RetrogeneDB ID: | retro_mmus_2047 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 2:75191075..75191822(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000081406 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
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_2047
ATGAAGCTGAACATCTCCTTCCCCGCCACCGGCTGTCAGAAGCTCATCGAGGTGGATGACGAGCGCAAGCTCCGCACCTT
CTATGAGAAGCGCATGGCCACGGAAGTAGCCGCTGATGCTCTTGGTGAAGAGTGGAAGGGTTATGTGGTCCGGATCAGCG
GTGGGAATGACAAGCAAGGTTTTCCCATGAAGCAAGGTGTTCTGACCCATGGCAGAGTGCGCCTGCTGTTGAGTAAGGGG
CATTCCTGTTACAGGCCAAGGAGAACTGGAGAGAGGAAGCGCAAGTCTGTTCGTGGATGCATTGTGGACGCTAATCTCAG
TGTTCTCAACTTGGTCATTGTAAAGAAAGGAGAGAAGGATATTCCTGGACTGACAGACACTACTGTGCCTCGTCGGTTGG
GACCTAAAAGGGCTAGTAGAATCCGCAAGCTTTTTAATCTCTCCAAAGAAGATGATGTCCGCCAGTATGTTGTCAGGAAG
CCCTTAAACAAAGAAGGTAAGAAGCCCAGGACCAAAGCACCCAAGATTCAGCGACTTGTTACTCCTCGTGTCCTGCAACA
CAAACGCCGACGTATTGCTCTGAAGAAGCAACGCACTAAGAAGAACAAGGAGGAGGCTGCAGAATACGCTAAACTTTTGG
CCAAGAGAATGAAGGAAGCCAAAGAAAAGCGCCAGGAACAGATTGCCAAGAGACGTAGGCTGTCCTCACTGAGAGCTTCT
ACTTCTAAGTCTGAGTCCAGTCAAAAA
ORF - retro_mmus_2047 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 | MKLNISFPATGCQKLIEVDDERKLRTFYEKRMATEVAADALGEEWKGYVVRISGGNDKQGFPMKQGVLTH |
| MKLNISFPATGCQKLIEVDDERKLRTFYEKRMATEVAADALGEEWKGYVVRISGGNDKQGFPMKQGVLTH | |
| Retrocopy | MKLNISFPATGCQKLIEVDDERKLRTFYEKRMATEVAADALGEEWKGYVVRISGGNDKQGFPMKQGVLTH |
| Parental | GRVRLLLSKGHSCYRPRRTGERKRKSVRGCIVDANLSVLNLVIVKKGEKDIPGLTDTTVPRRLGPKRASR |
| GRVRLLLSKGHSCYRPRRTGERKRKSVRGCIVDANLSVLNLVIVKKGEKDIPGLTDTTVPRRLGPKRASR | |
| Retrocopy | GRVRLLLSKGHSCYRPRRTGERKRKSVRGCIVDANLSVLNLVIVKKGEKDIPGLTDTTVPRRLGPKRASR |
| Parental | IRKLFNLSKEDDVRQYVVRKPLNKEGKKPRTKAPKIQRLVTPRVLQHKRRRIALKKQRTKKNKEEAAEYA |
| IRKLFNLSKEDDVRQYVVRKPLNKEGKKPRTKAPKIQRLVTPRVLQHKRRRIALKKQRTKKNKEEAAEYA | |
| Retrocopy | IRKLFNLSKEDDVRQYVVRKPLNKEGKKPRTKAPKIQRLVTPRVLQHKRRRIALKKQRTKKNKEEAAEYA |
| Parental | KLLAKRMKEAKEKRQEQIAKRRRLSSLRASTSKSESSQK |
| KLLAKRMKEAKEKRQEQIAKRRRLSSLRASTSKSESSQK | |
| Retrocopy | KLLAKRMKEAKEKRQEQIAKRRRLSSLRASTSKSESSQK |
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 | 43 .48 RPM |
| SRP007412_cerebellum | 0 .09 RPM | 37 .30 RPM |
| SRP007412_heart | 0 .25 RPM | 69 .30 RPM |
| SRP007412_kidney | 0 .23 RPM | 72 .19 RPM |
| SRP007412_liver | 0 .08 RPM | 80 .59 RPM |
| SRP007412_testis | 0 .00 RPM | 43 .50 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_2047 was not detected
No EST(s) were mapped for retro_mmus_2047 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_88962 | 563 libraries | 474 libraries | 35 libraries | 0 libraries | 0 libraries |
The graphical summary, for retro_mmus_2047 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_2047 was not experimentally validated.