RetrogeneDB ID: | retro_mmus_2688 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 5:110096919..110097461(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Rpl19 | ||
| Ensembl ID: | ENSMUSG00000017404 | ||
| Aliases: | None | ||
| Description: | ribosomal protein L19 [Source:MGI Symbol;Acc:MGI:98020] |
Retrocopy-Parental alignment summary:
>retro_mmus_2688
ATGAGTATGCTCAGGCTACAGAAGAGGCTTGCCTCTAGTGTCCTCCGCTGAGGGAAAAAGAAAGTCTGGTTGGACCCCAA
TGAGACCTATGAAATCGCCAATGCCAGCTCCTGTCAGCAGATCAGGAAGCCGATCAAAACTGGGCTGATCATCCAGAAGC
CTGTGACTGTCCGTTCCAGGGCTCGCTGCCGGAAGAACACCTTGGCCCGACGGAAGGGCAGGCATATGGGCATAGGGAAG
AGGAACGGTACTGCCAACGCTAGGATGCCAGAGAAGGTGACCTGGATGAGAAGGATGAGGATCCTACGTGGGCTTCTCAG
GAGATACCGGGAATCTAAGAAGATTGACCACCATATGTATCACAGCCTGTACCTGAAGGTCAAAGGGAATGTATTCAAAA
ACAAGTGGATTCTCATGAGCACATCCACAAGCTGAAGGCAGACAAGGCCCACAAGAAGCTCCTGGCTGACCAGGCTGAGG
CTCGCAGGTCTAAGACTAAGAAGCACGCGCGCCTCCAGGTGAGAAGGAAGAGATCACCAAGA
ORF - retro_mmus_2688 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 85.16 % |
| Parental protein coverage: | 92.35 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MSMLRLQKRLASSVLRCGKKKVWLDPNETNEIANANSRQQIRKLIKDGLIIRKPVTVHSRARCRKNTLAR |
| MSMLRLQKRLASSVLR.GKKKVWLDPNET.EIANA.S.QQIRK.IK.GLII.KPVTV.SRARCRKNTLAR | |
| Retrocopy | MSMLRLQKRLASSVLR*GKKKVWLDPNETYEIANASSCQQIRKPIKTGLIIQKPVTVRSRARCRKNTLAR |
| Parental | RKGRHMGIGKRKGTANARMPEKVTWMRRMRILRRLLRRYRESKKIDRHMYHSLYLKVKGNVFKNKRILM- |
| RKGRHMGIGKR.GTANARMPEKVTWMRRMRILR.LLRRYRESKKID.HMYHSLYLKVKGNVFKNK.ILM. | |
| Retrocopy | RKGRHMGIGKRNGTANARMPEKVTWMRRMRILRGLLRRYRESKKIDHHMYHSLYLKVKGNVFKNKWILM< |
| Parental | EHIHKLKADKARKKLLADQAEARRSKTKEARKRREERLQAKK |
| EHIHKLKADKA.KKLLADQAEARRSKTK........R..... | |
| Retrocopy | EHIHKLKADKAHKKLLADQAEARRSKTKKHARLQVRRKRSPR |
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 .07 RPM | 54 .16 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 33 .22 RPM |
| SRP007412_heart | 0 .00 RPM | 70 .85 RPM |
| SRP007412_kidney | 0 .02 RPM | 60 .93 RPM |
| SRP007412_liver | 0 .00 RPM | 55 .27 RPM |
| SRP007412_testis | 0 .00 RPM | 32 .47 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_2688 was not detected
No EST(s) were mapped for retro_mmus_2688 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_108037 | 139 libraries | 297 libraries | 593 libraries | 37 libraries | 6 libraries |
The graphical summary, for retro_mmus_2688 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_2688 was not experimentally validated.