RetrogeneDB ID: | retro_cjac_769 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 10:27929010..27930411(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | NUPL1 | ||
| Ensembl ID: | ENSCJAG00000019231 | ||
| Aliases: | None | ||
| Description: | nucleoporin like 1 [Source:HGNC Symbol;Acc:20261] |
Retrocopy-Parental alignment summary:
>retro_cjac_769
ATGTCCATGGGGTTCTCCTTCGGGTCCAGGACTTTGGACCCCACCACCGTAGCCCCTGGCAGGACCAGCACAGGTGGCAG
TTTCTCCTTTGGGACGGGAGTGTCTAGCAACCCTTCTGTGGGGCTCAATTTTGGAACTCTTGGAGGTCCTGCAACTCCAG
CAACTACACCTGCTCCTTCAAGCTGGTTTTGGAACCAGGCTCTTTGGATCTAAACCTGCTACTGGGTTCACTCTAGGAGG
AACAAATACAGGGACACCAGCCACTACATCTGCCCCTACAACAGGCTTCAGTTTAGGATTCAATAAACCTGCAGCATCTG
CCACACCATTTGCTCTACCTATTACTTCTACCTCAGCTAGCAGTCTCACTCTTTCCTCTGCTCTGACATCAACTCCAGCA
GCTTCCACAGGATTTACCCCAAATAATTTGGGTGGGACAATAGCCACAACTACAACTGCATCAACAGGCCTCTCTCTAGG
GGGAGCCTTAGCTGGTTTGGGAGGTTCACTTTTCCAGAGCACAGACACAGCAACATCAGGACTAGGACAGAATGCTTTAG
GCTTGACTTTGGGAACTACAGCAGCTACTTCAAGTGCAGGCAATGAAGGCCTTGGTGGCATAGATTTTAGTAGCTCCTCA
GATAAAAAGAGTGATAAAACAGGAACAAGACCAGAGGATAGTAAAGCTCTGAAGGATGAAAATCTACCTCCTGTCATCTG
CCAGGATGTTGAAAATCTCCAGAAATTTGTCAAGGAGCAGAAACAAGCTCAAGAAGAAATTAATAGAATGTCTTCAAAAG
CAATGCTTAAGGTACAAGAAGATATTAAAGCTCTGAAGCAGCTCCTGTCATTGGCTGCCAATAGACCACAGAGAAACACT
CTCAACATTGACAAATTGAAAATAGAAACTGCTCAGGAGTTAAAGAATGCTGAAATAGCTTTAAAAACCTAGAAGGCACC
ACCTGGACTTCAACATAAATATGCAGCTCCTGCTGACTACTTCAGAATCTTGGTTCAGCAATTTGAGGTACAGCTTCAGC
AATACAGACAACAGATTGAAGAACTAGAAAATTATCTTGCCACTCAAGCAAATAATTCACATATAACCCCTCAAGATTTG
TCAATGGCTATGCAGTAAATTTAAAAAACATTTGTAGCTTTAGCAGCACAACTTCAGTCTATTCATGAAAATGTAAAGGT
TCTGAAAAACAGTACCTTGGCTACAGGAAAATGTTCTTGGGAGATGCTGTTGATGTGTTTGAAGCAAGACGAGCAGAAGC
CAAGAAGTGGCAGAACACACCCAGAGTTACTACCGGACCCACCCCTTTCAGCACCATGCCAAATGCAGCAGCCATTGCCG
TGGCTGCAACACTTACACAGCAGCAACAGCCTGCTACAGGT
ORF - retro_cjac_769 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 92.54 % |
| Parental protein coverage: | 79.56 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | MSTGFSFGSGTLGSTTVAPGGTGTGGGFSFGTGASSNPSVGLNFGTLGSTATPTTTSAPSS-GFGTGLFG |
| MS.GFSFGS.TL..TTVAPG.T.TGG.FSFGTG.SSNPSVGLNFGTLG..ATP.TT.APSS.GFGT.LFG | |
| Retrocopy | MSMGFSFGSRTLDPTTVAPGRTSTGGSFSFGTGVSSNPSVGLNFGTLGGPATPATTPAPSS>GFGTRLFG |
