RetrogeneDB ID: | retro_mmus_2986 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 7:6533930..6534511(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | 4930453N24Rik | ||
| Ensembl ID: | ENSMUSG00000059920 | ||
| Aliases: | 4930453N24Rik, AI649104 | ||
| Description: | RIKEN cDNA 4930453N24 gene [Source:MGI Symbol;Acc:MGI:1914859] |
Retrocopy-Parental alignment summary:
>retro_mmus_2986
ATGTCGGAGCTTAGCCACTTAGAGTCAGAGGGATGCCGAAACCTATTTGGCATGCTGGACAATGATGAGATCATGGCCCT
TTGGGACACCATCACCACCACCTAGTGCAGCCTGTGGACCTCCAAGATGCTATTTGTGCAATATTAGTGTGTAGCCAACA
TGTAGAAGAACTTCTGAGGCTCAAAAAAGTCCACTGAGAAGTCATATTTAAGTATTTGGTAACACAAGGGGTGGTTGTAC
CTCCAACTACTGAAAATCACAATCTTATTCAGTATGTACAAGGTTACTCAGAAGAAGAGTCACCAAATCCAAAGGAGGCA
GCAGAGCCAGTTACAGAGACAGAGGACATCCAGCTCTTTGAACAGCAGACAAAAGAAGAGAAAGAAGCGGAAAAGGTTGA
TTATCATCACTTAGGAGAATTCTGTCACTGGTTCTTTGAAGTTCTTAATTCTCAGAATCCTTTTCTGGGACCACCTCAAG
ATGAATGTGGCCTACAGCACTTCTGGCATGATGTCCAGCTTAGGTTTTATTATAACACATCAGAACAAAGCATGACAGAC
TACCACAGAGCAGAAATTGTC
ORF - retro_mmus_2986 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 76.02 % |
| Parental protein coverage: | 56.03 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MSGLSHLESEGCRNLLGLLDNDEIMALCDTVT-NRLVQPVDRQDAIHAILVYSQNVEELLRRKKVHREVI |
| MS.LSHLESEGCRNL.G.LDNDEIMAL.DT.T...LVQPVD.QDAI.AILV.SQ.VEELLR.KKVH.EVI | |
| Retrocopy | MSELSHLESEGCRNLFGMLDNDEIMALWDTIT<HHLVQPVDLQDAICAILVCSQHVEELLRLKKVH*EVI |
| Parental | FKYLAKQGVVVPPTAEKHNLIQYAKDYWAKQSPKLKDTAEPVTKTEDIQLFKQQAKEDKEAEKVDFRRLG |
| FKYL..QGVVVPPT.E.HNLIQY...Y....SP..K..AEPVT.TEDIQLF.QQ.KE.KEAEKVD...LG | |
| Retrocopy | FKYLVTQGVVVPPTTENHNLIQYVQGYSEEESPNPKEAAEPVTETEDIQLFEQQTKEEKEAEKVDYHHLG |
| Parental | EEFCHWFFELLNSQNPFLGPPQDDWGPQHFWHDAKLRFYYNTSEQNTTDYQGAEIV |
| .EFCHWFFE.LNSQNPFLGPPQD..G.QHFWHD..LRFYYNTSEQ..TDY..AEIV | |
| Retrocopy | -EFCHWFFEVLNSQNPFLGPPQDECGLQHFWHDVQLRFYYNTSEQSMTDYHRAEIV |
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 | 16 .38 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 18 .11 RPM |
| SRP007412_heart | 0 .00 RPM | 14 .54 RPM |
| SRP007412_kidney | 0 .00 RPM | 18 .17 RPM |
| SRP007412_liver | 0 .00 RPM | 15 .70 RPM |
| SRP007412_testis | 0 .00 RPM | 354 .71 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_2986 was not detected
No EST(s) were mapped for retro_mmus_2986 retrocopy.
No TSS is located nearby retro_mmus_2986 retrocopy 5' end.
retro_mmus_2986 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_2986 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 | ENSMUSG00000059920 | 3 retrocopies |
retro_mmus_2986 , retro_mmus_376, retro_mmus_695,
|
| Tursiops truncatus | ENSTTRG00000002941 | 1 retrocopy |