RetrogeneDB ID: | retro_pabe_981 | ||
Retrocopy location | Organism: | Orangutan (Pongo abelii) | |
| Coordinates: | 13:19709831..19710448(+) | ||
| Located in intron of: | ENSPPYG00000005193 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | SLC35E1 | ||
| Ensembl ID: | ENSPPYG00000009692 | ||
| Aliases: | None | ||
| Description: | solute carrier family 35, member E1 [Source:HGNC Symbol;Acc:20803] |
Retrocopy-Parental alignment summary:
>retro_pabe_981
GCTGCCACGCTGTGCTTCTTGCTTCAGAACATTTTCTCCAAAAAGATATTGAGAGATTTGTGGATCCACCATCTCCCGCT
GCTCAACATCTTGGGCTGCGACGCTGTCTTTTTTATGATCCCCACCTGGGTTCTGGTGGACCTCTCAGCTTTCCTGGTCA
GCAGCGACTTGACTACGTCTCCCAGTGGCCCTGGATGCTCCTGCTTCTGGCTGTCAGTGGCTTCTGTAACTTTGCCCAGA
ATGTCATCGCCTTTAGCATCCTCAACCTCGTCAGCTCCCTGAGCTATTCGGTCGTCAATGCCACCAGGAGAATCATGGTC
ATCACAGTGTCCCTGATCATGCTGCCCAATGCAGTCACCAGCACCAATGTCCTGGGCATAATAACTGCCATCCTCGGGGT
CTTCCTCTACAACAAGACCAAGTAAGATGCAAACCAGCAAGTCAGGAAGCACCTCCTGCTGGCACCACAGTGGACCTGAG
CAGCAAGGAGCATCACCAGAGCCCGCTGGAGAAGCCCCACCAATGGCCTCCTCTTCCCCCAGCATGGGGACTATCATGGC
TCCAATAATATCTTAACAGACCACTTCCAGTACAGCTGGCAGAGCTACCCAAACTCG
ORF - retro_pabe_981 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 85.71 % |
| Parental protein coverage: | 77.82 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | AATLCFSLQNIFSKKVLRDSRIHHLRLLNILGCHAVFFMIPTWVLVDLSAFLVSSDLT-YVYQWPWTLLL |
| AATLCF.LQNIFSKK.LRD..IHHL.LLNILGC.AVFFMIPTWVLVDLSAFLVSSDLT.YV.QWPW.LLL | |
| Retrocopy | AATLCFLLQNIFSKKILRDLWIHHLPLLNILGCDAVFFMIPTWVLVDLSAFLVSSDLT<YVSQWPWMLLL |
| Parental | LAVSGFCNFAQNVIAFSILNLVSPLSYSVANATKRIMVITVSLIMLRNPVTSTNVLGMMTAILGVFLYNK |
| LAVSGFCNFAQNVIAFSILNLVS.LSYSV.NAT.RIMVITVSLIML.N.VTSTNVLG..TAILGVFLYNK | |
| Retrocopy | LAVSGFCNFAQNVIAFSILNLVSSLSYSVVNATRRIMVITVSLIMLPNAVTSTNVLGIITAILGVFLYNK |
| Parental | TKYDANQQARKHLLPV-TTADLSGKERHRSPLEKPH-NGLLFPQHGDYQYGRNNILTDHFQYSRQSYPNS |
| TK.DANQQ.RKHLL...TT.DLS.KE.H.SPLEKPH.NGLLFPQHGDY..G.NNILTDHFQYS.QSYPNS | |
| Retrocopy | TK*DANQQVRKHLLLA<TTVDLSSKEHHQSPLEKPH>NGLLFPQHGDY-HGSNNILTDHFQYSWQSYPNS |
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 | 23 .11 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 17 .63 RPM |
| SRP007412_heart | 0 .00 RPM | 8 .07 RPM |
| SRP007412_kidney | 0 .10 RPM | 15 .98 RPM |
| SRP007412_liver | 0 .03 RPM | 14 .57 RPM |
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_981 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_981 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_pabe_981 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 4 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Homo sapiens | ENSG00000127526 | 1 retrocopy | |
| Nomascus leucogenys | ENSNLEG00000005563 | 1 retrocopy | |
| Pongo abelii | ENSPPYG00000009692 | 1 retrocopy |
retro_pabe_981 ,
|
| Pan troglodytes | ENSPTRG00000010648 | 1 retrocopy |