RetrogeneDB ID: | retro_pabe_1731 | ||
Retrocopy location | Organism: | Orangutan (Pongo abelii) | |
| Coordinates: | 1_random:29279065..29279479(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | S100A10 | ||
| Ensembl ID: | ENSPPYG00000000850 | ||
| Aliases: | None | ||
| Description: | S100 calcium binding protein A10 [Source:HGNC Symbol;Acc:10487] |
Retrocopy-Parental alignment summary:
>retro_pabe_1731
CCCGCGCCGCCACCCTCTACCCACCCGCCGCACGTACTAAGGAAGGTGCACAGCCCGCCGCGCTCGCCTCTCTGCCCAGC
GTCCAGCTCGCCCAGCTCTCCCAGCGTCCGCCACGCCTCAGCCAAGGCTTCAACAGACCACACCAAAATGCCATCTCAAA
TGGAACACGCCATGGAAACCATGATGTTTACATTTCACAAATTCGCTGGGGATAAAGGCTACTTAACAAAGGAGGACCTG
AGAGTACTCATGGAAAAGGAGTTCCCTGGATTTTTGGAAAATCAAAAAGACCCTCTGGCTGTGGACAAAATAATGAGGGA
CCTGGACCAGTGCAGAGATGGCAAAGTGGGCTTCCAGAGCTTCTTTTTCCTAAGTGCGGGCCTCAGCATTGCATGCCATG
ACTATTTTGTAGTA
ORF - retro_pabe_1731 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 81.16 % |
| Parental protein coverage: | 62.16 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | PAPPPSTHQPHVLRKAHSSPRSPLRPASSSPSSPSVRRASVKASTDHTKMPSQMEHAMETMMFTFHKFAG |
| PAPPPSTH.PHVLRK.HS.PRSP..................KASTDHTKMPSQMEHAMETMMFTFHKFAG | |
| Retrocopy | PAPPPSTHPPHVLRKVHSPPRSPXXXXXXXXXXXXXXXXXXKASTDHTKMPSQMEHAMETMMFTFHKFAG |
| Parental | DKGYLTKEDLRVLMEKEFPGFLENQKDPLAVDKIMKDLDQCRDGKVGFQSFFSLIAGLTIACNDYFVV |
| DKGYLTKEDLRVLMEKEFPGFLENQKDPLAVDKIM.DLDQCRDGKVGFQSFF.L.AGL.IAC.DYFVV | |
| Retrocopy | DKGYLTKEDLRVLMEKEFPGFLENQKDPLAVDKIMRDLDQCRDGKVGFQSFFFLSAGLSIACHDYFVV |
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 |
|---|---|---|
| SRP007412_brain_prefrontal_cortex | 0 .11 RPM | 33 .51 RPM |
| SRP007412_cerebellum | 0 .73 RPM | 7 .78 RPM |
| SRP007412_heart | 0 .00 RPM | 22 .79 RPM |
| SRP007412_kidney | 0 .10 RPM | 50 .98 RPM |
| SRP007412_liver | 0 .31 RPM | 27 .63 RPM |
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_1731 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_1731 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_pabe_1731 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Pongo abelii | ENSPPYG00000000850 | 3 retrocopies |
retro_pabe_1455, retro_pabe_1731 , retro_pabe_498,
|