RetrogeneDB ID: | retro_mmus_2890 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 7:10745476..10746226(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Mtfmt | ||
| Ensembl ID: | ENSMUSG00000059183 | ||
| Aliases: | Mtfmt, 2310020P08Rik | ||
| Description: | mitochondrial methionyl-tRNA formyltransferase [Source:MGI Symbol;Acc:MGI:1916856] |
Retrocopy-Parental alignment summary:
>retro_mmus_2890
ATACTGAATGTGCACCCCAGTTGCCTCCCGAGGTGGCATGGTTCCGCTCCAATAATCCACAAGGTGCTTCATAAAGACAC
TGTCACTGGTGTAACGATTATGCAAATTAGACTCAAAAGATTTGATATAGGCCCAATTCTCCAACAGGAAACCATCCCTG
TGCCTCCCAAGAGCACATCAAAGGAATTGGAAGCAGTGTTGTCAAAACTTGGTGCCAACATGCTTATCTCAGTTTTGAAA
AAGTTGTCTGAAAGTCTGAACAATGGAAGGCCACAGGCAACCAAGGGAGTGACAAATGCAACCAAGGTCTCTGCTGGCAC
CATCTGTGTCAAGTGGGAGGAGCAAACCTCAGAGCAAGTACTCAGACTTCACCTTGCCATTGGGGATATAGTCCCACTGC
GGATGCTGTGGATGGAGAACACCATTAAACTTCTGGATCTCATAGAAGTTAACAACTCCATTCTTGCAGATCCGAAATTA
ACAGGACAAACTGTAACTCCGAGGTCCGTGGTGTACCACAGACCATCACAAATGCTACTAGTTCACTGTAAGGATGGCTG
GATCGGTGTTCAATCACTAATGCTTAAGAAAACACTAACAGCTACTGATTTCTACAATGGATATTTGCATGTGTGGTACC
AGAAAAATTCCCACGCTCACCCAAGCCAGTGCAGATTTCAGACTCTCAGACTACCAACAAAGATACAGCAGAAAACAAGG
TTGTTGCTATGCAGCAGTGCATTAAGTAGC
ORF - retro_mmus_2890 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 89.6 % |
| Parental protein coverage: | 64.77 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | ILNVHPSCLPRWRGPAPIIHTVLHGDTVTGVTIMQIRPKRFDIGPILQQETIPVPPKSTSKELEAVLSKL |
| ILNVHPSCLPRW.G.APIIH.VLH.DTVTGVTIMQIR.KRFDIGPILQQETIPVPPKSTSKELEAVLSKL | |
| Retrocopy | ILNVHPSCLPRWHGSAPIIHKVLHKDTVTGVTIMQIRLKRFDIGPILQQETIPVPPKSTSKELEAVLSKL |
| Parental | GANMLISVLKNLPESLNNGRPQPAEGVTYAPKVSAGTSCVKWEEQTSEQVLRLHLAIGDIVPLQTLWMEN |
| GANMLISVLK.L.ESLNNGRPQ...GVT.A.KVSAGT.CVKWEEQTSEQVLRLHLAIGDIVPL..LWMEN | |
| Retrocopy | GANMLISVLKKLSESLNNGRPQATKGVTNATKVSAGTICVKWEEQTSEQVLRLHLAIGDIVPLRMLWMEN |
| Parental | TVKLLDLVEVNNSILADPKLTGQTVTPGFVVYHRPSQMLLVRCKDGWIGVRSVMLKKTLTATDFYNGYLH |
| T.KLLDL.EVNNSILADPKLTGQTVTP..VVYHRPSQMLLV.CKDGWIGV.S.MLKKTLTATDFYNGYLH | |
| Retrocopy | TIKLLDLIEVNNSILADPKLTGQTVTPRSVVYHRPSQMLLVHCKDGWIGVQSLMLKKTLTATDFYNGYLH |
| Parental | AWYQKNSHAHPSQCRFQTLRLPTKMQQKTKLLLCNSALSS |
| .WYQKNSHAHPSQCRFQTLRLPTK.QQKT.LLLC.SALSS | |
| Retrocopy | VWYQKNSHAHPSQCRFQTLRLPTKIQQKTRLLLCSSALSS |
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 | 10 .77 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 9 .03 RPM |
| SRP007412_heart | 0 .03 RPM | 6 .01 RPM |
| SRP007412_kidney | 0 .02 RPM | 10 .55 RPM |
| SRP007412_liver | 0 .00 RPM | 4 .83 RPM |
| SRP007412_testis | 0 .00 RPM | 8 .28 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_2890 was not detected
No EST(s) were mapped for retro_mmus_2890 retrocopy.
No TSS is located nearby retro_mmus_2890 retrocopy 5' end.
retro_mmus_2890 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_2890 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Mus musculus | ENSMUSG00000059183 | 1 retrocopy |
retro_mmus_2890 ,
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