RetrogeneDB ID: | retro_pabe_2422 | ||
Retrocopy location | Organism: | Orangutan (Pongo abelii) | |
| Coordinates: | 4:3372700..3373027(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | XAGE3 | ||
| Ensembl ID: | ENSPPYG00000020369 | ||
| Aliases: | None | ||
| Description: | X antigen family, member 3 [Source:HGNC Symbol;Acc:14618] |
Retrocopy-Parental alignment summary:
>retro_pabe_2422
ATGAGTTGGCAAGGAAGATCAGCATGTAGGCTTAGACCAAGACGGTATCTGCAGCCCCTGAGCTAACTGGGTCTGTGCTT
GAGCCCAGTGATGAGAAGCCTCAACTAGAGGAACCACCACCTGAAAGTCGGGGTCCTACACCTGGCCAGGAGAGAGAGGA
TGATCACGGTGCCGCTGAGATTCTTGTGCTTGACCAGGAAGCTGATCTCTGGGAGCTGTCTCAAAAGACTGGGATGAATG
TGGAGATGGTCCTGATGTCCGGGGAAGATTCTGCCGAAATCAGAGCAATTTAAATTGCCAGAAGGAGGTGAAGGGCAACC
ACAGGTT
ORF - retro_pabe_2422 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 71.05 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | MIWRGRSTYRPRPRRSVPP-PELIGPMLEPSDEEPQQEEPPTESQDPAPGQEREEDQGAAEIQVPDLEAD |
| M.W.GRS..R.RPRR...P.PEL.G..LEPSDE.PQ.EEPP.ES..P.PGQERE.D.GAAEI.V.D.EAD | |
| Retrocopy | MSWQGRSACRLRPRRYLQP<PELTGSVLEPSDEKPQLEEPPPESRGPTPGQEREDDHGAAEILVLDQEAD |
| Parental | LQELSQSKTG-DECGNGPDDQ-GKILPKSEQFKMPEGGDRQPQV |
| L.ELSQ.KTG.DECG.GPD...GKILPKSEQFK.PEGG..QPQV | |
| Retrocopy | LWELSQ-KTG<DECGDGPDVR<GKILPKSEQFKLPEGGEGQPQV |
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 | 0 .00 RPM |
| SRP007412_cerebellum | 0 .24 RPM | 0 .00 RPM |
| SRP007412_heart | 0 .03 RPM | 0 .09 RPM |
| SRP007412_kidney | 0 .00 RPM | 0 .00 RPM |
| SRP007412_liver | 0 .00 RPM | 0 .03 RPM |
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_2422 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_2422 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_pabe_2422 has 1 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Callithrix jacchus | retro_cjac_2302 |
Parental genes homology:
Parental genes homology involve 4 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Gorilla gorilla | ENSGGOG00000027404 | 1 retrocopy | |
| Pongo abelii | ENSPPYG00000020345 | 1 retrocopy | |
| Pongo abelii | ENSPPYG00000020369 | 1 retrocopy |
retro_pabe_2422 ,
|
| Pan troglodytes | ENSPTRG00000021922 | 1 retrocopy |