RetrogeneDB ID: | retro_mmus_1521 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 16:55883220..55884508(-) | ||
| Located in intron of: | ENSMUSG00000075033 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Chuk | ||
| Ensembl ID: | ENSMUSG00000025199 | ||
| Aliases: | Chuk, AI256658, Chuk1, Fbx24, Fbxo24, IKBKA, IKK1, Ikka, NFKBIKA | ||
| Description: | conserved helix-loop-helix ubiquitous kinase [Source:MGI Symbol;Acc:MGI:99484] |
Retrocopy-Parental alignment summary:
>retro_mmus_1521
CCATGGAGGGCCCCCCTCCCCGGGGGGCTGTGGCCGGGCATGGGCGCCCCGGGAGATGTGGGAGTGGCCCGGTACTGGCT
GTACCAGCACGGGAACTTGCTCTCAAAAAAGCAATTAAGTCTTGTCACTTAGAGCTAAGTACCAAAACCAGAGAGCGATG
GTGCCATGAAATCCAGATCCTGAAAAAGTTGAGCCATGTGAATGTTGTAAAGGCCTGTGATGTTCCCGAGGGATTGAACT
TTTTAATTAACGATGTGCCTCTTCTAGCAATGGAGGACTGTTCTGGAGGGGACCTCCCGGAAGCGACTCAACAAATCAGA
ACATTGTTGTGGGCTTAAAGAAAGCCAGATACTTTCTTTACTGAGTGACATAGCATCTGGGATTTGATATTTGCATGAAA
ACAAAATTATACATCAGACCTAAAACCTGGAAATATAATTCTTCAGGATGTTGGTGGGAAGGTAATACATAAAATAATTG
ATTTGGGTTATGCCAAAGATGTTGATCAAGGAAGTCTCTGTACATCTTTTGTGGGAACATTGCAGTATTTGGCCCCAGGG
CTCTTTGAAGATAATCCATACACAGCCACTGTGGATTATTGGAACTTTGAGACCATTGTGTCTGAATGTACTGCTGGATA
TAGGCCCTTTATGCAGCACCTGCAGCCATTTACCTGGCATAAGAAGATTAAGAAGAAAGATCCAAAGTGTATATTTGCAT
GTGAAGAGATGACCGGAGAAGTTCGGTTTAGTAGCCATTTACCTCAGCCAAATGGCCTTTGTAGTTTAACGGTAGAGCCA
GTGGAAAGCTGGCTACAATTGATGTTGAATGGGGACCCACAGCAGAGAGGGGGACCCATTGATCTTACTTTGAAGTAGCC
AAGATGTTTTGCATCAATGGATCACATTTTCAATGTAAAGATAGTGCACATCCTAACTATGACTTCTGCAAAAATCATTT
CTTTTCTGTTACCATGGATGAATGTCTTCATTCACAACAGTCTCGAACTGAGCGTCAAACAGGAATAAATACAGGTTCTC
GAGAAGTTTTGTCAGAGGCAGGAATTTCTCTGGATCCACCGAAACCGGCCCCTCAGTGTGTGCTAGATGGAGTGAGAGGC
CGTGATAGCTACATGGTTCATTTGTTTGGTAAAAGTAAGACTGTATATGAAGGACCATTTGCCTCCAGAAGTTTATTTGA
TTGTGTAAATTATATTGTACAAGACAGCAAAATACAGCTGCCAACTATACAGCTGTGGAAAGTATGGGCTGAAGCAGTGC
ACTATGTA
ORF - retro_mmus_1521 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 82.03 % |
| Parental protein coverage: | 57.72 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 4 |
Retrocopy - Parental Gene Alignment:
| Parental | PGLRPGAGGPWEMRERLGTGGFGNVSLYQH-RELDLKIAIKSCRLELSSKNRERWCHEIQIMKKLDHANV |
| P...P..GG.W......G..G.....LYQH.REL.LK.AIKSC.LELS.K.RERWCHEIQI.KKL.H.NV | |