| Parental | SKPATGFTLGGTNTGTPATTSAPTTGFSLGFNKPAASATPFALPITSTSASGLTLSSALTSTPAASTGFT |
| SKPATGFTLGGTNTGTPATTSAPTTGFSLGFNKPAASATPFALPITSTSAS.LTLSSALTSTPAASTGFT | |
| Retrocopy | SKPATGFTLGGTNTGTPATTSAPTTGFSLGFNKPAASATPFALPITSTSASSLTLSSALTSTPAASTGFT |
| Parental | LNNLGGTTATTTTASTGLSLGGALAGLGGSLFQSTNTATSGLGQNALGLTLGTTAATSAAGNEGLGGIDF |
| .NNLGGT.ATTTTASTGLSLGGALAGLGGSLFQST.TATSGLGQNALGLTLGTTAATS.AGNEGLGGIDF | |
| Retrocopy | PNNLGGTIATTTTASTGLSLGGALAGLGGSLFQSTDTATSGLGQNALGLTLGTTAATSSAGNEGLGGIDF |
| Parental | SSSSDKKSDKTGTRPEDSKALKDENLPPVICQDVENLQKFVKEQKQVQEEISRMSSKAMLKVQEDIKALK |
| SSSSDKKSDKTGTRPEDSKALKDENLPPVICQDVENLQKFVKEQKQ.QEEI.RMSSKAMLKVQEDIKALK | |
| Retrocopy | SSSSDKKSDKTGTRPEDSKALKDENLPPVICQDVENLQKFVKEQKQAQEEINRMSSKAMLKVQEDIKALK |
| Parental | QLLSLAANGLQRNTLNIDKLKIETAQELKNAEIALRTQKTPPGLQHEYAAPADYFRILVQQFEVQLQQYR |
| QLLSLAAN..QRNTLNIDKLKIETAQELKNAEIAL.T.K.PPGLQH.YAAPADYFRILVQQFEVQLQQYR | |
| Retrocopy | QLLSLAANRPQRNTLNIDKLKIETAQELKNAEIALKT*KAPPGLQHKYAAPADYFRILVQQFEVQLQQYR |
| Parental | QQIEELENHLATQANNSHITPQDLSMAMQKIYQTFVALAAQLQSIHENVKVLK-EQYLGYRKMFLGDAVD |
| QQIEELEN.LATQANNSHITPQDLSMAMQ.I..TFVALAAQLQSIHENVKVLK..QYLGYRKMFLGDAVD | |
| Retrocopy | QQIEELENYLATQANNSHITPQDLSMAMQ*I*KTFVALAAQLQSIHENVKVLK<KQYLGYRKMFLGDAVD |
| Parental | VFEARRAEAKKWQNTPRVTTGPTPFSTMPNAAAVAMAATLTQQQQPATG |
| VFEARRAEAKKWQNTPRVTTGPTPFSTMPNAAA.A.AATLTQQQQPATG | |
| Retrocopy | VFEARRAEAKKWQNTPRVTTGPTPFSTMPNAAAIAVAATLTQQQQPATG |
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 .07 RPM | 22 .36 RPM |
| SRP051959_heart | 0 .12 RPM | 21 .29 RPM |
| SRP051959_kidney | 0 .22 RPM | 24 .27 RPM |
| SRP051959_liver | 0 .28 RPM | 14 .66 RPM |
| SRP051959_lung | 0 .20 RPM | 23 .99 RPM |
| SRP051959_lymph_node | 0 .07 RPM | 23 .20 RPM |
| SRP051959_skeletal_muscle | 0 .24 RPM | 24 .90 RPM |
| SRP051959_spleen | 0 .23 RPM | 22 .77 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_769 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_769 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_769 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 | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000019231 | 1 retrocopy |
retro_cjac_769 ,
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