RetrogeneDB ID: | retro_cjac_3631 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | ACFV01190418.1:3233..3975(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | 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_3631
ATGATGGGGTGTGGGGACCCAGAGTTGGAGTCGGGGGACGGGGAAGAAGCCGCGGTGGTCCCAGGGCCACCCCCGGAGCC
CCGAGTCCCGGAACCCCGACCCCCGGTGCCCGAGCCCAGCCTGGACTTGAGCCTGAGTCCATGCTCTGGCATCCCTGAGC
CACAGCACGGCAGCCCTGGGCGGCGGAAGAAGGGGGCGGAGCGGCAGGGCGCCGGTCGGCAGCGCGGCAGGTTGGTTTCC
GCCTGGCACCACCCTCCCCGGTGTAGTCCGAGCCGCAGCCCGCTGCGCTGCAGGAGCTAGAGATGGCCACGCTGCAGAGC
AACCTGGCCTTGGGGTCTGGAGCTGAGAGCCGCAGCCGTCCGGCAAAAGCCGTGGAAGAACAGCTGAAAAAGTCGTTCCA
GATCCACTGTGGCCCGGAGGAGAGTGTGTGCGAGGGGCCGAACGTGCCGCTCTCCAAGAGGCTCTTCCGAGACCTGGTGA
GCCTGCAGGTGCTGGAGGAACCGGTTCTGAACGCTGCGCTCGGGGAGAAATTGGCTCTCCTGCCGCCGCAGGCTCAACCC
AGCCCCCAAAGGAGCCACCTGGGCTGGGGCCAGACATGACCATCTTGTGTGACCCAGAAACACTATTTTACGAATCTCCA
CACCTGACCCTGGATGATCTGACCCCTCTCCGGCTTCAACTCCGGCCCCATCCTTCAGAGGACACCTTCCTTATGCACGG
GACACTGAGGCGTTGGGAAGCG
ORF - retro_cjac_3631 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 78.74 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | MIGCGDSELESVDGEEAAAVPGPPPEPRVPEPRAPVPEPGLDLSLSPQPDSPKPPHDRPGRRKERAERRG |
| M.GCGD.ELES.DGEEAA.VPGPPPEPRVPEPR.PVPEP.LDLSLSP....P.P.H..PGRRK..AER.G | |
| Retrocopy | MMGCGDPELESGDGEEAAVVPGPPPEPRVPEPRPPVPEPSLDLSLSPCSGIPEPQHGSPGRRKKGAERQG |
| Parental | AGRQR-RQVRFRLAPPSPVRSEPQPAASQELEMPALQSSLALGLELRAAAGSHFDAAKAVEEQLRKSFQI |
| AGRQR.RQV.FRLAPPSPV.SEPQPAA.QELEM..LQS.LALG......A.S....AKAVEEQL.KSFQI | |
| Retrocopy | AGRQR<RQVGFRLAPPSPV*SEPQPAALQELEMATLQSNLALG----SGAESRSRPAKAVEEQLKKSFQI |
| Parental | RCGLEESVSEGLNVPRSRRLFRDLVSLQVPEEQVLNAALREKLALLPPQAR-APPPKEPPGPGPDMTILC |
| .CG.EESV.EG.NVP.S.RLFRDLVSLQV.EE.VLNAAL.EKLALLPPQA....PPKEPPG.GPDMTILC | |
| Retrocopy | HCGPEESVCEGPNVPLSKRLFRDLVSLQVLEEPVLNAALGEKLALLPPQAQ<TQPPKEPPGLGPDMTILC |
| Parental | DPETLFYESPHLTLDGLPPLRLQLRPRPSEDTFLMHRTLRRWEA |
| DPETLFYESPHLTLD.L.PLRLQLRP.PSEDTFLMH.TLRRWEA | |
| Retrocopy | DPETLFYESPHLTLDDLTPLRLQLRPHPSEDTFLMHGTLRRWEA |
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 .72 RPM | 1 .81 RPM |
| SRP051959_kidney | 0 .13 RPM | 2 .82 RPM |
| SRP051959_liver | 0 .02 RPM | 2 .84 RPM |
| SRP051959_lung | 0 .08 RPM | 2 .96 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 2 .79 RPM |
| SRP051959_skeletal_muscle | 0 .02 RPM | 1 .70 RPM |
| SRP051959_spleen | 0 .02 RPM | 2 .16 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_3631 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_3631 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_3631 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 |