RetrogeneDB ID: | retro_pabe_1277 | ||
Retrocopy location | Organism: | Orangutan (Pongo abelii) | |
| Coordinates: | 15:23597428..23597978(-) | ||
| Located in intron of: | ENSPPYG00000006277 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | DUSP3 | ||
| Ensembl ID: | ENSPPYG00000008353 | ||
| Aliases: | DUSP3, VHR | ||
| Description: | Dual specificity protein phosphatase 3 [Source:UniProtKB/Swiss-Prot;Acc:Q5RD73] |
Retrocopy-Parental alignment summary:
>retro_pabe_1277
ATGACAGGCCCTTTCAAATGCTCCATGGAAGTTCTCAATGACCTGCTCTCAGATAGCAGTGGCTGCTACAGCCTCCCAAG
CCAGCCCTGCAATGAGGTCACCCTGAGGATTTACATGGGCAACACATCTGTGGCTCAGGATATCCCCAAGCTTCAGAAAC
TGGTCAGGATTCATGTCCTGAATGCCACTGAGGGCAGGTCTTTCATGCACATAAACAATGCCAACTTCTCCAAGGACTCT
GGCATCACCTACCTGGGCATCAAGACCATTGAAGTGCAGGAGTTCAACCTCAGCACCTATTTTGAAAGGGCTACAGACTT
CACTGACCAGGCCTTGGCTCAAAAGAATGGCCAGGTGCTCGTCCAGTGCTGGGAAGGTTACAGCCATCTCCAGCTCTAGT
TATCATGTACCTCACGATTGTAAGAAGTTGGACATCAAGTCCATCCTGAGTATCATGAGGCAGAACTGTGAGATCAGCCC
CAATGATGGGTTCCTGGCTCAGCTTTGCCATCTCAATGACAAACTAGCCAAGGAGGGGAAGGTGAAACCC
ORF - retro_pabe_1277 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 75.4 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | MSGSFELSVQDLNDLLSDGSGCYSLPSQPCNEVTPRIYVGNASVAQDIPKLQKLGITHVLNAAEGRSFMH |
| M.G.F..S...LNDLLSD.SGCYSLPSQPCNEVT.RIY.GN.SVAQDIPKLQKL...HVLNA.EGRSFMH | |
| Retrocopy | MTGPFKCSMEVLNDLLSDSSGCYSLPSQPCNEVTLRIYMGNTSVAQDIPKLQKLVRIHVLNATEGRSFMH |
| Parental | VNTNANFYKDSGITYLGIKANDTQEFNLSAYFERAADFIDQALAQKNGRVLVHCREGYSR-SPTLVIAYL |
| .N.NANF.KDSGITYLGIK....QEFNLS.YFERA.DF.DQALAQKNG.VLV.C.EGYS..SP.LVI.YL | |
| Retrocopy | IN-NANFSKDSGITYLGIKTIEVQEFNLSTYFERATDFTDQALAQKNGQVLVQCWEGYSH<SPALVIMYL |
| Parental | MM-RQKMDVKSALSIVRQNREIGPNDGFLAQLCQLNDRLAKEGKLKP |
| .....K.D.KS.LSI.RQN.EI.PNDGFLAQLC.LND.LAKEGK.KP | |
| Retrocopy | TI<CKKLDIKSILSIMRQNCEISPNDGFLAQLCHLNDKLAKEGKVKP |
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 .06 RPM | 170 .35 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 103 .12 RPM |
| SRP007412_heart | 0 .00 RPM | 152 .84 RPM |
| SRP007412_kidney | 0 .00 RPM | 120 .65 RPM |
| SRP007412_liver | 0 .00 RPM | 82 .10 RPM |
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_1277 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_1277 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_pabe_1277 has 3 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Homo sapiens | retro_hsap_1541 |
| Gorilla gorilla | retro_ggor_1174 |
| Macaca mulatta | retro_mmul_2205 |
Parental genes homology:
Parental genes homology involve 5 parental genes, and 5 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Homo sapiens | ENSG00000108861 | 1 retrocopy | |
| Gorilla gorilla | ENSGGOG00000023681 | 1 retrocopy | |
| Macaca mulatta | ENSMMUG00000002351 | 1 retrocopy | |
| Nomascus leucogenys | ENSNLEG00000005702 | 1 retrocopy | |
| Pongo abelii | ENSPPYG00000008353 | 1 retrocopy |
retro_pabe_1277 ,
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