RetrogeneDB ID: | retro_mmus_125 | ||
Retrocopylocation | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 11:48826004..48826349(-) | ||
| Located in intron of: | None | ||
Retrocopyinformation | Ensembl ID: | ENSMUSG00000078154 | |
| Aliases: | None | ||
| Status: | KNOWN_PROTEIN_CODING | ||
Parental geneinformation | Parental gene summary: | ||
| Parental gene symbol: | Cdk2ap1 | ||
| Ensembl ID: | ENSMUSG00000029394 | ||
| Aliases: | Cdk2ap1, Apc10, Cdkap1, DORC1, Doc1, ST19, doc-1, p12 | ||
| Description: | CDK2 (cyclin-dependent kinase 2)-associated protein 1 [Source:MGI Symbol;Acc:MGI:1202069] |
Retrocopy-Parental alignment summary:
>retro_mmus_125
ATGTCGTACAAGCCGAACTTGACCGCGCACATGCCCGCCGCCGCCCTCAACGCCGGAAGTGTCCACTCACCCTCTACTAG
CATGGCGACCTCCTCCCAATATCGCCAGCTGCTGAGTGACTATGGGCCTCCATCGCTAGGCTACACCCAGGGAACTGGAA
ATAGCCAGGTGCCTCAGAGTAAATATGCAGAGCTGCTGGCCATCATTGAAGAGTTGGGGAAAGAGATCAGACCGACGTAT
GCAGGGAGCAAGAGCGCCATGGAGAGGCTAAAACGAGGCATCATTCATGCCCGGAGCCTGGTTCGGGAGTGCTTGGCTGA
AACGGAACGGAATGCCAGGTCCTAG
ATGTCGTACAAGCCGAACTTGACCGCGCACATGCCCGCCGCCGCCCTCAACGCCGGAAGTGTCCACTCACCCTCTACTAG
CATGGCGACCTCCTCCCAATATCGCCAGCTGCTGAGTGACTATGGGCCTCCATCGCTAGGCTACACCCAGGGAACTGGAA
ATAGCCAGGTGCCTCAGAGTAAATATGCAGAGCTGCTGGCCATCATTGAAGAGTTGGGGAAAGAGATCAGACCGACGTAT
GCAGGGAGCAAGAGCGCCATGGAGAGGCTAAAACGAGGCATCATTCATGCCCGGAGCCTGGTTCGGGAGTGCTTGGCTGA
AACGGAACGGAATGCCAGGTCCTAG
ORF - retro_mmus_125 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 100. % |
| Parental protein coverage: | 100. % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MSYKPNLTAHMPAAALNAGSVHSPSTSMATSSQYRQLLSDYGPPSLGYTQGTGNSQVPQSKYAELLAIIE |
| MSYKPNLTAHMPAAALNAGSVHSPSTSMATSSQYRQLLSDYGPPSLGYTQGTGNSQVPQSKYAELLAIIE | |
| Retrocopy | MSYKPNLTAHMPAAALNAGSVHSPSTSMATSSQYRQLLSDYGPPSLGYTQGTGNSQVPQSKYAELLAIIE |
| Parental | ELGKEIRPTYAGSKSAMERLKRGIIHARSLVRECLAETERNARS |
| ELGKEIRPTYAGSKSAMERLKRGIIHARSLVRECLAETERNARS | |
| Retrocopy | ELGKEIRPTYAGSKSAMERLKRGIIHARSLVRECLAETERNARS |
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 | 9 .04 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 9 .60 RPM |
| SRP007412_heart | 0 .03 RPM | 6 .26 RPM |
| SRP007412_kidney | 0 .19 RPM | 4 .39 RPM |
| SRP007412_liver | 0 .00 RPM | 2 .54 RPM |
| SRP007412_testis | 0 .00 RPM | 3 .25 RPM |
RNA Polymerase II actvity near the 5' end of retro_mmus_125 was not detected
No EST(s) were mapped for retro_mmus_125 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_12962 | 216 libraries | 320 libraries | 490 libraries | 42 libraries | 4 libraries |
| TSS #2 | TSS_12963 | 459 libraries | 471 libraries | 138 libraries | 3 libraries | 1 library |
The graphical summary, for retro_mmus_125 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_125 was not experimentally validated.