RetrogeneDB ID: | retro_cjac_970 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 12:32999046..33000237(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | ENSCJAG00000020705 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_970
GACTCCTCCTTCGAGGGTACCAGCGGCAATGGCTCCCCCACCCTGAACTCATCCACTTCGAGCAGCACGCAGGGCGACCC
TGCCTTCCCCGAGATGAATGGCAGCGGTGCCGTGGCCCCCATGGACTTCACCACAGCAGCGGAGGACCAGCTCATCAACC
TGTGTGACAAGCTCCCACCAGCCACGGCGCTCGGCACACCCTCCTACCCCTCCGACGGCTGCGGCACTGACGGGCTGCGG
AGCCGCGTCAAATACGGGGTGAAGACCAACCCCTGAGTCCCCCTCTTACAGCCCTGGGAGCTACGATTCCATCAAGACCG
AGGTCAGCGGCTGCCCCTAGGACCTGACATAGGCCTGGCTTCCCGGCAGATGACGACGACGATGACCACGATGCCCATGA
GAACAATGACAAGATTAACGAGTCTGAAGGCATGGACCCCTGAGCGCCTTAAGGCCTTAAACATGTTTGTGCGTCTCTTT
GTGGACGAGACTCTGGTGTGCCCATCTCCAAGCAGCCCAAAAAGAAGATCCAGGCTATCACTGAGTCGGGCAGTCGGCAG
TTCCCCGAATTCCAGGAGTGAGCCCGCAAGCGCATCGGCACGTACCTCAAGTCCTGCCGCCGCATGAAGAAGAACTGCAT
GGAGATGACCAGACCCACGCCACCCCACCTGACCTCGGCCATGACAGAAAACATTCTGGCAGCTGCCTCTGAGAGCGAGA
CGAGAAAGGCAGCCAAGCGGATGCGCCTGGAGTTCTAACAATCCTCACGGGATGAGCCCGTAGCCCTGGATAAGCAGCAC
TCGCCGGACTTCGTAGCCATCACCCACTCCACCTACTCACTGCCCGCCTCCTCCTTCTCCCAGGACCCTGTGTACGCCAA
TGGCAGCCTCAACTACAGTTACGGCGGGTACTGGGCCTTGAGCAGCAACCTGCAGCCCCCTGCGTCCCCTCCAAACAGGA
AGCCACAGTAATGGGCCCACCGACCTCAACATGAAAGGCGGAGCCTCGACCACCTCCACCACCCCCACGCCCATCCCCTC
CAGCACCAGCACCAGCAGGCCCGTGCCCACCGCTCAGCTCAGCCCCACGGAGATCAGCGCCGTGCGGCAGCTCATCTCGG
GCTACCGGGAGTCTGCTGCCTTCCTGCTGCGCTCTGCAGACCAACTGGAAAACCTCATCCTACAGCAGAAC
ORF - retro_cjac_970 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 85.15 % |
| Parental protein coverage: | 99.75 % |
| Number of stop codons detected: | 4 |
| Number of frameshifts detected: | 5 |
Retrocopy - Parental Gene Alignment:
| Parental | DSSSESGSGNGSSTLNPSTSSSTQGDPAFPEMNGNGAVAPMDFTTAAEDQPINLCDKLPPATALGTPSYP |
| DSS.E..SGNGS.TLN.STSSSTQGDPAFPEMNG.GAVAPMDFTTAAEDQ.INLCDKLPPATALGTPSYP | |
| Retrocopy | DSSFEGTSGNGSPTLNSSTSSSTQGDPAFPEMNGSGAVAPMDFTTAAEDQLINLCDKLPPATALGTPSYP |
| Parental | SDGCGTDGLRSRVKYGVKT-TPESPPYSSGSYDSIKTEVSGCPEDLTVGRAP-TADDDDDDHDDHEDNDK |
| SDGCGTDGLRSRVKYGVKT.TPESP.YS.GSYDSIKTEVSGCP.DLT....P...DD.DDDHD.HE.NDK | |
| Retrocopy | SDGCGTDGLRSRVKYGVKT>TPESPSYSPGSYDSIKTEVSGCP*DLT*AWLP>ADDD-DDDHDAHENNDK |
| Parental | MNDSEGMD-PERLKAFNMFVRLFVDENLDRMVPISKQP-KEKIQAIIESCSRQFPEFQERARKRIRTYLK |
| .N.SEGMD.PERLKA.NMFVRLFVDE.L....P....P.K.KIQAI.ES.SRQFPEFQE.ARKRI.TYLK | |
| Retrocopy | INESEGMD>PERLKALNMFVRLFVDETL--VCPSPSSP<KKKIQAITESGSRQFPEFQE*ARKRIGTYLK |
| Parental | SCRRMKKNGMEMTRPTPPHLTSAMAENILAAACESETRKAAKRMRLEIYQSSQDEPIALDKQHSRDSAAI |
| SCRRMKKN.MEMTRPTPPHLTSAM.ENILAAA.ESETRKAAKRMRLE..QSS.DEP.ALDKQHS.D..AI | |
| Retrocopy | SCRRMKKNCMEMTRPTPPHLTSAMTENILAAASESETRKAAKRMRLEF*QSSRDEPVALDKQHSPDFVAI |
| Parental | THSTYSLPASSYSQDPVYANGGLNYSYRGYGALSSNLQPPAS-LQTGNHSNGPTDLSMKGGASTTSTTPT |
| THSTYSLPASS.SQDPVYANG.LNYSY.GY.ALSSNLQPPAS.LQTG.HSNGPTDL.MKGGASTTSTTPT | |
| Retrocopy | THSTYSLPASSFSQDPVYANGSLNYSYGGYWALSSNLQPPAS>LQTGSHSNGPTDLNMKGGASTTSTTPT |
| Parental | PTPSSTSTSRPVPTAQLSPTEISAVRQLIAGYRESAAFLLRSADELENLILQQN |
| P.PSSTSTSRPVPTAQLSPTEISAVRQLI.GYRESAAFLLRSAD.LENLILQQN | |
| Retrocopy | PIPSSTSTSRPVPTAQLSPTEISAVRQLISGYRESAAFLLRSADQLENLILQQN |
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 | 2 .33 RPM |
| SRP051959_heart | 0 .04 RPM | 0 .67 RPM |
| SRP051959_kidney | 0 .00 RPM | 1 .26 RPM |
| SRP051959_liver | 0 .04 RPM | 0 .54 RPM |
| SRP051959_lung | 0 .02 RPM | 1 .84 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 0 .55 RPM |
| SRP051959_skeletal_muscle | 0 .02 RPM | 0 .31 RPM |
| SRP051959_spleen | 0 .00 RPM | 0 .88 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_970 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_970 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_970 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 | ENSCJAG00000020705 | 1 retrocopy |
retro_cjac_970 ,
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