RetrogeneDB ID: | retro_mmus_448 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 1:60592250..60592712(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000082160 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Lix1 | ||
| Ensembl ID: | ENSMUSG00000047786 | ||
| Aliases: | Lix1, 5730466L18Rik | ||
| Description: | limb expression 1 homolog (chicken) [Source:MGI Symbol;Acc:MGI:1913893] |
Retrocopy-Parental alignment summary:
>retro_mmus_448
AAGGGCACGTTAGATGATGCGGATGACCCAAGCACAAGTGTGGGAGCCTATCACTACATGCTGGAGTCAAACATGGGGAA
GACTATGCTGGAGTTTCAGGAACTAATGACCATTTTCCAACTACTGCACTGGAATGGAAGCCTGAAAGCCCTCCGTGAAA
CAAAGTGCTCTCGACAGGAAGTCATCTCCTACTATTCCCAATATTCTTTAGATGAAAAGATGCGTAGCCACATGGCCCTG
GACTGGATTATGAAGGAGCGTGAATCACCAGGAATTCTCTCTCAAGAGCTGCGTGCAGCCCTAGGGCAGCTGGAGGAAGC
CAGGAAGGCTGGACAAGAACTACGATTTTACAAAGAAAAAAAAGAAATCCTGAGCTTGGCCCTGACTCAGATCTATAGTG
ACCCTGACCCTTCCTCACCCAGTGATGACCAGCTAAGCCTCACGGCTCTGTGTGGCTATCAT
ORF - retro_mmus_448 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 97.4 % |
| Parental protein coverage: | 54.61 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | RGTLDDADDPSTSVGAYHYMLESNMGKTMLEFQELMTIFQLLHWNGSLKALRETKCSRQEVISYYSQYSL |
| .GTLDDADDPSTSVGAYHYMLESNMGKTMLEFQELMTIFQLLHWNGSLKALRETKCSRQEVISYYSQYSL | |
| Retrocopy | KGTLDDADDPSTSVGAYHYMLESNMGKTMLEFQELMTIFQLLHWNGSLKALRETKCSRQEVISYYSQYSL |
| Parental | DEKMRSHMALDWIMKERESPGILSQELRAALGQLEEARKAGQELRFYKEKKEILSLALTQIYSDPDPSSP |
| DEKMRSHMALDWIMKERESPGILSQELRAALGQLEEARKAGQELRFYK...EILSLALTQIYSDPDPSSP | |
| Retrocopy | DEKMRSHMALDWIMKERESPGILSQELRAALGQLEEARKAGQELRFYKXXXEILSLALTQIYSDPDPSSP |
| Parental | SDDQLSLTALCGYH |
| SDDQLSLTALCGYH | |
| Retrocopy | SDDQLSLTALCGYH |
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 | 23 .60 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 4 .91 RPM |
| SRP007412_heart | 0 .00 RPM | 1 .90 RPM |
| SRP007412_kidney | 0 .00 RPM | 0 .96 RPM |
| SRP007412_liver | 0 .03 RPM | 0 .11 RPM |
| SRP007412_testis | 0 .00 RPM | 0 .59 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_448 was not detected
No EST(s) were mapped for retro_mmus_448 retrocopy.
No TSS is located nearby retro_mmus_448 retrocopy 5' end.
retro_mmus_448 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_448 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 | |
|---|---|---|---|
| Dasypus novemcinctus | ENSDNOG00000012335 | 1 retrocopy | |
| Equus caballus | ENSECAG00000021643 | 1 retrocopy | |
| Mus musculus | ENSMUSG00000047786 | 1 retrocopy |
retro_mmus_448 ,
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