RetrogeneDB ID: | retro_cjac_3945 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | GL286373.1:220978..222459(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | ALDH9A1 | ||
| Ensembl ID: | ENSCJAG00000004575 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_3945
ATGAGCACTGGCACCTTCGTTGTGTCGCAGCCGCTCAATTATCATGGCAGGACCCACGTGGAGCCGGCGGATGCTTCTGG
CACGGAGAAGGCTTTCGAGCCGGCAACCGGCTGAGGGATAGCTACTTTCCCATGTTCAGGAGAAAAGGAAGTAAATTTGA
CTGTTCAGAGTGCAAAGGCTGCTTTTAAAATATGGAGTCTAAAATCTGGTATGGAGCATTGCTGAATCCTTTTGGAGGCT
GCCAGAATAGTAAGGGAACGGAAGGATGAAATTGCCACTGTGGAATGCATCAACAACAGCAAGTCCATCTTTGAGGCCTG
CTTGGACATCAACACTGCCTGACAGTGCCTGGAGTATTTTGCAGGATTGGCTGCGTCCATGGCTGGTGAACACATCCAGC
TCCCAGGCGGATCCTTTGGTTATACCACAAGAGAACCACTTGGGGTATGTGTGGGAATAGGAGTGTGGAACTACCCCTTT
CAGATCACCTCTTGGAAGTCAGCTCCTGTGTTAGCCTGTGGTAATGCCATGGTCTTCAAACCTTCTCCCTTTACACCTGT
TTCTGCATTGCTACTGGCTGAAATCTACACTGAGGCTGCTGTGCCTCCTGGGCTCTTCAATGTGGTGCAGGGCGGGGCTG
CCACTGGCCAGTTTCTGTGTCAGCATCATGATGTGGCCCAAGTCTCCTTCACTGGAAGTGTGCCCACTGGCATGAAGATC
ATGGAGATGGCATCTAAAGGAGTCAAACCTGTTACCTAGGAACTTGGAGGCAAATCTCCACTCATCATCTTCTCAGACTG
TGATATTAACAATGCTGTGAAGGGGGCGCTGATGGCCAACTTCCTCACACAAGGCCAGGTTTGCTGTAATGGCACAAGAT
ATTTGTGCAGAAAGAAATTCTTGATAAATTTACAGAGGAAGTGGTGAAACAGACCCAAAGGATTAAAACTGGAGATCCCC
TTCTGGAAGACACAAGGATGGGTCCACTCATCAACCGACCACACCTGGAGCGAGTCCTTGGGTTTGTTAAAGTGGCAAAG
GAGCAGGGTGCTAAAGTGTTATGTGTTGGAGATATATATGCACCTCAAGATCCCAAATTAAAGGATGGATACTACATGAG
ACCTTGTGTATTAACTAATTGCAGAGATGACATGACCTGTGTGAAAGAAGAGATCTTTCGGCCTGTTATGTCTATTTTAC
CATTTGAGACTAAAGCTGAGGTTCTAGAAAGAGCCAATGATACCACTTTTGGACTAGCAGCTGGCGTCTTTACCAGGGAC
ATCCAGCGGGCTCATAGAGCGGTAGCTGAGCTTCAGGCTGGAACCTGCTTCATTAACAACTATAACGTCAGTCCAGTGAA
GTTGCCCTTTGGTGGATATAAGAAGTCAGGATTTGGCAGAGAGAACGGCTGTGTGACAATTGAATATTATTCACAACTGA
AGACTGTGTGTATGGAGATGGGTGATGTGGAATCTGCTTTT
ORF - retro_cjac_3945 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 90.71 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 4 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MSTGTFVVSQPLNYRGGTR-GAGGRSGTEKAFEPATGRVIATFTCSGEKEVNLAVQNAKAAFKIWSQKSG |
| MSTGTFVVSQPLNY.G.T.......SGTEKAFEPATG..IATF.CSGEKEVNL.VQ.AKAAFKIWS.KSG | |
| Retrocopy | MSTGTFVVSQPLNYHGRTHVEPADASGTEKAFEPATG*GIATFPCSGEKEVNLTVQSAKAAFKIWSLKSG |
