RetrogeneDB ID: | retro_mmus_3578 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | X:13927286..13928384(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000082736 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Mkrn2 | ||
| Ensembl ID: | ENSMUSG00000000439 | ||
| Aliases: | Mkrn2, 2610002L04Rik, C81377 | ||
| Description: | makorin, ring finger protein, 2 [Source:MGI Symbol;Acc:MGI:1914277] |
Retrocopy-Parental alignment summary:
>retro_mmus_3578
AGATATGATCATACAAAACCCCCAGCTGCAGCAGGTGGTGCTGTGGGTCCTGCATCCCACCCTTCACCCTCCTCAGGCCT
GCATAGTCCTCACCCTTATCCCGACATTGCCATATCTGTTATGAGGACACATTTGAATGAACCTGGAAAGCAGGAGAAGA
CAATGCTGGTGCTCACAGACAGCAATCTCACTGGTCTAGCTGAAGACAAGACTCCTCCAAGCACAGAGACTAGTCCAGGT
GGCTGTAGTGACCCTCAGACCAGCCCAGAGATGAAGCCCCATTTCTACCTAAATGCCATCAGAACTGGCCTGATGCTCCT
ACAGGAGGCCAGCAACTCCTGCAGCAATGAGCAGCAGTTGTGCTCCTATGCTGCCGCTGGGGAGTGCCAGTTTGAAGATG
CCTGTGTCTACCTGCATGGGGACATGTGTGAGATCTGCAGGCTTCAAATCCTCCACCCCTTTGACCCAAGAGCCAAGGAA
AGCTCATGAGAAGATGTGCAGGTCGACATTTGAACATGAGATGGAAAAGGCTTCGTCCAGGTAAGCCAGGACGAAGTGTG
CAGCATCTGTATGGAGGTGATCCTGGAGAAAGCATCTGCTTCTGAAAGGAGGTTTGGATTCTCTCCAACTGCAGCCACAC
CTACTGCCTGTCCTGCATCTGTCAATGAAGATGTGCCAAGCAGTTTGAAAACCCTATCATAAAGTCTTGTCCAGAGGGCC
GTGTGATAGCAAAGTTTGTAACTCCAAGTGTGTACTGGGTAGAAGATCAGAATAAAAAGAATGAATTAGTTGAAGTTTTC
AAACAGGGAATGGGGGTAAAAGGCATGTAAATACTTTGAACAAGGCAAGGAGACCTGCCCCTTTGGAAACAAGTGCCTTT
ACCACCACCATGCTTACCCTGATGGGCAGTTGGCAGAGCCAGAGAAACCTCAGAAGCAGCTAAGCTCTGAAGGCGCTGTG
AGGTTCTTTAACTCAGTGCGGCTTTGGGATTTTAACGAGAACCAAGAAACCCGGCAAGTTCCCAGCACTGATGATGTGGA
TGTGATGGAGCTAGGAGATCTCTTCATGCACCTTTCTGGAGTAGAGACATCAGAACCC
ORF - retro_mmus_3578 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 84.64 % |
| Parental protein coverage: | 87.74 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 4 |
Retrocopy - Parental Gene Alignment:
| Parental | RYDHTKPPAAAGGAVGPAPNPSPSSGLHSPHPSPDIATSVMRTHSNEPGKREKKTLVLRDRNLTGLAEDK |
| RYDHTKPPAAAGGAVGPA..PSPSSGLHSPHP.PDIA.SVMRTH.NEPGK.EK..LVL.D.NLTGLAEDK | |
| Retrocopy | RYDHTKPPAAAGGAVGPASHPSPSSGLHSPHPYPDIAISVMRTHLNEPGKQEKTMLVLTDSNLTGLAEDK |
| Parental | TPPSKVNNPGGCSDPQTSPEMKPHSYLDAIRTGLDDL-EASSSYSNEPQLCPYAAAGECRFGDACVYLHG |
| TPPS....PGGCSDPQTSPEMKPH.YL.AIRTGL..L.EAS.S.SNE.QLC.YAAAGEC.F.DACVYLHG | |
| Retrocopy | TPPSTETSPGGCSDPQTSPEMKPHFYLNAIRTGLMLLQEASNSCSNEQQLCSYAAAGECQFEDACVYLHG |
| Parental | DMCEICRLQVLHPFDP-EQRKAHEKMCMSTFEHEME-KAFAFQASQDKVCSICMEVILEKASASERRFG- |
| DMCEICRLQ.LHPFDP.E.RKAHEKMC.STFEHEME.K.F..Q.SQD.VCSICMEVILEKASASERRFG. | |
| Retrocopy | DMCEICRLQILHPFDP>EPRKAHEKMCRSTFEHEME<KGFV-QVSQDEVCSICMEVILEKASASERRFG< |
| Parental | ILSNCSHTYCLSCIRQWRCAKQFENPIIKSCPECRVISEFVIPSVYWVEDQNKKNELIEAFKQGMGKK-A |
| ILSNCSHTYCLSCI.Q.RCAKQFENPIIKSCPE.RVI..FV.PSVYWVEDQNKKNEL.E.FKQGMG.K.A | |
| Retrocopy | ILSNCSHTYCLSCICQ*RCAKQFENPIIKSCPEGRVIAKFVTPSVYWVEDQNKKNELVEVFKQGMGVK>A |
| Parental | CKYFEQGKGTCPFGSKCLYRH-AYPDGRLAEPEKPRKQLSSEGTVRFFNSVRLWDFIENRETRQVPSTDD |
| CKYFEQGK.TCPFG.KCLY.H.AYPDG.LAEPEKP.KQLSSEG.VRFFNSVRLWDF.EN.ETRQVPSTDD | |
| Retrocopy | CKYFEQGKETCPFGNKCLYHHHAYPDGQLAEPEKPQKQLSSEGAVRFFNSVRLWDFNENQETRQVPSTDD |
| Parental | VDVTELGDLFMHLSGVESSEP |
| VDV.ELGDLFMHLSGVE.SEP | |
| Retrocopy | VDVMELGDLFMHLSGVETSEP |
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 | 20 .19 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 19 .76 RPM |
| SRP007412_heart | 0 .00 RPM | 26 .99 RPM |
| SRP007412_kidney | 0 .00 RPM | 18 .23 RPM |
| SRP007412_liver | 0 .00 RPM | 9 .99 RPM |
| SRP007412_testis | 0 .05 RPM | 62 .62 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_3578 was not detected
No EST(s) were mapped for retro_mmus_3578 retrocopy.
No TSS is located nearby retro_mmus_3578 retrocopy 5' end.
retro_mmus_3578 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_3578 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 5 parental genes, and 6 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000016733 | 1 retrocopy | |
| Mus musculus | ENSMUSG00000000439 | 2 retrocopies |
retro_mmus_3578 , retro_mmus_544,
|
| Mus musculus | ENSMUSG00000029922 | 1 retrocopy | |
| Otolemur garnettii | ENSOGAG00000003255 | 1 retrocopy | |
| Pteropus vampyrus | ENSPVAG00000005822 | 1 retrocopy |