RetrogeneDB ID: | retro_cjac_1756 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 19:44207552..44209074(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | PAPSS1 | ||
| Ensembl ID: | ENSCJAG00000015905 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_1756
ATGGAGATCCCCGGGAGCCTGTGCAAGAAAGTCAAGCTGAGCAAGATGCAGAGAATGCAGAGAGCAACTAATGTCACCTA
CCAAGCCCATCATATCAGCAGGAACAAGAACGGTCAGGTTGTGGGGACCAGAGGTGGCTTTCGTGGCTGCACGTTTGGCT
CACAGGCTTGTCTAGAGCCAGAAAGACTACGGTCAGCGTGGCTTTGAAGAGTACCTGGTTTGCCATGATATTGCAGGCTA
CACTCTGGATGGTGCCGATATTCGTCAAGGTCTCAATAAAAATCTAGGCTTTAGTCCTGAAGACAGAGAAGGGAATGTTC
GACACGTGGCAGAAGTTACAGAGCTATTTGCAGGCGCTGGTTTAGTGTGCATCGCAAGTTTTATGTCACCTTATAGTCAG
GATCGCCATGATGCAAGACAAATTCATGAGGGGCAAGTTCGCCGTTTTCTGAAGTATTTGTTGATGCTCCTCTGCATGTT
TGTGAACAGAGGGATGTCAAAGGACTCTCCAAAAACCCCAGCCAGGAGAAATTAAAGGTTTCACTGGGATCGATTCTGAA
GATGAAAAGCCAGAGGCCCCTGAATTGGTGCTGAAAACAGACTCCTGTGAAGACTGTGTCCAGCAAGTTGCGGAACTTCT
ACAGGAACTAGATGTTGTACCTGTAGATGCATCTCGTGAGGTAAAATAACTGTATGTGCCAGGAAATAAACTTCATTTGG
CAAAAACAGATGCAGAAATGTTACCAGCACTGAAAATTAATCAAGTGGATATGCAGTGGGTGCAGGTTTTGACAGCAGGT
TGGGGAACCCCACTGAGTGGCTTCATGAGAGAGAGGGAATAATCGCAGTGCCTTCATTTTGATTGTCTTCTGGATGGAGG
TGTCATCAACTTGTCAGTACCTATAGTTCTGACAAGTTCTGCTACTCATGAAGTTAAACAGAGGCTGGACGGCTGGACAG
CATTTACTCTGATGTATGAGGACCGCCATGTGGCCATTCTTCACAATCCAGAGTTTTATGAGCACAGGGAAGAGGAGCAC
TGTGCCAGACGGTGGGGAACAACATGCAAGAACCACCCCCACATCAGGATGGTTATGGAACAAGGAGATTGGTTGATTGG
AGGAGATCTTCAAGTCTTGGACTGAGTTTATTGCAATGATGGTCTTGATCAGTATCGTCTTACTCCTACTGAGCTAAAGC
CGATATTTAAAGATATGAATGCTGACGCTGTCTTTGCATTTCAGTTACGCAACCCAGTGCACCATGGACATGCCCTGTTA
ATGCAGCATACCCATAAGCAATTTCTAGAGAGCAGCTACTGGTCCCCATCCTCCTCCTTCACTCTCTGGGTGGCTGGACA
AAGGATGATGATGTTCCTTTGATGTGGCATTTGAAGCAGCATGCTGCAGTGTTGGAGGAAGGAGTCCTGAATCCTGAGAT
GACAGTGGTGGCCATCTTCCCGTCTCCCATGAGGTATGCCAGACCAGCTGAGGTCCATTGGCATTGCAGGAGCCAACTTT
TA
ORF - retro_cjac_1756 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 81.5 % |
| Parental protein coverage: | 82.05 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 5 |
Retrocopy - Parental Gene Alignment:
| Parental | MESPGSLCKKVKLSNNAQNWGMQRATNVTYQAHHVSRNKRGQVVGTRGGFRGCT-VWLTGLSGAGKTTVS |
| ME.PGSLCKKVKLS.......MQRATNVTYQAHH.SRNK.GQVVGTRGGFRGCT.VWLTGLS.A.KTTVS | |
| Retrocopy | MEIPGSLCKKVKLSKMQR---MQRATNVTYQAHHISRNKNGQVVGTRGGFRGCT<VWLTGLSRARKTTVS |
| Parental | MAL-EEYLVCHGIPCYTLDGDNIRQGLNKNLGFSPEDREENVRRIAEVAKLFADAGLVCITSFISPYTQD |
