RetrogeneDB ID: | retro_mmus_70 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 6:136328542..136329778(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000094973 | |
| Aliases: | None | ||
| Status: | KNOWN_PROTEIN_CODING | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Eif4a3 | ||
| Ensembl ID: | ENSMUSG00000025580 | ||
| Aliases: | Eif4a3, 2400003O03Rik, Ddx48, eIF4A-III, mKIAA0111 | ||
| Description: | eukaryotic translation initiation factor 4A3 [Source:MGI Symbol;Acc:MGI:1923731] |
Retrocopy-Parental alignment summary:
>retro_mmus_70
ATGGCGACCACGACCAGGATGGCGACGTCTGGCTCGGCGCGGAAGCGGCTGCTCAAAGAGGACGGCATGACCAAAGTGGA
GTTCGAGACCAGCGAGGAGGTGGACGCGACCCCCACGTTCGACACCATGGGCCTGCGAGAGGACCTGCTGCGCGGCATCT
ACGCCTACGGTTTTGAAAAACCTTCAGCGATCCAGCAGCGTGCTATCAAGCAGATAATGAAAGGGAGAGATGTCATCGCA
CAGTCTCAGTCTGGCACAGGCAAGACGGCCACCTTCAGTATCTCAGTGCTCCAGTGCTTGGATATCCAGGTTCGAGAAAC
CCAAGCTTTGATCCTGGCTCCAACCAGAGAGTTAGCGGTGCAGATTCAGAAGGGTCTGCTCGCTCTGGGAGATTACATGA
ACGTGCAGTGCCATGCCTGCGTTGGGGGCACCAATGTCGGGGAGGACATCCGGAAGCTGGACTACGGGCAGCATGTGGTG
GCAGGCACGCCGGGACGCGTCTTTGATATGATCCGCCGGAGAAGTTTAACGACACGGGCTATCAAGATGCTGGTTTTGGA
TGAGGCTGATGAGATGTTGAACAGAGGTTTCAAGGAGCAGATCTATGATGTGTACAGGTATTTGCCACCAGCCACACAGG
TCGTTCTCGTCAGTGCCACACTGCCTCATGAGATCCTGGAGATGACCAACAAGTTCATGACCCACCCCATCCGCATCCTG
GTGAAGCGTGATGAGTTGACTCTGGAAGGCATCAAACAGTTCTTTGTGGCCGTGGAAAGAGAGGAATGGAAGTTTGATAC
TCTGTGTGATCTCTACGACACGCTGACCATCACCCAGGCCGTCATCTTCTGCATCACCAAGAGGAAGGTTGACTGGCTGA
CAGAGAAAATGAGAGAAGCCAATTTCACTGTGTCGTCCATGCATGGAGATATGCCCCAGAAAGAACGAGAGTCTATCATG
AAGGAGTTCCGGTCAGGTGCCAGCCGGGTGCTCATCTCCACAGATGTCTGGGCTCGAGGCCTGGATGTCCCTCAGGTGTC
CCTCATCATTAACTATGACCTGCCCAACAACAGAGAACTGTACATTCACAGAATTGGGAGATCGGGTCGGTATGGACGAA
AAGGTGTGGCCATCAATTTTGTGAAGAATGATGACATCCGGATTCTCAGGGACATCGAGCAGTACTACTCCACCCAGATA
GACGAGATGCCCATGAACCTGGCTGACCTCATCTGA
ORF - retro_mmus_70 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 96.11 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MAANATMATSGSARKRLLKEEDMTKVEFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIK |
| MA....MATSGSARKRLLKE..MTKVEFETSEEVD.TPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIK | |
| Retrocopy | MATTTRMATSGSARKRLLKEDGMTKVEFETSEEVDATPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIK |
| Parental | QIIKGRDVIAQSQSGTGKTATFSVSVLQCLDIQVRETQALILAPTRELAVQIQKGLLALGDYMNVQCHAC |
| QI.KGRDVIAQSQSGTGKTATFS.SVLQCLDIQVRETQALILAPTRELAVQIQKGLLALGDYMNVQCHAC | |
| Retrocopy | QIMKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPTRELAVQIQKGLLALGDYMNVQCHAC |
| Parental | IGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDVYRYLPP |
| .GGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSL.TRAIKMLVLDEADEMLN.GFKEQIYDVYRYLPP | |
| Retrocopy | VGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLTTRAIKMLVLDEADEMLNRGFKEQIYDVYRYLPP |
| Parental | ATQVVLISATLPHEILEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQA |
| ATQVVL.SATLPHEILEMTNKFMT.PIRILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQA | |
| Retrocopy | ATQVVLVSATLPHEILEMTNKFMTHPIRILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQA |
| Parental | VIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLII |
| VIFC.TKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLII | |
| Retrocopy | VIFCITKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLII |
| Parental | NYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMNVADLI |
| NYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMN.ADLI | |
| Retrocopy | NYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMNLADLI |
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 | 33 .13 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 42 .16 RPM |
| SRP007412_heart | 0 .00 RPM | 41 .78 RPM |
| SRP007412_kidney | 0 .02 RPM | 46 .58 RPM |
| SRP007412_liver | 0 .00 RPM | 31 .71 RPM |
| SRP007412_testis | 0 .00 RPM | 59 .92 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_70 was not detected
No EST(s) were mapped for retro_mmus_70 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_119675 | 685 libraries | 78 libraries | 289 libraries | 16 libraries | 4 libraries |
The graphical summary, for retro_mmus_70 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_70 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_70 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 6 parental genes, and 14 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Microcebus murinus | ENSMICG00000009136 | 2 retrocopies | |
| Myotis lucifugus | ENSMLUG00000009585 | 1 retrocopy | |
| Mus musculus | ENSMUSG00000025580 | 2 retrocopies |
retro_mmus_2752, retro_mmus_70 ,
|
| Mus musculus | ENSMUSG00000059796 | 7 retrocopies | |
| Ornithorhynchus anatinus | ENSOANG00000000334 | 1 retrocopy | |
| Otolemur garnettii | ENSOGAG00000007495 | 1 retrocopy |