RetrogeneDB ID: | retro_pabe_382 | ||
Retrocopy location | Organism: | Orangutan (Pongo abelii) | |
| Coordinates: | 1:46028138..46028506(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | C12orf45 | ||
| Ensembl ID: | ENSPPYG00000004897 | ||
| Aliases: | None | ||
| Description: | chromosome 12 open reading frame 45 [Source:HGNC Symbol;Acc:28628] |
Retrocopy-Parental alignment summary:
>retro_pabe_382
CCCAGGACTGCTACAGAGGGAGTCTTGGTGCCTAAGGAGTGGCTGACGGTAGGGAACAACAGCCAAGAGGTGTATCAGAC
AGGTTGCTCATCAACTCCCAGCCTGATTCTAGAAAGAACTCCACTCTCCAAACAGTCCAGATACAGAGGAGTCCCTTAGT
GGACCAAGGACAGACCTTTCTCCCACAGATGGCCCAGGCACATGAAAAGCTAAGAAAATAAATGGCGGGTTCACCACCTG
GTTGTTTCAATATTGAAAATATTGATGGTTCTCTTAGAAAAGTTATACAAATGGATGTGGTCTTGTTTGAGATGAACCAG
TCAGATTCAAAAGTGGACAGCTCAGAATCTGAGGATGAAGATGACAGC
ORF - retro_pabe_382 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 68.0 % |
| Parental protein coverage: | 67.03 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | PTRDSSGVPVSKELLTAGSDGRG-GIWDRLLINSQPKSRKTSTLQTVRIERSPLLDQVQTFLPQMARANE |
| P.....GV.V.KE.LT.G......G..DRLLINSQP.SRK.STLQTV.I.RSPL.DQ.QTFLPQMA.A.E | |
| Retrocopy | PRTATEGVLVPKEWLTVGNNSQE<GVSDRLLINSQPDSRKNSTLQTVQIQRSPLVDQGQTFLPQMAQAHE |
| Parental | KLRKEMAAAPPGRFNIENIDGPHGKVIQMDVALFEMNQSDSKEADSSEESSQDSS |
| KLRK.MA..PPG.FNIENIDG...KVIQMDV.LFEMNQSDSK..DSSE....D.S | |
| Retrocopy | KLRK*MAGSPPGCFNIENIDGSLRKVIQMDVVLFEMNQSDSK-VDSSESEDEDDS |
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 | 4 .59 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 3 .53 RPM |
| SRP007412_heart | 0 .00 RPM | 1 .63 RPM |
| SRP007412_kidney | 0 .10 RPM | 3 .94 RPM |
| SRP007412_liver | 0 .09 RPM | 6 .64 RPM |
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_382 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_382 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_pabe_382 has 4 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Homo sapiens | retro_hsap_292 |
| Pan troglodytes | retro_ptro_240 |
| Gorilla gorilla | retro_ggor_331 |
| Macaca mulatta | retro_mmul_551 |
Parental genes homology:
Parental genes homology involve 11 parental genes, and 12 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000014728 | 1 retrocopy | |
| Dasypus novemcinctus | ENSDNOG00000017235 | 1 retrocopy | |
| Homo sapiens | ENSG00000151131 | 1 retrocopy | |
| Gallus gallus | ENSGALG00000012694 | 1 retrocopy | |
| Gorilla gorilla | ENSGGOG00000027272 | 1 retrocopy | |
| Macaca mulatta | ENSMMUG00000017133 | 1 retrocopy | |
| Nomascus leucogenys | ENSNLEG00000006584 | 1 retrocopy | |
| Pongo abelii | ENSPPYG00000004897 | 1 retrocopy |
retro_pabe_382 ,
|
| Pan troglodytes | ENSPTRG00000005381 | 1 retrocopy | |
| Sus scrofa | ENSSSCG00000027792 | 2 retrocopies | |
| Tursiops truncatus | ENSTTRG00000005714 | 1 retrocopy |