RetrogeneDB ID: | retro_mmus_1590 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 17:74487270..74488021(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Rps6 | ||
| Ensembl ID: | ENSMUSG00000028495 | ||
| Aliases: | None | ||
| Description: | ribosomal protein S6 [Source:MGI Symbol;Acc:MGI:98159] |
Retrocopy-Parental alignment summary:
>retro_mmus_1590
ATGAAGCTGAACATCTCCTTCCCTGCCACTGGCTGTCAGAAGCTCATCGAGGTGGATGATGAGCGAGCGCAAGCTCCGCA
CCTTCTATGAGAAACGCATGGCCACGGAAGTAGCCGCTGATGCTCTTGGTGAAGAGTGGAAGGGTTATGTGGCCCGGATC
AGCGGTGGAAATGACAAGCAAGGTTTTCCCATGAAGCACGGTGTTCTGACCCATGGCAGAGTGCGCCTGCTGTTGAGTAA
GGGGCATTCCTGTTACAGACTAAGGAGAACTGGAGAGAGGAAGCGCAAGTCTGTTCGCGGATGCATTGTTGAAGCTAATC
TCAGTGTTCTCAACTTGGTTATTGTAAAGAAAGGAGAGAAGGATATTCCTGGACTGACAAATACTACTGTGCCTCATCGG
CTGGGACCTAAAAGAGCTAGTAGAATCCGAAAGCTTTTTAATCTCTCCAAAGAAGATCATGTCCGCCAGTATGTTGTCAG
GAAGCCCTTAAACAAAGAAGGTAAGAAGCCCAGGACCAAAGCACCCAAGATTCAGCGTCTTGTTACTCCACGCGTCCTGC
AACACAAACGCCGACGTATTGCTCTGAAGAAGCAACGCACTAAGAAGAACAAGGAGGAGGCTGCAGAATATGCTAAACTT
TTGGCCAAGAGAATGAAGGAAGCCAAAGAAAAGCGCCAGGAACAGATTGCCAAGAGACGTAGGCTGTCCTCTCTGAGAGC
TTCTACTTCTAAGTCTGAGTCCAGTCAAAAA
ORF - retro_mmus_1590 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 96.02 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MKLNISFPATGCQKLIEV-DD-ERKLRTFYEKRMATEVAADALGEEWKGYVVRISGGNDKQGFPMKQGVL |
| MKLNISFPATGCQKLIEV.D..ERKLRTFYEKRMATEVAADALGEEWKGYV.RISGGNDKQGFPMK.GVL | |
| Retrocopy | MKLNISFPATGCQKLIEVDDE>ERKLRTFYEKRMATEVAADALGEEWKGYVARISGGNDKQGFPMKHGVL |
| Parental | THGRVRLLLSKGHSCYRPRRTGERKRKSVRGCIVDANLSVLNLVIVKKGEKDIPGLTDTTVPRRLGPKRA |
| THGRVRLLLSKGHSCYR.RRTGERKRKSVRGCIV.ANLSVLNLVIVKKGEKDIPGLT.TTVP.RLGPKRA | |
| Retrocopy | THGRVRLLLSKGHSCYRLRRTGERKRKSVRGCIVEANLSVLNLVIVKKGEKDIPGLTNTTVPHRLGPKRA |
| Parental | SRIRKLFNLSKEDDVRQYVVRKPLNKEGKKPRTKAPKIQRLVTPRVLQHKRRRIALKKQRTKKNKEEAAE |
| SRIRKLFNLSKED.VRQYVVRKPLNKEGKKPRTKAPKIQRLVTPRVLQHKRRRIALKKQRTKKNKEEAAE | |
| Retrocopy | SRIRKLFNLSKEDHVRQYVVRKPLNKEGKKPRTKAPKIQRLVTPRVLQHKRRRIALKKQRTKKNKEEAAE |
| Parental | YAKLLAKRMKEAKEKRQEQIAKRRRLSSLRASTSKSESSQK |
| YAKLLAKRMKEAKEKRQEQIAKRRRLSSLRASTSKSESSQK | |
| Retrocopy | YAKLLAKRMKEAKEKRQEQIAKRRRLSSLRASTSKSESSQK |
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 .00 RPM | 43 .48 RPM |
| SRP007412_cerebellum | 0 .09 RPM | 37 .30 RPM |
| SRP007412_heart | 0 .06 RPM | 69 .30 RPM |
| SRP007412_kidney | 0 .06 RPM | 72 .19 RPM |
| SRP007412_liver | 0 .03 RPM | 80 .59 RPM |
| SRP007412_testis | 0 .00 RPM | 43 .50 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_1590 was not detected
No EST(s) were mapped for retro_mmus_1590 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_56690 | 63 libraries | 123 libraries | 634 libraries | 203 libraries | 49 libraries |
The graphical summary, for retro_mmus_1590 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_1590 was not experimentally validated.