RetrogeneDB ID: | retro_mmus_2967 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 7:115172020..115172608(+) | ||
| 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_2967
ATGAGTATGCTCAGGATACAGAAGAGGCTTGCCTCAGTGTCCTCCGCTGCAGGGGGGGGGGGGCCTGGTTGGATCCCTAT
GAGACCAATGAAATTGTCAATGCCAACTCCCGTCAACAGATCAAGAAGCTGATCAAAGATGGGTTGATCATCCGCAAGCC
TGTGACTGTCCATTCCCGGGCTCGTTGCCGGAAAAACACCCTGGCCCTATGGAAGGGCAGGCATATGGGCATAGGGAAGA
GGAAGAGTACTGCCAATGCTCCGATGCCCGAGAAGGTGACCTGGATGAGAAGGATGAGGATCCTGCGCCGGCTTCTCAGG
AGATACCGGGAATCCAAGAAGATTGACCGCCATATGTACCAAGCCTGTACATGAGAAGGTCAAAGGGAATGTATTCAAAA
ACAAGCGGATCCTCATGGAGCACATCCACAAACTGAAGGCTGACAAGGCCCGCAAGAAGCTCCTGGATGATCAGGCTGAG
ACTCACAGGTCTAAGACCAAGGAAGCATGAAAGCGCCGGGAGGAGCGCGTCCAGGCCAAGAAGGAAGAAATCATCAAGAC
TCTGTCGAAGGAGGAAGAGACCAAGAAA
ORF - retro_mmus_2967 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 87.37 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | MSMLRLQKRLAS-SVLRCGKKKVWLDPNETNEIANANSRQQIRKLIKDGLIIRKPVTVHSRARCRKNTLA |
| MSMLR.QKRLAS.SVLRC.....WLDP.ETNEI.NANSRQQI.KLIKDGLIIRKPVTVHSRARCRKNTLA | |
| Retrocopy | MSMLRIQKRLAS<SVLRCXXXXXWLDPYETNEIVNANSRQQIKKLIKDGLIIRKPVTVHSRARCRKNTLA |
| Parental | RRKGRHMGIGKRKGTANARMPEKVTWMRRMRILRRLLRRYRESKKIDRHMYHS-LYLKVKGNVFKNKRIL |
| ..KGRHMGIGKRK.TANA.MPEKVTWMRRMRILRRLLRRYRESKKIDRHMY......KVKGNVFKNKRIL | |
| Retrocopy | LWKGRHMGIGKRKSTANAPMPEKVTWMRRMRILRRLLRRYRESKKIDRHMYQA>VHEKVKGNVFKNKRIL |
| Parental | MEHIHKLKADKARKKLLADQAEARRSKTKEARKRREERLQAKKEEIIKTLSKEEETKK |
| MEHIHKLKADKARKKLL.DQAE..RSKTKEA.KRREER.QAKKEEIIKTLSKEEETKK | |
| Retrocopy | MEHIHKLKADKARKKLLDDQAETHRSKTKEA*KRREERVQAKKEEIIKTLSKEEETKK |
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 | 54 .16 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 33 .22 RPM |
| SRP007412_heart | 0 .09 RPM | 70 .85 RPM |
| SRP007412_kidney | 0 .00 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_2967 was not detected
No EST(s) were mapped for retro_mmus_2967 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_127973 | 34 libraries | 30 libraries | 560 libraries | 304 libraries | 144 libraries |
The graphical summary, for retro_mmus_2967 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_2967 was not experimentally validated.