RetrogeneDB ID: | retro_mmus_3696 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | X:121334990..121336574(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000083668 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Uhrf1 | ||
| Ensembl ID: | ENSMUSG00000001228 | ||
| Aliases: | Uhrf1, AL022808, ICBP90, Np95, RNF106 | ||
| Description: | ubiquitin-like, containing PHD and RING finger domains, 1 [Source:MGI Symbol;Acc:MGI:1338889] |
Retrocopy-Parental alignment summary:
>retro_mmus_3696
AACATCAGGCTCTTGAATGACTCTCAGCTCAACAACTGTCGGATCATGTTTGTGGATGAAGTCTTGATGATTGAGCTCCC
TAATGAGAGGAGGCCTTTGATCGCTAGCCCCTCGCAACCCCCTCCTGCCCTCCGGAACACAGGGAAGAGTGGCCCATCCT
GCCGGTTCTGCAAGGATGATGAAAACAAACCATGTCGAAAGTGTGCCTGCCACGTGTGTGGTGGGCGCGAGGCTCCTGAG
AAACAGCTGTTGTGTGATGACTGTGACATGGCCTTCCACCTGTACTGCCTGAAGCCACCGCTCACCTCTGTCCCCCCTGA
GCCGGAGTGGTACTGCCCCAGCTGCCGCACTGACTCAAGTGAGGTGGTACAAGCAGGGGAGCTGAAGGAGAACAAGAAGA
AGGCAAAGATGGCATCAGCCACTTCCTCCTCCCAGCGGGACTGGGGTAAGGGCATGGCATGTGTGGGCCGCACCACAGAG
TGTACCATTGTGCCCGCCAACCACTTTGGGCCCATCCCTGGTGTCCCTGTGGGCACCATGTGGCACTTCAGAGTCCAGGT
CAGTGAGTCCGGTGTGCATCGGCCTCATGTGGCAGGCATCCATGGCCGGAGCAACGACGGTGCCTACTCATTGGTCCTGG
CTGGTGGCTATGAGAATGATGTGGACAATGGCAATTACTTCACATACACAGGGAGTGGTGGCCGAGACCTCTCTGGCAAC
AAGCGTACAGCAGGCCAGTCCTCTGACCAGAAGCTCACTAATAACAATAGGGCTCTGGCACTCAATTGCCACTCCCCAAT
CAATGAGAAAGGTGCGGAGGCTGAAGACTGGCGCCAAGGGAAGCCAGTGTGTGTGGTCCGGAACATGAAGGGCGGGAAAC
ACAGCAAGTACGCTCCCGCAGAGGGCAACCGCTATGATGGCATCTACAAGGTGGTGAAGTACTGGCCAGAGAGAGGGAAA
TCTGGCTTCCTCATGTGGCATTATCTCCTTCGACGAGATGACACAGAGCCTGAGCCCTGGACCCGAAAGGGCAAGGACCG
CACTCGACAGCTGGGGCTCACTATGCAGTACCCTGAAGGCTACTTGGAGGCCTTGGCTAACAAGGAGAAGAGCAGGAAGC
GCCCGGCCAAGGCCTTGGAGCAGGGACCCTCATCTTCCAAGACAGGCAAAAGCAAACAGAAATCCACAGGGCCAACCCTC
TCCAGCCCCCGTGCCTCTAAGAATAGCAAGCTGGAGCCATACACACTCTCAGAGCAGCAGGCTAACCTCATCAAAGAGGA
CAAGGGCAACGCCAAGCTGTGGGATGATGTGCTAACTTCACTTCAGGATGGGCCGTACCAGATCTTCCTGAGCAAGGTGA
AAGAGGCTTTCCAGTGCATCTGCTGCCAGGAGCTGGTGTTCCGGCCAGTAACCACCGTGTGTCAGCACAACGTCTGTAAG
GACTGTCTGGACAGGTCCTTACGGGCCCAGGTGTTCAGCTGCCCAGCCTGTGGCTATGAGCTGGACCACAGCTCCCCAAC
CCGGGTGAACCAGCCCTTGCAGACCATTCTCAACCAGCTCTTCCCTGGCTATGGCAGCGGCCGG
ORF - retro_mmus_3696 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 97.16 % |
| Parental protein coverage: | 67.65 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | NIRLLNDSQLNNCRIMFVDEVLMIELPKERRPLIASPSQPPPALRNTGKSGPSCRFCKDDENKPCRKCAC |
| NIRLLNDSQLNNCRIMFVDEVLMIELP.ERRPLIASPSQPPPALRNTGKSGPSCRFCKDDENKPCRKCAC | |
