RetrogeneDB ID: | retro_pabe_2230 | ||
Retrocopy location | Organism: | Orangutan (Pongo abelii) | |
| Coordinates: | 3:98315368..98315956(+) | ||
| Located in intron of: | ENSPPYG00000013909 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | MRPS18A | ||
| Ensembl ID: | ENSPPYG00000017282 | ||
| Aliases: | None | ||
| Description: | mitochondrial ribosomal protein S18A [Source:HGNC Symbol;Acc:14515] |
Retrocopy-Parental alignment summary:
>retro_pabe_2230
ATGGCGGCCTTTGAGGCTCTGGTGTCTGGCTGTGGGCAGCTTCCCTGTGGGCTCCTAGCAGGCCCAGCAGTGACCAGCTG
ATCTCAGCTTCCAGCTCGCAGGTTCAGGGACGTGGTGGAGATCCAAGAAGGAAAGACAACTATAATTGAAGGCTGTATCA
CAGCGACTCCCAAGAAGAGTCCAAATCCTCCTAACCCCTCTGGCCAGTGCCCCATCTGCCATTGGAACCTGAACCACAAG
TAAAACTATGATGATCTTTTGCTGCTTAGCCAGTTCATCCAGCCTCATGGAGGCATGCTGCCCCGAAAGATCACAGGCCT
ATGACGGGAAGAGCACTGCAAGATCGAGGAGTGTGTGAAGATGGCCTACAGAGCAGGTCTGTTACCAAATCACAGGCCTC
AGCTTCCTGAAGGAGTTGTTCCAAAGGGCAAACCCCAACTCAACTAGTACCTGACCCACTGGGGTCCCCACACCCTCATG
CCCATCTACAAAAAAGGCCTCCCCTGGAACAGGGCGTTCATGGCCTTGGGGTCACCCCTCCTGAGGGACAATGTCTGCTA
CTCAAGAACACCTTGGAAGCTGTATCAC
ORF - retro_pabe_2230 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 80.61 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 4 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MAALKALVSGCGRFFRGLLAGPAATSWSRLPARGFREVVEIQEGKTTIIEGRITATPKESPNPPNPSGQC |
| MAA..ALVSGCG....GLLAGPA.TS.S.LPAR.FR.VVEIQEGKTTIIEG.ITATPK.SPNPPNPSGQC | |
| Retrocopy | MAAFEALVSGCGQLPCGLLAGPAVTS*SQLPARRFRDVVEIQEGKTTIIEGCITATPKKSPNPPNPSGQC |
| Parental | PICRWNLKHKYNYDDVLLLSQFIRPHGGMLPRKITGLCQEEHRKIEECVKMAHRAGLLPNHRPRLPEGVV |
| PIC.WNL.HK.NYDD.LLLSQFI.PHGGMLPRKITGL..EEH.KIEECVKMA.RAGLLPNHRP.LPEGVV | |
| Retrocopy | PICHWNLNHK*NYDDLLLLSQFIQPHGGMLPRKITGL*REEHCKIEECVKMAYRAGLLPNHRPQLPEGVV |
| Parental | PKSKPQLNRYLTRWAPGSVKPIYKKGPRWNRVRMPVGSPLLRDNVCYSGTPWKLYH |
| PK.KPQLN.YLT.W.P....PIYKKG..WNR..M..GSPLLRDNVCYS.TPWKLYH | |
| Retrocopy | PKGKPQLN*YLTHWGPHTLMPIYKKGLPWNRAFMALGSPLLRDNVCYSRTPWKLYH |
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 | 8 .68 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 4 .01 RPM |
| SRP007412_heart | 0 .00 RPM | 4 .70 RPM |
| SRP007412_kidney | 0 .00 RPM | 9 .65 RPM |
| SRP007412_liver | 0 .00 RPM | 5 .57 RPM |
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_2230 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_2230 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_pabe_2230 has 3 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Homo sapiens | retro_hsap_2787 |
| Pan troglodytes | retro_ptro_1888 |
| Callithrix jacchus | retro_cjac_1386 |
Parental genes homology:
Parental genes homology involve 6 parental genes, and 6 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000017382 | 1 retrocopy | |
| Homo sapiens | ENSG00000096080 | 1 retrocopy | |
| Macropus eugenii | ENSMEUG00000013986 | 1 retrocopy | |
| Pongo abelii | ENSPPYG00000017282 | 1 retrocopy |
retro_pabe_2230 ,
|
| Pan troglodytes | ENSPTRG00000018209 | 1 retrocopy | |
| Tarsius syrichta | ENSTSYG00000001390 | 1 retrocopy |