RetrogeneDB ID: | retro_mmus_708 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 11:46727946..46728627(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000080776 | |
| Aliases: | Gm12174, OTTMUSG00000005507 | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Rpl7 | ||
| Ensembl ID: | ENSMUSG00000043716 | ||
| Aliases: | Rpl7, Rpl7a, Surf-3 | ||
| Description: | ribosomal protein L7 [Source:MGI Symbol;Acc:MGI:98073] |
Retrocopy-Parental alignment summary:
>retro_mmus_708
CGAAGGAATTTCGCAGAGTTGAAGGTGAAGCGCCTGAGGAAGAAGTTTGCCCTGAAGACACTTTGAAAGGCAAGGAGGAA
GCTCATCTATGAGAAGGCAAAACACTATCACAAGGAGTACAGGCAGATGTACCGCACTGAGATTCGGATGGCCAGGATGG
CAAGGAAAGCTGGCAACTTCTATGTGCCCGCAGAACCAAAGCTGGCCTTTGTCATCAGAATCCGAGGTATCAATGGAGTA
AGCCCAAAGGTTCGTAAGGTTCTGCAGCTCCTTCGTCTTCGACAGATCTTCAATGGCACCTTTGTTAAGCTCAACAAGGC
TTCAATTAACATGCTGCAGATTGTGGAACCATACATTGCATGGGGGTACCCCAACCTGAAGTCAGTAAACGAGCTCATCT
ACAATCGCGGCTACGGCAAAATCAACAAGAAGCGGATTGCCTTGACAGATAATTCCTTGATTGCTCGGTCTCTTGGTAAG
TTTGGCATCATCTGCATGGAGGATCTAATTCATGAGATCTATATAGTTGGGAAACGCTTCAAGGAAGCAAATAACTTCCT
GTGGCCCTTCAAGTTATCTTCCCCACGAGGTGGGATGAAGAAAAAGACAACTCACTTTGTAGAAGGTGGAGATGCTGGCA
ACAGGGAAGACCAGATAAACAGGCTTATTAGACGGATGAAC
ORF - retro_mmus_708 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 98.24 % |
| Parental protein coverage: | 84.07 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | RRNFAELKVKRLRKKFALKTLRKARRKLIYEKAKHYHKEYRQMYRTEIRMARMARKAGNFYVPAEPKLAF |
| RRNFAELKVKRLRKKFALKTL.KARRKLIYEKAKHYHKEYRQMYRTEIRMARMARKAGNFYVPAEPKLAF | |
| Retrocopy | RRNFAELKVKRLRKKFALKTL*KARRKLIYEKAKHYHKEYRQMYRTEIRMARMARKAGNFYVPAEPKLAF |
| Parental | VIRIRGINGVSPKVRKVLQLLRLRQIFNGTFVKLNKASINMLRIVEPYIAWGYPNLKSVNELIYKRGYGK |
| VIRIRGINGVSPKVRKVLQLLRLRQIFNGTFVKLNKASINML.IVEPYIAWGYPNLKSVNELIY.RGYGK | |
| Retrocopy | VIRIRGINGVSPKVRKVLQLLRLRQIFNGTFVKLNKASINMLQIVEPYIAWGYPNLKSVNELIYNRGYGK |
| Parental | INKKRIALTDNSLIARSLGKFGIICMEDLIHEIYTVGKRFKEANNFLWPFKLSSPRGGMKKKTTHFVEGG |
| INKKRIALTDNSLIARSLGKFGIICMEDLIHEIY.VGKRFKEANNFLWPFKLSSPRGGMKKKTTHFVEGG | |
| Retrocopy | INKKRIALTDNSLIARSLGKFGIICMEDLIHEIYIVGKRFKEANNFLWPFKLSSPRGGMKKKTTHFVEGG |
| Parental | DAGNREDQINRLIRRMN |
| DAGNREDQINRLIRRMN | |
| Retrocopy | DAGNREDQINRLIRRMN |
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 .09 RPM | 108 .26 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 87 .10 RPM |
| SRP007412_heart | 0 .34 RPM | 118 .08 RPM |
| SRP007412_kidney | 0 .40 RPM | 156 .36 RPM |
| SRP007412_liver | 0 .14 RPM | 136 .76 RPM |
| SRP007412_testis | 0 .18 RPM | 77 .30 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_708 was not detected
No EST(s) were mapped for retro_mmus_708 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_12871 | 289 libraries | 421 libraries | 323 libraries | 34 libraries | 5 libraries |
The graphical summary, for retro_mmus_708 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_708 was not experimentally validated.