| Retrocopy | PWRAPLPGGLWPGMGAPGDVGVARYWLYQH<RELALKKAIKSCHLELSTKTRERWCHEIQILKKLSHVNV |
| Parental | VKACDVPEELNFLINDVPLLAMEYCSGGDL-RKLLNKPENCCGLKESQILSLLSDIGSGIRYLHENKIIH |
| VKACDVPE.LNFLINDVPLLAME.CSGGDL.RK.LNK.E.CCGLKESQILSLLSDI.SGI.YLHENKIIH | |
| Retrocopy | VKACDVPEGLNFLINDVPLLAMEDCSGGDL>RKRLNKSEHCCGLKESQILSLLSDIASGI*YLHENKIIH |
| Parental | R-DLKPENIVLQDVGGKTIHKIIDLGYAKDVDQGSLCTSFVGTLQYLAPELFENKPYTATVDYWSFGTMV |
| ..DLKP.NI.LQDVGGK.IHKIIDLGYAKDVDQGSLCTSFVGTLQYLAP.LFE..PYTATVDYW.F.T.V | |
| Retrocopy | Q<DLKPGNIILQDVGGKVIHKIIDLGYAKDVDQGSLCTSFVGTLQYLAPGLFEDNPYTATVDYWNFETIV |
| Parental | FECIAGYRPFLHHLQPFTWHEKIKKKDPKCIFACEEMTGEVRFSSHLPQPNSLCSLIVEPMESWLQLMLN |
| .EC.AGYRPF..HLQPFTWH.KIKKKDPKCIFACEEMTGEVRFSSHLPQPN.LCSL.VEP.ESWLQLMLN | |
| Retrocopy | SECTAGYRPFMQHLQPFTWHKKIKKKDPKCIFACEEMTGEVRFSSHLPQPNGLCSLTVEPVESWLQLMLN |
| Parental | WDPQQRGGPIDLTLKQPRCFALMDHILNLKIVHILNMTSAKIISFLLP-CDESLHSLQSRIERETGINTG |
| .DPQQRGGPIDLTLK.PRCFA.MDHI.N.KIVHIL.MTSAKIISFLLP..DE.LHS.QSR.ER.TGINTG | |
| Retrocopy | GDPQQRGGPIDLTLK*PRCFASMDHIFNVKIVHILTMTSAKIISFLLP<MDECLHSQQSRTERQTGINTG |
| Parental | SQELLSETGISLDPRKPASQCVLDGVRGCDSYMVYLFDKSKTVYEGPFASRSLSDCVNYIVQDSKIQLPI |
| S.E.LSE.GISLDP.KPA.QCVLDGVRG.DSYMV.LF.KSKTVYEGPFASRSL.DCVNYIVQDSKIQLP. | |
| Retrocopy | SREVLSEAGISLDPPKPAPQCVLDGVRGRDSYMVHLFGKSKTVYEGPFASRSLFDCVNYIVQDSKIQLPT |
| Parental | IQLRKVWAEAVHYV |
| IQL.KVWAEAVHYV | |
| Retrocopy | IQLWKVWAEAVHYV |
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 .12 RPM | 45 .37 RPM |
| SRP007412_cerebellum | 0 .04 RPM | 39 .99 RPM |
| SRP007412_heart | 0 .03 RPM | 23 .41 RPM |
| SRP007412_kidney | 0 .17 RPM | 100 .64 RPM |
| SRP007412_liver | 0 .00 RPM | 104 .89 RPM |
| SRP007412_testis | 0 .05 RPM | 17 .38 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_1521 was not detected
No EST(s) were mapped for retro_mmus_1521 retrocopy.
No TSS is located nearby retro_mmus_1521 retrocopy 5' end.
retro_mmus_1521 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_1521 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 | ENSMUSG00000025199 | 1 retrocopy |
retro_mmus_1521 ,
|
| Sarcophilus harrisii | ENSSHAG00000000038 | 1 retrocopy | |
| Ictidomys tridecemlineatus | ENSSTOG00000016412 | 1 retrocopy |