RetrogeneDB ID: | retro_mmus_3054 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 7:90107479..90107971(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000062235 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Btf3 | ||
| Ensembl ID: | ENSMUSG00000021660 | ||
| Aliases: | Btf3, 1700054E11Rik | ||
| Description: | basic transcription factor 3 [Source:MGI Symbol;Acc:MGI:1202875] |
Retrocopy-Parental alignment summary:
>retro_mmus_3054
AAGATGAAAGAACCGATCATGAACCAGGAAAAACTCGCCAAACTGCAGGCACAAGTGCGCATTGGTGGGAAAGGAACTGC
TCGTAGAAAGAAGAAGGTGGTTCAGAGAACAGCCACAGCAGACGGTAAGAAACTGCAGTTCTCCTTAGAGAAGTTAGGAG
TAAACAATATCACTGGTACTGAAGAAGTGAACATGTTTACAAACCAAGGAACAGAGATCCATCTTAACAATCCTAAAGTT
CAGGCGTCTCTGGCAGCAAACACCTTCACCATTACAGGCCACGCTGAGACGAAGCAGCGGACAACAATGCTTCCCAGCTT
CCTAAACCAGCTTGATGCAGACGGTCTGACTTGTTTAAGGAGCCGGGCTAAAGCTCTGCCCAAACAATCTGTGGACCGAA
AAGCACCACTTGCTACAACTGGACAGGAGGAGGAGGATGAAGTTCCAGGTCTGGGGGAAAACTTTGATGAGGCTTCTGAG
AATGAGGCAAAC
ORF - retro_mmus_3054 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 83.54 % |
| Parental protein coverage: | 79.9 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | QMKETIMNQEKLAKLQAQVRIGGKGTARRKKKVVHRTATADDKKLQFSLKKLGVNNISGIEEVNMFTNQG |
| .MKE.IMNQEKLAKLQAQVRIGGKGTARRKKKVV.RTATAD.KKLQFSL.KLGVNNI.G.EEVNMFTNQG | |
| Retrocopy | KMKEPIMNQEKLAKLQAQVRIGGKGTARRKKKVVQRTATADGKKLQFSLEKLGVNNITGTEEVNMFTNQG |
| Parental | TVIHFNNPKVQASLAANTFTITGHAETKQLTEMLPSILNQLGADSLTSLRRLAEALPKQSVDGKAPLA-T |
| T.IH.NNPKVQASLAANTFTITGHAETKQ.T.MLPS.LNQL.AD.LT.LR..A.ALPKQSVD.KAPLA.T | |
| Retrocopy | TEIHLNNPKVQASLAANTFTITGHAETKQRTTMLPSFLNQLDADGLTCLRSRAKALPKQSVDRKAPLATT |
| Parental | GEDDDDEVPDLVENFDEASKNEAN |
| G....DEVP.L.ENFDEAS.NEAN | |
| Retrocopy | GQEEEDEVPGLGENFDEASENEAN |
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 | 31 .21 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 33 .00 RPM |
| SRP007412_heart | 0 .00 RPM | 33 .90 RPM |
| SRP007412_kidney | 0 .04 RPM | 50 .80 RPM |
| SRP007412_liver | 0 .00 RPM | 44 .76 RPM |
| SRP007412_testis | 0 .00 RPM | 108 .54 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_3054 was not detected
No EST(s) were mapped for retro_mmus_3054 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_137985 | 279 libraries | 563 libraries | 227 libraries | 1 library | 2 libraries |
The graphical summary, for retro_mmus_3054 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_3054 was not experimentally validated.