||
| Located in intron of: | ENSMUSG00000025262 | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000084166 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Nsa2 | ||
| Ensembl ID: | ENSMUSG00000060739 | ||
| Aliases: | Nsa2, 5730427N09Rik, LNR42, Nsa2p, Tinp1, Yr29 | ||
| Description: | NSA2 ribosome biogenesis homolog (S. cerevisiae) [Source:MGI Symbol;Acc:MGI:1913883] |
Retrocopy-Parental alignment summary:
>retro_mmus_3713
ATGCCACAAAATGAATATATTGAATTGCACCACAAACGATATGGATATCGTTTGGACTACCATGAGAAAAAGAGAAAGAA
AGAAGGTCGGGAGGCCCATGAACGTTCAAAGAAGGCAAAAAAAAATGATTGGCCTGAAGGCTAAGCTCTACCATAAACAG
CGCCATGCCGAGAAAATACAAATGAAAAAGACTATTAAGATGCATGAGAAGAGAAACACCAAGCAGAAGGATGATGAGAA
GACGCCGCAGGGAGCAGTCCCCGCCTATCTGCTGGACAGAGAGGGCCAGTCAAGAGCAAAAGTCCTTTCTAACATGATTA
AGCAGAAACGGAAAGAAAAGGTGGGAAAATGGGAGGTCCCTCTACCCAAAGTTCGTGCCCAAGGAGAAACAGAAGTATTG
AAAGTTATTCGAACAGGAAAAAGGAAAAAGAGGGCATGGAAAAGAATGGTTACTAACGTCTGCTCTGTTGGTGATGGCTT
TACAAGAAAACCACCTAAATATGAAAGATTCATTAGGCCTATGGGTCTACGTTTCAAAAAAGCCCATGTCACACACCCTG
AGCTGAAAGCTACCTTTTGCCTGCCTATTCTCGGTGTGAAAAAGAATCCATCATCCCCATTATATACAACCCTGGGGGTG
ATCACCAAAGGCACAGTTATTGAAGTGAATGTGAGCGAGCTGGGCCTTGTGACACAAGGAGGCAAGGTTATTTGGGGAAA
GTATGCCCAAGTTACCAACAATCCTGAGAACGATGGGTGCATAAATGCGGTCTTGCTGGTC
ORF - retro_mmus_3713 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 96.17 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MPQNEYIELHRKRYGYRLDYHEKKRKKEGREAHERSKKAKKM-IGLKAKLYHKQRHAEKIQMKKTIKMHE |
| MPQNEYIELH.KRYGYRLDYHEKKRKKEGREAHERSKK.....IGLKAKLYHKQRHAEKIQMKKTIKMHE | |
| Retrocopy | MPQNEYIELHHKRYGYRLDYHEKKRKKEGREAHERSKKXXXX>IGLKAKLYHKQRHAEKIQMKKTIKMHE |
| Parental | KRNTKQKDDEKTPQGAVPAYLLDREGQSRAKVLSNMIKQKRKEKAGKWEVPLPKVRAQGETEVLKVIRTG |
| KRNTKQKDDEKTPQGAVPAYLLDREGQSRAKVLSNMIKQKRKEK.GKWEVPLPKVRAQGETEVLKVIRTG | |
| Retrocopy | KRNTKQKDDEKTPQGAVPAYLLDREGQSRAKVLSNMIKQKRKEKVGKWEVPLPKVRAQGETEVLKVIRTG |
| Parental | KRKKKAWKRMVTKVCFVGDGFTRKPPKYERFIRPMGLRFKKAHVTHPELKATFCLPILGVKKNPSSPLYT |
| KRKK.AWKRMVT.VC.VGDGFTRKPPKYERFIRPMGLRFKKAHVTHPELKATFCLPILGVKKNPSSPLYT | |
| Retrocopy | KRKKRAWKRMVTNVCSVGDGFTRKPPKYERFIRPMGLRFKKAHVTHPELKATFCLPILGVKKNPSSPLYT |
| Parental | TLGVITKGTVIEVNVSELGLVTQGGKVIWGKYAQVTNNPENDGCINAVLLV |
| TLGVITKGTVIEVNVSELGLVTQGGKVIWGKYAQVTNNPENDGCINAVLLV | |
| Retrocopy | TLGVITKGTVIEVNVSELGLVTQGGKVIWGKYAQVTNNPENDGCINAVLLV |
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 .21 RPM | 10 .05 RPM |
| SRP007412_cerebellum | 0 .04 RPM | 9 .99 RPM |
| SRP007412_heart | 0 .06 RPM | 16 .09 RPM |
| SRP007412_kidney | 0 .19 RPM | 22 .87 RPM |
| SRP007412_liver | 0 .08 RPM | 19 .72 RPM |
| SRP007412_testis | 0 .14 RPM | 25 .52 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_3713 was not detected
No EST(s) were mapped for retro_mmus_3713 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_155850 | 527 libraries | 480 libraries | 64 libraries | 0 libraries | 1 library |
The graphical summary, for retro_mmus_3713 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_3713 was not experimentally validated.