RetrogeneDB ID: | retro_mmus_3365 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 9:92334551..92335079(-) | ||
| Located in intron of: | ENSMUSG00000074139 | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000082623 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Ubald1 | ||
| Ensembl ID: | ENSMUSG00000039568 | ||
| Aliases: | None | ||
| Description: | UBA-like domain containing 1 [Source:MGI Symbol;Acc:MGI:1916255] |
Retrocopy-Parental alignment summary:
>retro_mmus_3365
ATGTCATTGAACATGGACCGGCTCAAACACCAGGTCATGATCAACCAGTTCATGCTGATAACAGGCTAAGCAGCCGATCA
GGCAAAGCAACTGCTGCAAGCAGCCCAGTAGCAGTTCGAGACACCCCTCAGTGCCCTTTTCCAGGAGACCAACATCCCCT
ACAGCCACCACCACCAGATGATGTTCACTCCGGCCAACACCCCTGCCACGCCCCCCAACTTCCCTGATGTTCTCACCATG
TTCTCCTATCCTAAGACCTCTGAAAGCATCTATGGTGGTGGCAGCAGCTGCAGCCCAATGGCCACTTTGGTCACGTCACC
CCCACTGCACTTCCCCCATGCCACTGGCAGCTTTGCAACACCCAGCAGGCCAACTGCAGCCTCGCCCCCAGGAGGCCCAC
AGCACCACCAGTCGCAGCCGCCCCTGTGGACACGAGCACCCCCTTCGCCAACTTCAGACTGGCCTTCCCTGGCTCCCCAA
CGGGTCACCTTAGAAACAAGGGCCCACTCTGCCATTGAGGCAGAGAGA
ORF - retro_mmus_3365 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 80.68 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MSVNMDELKHQVMINQFVLTAGCAADQAKQLLQAAHWQFETALSTFFQETNIPYSHHHQMMCTPANTPAT |
| MS.NMD.LKHQVMINQF.L..G.AADQAKQLLQAA..QFET.LS..FQETNIPYSHHHQMM.TPANTPAT | |
| Retrocopy | MSLNMDRLKHQVMINQFMLITG*AADQAKQLLQAAQ*QFETPLSALFQETNIPYSHHHQMMFTPANTPAT |
| Parental | PPNFPDALTMFSRLKASESFHGGGGSSSPMATSATSPPPHFPHATGSFATPSWPTAASPPGGPQQHQPQP |
| PPNFPD.LTMFS..K.SES..GGG.S.SPMAT..TSPP.HFPHATGSFATPS.PTAASPPGGPQ.HQ.QP | |
| Retrocopy | PPNFPDVLTMFSYPKTSESIYGGGSSCSPMATLVTSPPLHFPHATGSFATPSRPTAASPPGGPQHHQSQP |
| Parental | PLWTPAPPSPTSDWPPLAPQQATSEPRAHPAMEAER |
| PLWT.APPSPTSDWP.LAPQ..T.E.RAH.A.EAER | |
| Retrocopy | PLWTRAPPSPTSDWPSLAPQRVTLETRAHSAIEAER |
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 | 67 .87 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 47 .03 RPM |
| SRP007412_heart | 0 .00 RPM | 28 .42 RPM |
| SRP007412_kidney | 0 .00 RPM | 27 .58 RPM |
| SRP007412_liver | 0 .00 RPM | 15 .18 RPM |
| SRP007412_testis | 0 .05 RPM | 70 .26 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_3365 was not detected
No EST(s) were mapped for retro_mmus_3365 retrocopy.
No TSS is located nearby retro_mmus_3365 retrocopy 5' end.
retro_mmus_3365 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_3365 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 | |
|---|---|---|---|
| Mustela putorius furo | ENSMPUG00000014980 | 1 retrocopy | |
| Mus musculus | ENSMUSG00000039568 | 1 retrocopy |
retro_mmus_3365 ,
|
| Mus musculus | ENSMUSG00000050628 | 1 retrocopy |