RetrogeneDB ID: | retro_pabe_3452 | ||
Retrocopy location | Organism: | Orangutan (Pongo abelii) | |
| Coordinates: | 9:21956870..21957537(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | ARRDC3 | ||
| Ensembl ID: | ENSPPYG00000015628 | ||
| Aliases: | None | ||
| Description: | arrestin domain-containing protein 3 [Source:RefSeq peptide;Acc:NP_001127608] |
Retrocopy-Parental alignment summary:
>retro_pabe_3452
ACTGGCAAAATCAGAGTAAAAGCTCTTAAAATTCATGCAAGAGGACACTTGGAAATACGCTCTGTTGAATCTAGAAACAC
TGACGCCAATACTGCCTGTAGATGGAATTACGTGGAAGAAGTACAATATATCAACCATAAAGATATCTTAATTGGACACA
AAAGAGTCAACGATAATTCCAAAGAAGGCTTCAACACTATTCATTCAGGAAGGCTGAATATGCTTTCAGCTCTGAGCTTC
CAGAGACACCACTTGCTACCTCATTCAAAGGCAGTCGTGGTGTGTGCACTCTTGTGTGAAAGCTGAATCTCAAAAGTCCC
TGACTACTAACAGTAACATCACAGAAGGAATTTACAGTCTCTGAGTATATAAATATGAATACTCCTTCATCGCTGTCACC
CCAAGCAGGCACAGAAGAAAAGACACTAGGTTGCTGGTTTTCTACCTCAGGCTCAATATCCTTAAGTGCCAAAATTGAAA
AGAAGGGCTATACCATGGGTGAATCAACTCAGAAATTTGCTGAGACTGAGAACTGCTCTTTCCAAATGCTAGTGCCAAAG
TCAGCCATTACCAAACACGGGCCTTCCATGCCAAACGGAAGATGAAGGAAGTGAAACAGCATGTGGCTAACTTGCATGAG
GAATCCTTGTCATCTGGAAAGAGAGAC
ORF - retro_pabe_3452 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 68.44 % |
| Parental protein coverage: | 53.75 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | TGEIRVKSLKIHARGHAKVRWTESRNAGSNTAYTQNYTEEVEYFNHKDILIGHERDDDNSEEGFHTIHSG |
| TG.IRVK.LKIHARGH...R..ESRN...NTA...NY.EEV.Y.NHKDILIGH.R..DNS.EGF.TIHSG | |
| Retrocopy | TGKIRVKALKIHARGHLEIRSVESRNTDANTACRWNYVEEVQYINHKDILIGHKRVNDNSKEGFNTIHSG |
| Parental | R-HEYAFSFELPQTPLATSFEGRHGSVRYWVKAELHRPWLLPVKLKKEFTVFEHIDINTP-LLSPQAGTK |
| R..EYAFS.ELP.TPLATSF.G..G......K..L..P.LL.V...KEFTV.E.I..NTP..LSPQAGT. | |
| Retrocopy | R<AEYAFSSELPETPLATSFKGSRGVCTLV*KLNLKSP*LLTVTSQKEFTVSEYINMNTPSSLSPQAGTE |
| Parental | EKTLCCWFCTSGPISLSAKIERKGYTPGESIQIFAEIENCSSRMVVPKAAI-YQTQAFYAKGKMKEVKQL |
| EKTL.CWF.TSG.ISLSAKIE.KGYT.GES.Q.FAE.ENCS..M.VPK.AI.YQT.AF.AK.KMKEVKQ. | |
| Retrocopy | EKTLGCWFSTSGSISLSAKIEKKGYTMGESTQKFAETENCSFQMLVPKSAI<YQTRAFHAKRKMKEVKQH |
| Parental | VANLRGESLSSGKTE |
| VANL..ESLSSGK.. | |
| Retrocopy | VANLHEESLSSGKRD |
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 | 27 .15 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 64 .21 RPM |
| SRP007412_heart | 0 .00 RPM | 33 .96 RPM |
| SRP007412_kidney | 0 .00 RPM | 50 .75 RPM |
| SRP007412_liver | 0 .00 RPM | 42 .96 RPM |
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_3452 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_3452 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_pabe_3452 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000010525 | 1 retrocopy | |
| Nomascus leucogenys | ENSNLEG00000013887 | 1 retrocopy | |
| Pongo abelii | ENSPPYG00000015628 | 1 retrocopy |
retro_pabe_3452 ,
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