RetrogeneDB ID: | retro_pabe_2899 | ||
Retrocopy location | Organism: | Orangutan (Pongo abelii) | |
| Coordinates: | 6:108925092..108925351(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | TRAPPC6A | ||
| Ensembl ID: | ENSPPYG00000010109 | ||
| Aliases: | None | ||
| Description: | trafficking protein particle complex 6A [Source:HGNC Symbol;Acc:23069] |
Retrocopy-Parental alignment summary:
>retro_pabe_2899
TCCGTGAGGGGACAGAAGATAAGCCTGTTGATCCTGGAGAGTATGGATTTCTGTGTGAGCCAGGTTCTAGGTGAGAGACT
GCTGCTGGAGATGCTCGTCTCAGGGAGGAGCTGGGTGTCCTCAAGTTCATATGCAAAAATCTGTGGACGGCTGTGTTCCA
ATAGAAGGACAGCTTGTGCACCAATCACCAAGGGACCTACTTTTTGCAGGACAACAGCTTCTACTCCTCATCCCAATGAT
CTTGGGCCTGGATTCACTT
ORF - retro_pabe_2899 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 64.44 % |
| Parental protein coverage: | 51.46 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | ATKGQKMSLSVLEGMGFRVGQALGERLPREMLA-FREELDVLKFLCKDLWVAVFQKQMDSLRTNHQGTYV |
| ...GQK.SL..LE.M.F.V.Q.LGERL..EML...REEL.VLKF.CK.LW.AVFQ...DSL.TNHQGTY. | |
| Retrocopy | SVRGQKISLLILESMDFCVSQVLGERLLLEMLV<LREELGVLKFICKNLWTAVFQ*K-DSLCTNHQGTYF |
| Parental | LQDNSF-PLLLPMASGLQYL |
| LQDNSF..LL.PM..GL..L | |
| Retrocopy | LQDNSF<LLLIPMILGLDSL |
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 .00 RPM | 3 .98 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 2 .19 RPM |
| SRP007412_heart | 0 .00 RPM | 1 .54 RPM |
| SRP007412_kidney | 0 .00 RPM | 15 .51 RPM |
| SRP007412_liver | 0 .00 RPM | 6 .58 RPM |
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_2899 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_2899 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_pabe_2899 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 4 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000012869 | 1 retrocopy | |
| Macaca mulatta | ENSMMUG00000022932 | 1 retrocopy | |
| Pongo abelii | ENSPPYG00000010109 | 1 retrocopy |
retro_pabe_2899 ,
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