| Parental | MERCRILLEAARIIRERKDEIATVECINNGKSIFEARLDIDTSWQCLEYFAGLAASMAGEHIQLPGGSFG |
| ME.C.ILLEAARI.RERKDEIATVECINN.KSIFEA.LDI.T..QCLEYFAGLAASMAGEHIQLPGGSFG | |
| Retrocopy | MEHC*ILLEAARIVRERKDEIATVECINNSKSIFEACLDINTA*QCLEYFAGLAASMAGEHIQLPGGSFG |
| Parental | YTRREPLGVCVGIGAWNYPFQIASWKSAPALACGNAMVFKPSPFTPVSALLLAEIYTEAGVPPGLFNVVQ |
| YT.REPLGVCVGIG.WNYPFQI.SWKSAP.LACGNAMVFKPSPFTPVSALLLAEIYTEA.VPPGLFNVVQ | |
| Retrocopy | YTTREPLGVCVGIGVWNYPFQITSWKSAPVLACGNAMVFKPSPFTPVSALLLAEIYTEAAVPPGLFNVVQ |
| Parental | GGVATGQFLCQHHDVAKVSFTGSVPTGMKIMEMASKGVKPVTLELGGKSPLIIFSDCDMNNAVKGALMAN |
| GG.ATGQFLCQHHDVA.VSFTGSVPTGMKIMEMASKGVKPVT.ELGGKSPLIIFSDCD.NNAVKGALMAN | |
| Retrocopy | GGAATGQFLCQHHDVAQVSFTGSVPTGMKIMEMASKGVKPVT*ELGGKSPLIIFSDCDINNAVKGALMAN |
| Parental | FLTQGQVCCNGTR-VFVQKEILDKFTEEVVKQTQRIKIGDPLLEDTRMGPLINRPHLERVLGFVKVAKEQ |
| FLTQGQVCCNGTR..FVQKEILDKFTEEVVKQTQRIK.GDPLLEDTRMGPLINRPHLERVLGFVKVAKEQ | |
| Retrocopy | FLTQGQVCCNGTR<IFVQKEILDKFTEEVVKQTQRIKTGDPLLEDTRMGPLINRPHLERVLGFVKVAKEQ |
| Parental | GAKVLCGGDTYVPEDPKLKDGYYMRPCVLTNCRDDMTCVKEEIFGPVMSILPFDTEAEVLERANDTTFGL |
| GAKVLC.GD.Y.P.DPKLKDGYYMRPCVLTNCRDDMTCVKEEIF.PVMSILPF.T.AEVLERANDTTFGL | |
| Retrocopy | GAKVLCVGDIYAPQDPKLKDGYYMRPCVLTNCRDDMTCVKEEIFRPVMSILPFETKAEVLERANDTTFGL |
| Parental | AAGVFTRDIQRAHRVVAELQAGTCFINNYNVSPVELPFGGYKKSGFGRENGRVTIEYYSQLKTVCVEMGD |
| AAGVFTRDIQRAHR.VAELQAGTCFINNYNVSPV.LPFGGYKKSGFGRENG.VTIEYYSQLKTVC.EMGD | |
| Retrocopy | AAGVFTRDIQRAHRAVAELQAGTCFINNYNVSPVKLPFGGYKKSGFGRENGCVTIEYYSQLKTVCMEMGD |
| Parental | VESAF |
| VESAF | |
| Retrocopy | VESAF |
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 | 2 .02 RPM | 17 .84 RPM |
| SRP051959_heart | 1 .98 RPM | 10 .77 RPM |
| SRP051959_kidney | 3 .71 RPM | 23 .12 RPM |
| SRP051959_liver | 2 .21 RPM | 34 .25 RPM |
| SRP051959_lung | 2 .68 RPM | 16 .22 RPM |
| SRP051959_lymph_node | 3 .54 RPM | 25 .48 RPM |
| SRP051959_skeletal_muscle | 2 .40 RPM | 13 .06 RPM |
| SRP051959_spleen | 2 .96 RPM | 36 .39 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_3945 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_3945 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_3945 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 | ENSCJAG00000004575 | 1 retrocopy |
retro_cjac_3945 ,
|