RetrogeneDB ID: | retro_mmus_3299 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 9:94416588..94416855(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Tctex1d2 | ||
| Ensembl ID: | ENSMUSG00000014075 | ||
| Aliases: | Tctex1d2, 0610012D17Rik, 2410011K15Rik | ||
| Description: | Tctex1 domain containing 2 [Source:MGI Symbol;Acc:MGI:1913311] |
Retrocopy-Parental alignment summary:
>retro_mmus_3299
GGCTTGTGCGAGGTGGACAAGAACTCAGAGGAGCCTGAGAACACCTATATTCTGAGGCTCATTGTCCAGCAAAAGTTTAA
ACTCTCTGTGGTTAAAGACTGCATCCATGCTGTGCTCAAGGAAGAATTGGCAAGCACTGAATATTCTTCAGATAAAATGA
TTCAACTCACAAAACATCTATCAGAAATGATTAGAGATAAGCTAAAAGCACGACTGCTCACTGTTTCTGGGATGCAGACA
CCAACAACTACATTCACAATGTTTGCA
ORF - retro_mmus_3299 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 78.65 % |
| Parental protein coverage: | 85.58 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | GLSEVDKNSGEPENTYILRPIFQQRFRPSVVKDCIHTVLKEELASAEYSPDEMPQLTKRLSEMIKDKLKA |
| GL.EVDKNS.EPENTYILR.I.QQ.F..SVVKDCIH.VLKEELAS.EYS.D.M.QLTK.LSEMI.DKLKA | |
| Retrocopy | GLCEVDKNSEEPENTYILRLIVQQKFKLSVVKDCIHAVLKEELASTEYSSDKMIQLTKHLSEMIRDKLKA |
| Parental | WLLAVSGMQTRTTTLTMFS |
| .LL.VSGMQT.TTT.TMF. | |
| Retrocopy | RLLTVSGMQTPTTTFTMFA |
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 | 6 .96 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 5 .04 RPM |
| SRP007412_heart | 0 .00 RPM | 3 .77 RPM |
| SRP007412_kidney | 0 .00 RPM | 5 .52 RPM |
| SRP007412_liver | 0 .00 RPM | 0 .46 RPM |
| SRP007412_testis | 0 .00 RPM | 88 .64 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_3299 was not detected
No EST(s) were mapped for retro_mmus_3299 retrocopy.
No TSS is located nearby retro_mmus_3299 retrocopy 5' end.
retro_mmus_3299 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_3299 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Choloepus hoffmanni | ENSCHOG00000012543 | 1 retrocopy | |
| Mus musculus | ENSMUSG00000014075 | 2 retrocopies |
retro_mmus_2987, retro_mmus_3299 ,
|