RetrogeneDB ID: | retro_mmus_2720 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 6:18294561..18295148(+) | ||
| Located in intron of: | ENSMUSG00000041301 | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000080767 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Oas1d | ||
| Ensembl ID: | ENSMUSG00000032623 | ||
| Aliases: | Oas1d, AA536864, C85127, oasl8 | ||
| Description: | 2'-5' oligoadenylate synthetase 1D [Source:MGI Symbol;Acc:MGI:2140770] |
Retrocopy-Parental alignment summary:
>retro_mmus_2720
CCCCAGCGCTAGCAGGAAGTGGAATTTGATGTGCAGCCAGCCTATGATGTCCTTATGAAATGAGAAACTACAAGAACTTT
GACTCCAATAGCTACAACAAAATCTATACCCAACTCATCCATGAGTGCATCACGCTAAAGAAGAAGGATGAATTCTTGAT
CTGCTTCACAGACATCCATCAAAACTTCCTGAGGTATCGTGCACCCAGGCTATGGACTCTCCTCTGTCTGGTCAAGCACT
GGTATCAACTGTGTAAGGAGAAGCTGAGGGAGCCACTGTCCCCACAGTATCCCCTGGAGCTGCTCACAGTCTATGCCTGG
GAATGCAGGCTCCAAGACAGCTCTGGACTACATACAGCCCAGTGCTTCTGAACTGTCTTAGAACTGATCACTAACTATCC
ATGTCTTTGAATCTACTGGACATGGTGTTATGATTTTAAACATGAGATCTCTGACTACTTGCGCAGAGAGATCCAAAACG
ACAGGCCTCTGATCCTGGATCCAGCAGACTCAACAAGGAATGTGGCTGGGTCAGACTTACAGGCCTGGCACCTTCTGGCA
AGAAAGGCTCTGATCTGGATGCGTTCG
ORF - retro_mmus_2720 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 71.07 % |
| Parental protein coverage: | 54.29 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | PERQHELEFDVQPAYDAL-YEVRHFKPFDSSNYNKVYAQLTHECTTLEKEGEFSICFTDLHQSFLRYRAP |
| P.R..E.EFDVQPAYD.L.YE.R..K.FDS..YNK.Y.QL.HEC.TL.K..EF.ICFTD.HQ.FLRYRAP | |
| Retrocopy | PQR*QEVEFDVQPAYDVL<YEMRNYKNFDSNSYNKIYTQLIHECITLKKKDEFLICFTDIHQNFLRYRAP |
| Parental | KLWNLIRLVKHWYQLCKEKLRGPLPPQYALELLTVYVWEYGIHENPGLHTAQCFRTVLELVTKYKRLRIY |
| .LW.L..LVKHWYQLCKEKLR.PL.PQY.LELLTVY.WE.......GLHTAQCF.TVLEL.T.Y..L.IY | |
| Retrocopy | RLWTLLCLVKHWYQLCKEKLREPLSPQYPLELLTVYAWECRLQDSSGLHTAQCF*TVLELITNYPCL*IY |
| Parental | WTWCYDFQHEISDYLQGQIKKARPLILDPADPTRNVAGSDLQAWDLLAKEAQIWIDS |
| WTWCYDF.HEISDYL...I...RPLILDPAD.TRNVAGSDLQAW.LLA..A.IW..S | |
| Retrocopy | WTWCYDFKHEISDYLRREIQNDRPLILDPADSTRNVAGSDLQAWHLLARKALIWMRS |
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 | 0 .05 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 0 .04 RPM |
| SRP007412_heart | 0 .00 RPM | 0 .00 RPM |
| SRP007412_kidney | 0 .00 RPM | 0 .02 RPM |
| SRP007412_liver | 0 .00 RPM | 0 .00 RPM |
| SRP007412_testis | 0 .05 RPM | 0 .05 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_2720 was not detected
No EST(s) were mapped for retro_mmus_2720 retrocopy.
No TSS is located nearby retro_mmus_2720 retrocopy 5' end.
retro_mmus_2720 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_2720 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Myotis lucifugus | ENSMLUG00000015764 | 1 retrocopy | |
| Monodelphis domestica | ENSMODG00000003252 | 1 retrocopy | |
| Mus musculus | ENSMUSG00000032623 | 1 retrocopy |
retro_mmus_2720 ,
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