RetrogeneDB ID: | retro_mmus_3646 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | X:78855410..78858281(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000083258 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Zc3h18 | ||
| Ensembl ID: | ENSMUSG00000017478 | ||
| Aliases: | Zc3h18, 1190001B23Rik, 5830416A07Rik, Nhn1 | ||
| Description: | zinc finger CCCH-type containing 18 [Source:MGI Symbol;Acc:MGI:1923264] |
Retrocopy-Parental alignment summary:
>retro_mmus_3646
ATGAATGTGGCCGAGAGCCCTGAACTGGATCCTCACTCCCCAGAGGATGAAGAGCAGCCGGCACTCTCAGATGATGACAT
TCTGAGAGAAAGTGGATCTGAACAAGATTTGGATGGAGCTGGGGAAAGGGCTTCTGATTTGGAGGAGGAGGAAAATGCAA
CCAGGGTACAAAGCCAGGAGGAAACTTGCTCGGATGAGAAAGACCGAGCCAGTGAGCCCAAGTCCCAAGATCAGGATTCA
GAGGCTCATGAGCTGAGCAGGGGCCCAGAGGGATCCCCATGCGAGGAGGGGGATGATGTTGAAGAAGATGGGACAAGTGA
CCTCAGGGACGAAGCCTCCTCAGTGACCCGGGAACTGGATGAGCATAAACTAGACTATGATGAGGGGGTCCTTGAGGAGC
CAGCTCCTGCTGCCCAGGAGGAGGAGGCTGAGAAGGCTGGGGCTGAGGAGAAGGAGGAGAAGGGGGAAGGGGCTCCCGGA
GAGGAAGGGAAGCCTGATGTCCAAAGTGTGGGAGAACAAGAACCCACAGAAGCTGCCAAGGAGAAGAAGAAAGAGGATGA
CGACGGGGAGATTGATGATGGCGAGATAGACGATGATGACTTGGAAGAAGGCGAAGTGAAGGACCCCAGTGACCAGAACG
TGAGGCCTCGCCCCACCTGCCGATTCTTCATGAAAGATGTTGTGACACCATTATCCACTCTTCTTCCACCAATACCAAAT
TCCATACCACTCAGAGGCCAGGTTAAAGGAAACTGCACGTGGGGAATGAGCTGTAGGTTTATCCACCCTGGAGTGAATGA
CAAGGGCAACTACTCCCTCATCACCAAAGCGGAACCTTTTCCAACAAACGGTGCCCCGCCTCTTGGACCTCACCCACTGA
TGCCTGCCAACCCTTGGCGTGGGCCAGTGGTTGATGAAATTTTGCCTCCACCCCCTCCAGAGCCCCCAACAGAGAGCGCC
TGGGAACGTGGACTCCGACATGCAAAAGAGGTTTTGAAAAAAGCAACCATTCGGAAAGAACAGGAGCCGGACTTTGAAGA
AAAAAAGTTCACAGTAACCATTGGTGAAGATGACCAGGAGTTTGAGAAGGAGAATGAAGTCTTCCGAGATTGGAATTCTC
GAGTCCCGAGAGATGTCAGAGACACAACACTTGAGCCTTATGCAGACCCTTATTATTACTATGAGATAGAGCAGTTTTGG
CGTGGTGGACAGTACGAGAATTTCAGGGTGCAGTATACAGAAGCAGAGCCATATCATAACTATCGCGAACGAGAGAGGGA
ACGAGAGCGAGAAAACAGACAACTAGAACGCGAGCAGGAACGAGAGCGTGACCGAGAGCGGGAGCGCAGGCAGAGAGAGC
GGGAGCGAAAACAGGAAAGAGAGCGGGACAAGGAGCGGCAGCGGAGGAAAGAGTGGGAAAGAGAGAGAGCCAAGCGAGAC
GAGAAGGACCGGGAGAAGGACAAGGAGAAGCTGAAGTCCCGGTCCCCACAGCCACCAAGCCGTCAAGCTGAACTACCAAA
GAAGAGCACCTCTGTGGGGCCCCAGGTGAAGCGAGCCTATGAGTGGAAGGACCCCTGGCGCCGATCCAAGTCTCCCAAGA
AGAAGCATGGCGTGTCAGTCTCCCCAAGCTGGGCACGAAGACGTCACAAAACCTCCGCCTCCTCAGCCTCTGCTTCCAAT
TCCTCCAGGTCATCTTCACGGTCTTCATCCTACTCTGGCTCGTCCTGGTCCCGGTCCCGATCCTCCTCCTACAGCTCCTA
TTCTAGCCGCTCTTTCAGACACAGCTCCTTCTCAGGCAGCCGATCCAGGTCCCGGTCCTTCTCGTCCCCATCCCCGTCTC
CCACACCTTCCCCACACAGACCTCCAGTCAGAACCAAGGGGGAGCCGACCCCACCTTCCAGCAAAGCAAGGGAGAAGTCA
ATAAAGAAGCCAGCCACTCCCCCAGCCCCATCACAGGCCACCAAAAGTACTGCTCCTGGTCCTGAGCCTGCCAAACCTGG
AGATCTCCAAGAAGCCAGGAGAAAGGAGAGGCAAACCAGGACTCCCCCAAGGAGGAGGACGCCCAGCAGCAGTGGTAGCG
