RetrogeneDB ID: | retro_cjac_2792 | ||
Retrocopylocation | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 6:24730861..24731251(-) | ||
| Located in intron of: | ENSCJAG00000007856 | ||
Retrocopyinformation | Ensembl ID: | ENSCJAG00000008037 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental geneinformation | Parental gene summary: | ||
| Parental gene symbol: | ZDHHC18 | ||
| Ensembl ID: | ENSCJAG00000009969 | ||
| Aliases: | None | ||
| Description: | zinc finger, DHHC-type containing 18 [Source:HGNC Symbol;Acc:20712] |
Retrocopy-Parental alignment summary:
>retro_cjac_2792
CTGACGTTGCGCTCTCAGGGAAGTAACTTCCTCTCCACTCTGAAGGAGACACCAGCAAGCGGGCCGGAGTTGGTGATCTG
CTTCTTCTCCATCTGGTCCATTCTGGGCCTCTCAGGGTTTCACATGTACCTGGTCGCCTCCAGCCTGACTACTAATGAAA
ATATCAAAGGCTCGTGGTCCAGCAAGAGGGGCGGTGAGGCCTCTGTCAACCCCTGCAGCCATAAAAGTATTACCACCAAC
TGCTGCGCTGTGCTCTGTGGCCCCGTACCTCCCAGCCTGATTGACCCGAGGGGATTTGTGCAGTCCGACACCGTGTTGCC
CTCACCCAGCAGAAGCGATGAGCCAGCCTGCAGAACCAAGCCTGACGCCAGCATGGTAGGAGGCCACCCC
CTGACGTTGCGCTCTCAGGGAAGTAACTTCCTCTCCACTCTGAAGGAGACACCAGCAAGCGGGCCGGAGTTGGTGATCTG
CTTCTTCTCCATCTGGTCCATTCTGGGCCTCTCAGGGTTTCACATGTACCTGGTCGCCTCCAGCCTGACTACTAATGAAA
ATATCAAAGGCTCGTGGTCCAGCAAGAGGGGCGGTGAGGCCTCTGTCAACCCCTGCAGCCATAAAAGTATTACCACCAAC
TGCTGCGCTGTGCTCTGTGGCCCCGTACCTCCCAGCCTGATTGACCCGAGGGGATTTGTGCAGTCCGACACCGTGTTGCC
CTCACCCAGCAGAAGCGATGAGCCAGCCTGCAGAACCAAGCCTGACGCCAGCATGGTAGGAGGCCACCCC
ORF - retro_cjac_2792 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 92.31 % |
| Parental protein coverage: | 51.38 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | LTLRSQGSNFLSTLKETPASVLELVICFFSIWSILGLSGFHTYLVASNLTTNEDIKGSWSSKRGGEASVN |
| LTLRSQGSNFLSTLKETPAS..ELVICFFSIWSILGLSGFH.YLVAS.LTTNE.IKGSWSSKRGGEASVN | |
| Retrocopy | LTLRSQGSNFLSTLKETPASGPELVICFFSIWSILGLSGFHMYLVASSLTTNENIKGSWSSKRGGEASVN |
| Parental | PYSHKSIITNCCAVLCGPLPPSLIDRRGFVQSDTVLPSPSRSDEPACRAKPDASMVGGHP |
| P.SHKSI.TNCCAVLCGP.PPSLID.RGFVQSDTVLPSPSRSDEPACR.KPDASMVGGHP | |
| Retrocopy | PCSHKSITTNCCAVLCGPVPPSLIDPRGFVQSDTVLPSPSRSDEPACRTKPDASMVGGHP |
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 | 1 .95 RPM |
| SRP051959_heart | 0 .00 RPM | 4 .72 RPM |
| SRP051959_kidney | 0 .04 RPM | 2 .09 RPM |
| SRP051959_liver | 0 .00 RPM | 1 .75 RPM |
| SRP051959_lung | 0 .00 RPM | 4 .60 RPM |
| SRP051959_lymph_node | 0 .02 RPM | 7 .69 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 1 .62 RPM |
| SRP051959_spleen | 0 .00 RPM | 5 .44 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2792 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2792 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_2792 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 | ENSCJAG00000009969 | 1 retrocopy |
retro_cjac_2792 ,
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