RetrogeneDB ID: | retro_mmus_265 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 4:39450795..39451446(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000028287 | |
| Aliases: | 1700009N14Rik, AI429145 | ||
| Status: | KNOWN_PROTEIN_CODING | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Ran | ||
| Ensembl ID: | ENSMUSG00000029430 | ||
| Aliases: | None | ||
| Description: | RAN, member RAS oncogene family [Source:MGI Symbol;Acc:MGI:1333112] |
Retrocopy-Parental alignment summary:
>retro_mmus_265
ATGGCCGCAGAGGGCGATCCCCCAGTCCAATTCAAGCTTGTCCTCGTGGGCGATGGTGGTACTGGGAAGACAGCGTTTGT
GAAACGCCACTTGACTGGTGAATTTGAAAAGAAGTATGTGGCCACTCTGGGCGTAGAGGTACATCCTCTGATGTTCCACA
CCAGCAGAGGGCCCATCAAGTTTAACGTCTGGGACACTGCTGGCCAGGAAAAGTTTGGGGGCCTGCGAGACGGCTATTAC
ATCCAAGCCCAGGGTGCCATTATAATGTTCGATGTAACATCAAGAATTACTTACAAAAATGTGCCCAACTGGCATAGGGA
TCTGGTACGGGTGTGTGAAAACATCCCCATTGTGCTGTGTGGTAACAAAGTAGATGTTAAAGACAGAAAAGTGAAGGCGA
AGTCTATTGTCTTCCACCGCAAGAAGAACCTTCAGTATTACGACATTTCAGCCAAAAGCAACTACAACTTTGAGAAACCC
TTCCTCTGGCTCTCCAGAAGACTCACTGGAGACTCTAACTTGGAGTTCGTTGCCATGCCGGCTCTAGCCCCACCTGAGGT
GGTCATGGACCCAGCCTTAGCAAAGAAATACGAGCATGACTTGGAAGTGGCACAGGCCACTGCTCTCCCCGATGAGGATG
ATGACTTATGA
ORF - retro_mmus_265 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 92.59 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MAAQGEPQVQFKLVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGPIKFNVWDTAGQE |
| MAA.G.P.VQFKLVLVGDGGTGKT.FVKRHLTGEFEKKYVATLGVEVHPL.FHT.RGPIKFNVWDTAGQE | |
| Retrocopy | MAAEGDPPVQFKLVLVGDGGTGKTAFVKRHLTGEFEKKYVATLGVEVHPLMFHTSRGPIKFNVWDTAGQE |
| Parental | KFGGLRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLVRVCENIPIVLCGNKVDIKDRKVKAKSIVFHR |
| KFGGLRDGYYIQAQ.AIIMFDVTSR.TYKNVPNWHRDLVRVCENIPIVLCGNKVD.KDRKVKAKSIVFHR | |
| Retrocopy | KFGGLRDGYYIQAQGAIIMFDVTSRITYKNVPNWHRDLVRVCENIPIVLCGNKVDVKDRKVKAKSIVFHR |
| Parental | KKNLQYYDISAKSNYNFEKPFLWLARKLIGDPNLEFVAMPALAPPEVVMDPALAAQYEHDLEVAQTTALP |
| KKNLQYYDISAKSNYNFEKPFLWL.R.L.GD.NLEFVAMPALAPPEVVMDPALA..YEHDLEVAQ.TALP | |
| Retrocopy | KKNLQYYDISAKSNYNFEKPFLWLSRRLTGDSNLEFVAMPALAPPEVVMDPALAKKYEHDLEVAQATALP |
| Parental | DEDDDL |
| DEDDDL | |
| Retrocopy | DEDDDL |
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 .05 RPM | 81 .00 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 79 .29 RPM |
| SRP007412_heart | 0 .00 RPM | 57 .62 RPM |
| SRP007412_kidney | 0 .00 RPM | 56 .21 RPM |
| SRP007412_liver | 0 .05 RPM | 44 .62 RPM |
| SRP007412_testis | 337 .92 RPM | 249 .19 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_265 was not detected
No EST(s) were mapped for retro_mmus_265 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_104538 | 1001 libraries | 59 libraries | 5 libraries | 2 libraries | 5 libraries |
| TSS #2 | TSS_104539 | 1066 libraries | 1 library | 2 libraries | 0 libraries | 3 libraries |
The graphical summary, for retro_mmus_265 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_265 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_265 has 1 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Rattus norvegicus | retro_rnor_138 |