RetrogeneDB ID: | retro_mmus_1134 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 13:96080855..96081329(-) | ||
| Located in intron of: | ENSMUSG00000051111 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Btf3l4 | ||
| Ensembl ID: | ENSMUSG00000028568 | ||
| Aliases: | Btf3l4, 4632412E09Rik, 5730434I03Rik, AI316863, AU022207, AW552446 | ||
| Description: | basic transcription factor 3-like 4 [Source:MGI Symbol;Acc:MGI:1915312] |
Retrocopy-Parental alignment summary:
>retro_mmus_1134
ATGAATCAAGAAAAGTTAGCCAAACTTCAAGCTCAGGTCCGGATAGGGGGCAAGGGTACAGCTCGCAGGAAGAAGAAGGT
GGTACATAGGACAGCTACTGCTGATGACAAAAAGCTTCAGAGTTCACTAAAGAAACTGGCTGTGAACAATATAGCTGGTA
TTGAAGAGGTGAATATGATTAAAGACGATGGCACGGTTATTCATTTCAACAATCCCAAAGTCCAAGCTTCCCTCTCCGCT
AACACCTTTGCAATTACTGGTCATGCAGAAGCCAAACCAATCACAGAAATGCTTCCTGGGATATTAAGTCAGCTTGGTGC
TGACAGCTTAACGAGCCTTAGAAAGTTAGCTGAACAGTTCCCACGGCAAGTATTGGATAGTAAAGCGCCCAAACCAGAAG
ACATCGATGAAGAGGATGATGATGTTCCAGATCTTGTAGAAAATTTTGATGAAGCATCGAAAAATGAAGCTAAC
ORF - retro_mmus_1134 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 100.0 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MNQEKLAKLQAQVRIGGKGTARRKKKVVHRTATADDKKLQSSLKKLAVNNIAGIEEVNMIKDDGTVIHFN |
| MNQEKLAKLQAQVRIGGKGTARRKKKVVHRTATADDKKLQSSLKKLAVNNIAGIEEVNMIKDDGTVIHFN | |
| Retrocopy | MNQEKLAKLQAQVRIGGKGTARRKKKVVHRTATADDKKLQSSLKKLAVNNIAGIEEVNMIKDDGTVIHFN |
| Parental | NPKVQASLSANTFAITGHAEAKPITEMLPGILSQLGADSLTSLRKLAEQFPRQVLDSKAPKPEDIDEEDD |
| NPKVQASLSANTFAITGHAEAKPITEMLPGILSQLGADSLTSLRKLAEQFPRQVLDSKAPKPEDIDEEDD | |
| Retrocopy | NPKVQASLSANTFAITGHAEAKPITEMLPGILSQLGADSLTSLRKLAEQFPRQVLDSKAPKPEDIDEEDD |
| Parental | DVPDLVENFDEASKNEAN |
| DVPDLVENFDEASKNEAN | |
| Retrocopy | DVPDLVENFDEASKNEAN |
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 .02 RPM | 14 .44 RPM |
| SRP007412_cerebellum | 0 .09 RPM | 8 .12 RPM |
| SRP007412_heart | 0 .22 RPM | 6 .41 RPM |
| SRP007412_kidney | 0 .19 RPM | 5 .77 RPM |
| SRP007412_liver | 0 .25 RPM | 4 .01 RPM |
| SRP007412_testis | 0 .14 RPM | 10 .29 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_1134 was not detected
No EST(s) were mapped for retro_mmus_1134 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_31790 | 589 libraries | 452 libraries | 30 libraries | 1 library | 0 libraries |
| TSS #2 | TSS_31791 | 503 libraries | 414 libraries | 153 libraries | 2 libraries | 0 libraries |
The graphical summary, for retro_mmus_1134 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_1134 was not experimentally validated.