RetrogeneDB ID: | retro_cjac_522 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 1:43921904..43922656(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSCJAG00000032991 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | WDR74 | ||
| Ensembl ID: | ENSCJAG00000018581 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_522
AGGATGCGCCAAGACCCAGCCCACCCCCATATGGTTGCCACAGGTGGGAAAGAGAATGCCTTGAAGATGTGGGACCTGCA
GGGCTCTGAGGAACCTGTGTTTAGGGCCAAGAACGTGCGGAATGACTGGCTAGACCTGCGAGTTCCCATCTGGGACCAGG
GCATACAGTTTCTCCCAGGATCACATAAGCTTGTCACCTGTGCAGGGTACCACCAGATTCGTGTCTATGATCCAGCCTCC
CCTCAGCGCTGGCCAGTCCTAGAGACCACCTATGGAGAGTACCCACTGACAGCTATGACCCTCACTCCTGGAGGCAACTC
AGTGATTGTGGGAAACATTCATGGGCAGCTGGCAGAAATTGACCTTCGGCAAGGGCGTCTACTGGGCTGTCTGAAGGGGC
TGGCAGGCAGCGTCTGTGGGTTGCAGTGCCACCCTTCCAAGCCTCTACTAGCCTCCTGTGGCTTGGACAGAGTCTTGAGG
ATACACAGGATCCAGAATCCACGGGGTCTGGCACATAAGGTTTATCTCAAGTCTCAATTGAACTGCCTCCTCCTGTCAGA
CAGGGACAACTGGGAGGATGAGTCCCAAGAACCTCAAGAACCCAACAACGTGCCCCTAGAAGACACAGAGACAGATGAAC
TTTGGGCATCCTTGGAGGCAGCTGCCAAGCAGAAGCTTCGGATTTGGAGCAGACCCAAGGAGCTCTCCAAACCAGGCGGA
GAAAGAAGAAGTGGCCTGGGTCCACCAGCCCC
ORF - retro_cjac_522 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 94.84 % |
| Parental protein coverage: | 65.19 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | RMRQDPAHPHVVATGGKENALKMWDLQGSEEPVFRAKNVRNDWLDLRVPIWDQDIQFLPGSQKLVTCTGY |
| RMRQDPAHPH.VATGGKENALKMWDLQGSEEPVFRAKNVRNDWLDLRVPIWDQ.IQFLPGS.KLVTC.GY | |
| Retrocopy | RMRQDPAHPHMVATGGKENALKMWDLQGSEEPVFRAKNVRNDWLDLRVPIWDQGIQFLPGSHKLVTCAGY |
| Parental | HQVRVYDPASPQRRPVLETTYGEYPLTAMTLTPGGNSVIVGNTHGQLAEIDLRQGRLLGCLKGLAGSVRG |
| HQ.RVYDPASPQR.PVLETTYGEYPLTAMTLTPGGNSVIVGN.HGQLAEIDLRQGRLLGCLKGLAGSV.G | |
| Retrocopy | HQIRVYDPASPQRWPVLETTYGEYPLTAMTLTPGGNSVIVGNIHGQLAEIDLRQGRLLGCLKGLAGSVCG |
| Parental | LQCHPSKPLLASCGLDRVLRIHRIQNPRGLEHKVYLKSQLNCLLLSDRDNWEDEPQEPQEPNNVPLEDTE |
| LQCHPSKPLLASCGLDRVLRIHRIQNPRGL.HKVYLKSQLNCLLLSDRDNWEDE.QEPQEPNNVPLEDTE | |
| Retrocopy | LQCHPSKPLLASCGLDRVLRIHRIQNPRGLAHKVYLKSQLNCLLLSDRDNWEDESQEPQEPNNVPLEDTE |
| Parental | TDELWASLEAAAKRKL-SDLEQTQGALQTRRRKKKRPGSTSP |
| TDELWASLEAAAK.KL.SDLEQTQGALQTRRRKKK.PGSTSP | |
| Retrocopy | TDELWASLEAAAKQKL<SDLEQTQGALQTRRRKKKWPGSTSP |
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 | 4 .81 RPM |
| SRP051959_heart | 0 .02 RPM | 6 .61 RPM |
| SRP051959_kidney | 0 .02 RPM | 6 .12 RPM |
| SRP051959_liver | 0 .00 RPM | 6 .11 RPM |
| SRP051959_lung | 0 .02 RPM | 6 .86 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 8 .58 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 9 .85 RPM |
| SRP051959_spleen | 0 .00 RPM | 7 .56 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_522 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_522 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_522 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 | ENSCJAG00000018581 | 1 retrocopy |
retro_cjac_522 ,
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