RetrogeneDB ID: | retro_cjac_549 | ||
Retrocopylocation | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 1:74921052..74921548(-) | ||
| Located in intron of: | None | ||
Retrocopyinformation | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental geneinformation | Parental gene summary: | ||
| Parental gene symbol: | PPP1R35 | ||
| Ensembl ID: | ENSCJAG00000015345 | ||
| Aliases: | None | ||
| Description: | protein phosphatase 1, regulatory subunit 35 [Source:HGNC Symbol;Acc:28320] |
Retrocopy-Parental alignment summary:
>retro_cjac_549
GTGCGGTTGGAGCCGCAGCCCGCGGCGCCGCAGGAGCTGGAGATGCCCTCGCTGCAGAGCAGCCTGGCCTTGGGCCTGGA
GCTGAGAGCCGCAGCCGGGAGCCACTTTGATGCCGCGAAAGCCGTGGAGGAACAGCTGAGAAAGTCGTTCCAGATCCACT
GCGGCCTGGAGGAGAGCGTGTCTGAGGGGCTGAACGTGCCGCGCTCCAAGAGGCTCTTCCGAGACCTGGTGAGCCGGCAG
ATGCCGGAGGAACAGGTTCTGAACGCCGCGCTCGGGGAGAAATTGGCTCTCCTGCAGCCGCAGGCTCCAGCCCCGCCCCC
CGAAGGAGCCACCTGGGCCGGGGCCAGACATGACCATCTTGTGTGACCCAGAAACACTATTTTATGAATCTCCACACCTG
ACCCTGGACGGTCTGCCCCCTCTCCGGCTTCAACTCCGGCCCCGCCCTTCAGAGGACACCTTCCTCATGCACCGGACACT
GAGGCGATGGGAAGCA
GTGCGGTTGGAGCCGCAGCCCGCGGCGCCGCAGGAGCTGGAGATGCCCTCGCTGCAGAGCAGCCTGGCCTTGGGCCTGGA
GCTGAGAGCCGCAGCCGGGAGCCACTTTGATGCCGCGAAAGCCGTGGAGGAACAGCTGAGAAAGTCGTTCCAGATCCACT
GCGGCCTGGAGGAGAGCGTGTCTGAGGGGCTGAACGTGCCGCGCTCCAAGAGGCTCTTCCGAGACCTGGTGAGCCGGCAG
ATGCCGGAGGAACAGGTTCTGAACGCCGCGCTCGGGGAGAAATTGGCTCTCCTGCAGCCGCAGGCTCCAGCCCCGCCCCC
CGAAGGAGCCACCTGGGCCGGGGCCAGACATGACCATCTTGTGTGACCCAGAAACACTATTTTATGAATCTCCACACCTG
ACCCTGGACGGTCTGCCCCCTCTCCGGCTTCAACTCCGGCCCCGCCCTTCAGAGGACACCTTCCTCATGCACCGGACACT
GAGGCGATGGGAAGCA
ORF - retro_cjac_549 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 93.37 % |
| Parental protein coverage: | 65.48 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | VRSEPQPAASQELEMPALQSSLALGLELRAAAGSHFDAAKAVEEQLRKSFQIRCGLEESVSEGLNVPRSR |
| VR.EPQPAA.QELEMP.LQSSLALGLELRAAAGSHFDAAKAVEEQLRKSFQI.CGLEESVSEGLNVPRS. | |
| Retrocopy | VRLEPQPAAPQELEMPSLQSSLALGLELRAAAGSHFDAAKAVEEQLRKSFQIHCGLEESVSEGLNVPRSK |
| Parental | RLFRDLVSLQVPEEQVLNAALREKLALLPPQARAP-PPKEPPGPGPDMTILCDPETLFYESPHLTLDGLP |
| RLFRDLVS.Q.PEEQVLNAAL.EKLALL.PQA.AP.PPKEPPGPGPDMTILCDPETLFYESPHLTLDGLP | |
| Retrocopy | RLFRDLVSRQMPEEQVLNAALGEKLALLQPQAPAP>PPKEPPGPGPDMTILCDPETLFYESPHLTLDGLP |
| Parental | PLRLQLRPRPSEDTFLMHRTLRRWEA |
| PLRLQLRPRPSEDTFLMHRTLRRWEA | |
| Retrocopy | PLRLQLRPRPSEDTFLMHRTLRRWEA |
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 .51 RPM |
| SRP051959_heart | 0 .00 RPM | 1 .81 RPM |
| SRP051959_kidney | 0 .00 RPM | 2 .82 RPM |
| SRP051959_liver | 0 .00 RPM | 2 .84 RPM |
| SRP051959_lung | 0 .00 RPM | 2 .96 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 2 .79 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 1 .70 RPM |
| SRP051959_spleen | 0 .00 RPM | 2 .16 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_549 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_549 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_549 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 5 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000015345 | 5 retrocopies |