RetrogeneDB ID: | retro_mmus_2835 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 6:70429669..70429981(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Slc5a6 | ||
| Ensembl ID: | ENSMUSG00000006641 | ||
| Aliases: | Slc5a6, E430023I20 | ||
| Description: | solute carrier family 5 (sodium-dependent vitamin transporter), member 6 [Source:MGI Symbol;Acc:MGI:2660847] |
Retrocopy-Parental alignment summary:
>retro_mmus_2835
AGTTCCCACTCGGAGAGAGCTGCTGTGCTCTCCTGCTATGCAGTGTTCCCTTGCCAGCAAGTGGCCCTCTGCATGAGCTG
CCTCATTGGTCTGTTCATGTTTGCCTATTATAACATGTATAGCATGAGCACCGAGCTGAAGCAAGCAGCCCCTGACCAGT
TAGTCCTCTATTTTGTGATGGACCTCCTGAAAGACATGCCAGGGCTGCCTGGGTTCTTCGTTGCCTGTCTCTTCAGTGGA
TCTCTCAGCACCATATCCTCTGCATTCAATTCACTGGCAACTGTCACAATGGAAGACCTGATCCAGCCCTGG
ORF - retro_mmus_2835 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 89.42 % |
| Parental protein coverage: | 53.33 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | SQHGLISGINSCYAVFPCQQVALCMSCLIGLVMFAYYNMYSMSPELKQAAPDQLVLYFVMDLLKDMPGLP |
| S.H.......SCYAVFPCQQVALCMSCLIGL.MFAYYNMYSMS.ELKQAAPDQLVLYFVMDLLKDMPGLP | |
| Retrocopy | SSHSERAAVLSCYAVFPCQQVALCMSCLIGLFMFAYYNMYSMSTELKQAAPDQLVLYFVMDLLKDMPGLP |
| Parental | GLFVACLFSGSLSTISSAFNSLATVTMEDLIQPW |
| G.FVACLFSGSLSTISSAFNSLATVTMEDLIQPW | |
| Retrocopy | GFFVACLFSGSLSTISSAFNSLATVTMEDLIQPW |
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 .18 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 28 .01 RPM |
| SRP007412_heart | 0 .03 RPM | 13 .20 RPM |
| SRP007412_kidney | 0 .00 RPM | 33 .17 RPM |
| SRP007412_liver | 0 .00 RPM | 20 .13 RPM |
| SRP007412_testis | 0 .00 RPM | 2 .52 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_2835 was not detected
No EST(s) were mapped for retro_mmus_2835 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_124195 | 1029 libraries | 26 libraries | 12 libraries | 4 libraries | 1 library |
The graphical summary, for retro_mmus_2835 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_2835 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_2835 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Mus musculus | ENSMUSG00000006641 | 2 retrocopies |
retro_mmus_2835 , retro_mmus_2836,
|
| Mus musculus | ENSMUSG00000030781 | 1 retrocopy |