| .AL.EEYLVCH.I..YTLDG..IRQGLNKNLGFSPEDRE.NVR..AEV..LFA.AGLVCI.SF.SPY.QD | |
| Retrocopy | VAL<EEYLVCHDIAGYTLDGADIRQGLNKNLGFSPEDREGNVRHVAEVTELFAGAGLVCIASFMSPYSQD |
| Parental | RNNARQIHEG-ASLPFFEVFVDAPLHVCEQRDVKGLYK-KARAGEIKGFTGIDSEYEKPEAPELVLKTDS |
| R..ARQIHEG.AS.PF.EVFVDAPLHVCEQRDVKGL.K.K...GEIKGFTGIDSE.EKPEAPELVLKTDS | |
| Retrocopy | RHDARQIHEG<ASSPFSEVFVDAPLHVCEQRDVKGLSK<KPQPGEIKGFTGIDSEDEKPEAPELVLKTDS |
| Parental | CDVNDCVQQVVELLQERDIVPVDASYEVKELYVPENKLHLAKTDAETLPALKINKVDMQWVQVLAEGWAT |
| C...DCVQQV.ELLQE.D.VPVDAS.EVK.LYVP.NKLHLAKTDAE.LPALKIN.VDMQWVQVL..GW.T | |
| Retrocopy | CE--DCVQQVAELLQELDVVPVDASREVK*LYVPGNKLHLAKTDAEMLPALKINQVDMQWVQVLTAGWGT |
| Parental | PLNGFMREREYLQCLHFDCLLDGGVINLSVPIVLT--ATHEDKERLDGCTAFALMYEGRRVAILRNPEFY |
| PL.GFMRERE..QCLHFDCLLDGGVINLSVPIVLT..ATHE.K.RLDG.TAF.LMYE.R.VAIL.NPEFY | |
| Retrocopy | PLSGFMRERE*SQCLHFDCLLDGGVINLSVPIVLTSSATHEVKQRLDGWTAFTLMYEDRHVAILHNPEFY |
| Parental | EHRKEERCARQWGTTCKNHPYIKMVMEQGDWLIGGDLQVLDRVYWNDGLDQYRLTPTELKQKFKDMNADA |
| EHR.EE.CAR.WGTTCKNHP.I.MVMEQGDWLIGGDLQVLD.VY.NDGLDQYRLTPTELK..FKDMNADA | |
| Retrocopy | EHREEEHCARRWGTTCKNHPHIRMVMEQGDWLIGGDLQVLD*VYCNDGLDQYRLTPTELKPIFKDMNADA |
| Parental | VFAFQLRNPVHNGHALLMQDTHKQLLERGYRR-PVLLLHPLGGWTKDDDVPLMWRMKQHAAVLEEGVLNP |
| VFAFQLRNPVH.GHALLMQ.THKQ.LE..Y...P.LLLH.LGGWTKDDDVPLMW..KQHAAVLEEGVLNP | |
| Retrocopy | VFAFQLRNPVHHGHALLMQHTHKQFLESSYWS<PILLLHSLGGWTKDDDVPLMWHLKQHAAVLEEGVLNP |
| Parental | ETTVVAIFPSPMMYAGPTEVQWHCRARMV |
| E.TVVAIFPSPM.YA.P.EV.WHCR.... | |
| Retrocopy | EMTVVAIFPSPMRYARPAEVHWHCRSQLL |
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 |
|---|---|---|
| SRP051959_colon | 0 .00 RPM | 33 .59 RPM |
| SRP051959_heart | 0 .02 RPM | 28 .82 RPM |
| SRP051959_kidney | 0 .00 RPM | 41 .09 RPM |
| SRP051959_liver | 0 .00 RPM | 14 .49 RPM |
| SRP051959_lung | 0 .02 RPM | 35 .24 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 29 .79 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 9 .83 RPM |
| SRP051959_spleen | 0 .00 RPM | 30 .76 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_1756 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_1756 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_1756 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 | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000015905 | 1 retrocopy |
retro_cjac_1756 ,
|
| Equus caballus | ENSECAG00000021678 | 1 retrocopy |