RetrogeneDB ID: | retro_mmus_2479 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 4:90543644..90544370(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000082502 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Usp46 | ||
| Ensembl ID: | ENSMUSG00000054814 | ||
| Aliases: | None | ||
| Description: | ubiquitin specific peptidase 46 [Source:MGI Symbol;Acc:MGI:1916977] |
Retrocopy-Parental alignment summary:
>retro_mmus_2479
TGTACCATGGGTGCCAATGCTTCAGCATTAGAGAAAGAGATTGGCTCAGAATAGTTTCTGGTCAATGAGCATTATTTTAG
ATTAGAGAATTTTGGGAATACCTGCTACTGCAACTCAGTTCTTCAAGCAATTATTTTTGTCCATTTCAGGAAAAAATTCT
AGCATACAAAAGTCAGCCCAGATAAAAGGAGAACCTTCTCACCTGTCTGGCATACCTCTTCCACAGCCTAACTACTCAGA
AGAGGAAGGTCAGTGTGATCCTGCCCAAGGAGTTCATCACAAGATTTCAGAAAGAAATTGAGTTGTTTGACAACTACAAT
AAGATGTCCATAAATTTTAAAATTACCTACTCAGTACAATTGCTGGTATTTCTAAGAAGAAAGAAAACGGGAGAAGCAAA
ATAACCTATTACATAAAGGGGACGTGGACAGCGAGGATAAAAATAGCATACCAGACCCAACAAGAGTCCATGAGATTTTT
CAGGGAACATTAACTAATGAAATCTGGTTTCTTACTTATGAAACTATAAACAGCAAAGATGAAGATTTTTTTTTAGACCT
TTCTGTTGACGTGGAATGAAACACATCAGTTACTCAATGCTTAAGAGGGTTCAGTAACACAGAGCAAGTCTTAATGAGGT
TTTGTCTAACCTTACTGTCAAGAAAGTAAAGGGCACACTCAGGAAGAGTAGCAGCCTTACCTCTGTACTCTAGCATGCTG
ATAAGG
ORF - retro_mmus_2479 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 53.6 % |
| Parental protein coverage: | 67.49 % |
| Number of stop codons detected: | 4 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | CNMGTNASALEKDIGPEQFPINEHYFGLVNFGNTCYCNSVLQAL-YFCRPFRENVLAYKAQQKKKENLLT |
| C.MG.NASALEK.IG.E.F..NEHYF.L.NFGNTCYCNSVLQA..YFC.PF.E..LAYK.Q...KENLLT | |
| Retrocopy | CTMGANASALEKEIGSE*FLVNEHYFRLENFGNTCYCNSVLQAI<YFC-PFQEKILAYKSQPR*KENLLT |
| Parental | CLADLFHSIATQKKKVGVIPPKKFISRLRKENDLFDNYMQQDAHEFLNYLLNTIADILQEEKK-QEKQNG |
| CLA.LFHS..TQK.KV.VI.PK.FI.R..KE..LFDNY..........Y............KK..EKQN. | |
| Retrocopy | CLAYLFHSLTTQKRKVSVILPKEFITRFQKEIELFDNYNKMSINFKITYSVQLL--VFLRRKK>REKQNN |
| Parental | KLKNGNMNEPAENNKPELTWVHEIFQGTLTNETRCLNCETVSSKDE-DFLDLSVDVEQNTSITHCLRDFS |
| .L..G.......N..P..T.VHEIFQGTLTNE...L..ET..SKDE....DLSVDVE.NTS.T.CLR.FS | |
| Retrocopy | LLHKGDVDSEDKNSIPDPTRVHEIFQGTLTNEIWFLTYETINSKDEXXXXDLSVDVE*NTSVTQCLRGFS |
| Parental | NTETLCSEQKYYCETCCSKQEAQKRMRVKKLPMILALHLK |
| NTE.........C.T..S........RV..LP........ | |
| Retrocopy | NTEQVLMR---FCLTLLSRK*RAHSGRVAALPLYSSMLIR |
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 | 117 .59 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 117 .54 RPM |
| SRP007412_heart | 0 .00 RPM | 27 .27 RPM |
| SRP007412_kidney | 0 .00 RPM | 33 .19 RPM |
| SRP007412_liver | 0 .00 RPM | 10 .32 RPM |
| SRP007412_testis | 0 .00 RPM | 26 .07 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_2479 was not detected
No EST(s) were mapped for retro_mmus_2479 retrocopy.
No TSS is located nearby retro_mmus_2479 retrocopy 5' end.
retro_mmus_2479 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_2479 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 | |
|---|---|---|---|
| Mus musculus | ENSMUSG00000028560 | 1 retrocopy | |
| Mus musculus | ENSMUSG00000054814 | 1 retrocopy |
retro_mmus_2479 ,
|
| Oryctolagus cuniculus | ENSOCUG00000017031 | 1 retrocopy |