RetrogeneDB ID: | retro_mmus_2685 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 5:109016459..109016915(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000093545 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Smndc1 | ||
| Ensembl ID: | ENSMUSG00000025024 | ||
| Aliases: | Smndc1, 2410004J23Rik, 4933440I19Rik | ||
| Description: | survival motor neuron domain containing 1 [Source:MGI Symbol;Acc:MGI:1923729] |
Retrocopy-Parental alignment summary:
>retro_mmus_2685
ATGTCAGAGGATCTAGCAAAACAGTTGGCTAGCTACAAAGCTCAACTCCAGCAAGTAGAAGCTGCTCTTTCTGGAAATGG
AGAAAATGAAGATCTATTGAAACTGAAAAAGGCTTTGAAAGAAGTAATAGAACTGACCAAAGACCTTCTGTCAACTCAGC
CTTCAGAGACGCTTGCAAGTTCAGACAGTTTTGCTTCTACTCAGCCCACTCATTCATGGAAAGTAGGGGACAAGTGCATG
GCCATGTGGAATGAAGACGGACAGTGTTACGAAGTGGAGATTGAAGAGATAGATGAAGAAAATGGCACCCCTGCAATCAC
CTTTGCTGTTTACAGCAATGCCGAAGTGACGCCATTGCTGAACCTCAAGCCTATAGAAGAAGGAAGGAAGGCGAAAGAGG
ACAGCGGCAACAAACCCATGTCAAAAAAAGAAATGATCGCCCAGCAGAGTGAATAT
ORF - retro_mmus_2685 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 94.08 % |
| Parental protein coverage: | 63.87 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MSEDLAKQLASYKAQLQQVEAALSGNGENEDLLKLKKDLQEVIELTKDLLSTQPSETLASSDSFASTQPT |
| MSEDLAKQLASYKAQLQQVEAALSGNGENEDLLKLKK.L.EVIELTKDLLSTQPSETLASSDSFASTQPT | |
| Retrocopy | MSEDLAKQLASYKAQLQQVEAALSGNGENEDLLKLKKALKEVIELTKDLLSTQPSETLASSDSFASTQPT |
| Parental | HSWKVGDKCMAVWSEDGQCYEAEIEEIDEENGTAAITFAVYGNAEVTPLLNLKPVEEGRKAKEDSGNKPM |
| HSWKVGDKCMA.W.EDGQCYE.EIEEIDEENGT.AITFAVY.NAEVTPLLNLKP.EEGRKAKEDSGNKPM | |
| Retrocopy | HSWKVGDKCMAMWNEDGQCYEVEIEEIDEENGTPAITFAVYSNAEVTPLLNLKPIEEGRKAKEDSGNKPM |
| Parental | SKKEMIAQQREY |
| SKKEMIAQQ.EY | |
| Retrocopy | SKKEMIAQQSEY |
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 | 23 .43 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 23 .19 RPM |
| SRP007412_heart | 0 .00 RPM | 16 .62 RPM |
| SRP007412_kidney | 0 .00 RPM | 25 .33 RPM |
| SRP007412_liver | 0 .00 RPM | 13 .57 RPM |
| SRP007412_testis | 0 .00 RPM | 37 .87 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_2685 was not detected
No EST(s) were mapped for retro_mmus_2685 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_108007 | 338 libraries | 475 libraries | 253 libraries | 4 libraries | 2 libraries |
The graphical summary, for retro_mmus_2685 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_2685 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_2685 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Macaca mulatta | ENSMMUG00000007775 | 2 retrocopies | |
| Mus musculus | ENSMUSG00000025024 | 1 retrocopy |
retro_mmus_2685 ,
|
| Tarsius syrichta | ENSTSYG00000006636 | 1 retrocopy |