RetrogeneDB ID: | retro_mmus_746 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 11:99932237..99933098(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000086688 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Ybx1 | ||
| Ensembl ID: | ENSMUSG00000028639 | ||
| Aliases: | Ybx1, 1700102N10Rik, C79409, EF1A, MSY1, Nsep1, YB-1, dbpB, mYB-1a | ||
| Description: | Y box protein 1 [Source:MGI Symbol;Acc:MGI:99146] |
Retrocopy-Parental alignment summary:
>retro_mmus_746
GCGGCAGGGGTAGTGGCGCTCATATCGGCGGCGCCCACCAGCGGGGACAAGAAGGTCATCGCAACGAAGGTTTTGGGGAC
AGTCAAATGGTTCAATATAAGGAACGGATACAGTTTCATCAACAGGAATGACACCAAGGAAGACGTATTTGTACACCAGA
CTGCCAAAAAGAAGAATAACCCCAGGAAGTACCTTCGCAGTGTAGGCGATGGAGAGACTGTGGAGTTTGATGTTGTTGAA
GGAGAAAAGGGTGCGGAGGCAGCAAAAGTTACAGGCCCTGGTGGAGTTCCAGTTCAAGGCAGTAAATACGCAGCAGACCG
TAACCATTATAGACGTTATCCACGTCGTAGGGGTCCTCCACGCAATTACCAGCAAAATTACCAGAATAGTGAGAGTGGAG
AAAAGAACGAGGGATCGGAAAGCGCTCCTGAAGGCCAGGCCCAACAATGCCAGCCCTATCGCAGGCGAAGGTTCCCACCT
TACTACATGCGGAGACCCTATGCGCGTCGACCACAGTATTCCAACCCCCCTGTGCAAGGAGAAGTGATGGAGGGTGCTGA
CAACCAGGGTGCAGGAGAGCAAGGTAGACCAGTGAGACAGAGTATGTATCGGGGTTACAGACCACGATTCAGAAGGGGCC
CTCCTCGCCAAAGACAGCCTAGAGAGGTTGGCAATGAAGAGGACAAAGAAAATCAAAGAGATGAGACCCAAGGTCAGCAG
CCACCTCAACGTCGGTATCGCCGCAACTTCAATTACCGACGCAGACGCCCAGAGAACCCTAAACCACAAGATGGCAAAGA
GACAAAAGCAGCCGATCCACCAGCTGAGAATTTGTCCGCTCCCAAGGCTGAGCAGGGCGGG
ORF - retro_mmus_746 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 93.38 % |
| Parental protein coverage: | 89.13 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | SGGPGGLTSAAPAGGDKKVIATKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKYLRSVGD |
| ..G...L.SAAP..GDKKVIATKVLGTVKWFN.RNGY.FINRNDTKEDVFVHQTA.KKNNPRKYLRSVGD | |
| Retrocopy | AAGVVALISAAPTSGDKKVIATKVLGTVKWFNIRNGYSFINRNDTKEDVFVHQTAKKKNNPRKYLRSVGD |
| Parental | GETVEFDVVEGEKGAEAANVTGPGGVPVQGSKYAADRNHYRRYPRRRGPPRNYQQNYQNSESGEKNEGSE |
| GETVEFDVVEGEKGAEAA.VTGPGGVPVQGSKYAADRNHYRRYPRRRGPPRNYQQNYQNSESGEKNEGSE | |
| Retrocopy | GETVEFDVVEGEKGAEAAKVTGPGGVPVQGSKYAADRNHYRRYPRRRGPPRNYQQNYQNSESGEKNEGSE |
| Parental | SAPEGQAQQRRPYRRRRFPPYYMRRPYARRPQYSNPPVQGEVMEGADNQGAGEQGRPVRQNMYRGYRPRF |
| SAPEGQAQQ..PYRRRRFPPYYMRRPYARRPQYSNPPVQGEVMEGADNQGAGEQGRPVRQ.MYRGYRPRF | |
| Retrocopy | SAPEGQAQQCQPYRRRRFPPYYMRRPYARRPQYSNPPVQGEVMEGADNQGAGEQGRPVRQSMYRGYRPRF |
| Parental | RRGPPRQRQPREDGNEEDKENQGDETQGQQPPQRRYRRNFNYRRRRPENPKPQDGKETKAADPPAENSSA |
| RRGPPRQRQPRE.GNEEDKENQ.DETQGQQPPQRRYRRNFNYRRRRPENPKPQDGKETKAADPPAEN.SA | |
| Retrocopy | RRGPPRQRQPREVGNEEDKENQRDETQGQQPPQRRYRRNFNYRRRRPENPKPQDGKETKAADPPAENLSA |
| Parental | PEAEQGG |
| P.AEQGG | |
| Retrocopy | PKAEQGG |
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 .12 RPM | 68 .08 RPM |
| SRP007412_cerebellum | 0 .17 RPM | 66 .22 RPM |
| SRP007412_heart | 0 .62 RPM | 456 .18 RPM |
| SRP007412_kidney | 0 .62 RPM | 372 .40 RPM |
| SRP007412_liver | 0 .08 RPM | 136 .16 RPM |
| SRP007412_testis | 1 .46 RPM | 864 .37 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_746 was not detected
No EST(s) were mapped for retro_mmus_746 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_20237 | 49 libraries | 111 libraries | 323 libraries | 228 libraries | 361 libraries |
The graphical summary, for retro_mmus_746 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_746 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_746 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Mus musculus | ENSMUSG00000028639 | 3 retrocopies |
retro_mmus_1623, retro_mmus_2813, retro_mmus_746 ,
|
| Rattus norvegicus | ENSRNOG00000023786 | 1 retrocopy |