RetrogeneDB ID: | retro_cjac_3286 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 9:27047988..27049127(-) | ||
| Located in intron of: | ENSCJAG00000013333 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | COASY | ||
| Ensembl ID: | ENSCJAG00000005064 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_3286
GCCTCAGCCGCAGGCCCCTCAATCACCGTCACTTCATCTCCCTGACTGTCCGCAGGCCTGGGCAGAATGGCCTTATTCAT
GGTCTGGCCTCCTGGTGCTGATGACGCCGCTGGCCTCCCTGGCCCCTCGCCTGGCCCCCATCCTGACCTCGGCAGCCTGG
CTGGTGAATGACACACTCTATGTACACCTGCAGCCAGGCATGAGCCTGGAAGGCCCGGCTCAGCCCCAGTCCACCCCCAT
GTGGGCCACGTTTGAGGTTCTTGATTTCATCACACACCTCTATGCTGGCCCCGACATCCACAGGCATCTGGATGTCAGAA
TCCTACTGACCAATATCCGAACCAAGAGCAGCTTTCTCCCTCCCCTGCCTACCTCAGTCCAGAATCTCGCCCACCTGCCA
GAAGTCATGTTGACAGACTTCCAGACCCTGGATGGAAGCCAGTACAACTCAGTCAAGCAGCAGGTAGTGTGTTATGCCAC
CAGCTGTTACAGCTGTTGTCTGCAACTGGCCTCAGTGCTGCTATACCCCGATTATGGGACAGGAGAAGTGCGTGTGGAGC
CCCTGGATATCCCCTTATCCTCGACGATCAGGCCAGCTTCCCCCATGTCCAGGTCTCCAAAGCAGCCAGTGTGTGGCTAC
TACCGTGGCTCTGTGGGTGACACGTTTGACCACCTGCACAATGCCCACAAGGTGTTGCTCAGTGTGTACGTCCTGGCCCA
GGAGCAGCTGGTGGTGGGAATAGCAGACCAAGATCTGTTGAAGAGCAAGTTGCTCCCTGAGCTGCTCCAACCTTATACAG
GACACATGGAACATCTGAGTGAGTTCCTGATGGATGTCAAGCCCTCCTTGACTTTCCATGTTGTCCCCCTGCTGGACCCC
TATGGGCCCACTGGCTTTGACCCCCTCCCTGGAGTTCCTGGTGGTCAGCAAGGAGACCTATCATGGGGGAATGGCCATCA
ACCGCTTCTGCCTGGAGAATGACCTGGAGGAGCTTGCCTTGTACCAGGTCCAGCTGCTGAAGGACCTAAGTCATATGGAG
AATGACGAGGACAAAGTCAGCTCCTCCAGCTTCCATCAGCAAATTCTGGGAAACCTGCTTTGGCCTTCATATGAGAGGCC
AGAGCTCCCCTAGTCTCTA
ORF - retro_cjac_3286 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 81.94 % |
| Parental protein coverage: | 64.08 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | AQPRGSVCQAPSPPPAPLGLGRMAVFQ-SGLLVLTTPLASLAPRLAPILTSAARLVNDTLYVHLQPGMSL |
| A...G......S.P....GLGRMA.F..SGLLVL.TPLASLAPRLAPILTSAA.LVNDTLYVHLQPGMSL | |
| Retrocopy | ASAAGPSITVTSSP*LSAGLGRMALFM>SGLLVLMTPLASLAPRLAPILTSAAWLVNDTLYVHLQPGMSL |
| Parental | EGPAQPQSTPVQATFEVLDFITHLYAGADVHRHLDVRILLTNIRTKSTFLPPMPTSVQNLAHPPEVVLTD |
| EGPAQPQSTP..ATFEVLDFITHLYAG.D.HRHLDVRILLTNIRTKS.FLPP.PTSVQNLAH.PEV.LTD | |
| Retrocopy | EGPAQPQSTPMWATFEVLDFITHLYAGPDIHRHLDVRILLTNIRTKSSFLPPLPTSVQNLAHLPEVMLTD |
| Parental | FQTLDGSQYNPVKQQLVRYATSCYSCCPRLASVLLYPDYGTGEVPVEPLDVPLPSTIRPASPVARSPKQP |
| FQTLDGSQYN.VKQQ.V.YATSCYSCC..LASVLLYPDYGTGEV.VEPLD.PL.STIRPASP..RSPKQP | |
| Retrocopy | FQTLDGSQYNSVKQQVVCYATSCYSCCLQLASVLLYPDYGTGEVRVEPLDIPLSSTIRPASPMSRSPKQP |
| Parental | VRGYYRGAVGGTFDRLHNAHKVLLSVACVLAQEQLVVGVADKDLLKSKLLPELLQPYTERVEHLSEFLVD |
| V.GYYRG.VG.TFD.LHNAHKVLLSV..VLAQEQLVVG.AD.DLLKSKLLPELLQPYT...EHLSEFL.D | |
| Retrocopy | VCGYYRGSVGDTFDHLHNAHKVLLSV-YVLAQEQLVVGIADQDLLKSKLLPELLQPYTGHMEHLSEFLMD |
| Parental | VKPSLTFDVIPLLDPYGPAGSD-PSLEFLVVSEETYRGGMAVNRFRLENDLEELALYQIQLLKDLRHTEN |
| VKPSLTF.V.PLLDPYGP.G.D.PSLEFLVVS.ETY.GGMA.NRF.LENDLEELALYQ.QLLKDL.H.EN | |
| Retrocopy | VKPSLTFHVVPLLDPYGPTGFD>PSLEFLVVSKETYHGGMAINRFCLENDLEELALYQVQLLKDLSHMEN |
| Parental | EEDKVSSSSFRQRMLGDLLRPPYERPELPPSL |
| .EDKVSSSSF.Q..LG.LL.P.YERPELP.SL | |
| Retrocopy | DEDKVSSSSFHQQILGNLLWPSYERPELP*SL |
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 .20 RPM | 3 .64 RPM |
| SRP051959_heart | 0 .23 RPM | 4 .14 RPM |
| SRP051959_kidney | 0 .27 RPM | 6 .97 RPM |
| SRP051959_liver | 0 .17 RPM | 5 .70 RPM |
| SRP051959_lung | 0 .10 RPM | 4 .29 RPM |
| SRP051959_lymph_node | 0 .07 RPM | 4 .98 RPM |
| SRP051959_skeletal_muscle | 0 .24 RPM | 5 .35 RPM |
| SRP051959_spleen | 0 .08 RPM | 4 .58 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_3286 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_3286 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_3286 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 | ENSCJAG00000005064 | 1 retrocopy |
retro_cjac_3286 ,
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