RetrogeneDB ID: | retro_mmus_2143 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 3:25731241..25731590(+) | ||
| Located in intron of: | ENSMUSG00000063887 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Acp1 | ||
| Ensembl ID: | ENSMUSG00000044573 | ||
| Aliases: | Acp1, 4632432E04Rik, AI427468, Acp-1, LMW-PTP | ||
| Description: | acid phosphatase 1, soluble [Source:MGI Symbol;Acc:MGI:87881] |
Retrocopy-Parental alignment summary:
>retro_mmus_2143
ATGGCAGAGGTTGGGTCCAAGTCAGTGCTGTTCGTGTGTCTCGGTAACATTTGCTGGTCACCCATTGCAGAAGCAGTATT
TAGAAAATTGGTAACTGATAAAAGGGTTTCAGGTAATTGGGCCATTGACAGCAGCGCCGTTTCCTGACCGGAACAAGGGC
CGGCCCCCAGACCCAAGAGCTGTCAGCTGCCTAAGAAATCATGGCATAAGCACAGCCCATAAGGCAAGACAGATTACAAA
AGAAGACTTTGCCACATTCGATTATATACTATGTATGGATGAAAGCAATCTGAGAGATCTCAATAGAAAAAGTAATCAAG
TTAAAAACTGCAAAGCTACTTGGGAGCTA
ORF - retro_mmus_2143 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 92.31 % |
| Parental protein coverage: | 73.42 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MAEVGSKSVLFVCLGNICRSPIAEAVFRKLVTDEKVSDNWAIDSSAVS-DWNVGRPPDPRAVSCLRNHGI |
| MAEVGSKSVLFVCLGNIC.SPIAEAVFRKLVTD..VS.NWAIDSSAVS.D.N.GRPPDPRAVSCLRNHGI | |
| Retrocopy | MAEVGSKSVLFVCLGNICWSPIAEAVFRKLVTDKRVSGNWAIDSSAVS>DRNKGRPPDPRAVSCLRNHGI |
| Parental | STAHKARQITKEDFATFDYILCMDESNLRDLNRKSNQVKNCKAKIEL |
| STAHKARQITKEDFATFDYILCMDESNLRDLNRKSNQVKNCKA..EL | |
| Retrocopy | STAHKARQITKEDFATFDYILCMDESNLRDLNRKSNQVKNCKATWEL |
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 | 16 .31 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 4 .86 RPM |
| SRP007412_heart | 0 .00 RPM | 10 .06 RPM |
| SRP007412_kidney | 0 .00 RPM | 11 .45 RPM |
| SRP007412_liver | 0 .00 RPM | 19 .03 RPM |
| SRP007412_testis | 0 .00 RPM | 11 .53 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_2143 was not detected
No EST(s) were mapped for retro_mmus_2143 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_94053 | 447 libraries | 53 libraries | 351 libraries | 200 libraries | 21 libraries |
The graphical summary, for retro_mmus_2143 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_2143 was not experimentally validated.