GCAGTGGTAGCAGCTACAGTGGCTCCAGTTCCAGATCCAGGTCTCTGAGTGTGAGTAGCCTTTCCTCAGTGTCCAGCGCC
ACCTCGAGTAGCAGCTCAGTGCACAGTGTGGACTCAGATGACATGTATGCAGACCTGGCCAGTCCTGTGTCCTCAGCCAG
CTCTCGATCCCCAACTCCTGCCCAGACCAAGAAGGAGAGAGGGAAATCCAAGAAAGAAGACGGAGTGAGAGAGGAAAAGC
GGAAGCGGGATCCATCCACGCAGCCACCCAAGTCCTCTAAAGCTCCAGCAGGTGGGAAGGCCTCCCAGCAGGCAGCGGCA
CCTCAGCCGGCGGCCCCCGGACAGCCCCAACAGGGCTCCTTTGTTGCCCACAAGGAGATAAAGCTGACACTGCTGAACAA
GGCGGCTGATAAAGGAAGCCGGAAGCGCTATGAGCCATCAGACAAGGACCACCGGCAGAGCCCTCCTGCTAAGAAGGCCA
ACTTGTCCCCAGACCGAGGTTCTGGAGACCGGAAATCAGGTGGAAGAATGGGCTCCCCAAAACCAGAGATGCAGAGAGGC
CAGAACGCTAAAGCTCCTGCTGCCCCAGCGGACAGGAAGCGTCCACTGTCACCCCAGTCTAAGGGCTCCAGCAAGGTCAC
CATCGTGCCTGGCAAAGCCACAGATACTGCCACAGCAGGCACCAAGTCAGGGAAGGCCAGCACATTGTCACGGCGAGAGG
AGCTCCTTAAACAGCTCAAGAAGGTTGAGGAAGCCATCGCTCGCAAGCGGGCCAAGATCCCCGGGAAAATG
ORF - retro_mmus_3646 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 76.41 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MDVAESPELDPHSPEDEEQPALSDDDILRESGSEQDLDGAGERASDLEEEENATRVQSQEETRSDEEDRA |
| M.VAESPELDPHSPEDEEQPALSDDDILRESGSEQDLDGAGERASDLEEEENATRVQSQEET.SDE.DRA | |
| Retrocopy | MNVAESPELDPHSPEDEEQPALSDDDILRESGSEQDLDGAGERASDLEEEENATRVQSQEETCSDEKDRA |
| Parental | SEPKSQDQDSEAHELSRGPAGSPCEEGDDVEEDGTSDLRDEASSVTRELDEHELDYDEEVPEEPAPAAQE |
| SEPKSQDQDSEAHELSRGP.GSPCEEGDDVEEDGTSDLRDEASSVTRELDEH.LDYDE.V.EEPAPAA.. | |
| Retrocopy | SEPKSQDQDSEAHELSRGPEGSPCEEGDDVEEDGTSDLRDEASSVTRELDEHKLDYDEGVLEEPAPAAXX |
| Parental | EEAEKAGAEEEEEKGEGAPGEEGKPDVQSVGEQEPTEAAKEKKKEDDDGEIDDGEIDDDDLEEGEVKDPS |
| ................GAPGEEGKPDVQSVGEQEPTEAAKEKKKEDDDGEIDDGEIDDDDLEEGEVKDPS | |
| Retrocopy | XXXXXXXXXXXXXXXXGAPGEEGKPDVQSVGEQEPTEAAKEKKKEDDDGEIDDGEIDDDDLEEGEVKDPS |
| Parental | DRKVRPRPTCRFFMKDVVTPLSTLLPPIPNSIPLRGQVKGNCTWGMSCRFIHPGVNDKGNYSLITKAEPF |
| D..VRPRPTCRFFMKDVVTPLSTLLPPIPNSIPLRGQVKGNCTWGMSCRFIHPGVNDKGNYSLITKAEPF | |
| Retrocopy | DQNVRPRPTCRFFMKDVVTPLSTLLPPIPNSIPLRGQVKGNCTWGMSCRFIHPGVNDKGNYSLITKAEPF |
| Parental | PPNGAPPLGPHPLMPANPWGGPVVDEILPPPPPEPPTESAWERGLRHAKEVLKKATIRKEQEPDFEEKRF |
| P.NGAPPLGPHPLMPANPW.GPVVDEILPPPPPEPPTESAWERGLRHAKEVLKKATIRKEQEPDFEEK.F | |
| Retrocopy | PTNGAPPLGPHPLMPANPWRGPVVDEILPPPPPEPPTESAWERGLRHAKEVLKKATIRKEQEPDFEEKKF |
| Parental | TVTIGEDDREFDKENEVFRDWNSRVPRDVRDTTLEPYADPYYDYEIERFWRGGQYENFRVQYTEAEPYHN |
| TVTIGEDD.EF.KENEVFRDWNSRVPRDVRDTTLEPYADPYY.YEIE.FWRGGQYENFRVQYTEAEPYHN | |
| Retrocopy | TVTIGEDDQEFEKENEVFRDWNSRVPRDVRDTTLEPYADPYYYYEIEQFWRGGQYENFRVQYTEAEPYHN |
| Parental | YRERERERERENRQRERERERERDRERERRQRERERERERERDKERQRRKEEWERERAKRD----EKDRQ |
