RetrogeneDB ID: | retro_pabe_3719 | ||
Retrocopy location | Organism: | Orangutan (Pongo abelii) | |
| Coordinates: | X:8517804..8518527(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | DRAXIN | ||
| Ensembl ID: | ENSPPYG00000001884 | ||
| Aliases: | None | ||
| Description: | dorsal inhibitory axon guidance protein [Source:HGNC Symbol;Acc:25054] |
Retrocopy-Parental alignment summary:
>retro_pabe_3719
CTAGTCCTAGTCCTCCTGCTGCCCCTGGAGCTGAGCCTGGCAAACGCCCTTGCACCTGGGACCCCTGCTCAGAATCTACC
CGAGAATCACATCGACCTCCCAGGCCCAGCGCTGTGGTCGCCTCAGGCCAGCCACCGCCGCCAGCGCGACCCGGGCAAGA
AGGAGTGGGGCTCAGGCCTGCCCAGGTAGGCCCAGGATAGGGCTGTGCTCACCGCCACCAGGCAGGCTTCCAGGCTGCCA
GGGCCTGAGGGGCCGCTGCCTGAGCAGAGTCCTGCAGGCCTGCTGCGGGTCAAGGACCTGCTCCTGGGGCTCGAGTTGCC
CTACCCCAAGAAGGAGAATCGGTGTCCAGGGTGGGAGAGGGCCAGGAAACGCAGCAGGGAGTACAAGAGACGCAGGGACA
GGCTGAGGCTGCACCGAGGCCGAGCCTTGGTCGGAGGTCCCAGTTACCTGATGAAGGCAGAGCTTTCCGAAGCCAAGGCG
CTGGATGCGACCATGAAGGATTCTTCCGCCAGTCTGGCCCCCACCATGCTCTTCCTCACGACCTTTGAGGCAGCACCTGC
CACAGAAGAGTCCTTAATCTTGCTCATCGCCCCCCTGCGGCCCCAGGCACAGCACAGGCCTGACGGGGAGGCGATACCCA
CACTGGACGTGGCCTTGTTCGACTGGACCGATTATGAAGACTTAAAACCTGATGGCGGGCCCTCTGCAAAGAAGAAAGAA
AAA
ORF - retro_pabe_3719 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 80.66 % |
| Parental protein coverage: | 69.43 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | LFFVLLLPLELSLADALALGTPAWNLPENHIDLPGPALWTPQASHYRRRGPGKKEWGPGLPSQAQDGAVA |
| L..VLLLPLELSLA.ALA.GTPA.NLPENHIDLPGPALW.PQASH.R.R.PGKKEWG.GLP..AQD.AV. | |
| Retrocopy | LVLVLLLPLELSLANALAPGTPAQNLPENHIDLPGPALWSPQASHRRQRDPGKKEWGSGLPR*AQDRAVL |
| Parental | TTTRQASRLPEAEGLLPEQSPAGLLQDKDLLLGLALPYPEKENRPPGWERTRKRSREHKRRRDRLRLHRG |
| T.TRQASRLP..EG.LPEQSPAGLL..KDLLLGL.LPYP.KENR.PGWER.RKRSRE.KRRRDRLRLHRG | |
| Retrocopy | TATRQASRLPGPEGPLPEQSPAGLLRVKDLLLGLELPYPKKENRCPGWERARKRSREYKRRRDRLRLHRG |
| Parental | RALVRGPSSLMKKAEFSEAQVLDAAMEESSTSLAPTMFFLTTFEAAPATEESLILPVTSLRPQQAQPRSD |
| RALV.GPS.LM.KAE.SEA..LDA.M..SS.SLAPTM.FLTTFEAAPATEESLIL....LRP.QAQ.R.D | |
| Retrocopy | RALVGGPSYLM-KAELSEAKALDATMKDSSASLAPTMLFLTTFEAAPATEESLILLIAPLRP-QAQHRPD |
| Parental | GEVMPTLDMALFDWTDYEDLKPDGWPSAKKKEK |
| GE..PTLD.ALFDWTDYEDLKPDG.PSAKKKEK | |
| Retrocopy | GEAIPTLDVALFDWTDYEDLKPDGGPSAKKKEK |
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 .28 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 0 .00 RPM |
| SRP007412_heart | 0 .00 RPM | 0 .00 RPM |
| SRP007412_kidney | 0 .00 RPM | 0 .00 RPM |
| SRP007412_liver | 0 .03 RPM | 0 .00 RPM |
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_3719 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_3719 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_pabe_3719 has 2 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Homo sapiens | retro_hsap_4779 |
| Macaca mulatta | retro_mmul_2550 |
Parental genes homology:
Parental genes homology involve 4 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Homo sapiens | ENSG00000162490 | 1 retrocopy | |
| Macaca mulatta | ENSMMUG00000001652 | 1 retrocopy | |
| Pongo abelii | ENSPPYG00000001884 | 1 retrocopy |
retro_pabe_3719 ,
|
| Pan troglodytes | ENSPTRG00000000150 | 1 retrocopy |