RetrogeneDB ID: | retro_pabe_102 | ||
Retrocopylocation | Organism: | Orangutan (Pongo abelii) | |
| Coordinates: | 12:122462726..122463185(+) | ||
| Located in intron of: | None | ||
Retrocopyinformation | Ensembl ID: | ENSPPYG00000005024 | |
| Aliases: | None | ||
| Status: | KNOWN_PROTEIN_CODING | ||
Parental geneinformation | Parental gene summary: | ||
| Parental gene symbol: | NME3 | ||
| Ensembl ID: | ENSPPYG00000006961 | ||
| Aliases: | None | ||
| Description: | NME/NM23 nucleoside diphosphate kinase 3 [Source:HGNC Symbol;Acc:7851] |
Retrocopy-Parental alignment summary:
>retro_pabe_102
ATGGCCAACCTCGAGCGCACCTTCGTCGCCATCAAGCCGGACGGCGTGCAGCGCGGCCTGGTGGGCGAGATCATCAAGCG
CTTCGAGCAGAAGGGTTTCCGCCTCGTGGCCATGAAGTTCCTCCCGGCCTCTGAAGAACACCTGAAGCAGCACTACATTG
ACCTGAAGGACTGCCCATTCTTCCCTGGGCTGGTGAAGTACATGAACTCAGGGCCGGTCGTGGCCATGGTCTGGGAGGGG
CTGAACGTGGTGAAGACAGGCCGAGTGATGCTTGGGGAGACCAATCCAGCAGATTCTAAGCCAGGCACCATTCGTGGGGA
CTTCTGCATTCAGGTTGGCAGGAACATCATGTATGGCAGTGATTCAGTAAAAAGTGCTGAAAAAGAAATCAGCCTATGGT
TTAAGCCTGAAGAATTGGTTGACTACAAGTCTCCTGCTCATGACTGGCTCTATGAATAA
ATGGCCAACCTCGAGCGCACCTTCGTCGCCATCAAGCCGGACGGCGTGCAGCGCGGCCTGGTGGGCGAGATCATCAAGCG
CTTCGAGCAGAAGGGTTTCCGCCTCGTGGCCATGAAGTTCCTCCCGGCCTCTGAAGAACACCTGAAGCAGCACTACATTG
ACCTGAAGGACTGCCCATTCTTCCCTGGGCTGGTGAAGTACATGAACTCAGGGCCGGTCGTGGCCATGGTCTGGGAGGGG
CTGAACGTGGTGAAGACAGGCCGAGTGATGCTTGGGGAGACCAATCCAGCAGATTCTAAGCCAGGCACCATTCGTGGGGA
CTTCTGCATTCAGGTTGGCAGGAACATCATGTATGGCAGTGATTCAGTAAAAAGTGCTGAAAAAGAAATCAGCCTATGGT
TTAAGCCTGAAGAATTGGTTGACTACAAGTCTCCTGCTCATGACTGGCTCTATGAATAA
ORF - retro_pabe_102 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 64.19 % |
| Parental protein coverage: | 87.57 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | ERTFLAVKPDGVQRRLVGEIVRRFERKGFKLVALKLVQASEELLREHYAELRERPFYGRLVKYMASGPVV |
| ERTF.A.KPDGVQR.LVGEI..RFE.KGF.LVA.K...ASEE.L..HY..L...PF...LVKYM.SGPVV | |
| Retrocopy | ERTFVAIKPDGVQRGLVGEIIKRFEQKGFRLVAMKFLPASEEHLKQHYIDLKDCPFFPGLVKYMNSGPVV |
| Parental | AMVWQGLDVVRTSRALIGATNPADAPPGTIRGDFCIEVGKNLIHGSDSVESARREIALWFRADELLCWED |
| AMVW.GL.VV.T.R...G.TNPAD..PGTIRGDFCI.VG.N...GSDSV.SA..EI.LWF...EL..... | |
| Retrocopy | AMVWEGLNVVKTGRVMLGETNPADSKPGTIRGDFCIQVGRNIMYGSDSVKSAEKEISLWFKPEELVDYKS |
| Parental | SAGHWLYE |
| .A..WLYE | |
| Retrocopy | PAHDWLYE |
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 | 37 .10 RPM | 0 .00 RPM |
| SRP007412_cerebellum | 9 .36 RPM | 0 .00 RPM |
| SRP007412_heart | 19 .60 RPM | 0 .00 RPM |
| SRP007412_kidney | 64 .93 RPM | 0 .00 RPM |
| SRP007412_liver | 30 .94 RPM | 0 .00 RPM |
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_102 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_102 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_pabe_102 has 3 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Homo sapiens | retro_hsap_1063 |
| Pan troglodytes | retro_ptro_91 |
| Gorilla gorilla | retro_ggor_71 |
Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Pongo abelii | ENSPPYG00000006908 | 1 retrocopy | |
| Pongo abelii | ENSPPYG00000006961 | 1 retrocopy |
retro_pabe_102 ,
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