RetrogeneDB ID: | retro_pabe_3385 | ||
Retrocopy location | Organism: | Orangutan (Pongo abelii) | |
| Coordinates: | 9:23095233..23096218(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | ARMC8 | ||
| Ensembl ID: | ENSPPYG00000014140 | ||
| Aliases: | None | ||
| Description: | armadillo repeat-containing protein 8 [Source:RefSeq peptide;Acc:NP_001126485] |
Retrocopy-Parental alignment summary:
>retro_pabe_3385
GTATTAAAGACATTGTCTTATTCGGTTCAAATGTGCAGTAAGAAGAGATTACTAGAGGAGAGAGTTAAAGGAGCTGAGAC
ACTTGCCTATCTGATTGAACCAGATATTGAGCTACAGAGAATCGCTAGTGTAACTGATCACCTCATTGTCATGCTTGCTG
ACTATTTCAAGTATCCCAACTCATTGAGTGCCATCACTGATATTAAAAGGCTTGATCATGTTTTAAAACATGCTCATGAA
CTCTGCCAGGCTGCATTTAATCTCTACGACTCTCTTAGAGCAAATGATGAAGACATTCAGAAGAAAAGCCCTGAGACTGG
AAATATGATGGACTGAATTGTGACTGGCTTGTCTGAGTCTAGTGTCAAGGTGCAGTTTCCTGCTGTCAGATGTTTTCACC
GTTTATCCAGATCTGTGCAGCAGCTTCAAAACAGTTTCTAGGATCACACTCTGTGAAAACCTTTAATGAAGGTTTTACAA
AATGCACCAGATGAAATCCTAGTAGTAGCATCTTCCATGGTATATAATCTTCTTGAATTTTCTCCAAGGAAAGAGTCAAT
TTTAAAATCAGGAGTTGTAAAGCTACTTTGTGGATTAACCCAGAGTGAAAATCCTGCTTTACGAGTGAGCAGAATTTGGG
CTTTAATGAGTATGGCATTTCAGGCTGAACAAAAAATAAAAGCAGACATGTTACAAAGCTTGAGTACTGAACAGCTATTC
TGGTTATTATCAGATTCAGATTTGAATGTGCTGATGAAGACACTGGGACTTCTTAGAAATCTCCTCTTGACCTGGCTTCA
TATAATAAAATAATGAGTACTCATGGAAAGCAAATTATGCAAGCTGTCATCCTTATTCTGGAAGGGGAACATAACTTTAA
GGTCAAAGAGTAGATACTGTGCATCTTAGCCAATATAGAAGATGAGACAACAGCAAAGAATGTATTATGACCAATGATGA
TATCCTTCAGAAAATCAAATATTAC
ORF - retro_pabe_3385 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 81.33 % |
| Parental protein coverage: | 55.46 % |
| Number of stop codons detected: | 4 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | VLKTLPCLVRMCSKERLLEERVEGAETLAYLIEPDVELQRIASITDHLIAMLADYFKYPSSVSAITDIKR |
| VLKTL...V.MCSK.RLLEERV.GAETLAYLIEPD.ELQRIAS.TDHLI.MLADYFKYP.S.SAITDIKR | |
| Retrocopy | VLKTLSYSVQMCSKKRLLEERVKGAETLAYLIEPDIELQRIASVTDHLIVMLADYFKYPNSLSAITDIKR |
| Parental | LDHDLKHAHELRQAAFKLYASLGANDEDIRKKIIETENMMDRIVTGLSESSVKVRLAAVRCLHSLSRSVQ |
| LDH.LKHAHEL.QAAF.LY.SL.ANDEDI.KK..ET.NMMD.IVTGLSESSVKV...AVRC.H.LSRSVQ | |
| Retrocopy | LDHVLKHAHELCQAAFNLYDSLRANDEDIQKKSPETGNMMD*IVTGLSESSVKVQFPAVRCFHRLSRSVQ |
| Parental | QLRTSFQDHAVWKPLMKVLQNAPDEILVVASSMLCNLLLEFSPSKEPILESGAVELLCGLTQSENPALRV |
| QL..SF.DH...KPLMKVLQNAPDEILVVASSM..N.LLEFSP.KE.IL.SG.V.LLCGLTQSENPALRV | |
| Retrocopy | QLQNSF*DHTL*KPLMKVLQNAPDEILVVASSMVYN-LLEFSPRKESILKSGVVKLLCGLTQSENPALRV |
| Parental | NGIWALMNMAFQAEQKIKADILRSLSTEQLFRLLSDSDLNVLMKTLGLLRNLLSTRPHI-DKIMSTHGKQ |
| ..IWALM.MAFQAEQKIKAD.L.SLSTEQLF.LLSDSDLNVLMKTLGLLRNLL.T..HI..KIMSTHGKQ | |
| Retrocopy | SRIWALMSMAFQAEQKIKADMLQSLSTEQLFWLLSDSDLNVLMKTLGLLRNLLLTWLHI<NKIMSTHGKQ |
| Parental | IMQAVTLILEGEHNIEVKEQTLCILANIADGTTAKDL-IMTNDDILQKIKNY |
| IMQAV.LILEGEHN..VKE..LCILANI.D.TTAK...IMTNDDILQKIK.Y | |
| Retrocopy | IMQAVILILEGEHNFKVKE*ILCILANIEDETTAKNV<IMTNDDILQKIKYY |
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 | 25 .82 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 45 .60 RPM |
| SRP007412_heart | 0 .00 RPM | 6 .71 RPM |
| SRP007412_kidney | 0 .00 RPM | 9 .65 RPM |
| SRP007412_liver | 0 .00 RPM | 7 .28 RPM |
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_3385 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_3385 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_pabe_3385 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 4 parental genes, and 5 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Homo sapiens | ENSG00000114098 | 1 retrocopy | |
| Gorilla gorilla | ENSGGOG00000023535 | 1 retrocopy | |
| Macaca mulatta | ENSMMUG00000021285 | 1 retrocopy | |
| Pongo abelii | ENSPPYG00000014140 | 2 retrocopies |
retro_pabe_3384, retro_pabe_3385 ,
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