RetrogeneDB ID: | retro_mmus_1421 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 15:92026358..92027597(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Lgi1 | ||
| Ensembl ID: | ENSMUSG00000067242 | ||
| Aliases: | Lgi1, BB130740 | ||
| Description: | leucine-rich repeat LGI family, member 1 [Source:MGI Symbol;Acc:MGI:1861691] |
Retrocopy-Parental alignment summary:
>retro_mmus_1421
AGTCTTGCAAACAACAATCTCCAGACACTCCCAAAAGACATTTTCAAAGGCCTGGATTCCTTAACAAATGTGGACCTAAG
AGGGAACGCATTTAATTGTGACTGTAAGTTGAAGTGGCTGGTGGAATGGCTCGGCCATACCAATGCAACTGTGGAAGACA
TCTACTGTGAAGGCCCACCGGAATATAAGAAACGGAAAATCAATAGCCTCTCCCCCAAGGATTTTGACTGTATCATTACA
GAATTTGCAAAGTCCCAAGACCTACCTTATCAGTCGCTGTCCATAGACACTTTTTCTTATTTGAATGATGAATATGTAGT
CATTGCTCAGCCTTTTACTGGAAAATGCATTTTCCTGGAATGGGACCACGTAGAGAAGACCTTCCGGAATTATGACAACA
TTACAGGCACGTCCACTGTGGTGTGCAAGCCCATAGTTATTGACACTCAGCTCTATGTCATTGTGGCCCAGCTGTTTGGT
GGCTCTCATATCTATAAGCGAGATGGTTTTGCAAACAAATTCATAAAAATCCAAGATATTGAAGTTCTCAAAATTCGAAA
ACCCAATGACATCGAAACATTCAAGATTGAAGACAACTGGTACTTCGTTGTCGCTGACAGTTCCAAAGCTGGGTTTACTA
CCATTTACAAGTGGAATGGAAACGGATTCTACTCCCACCAATCCTTACATGCCTGGTACAGGGATACTGATGTGGAATAC
CTTGAAATAGCCAGACCACCATTGGCCCTCAGAACACCTCATTTAATCCTGTCCAGTAGTTCTCAGCGCCCTGTTATTTA
CCAGTGGAGCAAAGCAACACAGCTATTCACTAACCAAACCGACATTCCTAACATGGAGGACGTATACGCGGTGAAGCACT
TCTCTGTGAAAGGTGATGTGTACATCTGCTTGACCAGATTCATTGGCGACTCTAAAGTCATGAAGTGGGGCGGCTCCTCC
TTCTAGGACATCCAGAGGATGCCATCTCGAGGATCCATGGTGTTCCAACCTCTTCAGATAAATAATTACCAATATGCAAT
TCTCGGAAGCGATTACTCCTTTACTCAAGTGTATAACTGGGATGCAGAGAAAGCCAAATTTGTGAAGTTTCAGGAGTTAA
ACGTTCAGGCACCCAGATCATTCACACACGTATCCATTAATAAGCGTAATTTTCTCTTTGCTTCCAGTTTTAAGGGAAAC
ACGCAGATTTACAAACATGTCATAGTTGACTTAAGCGCA
ORF - retro_mmus_1421 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 99.76 % |
| Parental protein coverage: | 74.15 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | SLANNNLQTLPKDIFKGLDSLTNVDLRGNAFNCDCKLKWLVEWLGHTNATVEDIYCEGPPEYKKRKINSL |
| SLANNNLQTLPKDIFKGLDSLTNVDLRGNAFNCDCKLKWLVEWLGHTNATVEDIYCEGPPEYKKRKINSL | |
| Retrocopy | SLANNNLQTLPKDIFKGLDSLTNVDLRGNAFNCDCKLKWLVEWLGHTNATVEDIYCEGPPEYKKRKINSL |
| Parental | SPKDFDCIITEFAKSQDLPYQSLSIDTFSYLNDEYVVIAQPFTGKCIFLEWDHVEKTFRNYDNITGTSTV |
| SPKDFDCIITEFAKSQDLPYQSLSIDTFSYLNDEYVVIAQPFTGKCIFLEWDHVEKTFRNYDNITGTSTV | |
| Retrocopy | SPKDFDCIITEFAKSQDLPYQSLSIDTFSYLNDEYVVIAQPFTGKCIFLEWDHVEKTFRNYDNITGTSTV |
| Parental | VCKPIVIDTQLYVIVAQLFGGSHIYKRDGFANKFIKIQDIEVLKIRKPNDIETFKIEDNWYFVVADSSKA |
| VCKPIVIDTQLYVIVAQLFGGSHIYKRDGFANKFIKIQDIEVLKIRKPNDIETFKIEDNWYFVVADSSKA | |
| Retrocopy | VCKPIVIDTQLYVIVAQLFGGSHIYKRDGFANKFIKIQDIEVLKIRKPNDIETFKIEDNWYFVVADSSKA |
| Parental | GFTTIYKWNGNGFYSHQSLHAWYRDTDVEYLEIARPPLALRTPHLILSSSSQRPVIYQWSKATQLFTNQT |
| GFTTIYKWNGNGFYSHQSLHAWYRDTDVEYLEIARPPLALRTPHLILSSSSQRPVIYQWSKATQLFTNQT | |
| Retrocopy | GFTTIYKWNGNGFYSHQSLHAWYRDTDVEYLEIARPPLALRTPHLILSSSSQRPVIYQWSKATQLFTNQT |
| Parental | DIPNMEDVYAVKHFSVKGDVYICLTRFIGDSKVMKWGGSSFQDIQRMPSRGSMVFQPLQINNYQYAILGS |
| DIPNMEDVYAVKHFSVKGDVYICLTRFIGDSKVMKWGGSSF.DIQRMPSRGSMVFQPLQINNYQYAILGS | |
| Retrocopy | DIPNMEDVYAVKHFSVKGDVYICLTRFIGDSKVMKWGGSSF*DIQRMPSRGSMVFQPLQINNYQYAILGS |
| Parental | DYSFTQVYNWDAEKAKFVKFQELNVQAPRSFTHVSINKRNFLFASSFKGNTQIYKHVIVDLSA |
| DYSFTQVYNWDAEKAKFVKFQELNVQAPRSFTHVSINKRNFLFASSFKGNTQIYKHVIVDLSA | |
| Retrocopy | DYSFTQVYNWDAEKAKFVKFQELNVQAPRSFTHVSINKRNFLFASSFKGNTQIYKHVIVDLSA |
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 .14 RPM | 92 .03 RPM |
| SRP007412_cerebellum | 0 .04 RPM | 48 .94 RPM |
| SRP007412_heart | 0 .00 RPM | 2 .65 RPM |
| SRP007412_kidney | 0 .00 RPM | 0 .19 RPM |
| SRP007412_liver | 0 .00 RPM | 0 .03 RPM |
| SRP007412_testis | 0 .00 RPM | 0 .50 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_1421 was not detected
No EST(s) were mapped for retro_mmus_1421 retrocopy.
No TSS is located nearby retro_mmus_1421 retrocopy 5' end.
retro_mmus_1421 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_1421 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 | ENSMUSG00000067242 | 1 retrocopy |
retro_mmus_1421 ,
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