RetrogeneDB ID: | retro_cjac_2380 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 4:135600858..135601315(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSCJAG00000033406 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | CLPP | ||
| Ensembl ID: | ENSCJAG00000016699 | ||
| Aliases: | None | ||
| Description: | ClpP caseinolytic peptidase, ATP-dependent, proteolytic subunit homolog (E. coli) [Source:HGNC Symbol;Acc:2084] |
Retrocopy-Parental alignment summary:
>retro_cjac_2380
ATATTGGGGGAGGGGGGGCAGGGTGGCGGAGGCAGGTACCCCGCGCTGGGGCTTCGCCTCGCCTCGCCTCTCGCTTTCCA
GAGCAGCGGAAGCCCCAGAGCGGCCTGGCCCTGTAGCAGAGCCTGCACGTTCGGCCCGAGCTCTCCCGCTCATACCCATC
GCGGTGGAGCAGACCCGTCGCGGGTAGCGCGCCTATGACATCTACTCGCGGCTGCTGCGGGAGCGCATCGTGTGCGAAAT
GGGCCCGATAGATGACAGCGTTGCCCTCCTGGTTATTGCACAGCTCCTCTTCCTGCAATCCGAGAGCAACAAGAAGCCCA
TCCACATGTACATCAACAGCCCTGGTGGTGTGGTGACCGCGGGCATGGCCATCTACGATACGATGCTGTATATCCTCAAT
CCAATCTGCACATGGTGCGTGGGCCAGGCAGCCAGCATGGGCTCCCTGCTTCTAGCC
ORF - retro_cjac_2380 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 79.74 % |
| Parental protein coverage: | 55.68 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | ILVGGGRVAAGRYPALGLRLASRFAAQRTPQSGPALQRSLHVT-AARALPLIPIVVEQTGRGERAYDIYS |
| IL..GG....GRYPALGLRLAS..A.Q.......A...S...T..ARALPLIPI.VEQT.RG.RAYDIYS | |
| Retrocopy | ILGEGGQGGGGRYPALGLRLASPLAFQSSGSPRAAWPCSRACT>SARALPLIPIAVEQTRRG*RAYDIYS |
| Parental | RLLRERIVCVMGPIDDSVASLVIAQLLFLQSESNKKPIHMYINSPGGVVTAGLAIYDTMQYILNPICTWC |
| RLLRERIVC.MGPIDDSVA.LVIAQLLFLQSESNKKPIHMYINSPGGVVTAG.AIYDTM.YILNPICTWC | |
| Retrocopy | RLLRERIVCEMGPIDDSVALLVIAQLLFLQSESNKKPIHMYINSPGGVVTAGMAIYDTMLYILNPICTWC |
| Parental | VGQAASMGSLLLA |
| VGQAASMGSLLLA | |
| Retrocopy | VGQAASMGSLLLA |
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 | 3 .64 RPM |
| SRP051959_heart | 0 .02 RPM | 4 .19 RPM |
| SRP051959_kidney | 0 .00 RPM | 6 .15 RPM |
| SRP051959_liver | 0 .00 RPM | 7 .34 RPM |
| SRP051959_lung | 0 .00 RPM | 3 .43 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 4 .18 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 6 .57 RPM |
| SRP051959_spleen | 0 .00 RPM | 3 .55 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2380 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2380 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_2380 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 4 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000016699 | 1 retrocopy |
retro_cjac_2380 ,
|
| Microcebus murinus | ENSMICG00000006284 | 1 retrocopy | |
| Myotis lucifugus | ENSMLUG00000007981 | 1 retrocopy | |
| Xenopus tropicalis | ENSXETG00000005576 | 1 retrocopy |