RetrogeneDB ID: | retro_mmus_712 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 11:54199429..54199689(+) | ||
| Located in intron of: | ENSMUSG00000086209 | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000060068 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Dbi | ||
| Ensembl ID: | ENSMUSG00000026385 | ||
| Aliases: | Dbi, ACBD1, Acbp, EP, endozepine | ||
| Description: | diazepam binding inhibitor [Source:MGI Symbol;Acc:MGI:94865] |
Retrocopy-Parental alignment summary:
>retro_mmus_712
GTTTCTCAGGCTGAATTTGACAAAGCTGCTGAGGAGGTGAAGCACCTCAAGACTCAGCCAACTGATGAAGAGATGCTGTT
CATCTACAGTCACTTCAAACAAGCTACCATGGGTGATGTAAATACAGATCGGCTGGGGCTATTGGACCTCAAGGGCAAAG
CCAAGCGGGACACATGGAACAAGCTGAAAGGGACTTCCAAGGGAAGTGCCATGAAGACCTATATGGAAAAAGTAGAAGAG
CTAAAGAGAAATATGGAATA
ORF - retro_mmus_712 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 87.5 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MSQAEFDKAAEEVKRLKTQPTDEEMLFIYSHFKQATVGDVNTDRPGLLDLKGKAKWDSWNKLKGTSKESA |
| .SQAEFDKAAEEVK.LKTQPTDEEMLFIYSHFKQAT.GDVNTDR.GLLDLKGKAK.D.WNKLKGTSK.SA | |
| Retrocopy | VSQAEFDKAAEEVKHLKTQPTDEEMLFIYSHFKQATMGDVNTDRLGLLDLKGKAKRDTWNKLKGTSKGSA |
| Parental | MKTYVEKVDELKK-KYGI |
| MKTY.EKV.ELK..KYGI | |
| Retrocopy | MKTYMEKVEELKR<KYGI |
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 | 66 .65 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 114 .55 RPM |
| SRP007412_heart | 0 .00 RPM | 67 .43 RPM |
| SRP007412_kidney | 0 .06 RPM | 222 .26 RPM |
| SRP007412_liver | 0 .14 RPM | 387 .78 RPM |
| SRP007412_testis | 0 .09 RPM | 21 .54 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_712 was not detected
No EST(s) were mapped for retro_mmus_712 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_13687 | 383 libraries | 301 libraries | 261 libraries | 78 libraries | 49 libraries |
The graphical summary, for retro_mmus_712 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_712 was not experimentally validated.