| YRERERERERENRQ.ERE.ERERDRERERRQRERER..ERERDKERQRRKE.WERERAKRD....EKD.. | |
| Retrocopy | YRERERERERENRQLEREQERERDRERERRQRERERKQERERDKERQRRKE-WERERAKRDEKDREKDKE |
| Parental | HRDRDRDKDREKDKEKPKPRSPQPPS--RQAEPPKKESTSVGPQVKRADEWKDPWRRSKSPKKKLGVSVS |
| ..............E.PK......P...R..E.......S..P..K........W.R..........S.S | |
| Retrocopy | KLKSRSPQPPSRQAELPKKSTSVGPQVKRAYEWKDPWRRSKSPKKKHGVSVSPSWARRRHKTSASSASAS |
| Parental | PSRARRRRKTSASSASASNSSRSSSRS-SSYSGSGSSRSRSRSSSYSSYSSRSSRHSSFSGSRSRSRSFS |
| .S.....R..S.S..S.S.S..SS..S.SS.S...SS.S.SRS.S.S..S...S...S......R..... | |
| Retrocopy | NSSRSSSRSSSYSGSSWSRSRSSSYSSYSSRSFRHSSFSGSRSRSRSFSSPSPSPTPSPHRPPVRTKGEP |
| Parental | SSPSPSPTPSPHRPPVRTKGEPAPPPGKAGEKSIKKPAPPPAPPQATKTTAPGPEPAKPGDLREARRKER |
| ..PS..........P.............A......KP............T...P....P........... | |
| Retrocopy | TPPSSKAREKSIKKPATPPAPSQATKSTAPGPEPAKPGDLQEARRKERQTRTPPRRRTPSSSGSGSGSSY |
| Parental | QTRTPPRRSLSVSSVSSVSSATSSSSSVHSVDSDDMYADLASPVSSASSRSPTPAQTKKERGKSKKEDGV |
| .......RSLSVSS.SSVSSATSSSSSVHSVDSDDMYADLASPVSSASSRSPTPAQTKKERGKSKKEDGV | |
| Retrocopy | SGSSSRSRSLSVSSLSSVSSATSSSSSVHSVDSDDMYADLASPVSSASSRSPTPAQTKKERGKSKKEDGV |
| Parental | REEKRRRDPSAQPPKSSKAPAGGKASQQAAAPQPAVPGQPQQGSFVAHKEIKLTLLNKAADKGSRKRYEP |
| REEKR.RDPS.QPPKSSKAPAGGKASQQAAAPQPA.PGQPQQGSFVAHKEIKLTLLNKAADKGSRKRYEP | |
| Retrocopy | REEKRKRDPSTQPPKSSKAPAGGKASQQAAAPQPAAPGQPQQGSFVAHKEIKLTLLNKAADKGSRKRYEP |
| Parental | SDKD-RQSPPAKKANLSPDRGSRDRKSGGRMGSPKPERQRGQNAKAPAAPADRKRPLSPQSKGSSKVTSV |
| SDKD.RQSPPAKKANLSPDRGS.DRKSGGRMGSPKPE.QRGQNAKAPAAPADRKRPLSPQSKGSSKVT.V | |
| Retrocopy | SDKDHRQSPPAKKANLSPDRGSGDRKSGGRMGSPKPEMQRGQNAKAPAAPADRKRPLSPQSKGSSKVTIV |
| Parental | PGKATDTATAGTKSGKASTLSRREELLKQLKAVEDAIARKRAKIPGKV |
| PGKATDTATAGTKSGKASTLSRREELLKQLK.VE.AIARKRAKIPGK. | |
| Retrocopy | PGKATDTATAGTKSGKASTLSRREELLKQLKKVEEAIARKRAKIPGKM |
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 .05 RPM | 39 .09 RPM |
| SRP007412_cerebellum | 0 .09 RPM | 66 .74 RPM |
| SRP007412_heart | 0 .00 RPM | 42 .24 RPM |
| SRP007412_kidney | 0 .10 RPM | 75 .71 RPM |
| SRP007412_liver | 0 .03 RPM | 64 .72 RPM |
| SRP007412_testis | 0 .05 RPM | 86 .22 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_3646 was not detected
No EST(s) were mapped for retro_mmus_3646 retrocopy.
No TSS is located nearby retro_mmus_3646 retrocopy 5' end.
retro_mmus_3646 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_3646 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Mus musculus | ENSMUSG00000017478 | 1 retrocopy |
retro_mmus_3646 ,
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