RetrogeneDB ID: | retro_pabe_1163 | ||
Retrocopy location | Organism: | Orangutan (Pongo abelii) | |
| Coordinates: | 14:38841055..38841494(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | RIPPLY3 | ||
| Ensembl ID: | ENSPPYG00000011408 | ||
| Aliases: | None | ||
| Description: | ripply3 homolog (zebrafish) [Source:HGNC Symbol;Acc:3047] |
Retrocopy-Parental alignment summary:
>retro_pabe_1163
TGGAGACCTATGATCCTGACACCTGCAGATGCTGAGCTGACCAGAACTGGAAGCCAGTTTAAACTCGGGGGAGATCAAGA
AACTTTTGGATTAAAGGAAGTCTTCAGGTTTCAGCATCCTGTAAGACTTTACTTACCCTTTTTGAAATGTCAAGAATATT
TTCAGTGTTCTGGGGAATAAGTGCTGGTCTGTTTTCCAGTGCAAGCCGTGATATACTTCTATAACGATGAGTCTGATTCA
GATGATGAAGAGCAAGAGGAAGAAACCAGCTCTTCCATTTTCTGTGCCAGGAGGCGGAAGGTCTGGAGGAAACTGTCCTG
GGGGAAAGGGCAGAGACAGGATCATAAACTGAGGATGGCAATCTGAAAGAAGGGGTGGCCTCTGTGTGGAGGACCAGCTC
CCCTGAGGTGAGTCCTCAAGGGGCAGGGAGTGCTCCTCA
ORF - retro_pabe_1163 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 56.58 % |
| Parental protein coverage: | 78.95 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | WRPWIQTPGDAELTRTGRPLEPRADQHAFGSKGAFGFQHPVRVYLPMSKRQEYLQSSGEQVLASFPVQAT |
| WRP.I.TP.DAELTRTG.......DQ..FG.K..F.FQHPVR.YLP..K.QEY.Q.SGE.VL..FPVQA. | |
| Retrocopy | WRPMILTPADAELTRTGSQFKLGGDQETFGLKEVFRFQHPVRLYLPFLKCQEYFQCSGE*VLVCFPVQAV |
| Parental | IDFYDDESTESASEAEEPEEGTPP-LHPLLQEVGGLQE-NCPGGKGRDQGSNRGQRSSGGGDPWGEGLLP |
| I.FY.DES....S..EE.EE.T....H.L.QE..GL.E.NCPGGKGRD...N.G..S...G....E..LP | |
| Retrocopy | IYFYNDESD---SDDEEQEEETSS<FHFLCQEAEGLEE<NCPGGKGRDRIIN*GWQSERRGGLCVEDQLP |
| Parental | HSVSSRGGKCSS |
| ...SSRG..CSS | |
| Retrocopy | *GESSRGRECSS |
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 .17 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 0 .73 RPM |
| SRP007412_heart | 0 .00 RPM | 0 .03 RPM |
| SRP007412_kidney | 0 .00 RPM | 0 .93 RPM |
| SRP007412_liver | 0 .00 RPM | 0 .40 RPM |
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_1163 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_1163 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_pabe_1163 has 3 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Homo sapiens | retro_hsap_1407 |
| Pan troglodytes | retro_ptro_964 |
| Gorilla gorilla | retro_ggor_1091 |
Parental genes homology:
Parental genes homology involve 6 parental genes, and 6 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Bos taurus | ENSBTAG00000036019 | 1 retrocopy | |
| Homo sapiens | ENSG00000183145 | 1 retrocopy | |
| Gorilla gorilla | ENSGGOG00000006091 | 1 retrocopy | |
| Nomascus leucogenys | ENSNLEG00000004521 | 1 retrocopy | |
| Pongo abelii | ENSPPYG00000011408 | 1 retrocopy |
retro_pabe_1163 ,
|
| Pan troglodytes | ENSPTRG00000013896 | 1 retrocopy |