RetrogeneDB ID: | retro_mmus_3170 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 8:4039856..4040183(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Cdc42 | ||
| Ensembl ID: | ENSMUSG00000006699 | ||
| Aliases: | Cdc42, AI747189, AU018915 | ||
| Description: | cell division cycle 42 [Source:MGI Symbol;Acc:MGI:106211] |
Retrocopy-Parental alignment summary:
>retro_mmus_3170
ACAGTGGTCTCTCCATCCTCATTTGAAAATGTGAAAGAAAAATGGGCGCCTGAGATAACTCACCACTGTCCAAAGACTCC
TTTCTTGCTTGTTGGGACCCAAATTGATCTCAAAGATGACCCCTCTACTATCGAGAAACTTGCCATGAACAAACAGAAGC
ATATTACTCCAGAGACTGCTGAAAAGCTGGCGCAGGATCTGAAGGCTGTCAAGTATGTGGAGTGCTCCGCTCTCACACAG
AAAGGCCTAAAGAATGTATTTGATGAAGCAATATTGGCTGCCCTGGAGCTTCCAGAACCGAAGAAGAGCCACAGGTATGT
GCTGCTA
ORF - retro_mmus_3170 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 91.74 % |
| Parental protein coverage: | 57.07 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | SVVSPSSFENVKEKWVPEITHHCPKTPFLLVGTQIDLRDDPSTIEKLAKNKQKPITPETAEKLARDLKAV |
| .VVSPSSFENVKEKW.PEITHHCPKTPFLLVGTQIDL.DDPSTIEKLA.NKQK.ITPETAEKLA.DLKAV | |
| Retrocopy | TVVSPSSFENVKEKWAPEITHHCPKTPFLLVGTQIDLKDDPSTIEKLAMNKQKHITPETAEKLAQDLKAV |
| Parental | KYVECSALTQKGLKNVFDEAILAALEPPEPKKSRRCVLL |
| KYVECSALTQKGLKNVFDEAILAALE.PEPKKS.R.VLL | |
| Retrocopy | KYVECSALTQKGLKNVFDEAILAALELPEPKKSHRYVLL |
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 | 215 .97 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 169 .26 RPM |
| SRP007412_heart | 0 .00 RPM | 99 .83 RPM |
| SRP007412_kidney | 0 .06 RPM | 164 .91 RPM |
| SRP007412_liver | 0 .00 RPM | 103 .20 RPM |
| SRP007412_testis | 0 .05 RPM | 39 .11 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_3170 was not detected
No EST(s) were mapped for retro_mmus_3170 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_141913 | 18 libraries | 5 libraries | 51 libraries | 57 libraries | 941 libraries |
The graphical summary, for retro_mmus_3170 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_3170 was not experimentally validated.