RetrogeneDB ID: | retro_mmus_2113 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 2:156347204..156347840(-) | ||
| Located in intron of: | ENSMUSG00000038085 | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000082321 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Pdcd10 | ||
| Ensembl ID: | ENSMUSG00000027835 | ||
| Aliases: | Pdcd10, 2410003B13Rik, Ccm3, Tfa15, Tfar15 | ||
| Description: | programmed cell death 10 [Source:MGI Symbol;Acc:MGI:1928396] |
Retrocopy-Parental alignment summary:
>retro_mmus_2113
ATGAGGATGACAATGGAAGAGATGAAGAATGAAGCTGAGATCACTTCCATGGTTTCTATGCCTCTCTATGCAGTCATGTA
TCCTGTGTTTAATGAGCTAGAACGAGTAAATTTGTCTGCAGCTCAGACTCTGAGAGCCGCTTTCATTAAGGCTGAAAAGG
AAAATCCAGGCCTCACACAAGACATCATTATGAAAATATTAGAGAAAAAAAGTGTAGAAGTTAACTTCACTGAGTCCCTC
CTTCGTATGGCAGCTGATGACGTAGAAGAGTACATGATTGAGCGGCCAGAGCCAGAATTCCAGGACCTAAATGAAAAGGC
ACGGGCACTTAAACAGATTCTCAGTAAGATTCCCGATGAGATCAATGACAGAGTGAGGTTTCTGCAGACAATCAAGGATA
TAGCTAGTGCAATAAAAGAACTACTTGATACAGTGAATAATGTCTTCAAAAAATATCAGTACCAGAACCGCAGGGCACTT
GAACACCAAAAGAAAGAATTTGTAAAATACTCCAAAAGTTTCAGTGACACTCTAAAGACTTATTTTAAAGATGGCAAGGC
AATAAATGTGTTCATAAGTGCCAACCGGCTAATTCATCAAACCAACTTGATACTTCAGACCTTCAAAACTGTGGCC
ORF - retro_mmus_2113 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 99.53 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MRMTMEEMKNEAETTSMVSMPLYAVMYPVFNELERVNLSAAQTLRAAFIKAEKENPGLTQDIIMKILEKK |
| MRMTMEEMKNEAE.TSMVSMPLYAVMYPVFNELERVNLSAAQTLRAAFIKAEKENPGLTQDIIMKILEKK | |
| Retrocopy | MRMTMEEMKNEAEITSMVSMPLYAVMYPVFNELERVNLSAAQTLRAAFIKAEKENPGLTQDIIMKILEKK |
| Parental | SVEVNFTESLLRMAADDVEEYMIERPEPEFQDLNEKARALKQILSKIPDEINDRVRFLQTIKDIASAIKE |
| SVEVNFTESLLRMAADDVEEYMIERPEPEFQDLNEKARALKQILSKIPDEINDRVRFLQTIKDIASAIKE | |
| Retrocopy | SVEVNFTESLLRMAADDVEEYMIERPEPEFQDLNEKARALKQILSKIPDEINDRVRFLQTIKDIASAIKE |
| Parental | LLDTVNNVFKKYQYQNRRALEHQKKEFVKYSKSFSDTLKTYFKDGKAINVFISANRLIHQTNLILQTFKT |
| LLDTVNNVFKKYQYQNRRALEHQKKEFVKYSKSFSDTLKTYFKDGKAINVFISANRLIHQTNLILQTFKT | |
| Retrocopy | LLDTVNNVFKKYQYQNRRALEHQKKEFVKYSKSFSDTLKTYFKDGKAINVFISANRLIHQTNLILQTFKT |
| Parental | VA |
| VA | |
| Retrocopy | VA |
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 .23 RPM | 13 .11 RPM |
| SRP007412_cerebellum | 0 .04 RPM | 8 .73 RPM |
| SRP007412_heart | 0 .06 RPM | 4 .42 RPM |
| SRP007412_kidney | 0 .15 RPM | 9 .97 RPM |
| SRP007412_liver | 0 .03 RPM | 7 .24 RPM |
| SRP007412_testis | 0 .00 RPM | 10 .79 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_2113 was not detected
No EST(s) were mapped for retro_mmus_2113 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_82192 | 433 libraries | 511 libraries | 123 libraries | 4 libraries | 1 library |
| TSS #2 | TSS_82193 | 524 libraries | 499 libraries | 47 libraries | 1 library | 1 library |
The graphical summary, for retro_mmus_2113 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_2113 was not experimentally validated.