| Retrocopy | NIRLLNDSQLNNCRIMFVDEVLMIELPNERRPLIASPSQPPPALRNTGKSGPSCRFCKDDENKPCRKCAC |
| Parental | HVCGGREAPEKQLLCDECDMAFHLYCLKPPLTSVPPEPEWYCPSCRTDSSEVVQAGEKLKESKKKAKMAS |
| HVCGGREAPEKQLLCD.CDMAFHLYCLKPPLTSVPPEPEWYCPSCRTDSSEVVQAGE.LKE.KKKAKMAS | |
| Retrocopy | HVCGGREAPEKQLLCDDCDMAFHLYCLKPPLTSVPPEPEWYCPSCRTDSSEVVQAGE-LKENKKKAKMAS |
| Parental | ATSSSRRDWGKGMACVGRTTECTIVPANHFGPIPGVPVGTMWRFRVQVSESGVHRPHVAGIHGRSNDGAY |
| ATSSS.RDWGKGMACVGRTTECTIVPANHFGPIPGVPVGTMW.FRVQVSESGVHRPHVAGIHGRSNDGAY | |
| Retrocopy | ATSSSQRDWGKGMACVGRTTECTIVPANHFGPIPGVPVGTMWHFRVQVSESGVHRPHVAGIHGRSNDGAY |
| Parental | SLVLAGGYEDDVDNGNYFTYTGSGGRDLSGNKRTAGQSSDQKLTNNNRALALNCHSPINEKGAEAEDWRQ |
| SLVLAGGYE.DVDNGNYFTYTGSGGRDLSGNKRTAGQSSDQKLTNNNRALALNCHSPINEKGAEAEDWRQ | |
| Retrocopy | SLVLAGGYENDVDNGNYFTYTGSGGRDLSGNKRTAGQSSDQKLTNNNRALALNCHSPINEKGAEAEDWRQ |
| Parental | GKPVRVVRNMKGGKHSKYAPAEGNRYDGIYKVVKYWPERGKSGFLVWRYLLRRDDTEPEPWTREGKDRTR |
| GKPV.VVRNMKGGKHSKYAPAEGNRYDGIYKVVKYWPERGKSGFL.W.YLLRRDDTEPEPWTR.GKDRTR | |
| Retrocopy | GKPVCVVRNMKGGKHSKYAPAEGNRYDGIYKVVKYWPERGKSGFLMWHYLLRRDDTEPEPWTRKGKDRTR |
| Parental | QLGLTMQYPEGYLEALANKEKSRKRPAKALEQGPSSSKTGKSKQKSTGPTLSSPRASKKSKLEPYTLSEQ |
| QLGLTMQYPEGYLEALANKEKSRKRPAKALEQGPSSSKTGKSKQKSTGPTLSSPRASK.SKLEPYTLSEQ | |
| Retrocopy | QLGLTMQYPEGYLEALANKEKSRKRPAKALEQGPSSSKTGKSKQKSTGPTLSSPRASKNSKLEPYTLSEQ |
| Parental | QANLIKEDKGNAKLWDDVLTSLQDGPYQIFLSKVKEAFQCICCQELVFRPVTTVCQHNVCKDCLDRSFRA |
| QANLIKEDKGNAKLWDDVLTSLQDGPYQIFLSKVKEAFQCICCQELVFRPVTTVCQHNVCKDCLDRS.RA | |
| Retrocopy | QANLIKEDKGNAKLWDDVLTSLQDGPYQIFLSKVKEAFQCICCQELVFRPVTTVCQHNVCKDCLDRSLRA |
| Parental | QVFSCPACRFELDHSSPTRVNQPLQTILNQLFPGYGSGR |
| QVFSCPAC..ELDHSSPTRVNQPLQTILNQLFPGYGSGR | |
| Retrocopy | QVFSCPACGYELDHSSPTRVNQPLQTILNQLFPGYGSGR |
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 | 1 .17 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 0 .48 RPM |
| SRP007412_heart | 0 .00 RPM | 1 .90 RPM |
| SRP007412_kidney | 0 .00 RPM | 3 .77 RPM |
| SRP007412_liver | 0 .00 RPM | 0 .85 RPM |
| SRP007412_testis | 0 .41 RPM | 102 .04 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_3696 was not detected
No EST(s) were mapped for retro_mmus_3696 retrocopy.
No TSS is located nearby retro_mmus_3696 retrocopy 5' end.
retro_mmus_3696 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_3696 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Mus musculus | ENSMUSG00000001228 | 1 retrocopy |
retro_mmus_3696 ,
|
| Nomascus leucogenys | ENSNLEG00000013406 | 1 retrocopy |