RetrogeneDB ID: | retro_mmus_3351 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 9:67748134..67748547(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Spin1 | ||
| Ensembl ID: | ENSMUSG00000021395 | ||
| Aliases: | Spin1, Spin | ||
| Description: | spindlin 1 [Source:MGI Symbol;Acc:MGI:109242] |
Retrocopy-Parental alignment summary:
>retro_mmus_3351
GTTTATCCACTGGAAGTCCTCCCTGATAGAGTTGCAACATCTCGGATCAGCTATGCACACTTAGCGGACACGATAATTGG
CAAAGCAGTGGAACACATGTTTGAGACAGAGGATGGCTCTAAAGATGAGTGGAGGGGGATGGTCTTGGCACGGGCGCCTG
TCATGAACACATGGTTTTACATCACCTATGAGAAAGACCCTGTCTTGTACATGTACCAGCTCCTCGATGATTACAAGAAG
GCAACTTCAGTTTTATATTATGCCTGCCTGATTCCAGTGATTCGCCTCCAGCAGAAAAGGAGCCAGGAGAAGTTGTGGAC
AGCCTGGTAGGCAAGCAAGTGGGATATGCAGAAGAAGACGGCTTGAAAAGGACTGGCATGGTCATCTACCAAGTAGAGGC
CAAGCCCTCTATT
ORF - retro_mmus_3351 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 84.89 % |
| Parental protein coverage: | 51.53 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | VSALEVLPDRVATSRISDAHLADTMIGKAVEHMFETEDGSKDEWRGMVLARAPVMNTWFYITYEKDPVLY |
| V..LEVLPDRVATSRIS.AHLADT.IGKAVEHMFETEDGSKDEWRGMVLARAPVMNTWFYITYEKDPVLY | |
| Retrocopy | VYPLEVLPDRVATSRISYAHLADTIIGKAVEHMFETEDGSKDEWRGMVLARAPVMNTWFYITYEKDPVLY |
| Parental | MYQLLDDY-KEGDLRI---MPDSNDSPPAEREPGEVVDSLVGKQVEYAKEDGSKRTGMVIHQVEAKPSV |
| MYQLLDDY..EG........PDS.DSPPAE.EPGEVVDSLVGKQV.YA.EDG.KRTGMVI.QVEAKPS. | |
| Retrocopy | MYQLLDDY<QEGNFSFILCLPDSSDSPPAEKEPGEVVDSLVGKQVGYAEEDGLKRTGMVIYQVEAKPSI |
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 | 167 .51 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 95 .61 RPM |
| SRP007412_heart | 0 .00 RPM | 31 .35 RPM |
| SRP007412_kidney | 0 .00 RPM | 70 .16 RPM |
| SRP007412_liver | 0 .00 RPM | 54 .51 RPM |
| SRP007412_testis | 0 .82 RPM | 23 .42 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_3351 was not detected
No EST(s) were mapped for retro_mmus_3351 retrocopy.
No TSS is located nearby retro_mmus_3351 retrocopy 5' end.
retro_mmus_3351 was not experimentally validated.