RetrogeneDB ID: | retro_cjac_2271 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 3:124722910..124724000(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | DDX59 | ||
| Ensembl ID: | ENSCJAG00000005183 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_2271
TATGAGGTGTCAATCCCCATCCAAATACAGATGATTCCTGTGGGACTTCTGGGAAGAGACATTCTGGCCAGTGCAGATAC
TGGCTCAGGAAAAACAGCTGTTTTTCTTCTTTCTGTTATCATGCAAGCTTTATTTGAGAGCAAAACTCCATTTGCACTCA
TTCTTACACCAACCAGAGAGTTAGCCATTCAGCTGGTTAGACAAACTAAAGAATTGATGAGTGGCCTTCCACACATGAAA
ACCGTGCTTCTTGTATGGGACTTACCCTTACCCCCACAGCTTTATCGTCTGCAACATGTTAAGGTTATTATAGCAACCCC
TGAGCGACTTCTGGATATAATAAACTAGAGCTCTGTAGAACTCTGTGGTATAAAGATTGGTAGTAGATGAAGCTGATACC
ATGTTAGAGATGGGCTTTCAACAAGTGCTTGACATTTTGGAAAATGTTCCTATTGATTGTCAGACCATTTTGGTTTCGGC
CACAATTCCAACTAGCATAGAACAACTAGTAAGCCATTGTCTGCATAATCCTGTGAGAATTATAACTGGAGAAAAGAATC
TACCTTGTGTCAATGTGCACAAGATTATTGTGGGTAGAAGACCCAGCCAAAAAGAAAAAATTATTTGAAATTTTAAATGA
TAAGAAATTATTTAGCTTCCAGTGTTAGTATTTGTGGACAGCAAAGTAGGAGTAGATCTGTTGAGTGAAGCCATTCAGAA
AATCACAGGGCGGAAAAGTGTATCTATACATTCAGAGAAGTCACAAATATAAAGGAAAAATATATTGAAGGGACTACTTG
AAGGAGACTGTGAAGGTGCAGTGAGCACAGGAGTCTTGGGATGAGGACTAGACTTGATCAGTGTCTGGCTGGTTGTCAAT
TTTGGTATGCCTTCAGGAATGGACAAGTACGTCCATCAGGTTGGAAGAGTAGGCAGATTAGGTCAAAAGGAAACAGCAAT
TACTTTCATCAATAATAATTCAAAAAGACTCTTCTGGGATATTGCAAAACGAGTAAATCCCACAGGATCCATTCTTCCCC
CACGGTTATTAAATTCCCCATACCTTCATGACTAGAGGAAAAAGGATCAA
ORF - retro_cjac_2271 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 82.16 % |
| Parental protein coverage: | 59.19 % |
| Number of stop codons detected: | 4 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | YEVPTPIQMQMIPVGLLGRDILASADTGSGKTAAFLLPVIMRALFERKTPSALILTPTRELAIQIERQAK |
| YEV..PIQ.QMIPVGLLGRDILASADTGSGKTA.FLL.VIM.ALFE.KTP.ALILTPTRELAIQ..RQ.K | |
| Retrocopy | YEVSIPIQIQMIPVGLLGRDILASADTGSGKTAVFLLSVIMQALFESKTPFALILTPTRELAIQLVRQTK |
| Parental | ELMSGLPRMKTVLLVGGLPLPPQLYRLQQHVKVIIATPGRLLDIMKQSSVELCGIKI-VVVDEADTMLKM |
| ELMSGLP.MKTVLLV..LPLPPQLYRL.QHVKVIIATP.RLLDI...SSVELCGIKI.VV.DEADTML.M | |
| Retrocopy | ELMSGLPHMKTVLLVWDLPLPPQLYRL-QHVKVIIATPERLLDIIN*SSVELCGIKI>VV-DEADTMLEM |
| Parental | GFQQQVLDILENIPNDCQTILVSATIPTSIEQLASQLLHNPVRIITGEENLPCANVRQIILWVEDPAKK- |
| GF.QQVLDILEN.P.DCQTILVSATIPTSIEQL.S..LHNPVRIITGE.NLPC.NV..II.....P..K. | |
| Retrocopy | GF-QQVLDILENVPIDCQTILVSATIPTSIEQLVSHCLHNPVRIITGEKNLPCVNVHKIIVG-RRPSQK> |
| Parental | KKLFEILNDKKLFK-PPVLVFVDCKLGADLLSEAVQKITGLKSISIHSEKSQIERKNILKGLLEGDFEVV |
| KKLFEILNDKKLF...PVLVFVD.K.G.DLLSEA.QKITG.KS.SIHSEKSQI.RKNILKGLLEGD.E.. | |
| Retrocopy | KKLFEILNDKKLFS<LPVLVFVDSKVGVDLLSEAIQKITGRKSVSIHSEKSQI*RKNILKGLLEGDCEGA |
| Parental | VSTGVLGRGLDLISVRLVVNFDMPSSMDEYVHQVGRVGRLGQNGTAITFINNNSKRLFWDIAKRVKPTGS |
| VSTGVLG.GLDLISV.LVVNF.MPS.MD.YVHQVGRVGRLGQ..TAITFINNNSKRLFWDIAKRV.PTGS | |
| Retrocopy | VSTGVLG*GLDLISVWLVVNFGMPSGMDKYVHQVGRVGRLGQKETAITFINNNSKRLFWDIAKRVNPTGS |
| Parental | ILPPQLLNSPYLHDQKRKEQ |
| ILPP.LLNSPYLHD...K.Q | |
| Retrocopy | ILPPRLLNSPYLHD*RKKDQ |
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 | 6 .23 RPM |
| SRP051959_heart | 0 .00 RPM | 5 .53 RPM |
| SRP051959_kidney | 0 .00 RPM | 6 .54 RPM |
| SRP051959_liver | 0 .00 RPM | 4 .68 RPM |
| SRP051959_lung | 0 .00 RPM | 7 .42 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 5 .52 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 4 .54 RPM |
| SRP051959_spleen | 0 .00 RPM | 5 .99 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2271 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2271 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_2271 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 | ENSCJAG00000005183 | 1 retrocopy |
retro_cjac_2271 ,
|