RetrogeneDB ID: | retro_cjac_3887 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | GL285848.1:8867..10057(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | FUBP3 | ||
| Ensembl ID: | ENSCJAG00000020542 | ||
| Aliases: | None | ||
| Description: | far upstream element (FUSE) binding protein 3 [Source:HGNC Symbol;Acc:4005] |
Retrocopy-Parental alignment summary:
>retro_cjac_3887
GGGGCCATGGTACATCAAAGGACCGTAATAAGGGAAGAATTCAAAGTGCCTGACGAAATGGTTGGATTTATTATCGGCAG
GGGAGGTGAGCAGATTTCACGGATTCAAGCAGAATCTGGTTGCAAAATTCAGATTGCTTCAGAGAGTTCTGGGATTCCAG
AGAGGCCCTGGGTACTTACTGGAACCACAGAAATTATTGAACACGCCAAACAACTCCTGGGGCAGATTGCGGACCGCTGT
CTAAATGGACCTGGCTTTCATCATGACATAGACAGCAACAGCACAATCCAGGAGATTCTCATTCCCGCATCTAAAGTGGG
TCTTGTCATCGGCAGAGGACGGGAAACAATCAAGCAGTTGCAGGAGCCGAAAGGCGTGAAGATGGTTATGATCCAGGACG
GCCCATTGCCCACGGGAGCAGACAAGGCTCTTCGTATCACTGGAGACCCATTTAAAGTACAACAAGCAAGAGAAATGGTA
CTAGAGATTTTCCGAGAAAAAGACCAAGCTGACTTTCGGGGTGTACACTCCCGGGGTGATTTCAGCTCCCGAATGGGAGG
AGGCAGTATTGAGGTATCTGTGCCTAGATTCGCTGTGGGGATTGTAATAGGAAGAAACGGGGAAATGATCAAAAAGATCC
AGAGTGATGCTGGTGTGAGGATTCAGTTTAAACCAGACGATGGGATTAGTCCAGAAAGAGCTGCGCAGGTCATGGGCCCT
CCGGATCGGTGTCAGCATGCAGTGCACATCATCAACGAGCTGATTCTTACAGCCCAGGAAAGAGACGGCTTTGGAGGCCT
GGCAGTAGCCAGAGGAAGAGGTCGTGGCCGTGGCGACTGCAGTGTGGGAGCCCCTGGTGGCGTCCAGGAGATAACATACA
TGGTGCCAGCCCATAAATGTGGCCTTGTCATAGGCAAAGGGGGTGAGAACATCAAAAGCATCAACCAGCAGTCAGGGGCG
CATGTGGAGCTCCAGAGGAACCCCCCTCCCAACTGGACCCTAACCTGCGGAGATTCACCATCAAGGGGATTCCCCAGCAG
ATCGAGGTGGCCAGGCAGCTCACAGATGAGAAAGTTGGTGGGACCAGTCTTGGAGCACCTGGAGCCTTCGGACAGAGTCC
CTTCAGCCAGCCACCTGCCCTACATCATCAAAACGCCTTTCCTCCAAGGAGCTCTGGGTGCTTCCCCCAC
ORF - retro_cjac_3887 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 91.96 % |
| Parental protein coverage: | 69.06 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | GALVHQRTVITEEFKVPDKMVGFIIGRGGEQISRIQAESGCKIQIASESSGIPERPCVLTGTPESIEQAK |
| GA.VHQRTVI.EEFKVPD.MVGFIIGRGGEQISRIQAESGCKIQIASESSGIPERP.VLTGT.E.IE.AK | |
| Retrocopy | GAMVHQRTVIREEFKVPDEMVGFIIGRGGEQISRIQAESGCKIQIASESSGIPERPWVLTGTTEIIEHAK |
| Parental | RLLGQIVDRCRNGPGFHNDIDSNSTIQEILIPASKVGLVIGRGGETIKQLQERTGVKMVMIQDGPLPTGA |
| .LLGQI.DRC.NGPGFH.DIDSNSTIQEILIPASKVGLVIGRG.ETIKQLQE..GVKMVMIQDGPLPTGA | |
| Retrocopy | QLLGQIADRCLNGPGFHHDIDSNSTIQEILIPASKVGLVIGRGRETIKQLQEPKGVKMVMIQDGPLPTGA |
| Parental | DKPLRITGDPFKVQQAREMVLEIIREKDQADFRGV--RGDFSSRMGGGSIEVSVPRFAVGIVIGRNGEMI |
| DK.LRITGDPFKVQQAREMVLEI.REKDQADFRGV..RGDFSSRMGGGSIEVSVPRFAVGIVIGRNGEMI | |
| Retrocopy | DKALRITGDPFKVQQAREMVLEIFREKDQADFRGVHSRGDFSSRMGGGSIEVSVPRFAVGIVIGRNGEMI |
| Parental | KKIQNDAGVRIQFKPDDGISPERAAQVMGPPDRCQHAAHIINELILTAQERDGFGGLAVARGRGRGRGDW |
| KKIQ.DAGVRIQFKPDDGISPERAAQVMGPPDRCQHA.HIINELILTAQERDGFGGLAVARGRGRGRGD. | |
| Retrocopy | KKIQSDAGVRIQFKPDDGISPERAAQVMGPPDRCQHAVHIINELILTAQERDGFGGLAVARGRGRGRGDC |
| Parental | SVGAPGGVQEITYTVPADKCGLVIGKGGENIKSINQQSGAHVELQRNPPPN-SDPNLRRFTIRGVPQQIE |
| SVGAPGGVQEITY.VPA.KCGLVIGKGGENIKSINQQSGAHVELQRNPPPN..DPNLRRFTI.G.PQQIE | |
| Retrocopy | SVGAPGGVQEITYMVPAHKCGLVIGKGGENIKSINQQSGAHVELQRNPPPN<LDPNLRRFTIKGIPQQIE |
| Parental | VARQLIDEKVGGTSLGAPGAFGQSPFSQPPAPPHQNTFPPRSSGCFPN |
| VARQL.DEKVGGTSLGAPGAFGQSPFSQPPA..HQN.FPPRSSGCFP. | |
| Retrocopy | VARQLTDEKVGGTSLGAPGAFGQSPFSQPPALHHQNAFPPRSSGCFPH |
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 | 19 .97 RPM |
| SRP051959_heart | 0 .04 RPM | 14 .54 RPM |
| SRP051959_kidney | 0 .02 RPM | 22 .56 RPM |
| SRP051959_liver | 0 .09 RPM | 31 .34 RPM |
| SRP051959_lung | 0 .13 RPM | 23 .33 RPM |
| SRP051959_lymph_node | 0 .05 RPM | 17 .99 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 7 .40 RPM |
| SRP051959_spleen | 0 .04 RPM | 20 .06 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_3887 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_3887 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_3887 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000016627 | 1 retrocopy | |
| Callithrix jacchus | ENSCJAG00000020542 | 1 retrocopy |
retro_cjac_3887 ,
|
| Microcebus murinus | ENSMICG00000015452 | 1 retrocopy |