RetrogeneDB ID: | retro_cjac_4029 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | GL289951.1:236152..236550(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSCJAG00000020534 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | PFN2 | ||
| Ensembl ID: | ENSCJAG00000001271 | ||
| Aliases: | None | ||
| Description: | Profilin [Source:UniProtKB/TrEMBL;Acc:F7HQH2] |
Retrocopy-Parental alignment summary:
>retro_cjac_4029
CAGAGCTACGTGGATAACCTGCTGTGCGATGGCTGCTGCCAGGGGGCCGCCATTGTCGGCTACTGCGACGCCAAATACGT
CTGGGCAGCCAGGGCCAGGGGTGTCTTTCAGAGCATTACGCCAATAGAAGTAGGTATGATTGTAGGAAAAGACCGGGAAG
GTTTCTTTACCAATGGTTTGACTCTTGGCGCGAAGAAATGCTCAGTGATCAGAATAGCCTACACGTCGATGGTGACTGCA
CAATGGACATGCGGACAAAGTGTCAAGGTGGGGAGCCAACATACAATGTTGCTGTCGGCAGAGCTGGTAGAGCATTGGTT
ATAGTCTTGGGAAAGGAAGGTGTCCACGGAGGCACACTTAACAAGAAAGCATATGAACTCCCTTTATACCTGAGGAGG
ORF - retro_cjac_4029 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 90.3 % |
| Parental protein coverage: | 70.74 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | QSYVDNLMCDGCCQEAAIVGYCDAKYVWAATAGGVFQSITPIEIDMIVGKDREGFFTNGLTLGAKKCSVI |
| QSYVDNL.CDGCCQ.AAIVGYCDAKYVWAA.A.GVFQSITPIE..MIVGKDREGFFTNGLTLGAKKCSVI | |
| Retrocopy | QSYVDNLLCDGCCQGAAIVGYCDAKYVWAARARGVFQSITPIEVGMIVGKDREGFFTNGLTLGAKKCSVI |
| Parental | R-DSLYVDGDCTMDIRTKSQGGEPTYNVAVGRAGRALVIVMGKEGVHGGTLNKKAYELALYLRR |
| R..SL.VDGDCTMD.RTK.QGGEPTYNVAVGRAGRALVIV.GKEGVHGGTLNKKAYEL.LYLRR | |
| Retrocopy | R<NSLHVDGDCTMDMRTKCQGGEPTYNVAVGRAGRALVIVLGKEGVHGGTLNKKAYELPLYLRR |
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 .97 RPM |
| SRP051959_heart | 0 .00 RPM | 16 .40 RPM |
| SRP051959_kidney | 0 .02 RPM | 38 .65 RPM |
| SRP051959_liver | 0 .00 RPM | 0 .95 RPM |
| SRP051959_lung | 0 .00 RPM | 9 .91 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 1 .48 RPM |
| SRP051959_skeletal_muscle | 0 .02 RPM | 176 .71 RPM |
| SRP051959_spleen | 0 .00 RPM | 4 .22 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_4029 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_4029 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_4029 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 | ENSCJAG00000001271 | 1 retrocopy |
retro_cjac_4029 ,
|
| Callithrix jacchus | ENSCJAG00000011719 | 2 retrocopies |