RetrogeneDB ID: | retro_cjac_1000 | ||
Retrocopylocation | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 12:89181626..89182017(+) | ||
| Located in intron of: | ENSCJAG00000017743 | ||
Retrocopyinformation | Ensembl ID: | ENSCJAG00000017775 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental geneinformation | Parental gene summary: | ||
| Parental gene symbol: | SZRD1 | ||
| Ensembl ID: | ENSCJAG00000008232 | ||
| Aliases: | None | ||
| Description: | SUZ RNA binding domain containing 1 [Source:HGNC Symbol;Acc:30232] |
Retrocopy-Parental alignment summary:
>retro_cjac_1000
AGGTCGCTGAGAGCTGGGAAGAGGCGGCAGACAGCGGGCAGGAAATCCAAATCTCTGCCCAAAGTGCCCATTGTGATTCA
GGACGACAGCCTTCCTGCGGGACCCCCTGCACAGATCCATATCCCCAAGAGGCCTACCAGCAACGTGTGGTCAACAGCCC
CAACTCCACCAGCAGGCCTGCCATTCCGGTCAAGTCCTTAGCACAGCGGGAGGCCGAGTACCTCGAGGCCCGAAAGCAGA
TCCTGGGCAGCGCCAGCCCAGAGGAGGAGCAAGAGAAACCCATCCTCGACAGGCCAACCAGGATCTCCCAAGCAGAAGAC
AGCAGGAGCCCAATAATGTGATCAGACAGCCTTTGGGTCCTGATGGGTCACAAGGCTTCAAACAGCGCAGA
AGGTCGCTGAGAGCTGGGAAGAGGCGGCAGACAGCGGGCAGGAAATCCAAATCTCTGCCCAAAGTGCCCATTGTGATTCA
GGACGACAGCCTTCCTGCGGGACCCCCTGCACAGATCCATATCCCCAAGAGGCCTACCAGCAACGTGTGGTCAACAGCCC
CAACTCCACCAGCAGGCCTGCCATTCCGGTCAAGTCCTTAGCACAGCGGGAGGCCGAGTACCTCGAGGCCCGAAAGCAGA
TCCTGGGCAGCGCCAGCCCAGAGGAGGAGCAAGAGAAACCCATCCTCGACAGGCCAACCAGGATCTCCCAAGCAGAAGAC
AGCAGGAGCCCAATAATGTGATCAGACAGCCTTTGGGTCCTGATGGGTCACAAGGCTTCAAACAGCGCAGA
ORF - retro_cjac_1000 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 90.98 % |
| Parental protein coverage: | 98.5 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | RSLRAGKRRQTAGRKSKSPPKVPIVIQDDSLPAGPPPQIRILKRPTSN-GVVNSPNSTSRPALPVKSLAQ |
| RSLRAGKRRQTAGRKSKS.PKVPIVIQDDSLPAGPP.QI.I.KRPTSN..VVNSPNSTSRPA.PVKSLAQ | |
| Retrocopy | RSLRAGKRRQTAGRKSKSLPKVPIVIQDDSLPAGPPAQIHIPKRPTSN<RVVNSPNSTSRPAIPVKSLAQ |
| Parental | REAEYAEARKRILGSASPEEEQEKPILDRPTRISQPEDSR-QPNNVIRQPLGPDGSQGFKQRR |
| REAEY.EARK.ILGSASPEEEQEKPILDRPTRISQ.EDSR..PNNVIRQPLGPDGSQGFKQRR | |
| Retrocopy | REAEYLEARKQILGSASPEEEQEKPILDRPTRISQAEDSR<EPNNVIRQPLGPDGSQGFKQRR |
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 .13 RPM | 37 .23 RPM |
| SRP051959_heart | 0 .16 RPM | 42 .62 RPM |
| SRP051959_kidney | 0 .07 RPM | 39 .29 RPM |
| SRP051959_liver | 0 .06 RPM | 28 .85 RPM |
| SRP051959_lung | 0 .13 RPM | 42 .41 RPM |
| SRP051959_lymph_node | 0 .18 RPM | 43 .97 RPM |
| SRP051959_skeletal_muscle | 0 .13 RPM | 28 .43 RPM |
| SRP051959_spleen | 0 .08 RPM | 38 .93 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_1000 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_1000 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_1000 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000008232 | 2 retrocopies |
retro_cjac_1000 , retro_cjac_3307,
|
| Dasypus novemcinctus | ENSDNOG00000011616 | 1 retrocopy |