RetrogeneDB ID: | retro_pabe_759 | ||
Retrocopy location | Organism: | Orangutan (Pongo abelii) | |
| Coordinates: | 11:43540704..43541496(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | NAE1 | ||
| Ensembl ID: | ENSPPYG00000007428 | ||
| Aliases: | None | ||
| Description: | NEDD8 activating enzyme E1 subunit 1 [Source:HGNC Symbol;Acc:621] |
Retrocopy-Parental alignment summary:
>retro_pabe_759
ATTCAAGATCTGTGACTGGATAAAGTGTTTTCTGAGCTGAGAGAATATTTCAGTCTTATATTTTGGATCATATGTTGAAA
AAAACTATAGCCATACCCCAAGGATTGTGATCATAGATAAATATTTAGCACAGTAGAGTAGTAAAACAAACGGGTGAATA
TCTAAAATGTATGAAGAAAAAGAGCACTTAAGAGATTTGATTATACAAAAGATTCTAAATAATACAAATAGGACTTCAGA
AGATGAAAAGAATTCTGAAGAAACTATTAAAATATGAACATGGCAATAAATACTACTTAGATACCAAACAATATTTAAGA
TATATTTAATAATAATTTCTGAATAAATATCAGCAAACAGACTTCATCCTTTGGGGTTTTAGCTTATGCCTCAAAGGAAT
TTGTGGCCAAGGAAGGTCATGGAAATTTACCTATTCAAGCACAATTTCTGACACAATTGCCGACTTGAAAAAATATATAA
ATACGCAAAGTATTTACTGTGTGAAAGCAAATGAATATGTTTCTCCTGTGAATAAATCATGCCAACAAAATGCTGCAGTC
CATAGACCAGGCGAACAATGACACTGCAAAGAAAGAATTAAAATTACTCTGTAGCAATTCTTCATTTCTTAGAGTCTTAA
GATGTGAATCCTTTACTGAAGAATATGGTTTGGATACAATTAACAAGAATAAAATCTTTTCCAGCATGGGCACTGCAGAT
AATGAAATAGTATTGTACTTAATATTATGGACTATTGATAGATTTTATATGCAACAATATAGATGTCCAGGA
ORF - retro_pabe_759 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 61.11 % |
| Parental protein coverage: | 59.15 % |
| Number of stop codons detected: | 6 |
| Number of frameshifts detected: | 5 |
Retrocopy - Parental Gene Alignment:
| Parental | LEDLRLDKPFPELREHF-QSYDLDHMEKK-DHSHTPWIVIIAKYLAQWHSETNGRIPKTYKEKEDFRDLI |
| ..DL.LDK.F.ELRE.F.QSY.LDHM.KK...SHTP.IVII.KYLAQ..S.TNG.I.K.Y.EKE..RDLI | |
| Retrocopy | IQDL*LDKVFSELREYF<QSYILDHMLKK<NYSHTPRIVIIDKYLAQ*SSKTNG*ISKMYEEKEHLRDLI |
| Parental | RQGILKNENGAPEDEENFEEAIK-NVNTALNTTQIPSSIEDIFNDDRCINITKQTPSFWILARALKEFVA |
| .Q.IL.N.N...EDE.N.EE.IK.N.N.A.NTT.IP..I.DIFN....INI.KQT.SF..LA.A.KEFVA | |
| Retrocopy | IQKILNNTNRTSEDEKNSEETIK<NMNMAINTT*IPNNI*DIFNNNF*INISKQTSSFGVLAYASKEFVA |
| Parental | KEGQGNLPVRG-TIPDMIADSGKYVKLQNVYREKAKKDAAAVG-NHVAKLLQSIGQAPESISEKELKLLC |
| KEG.GNLP....TI.D.IAD..KY...Q..Y..KA......V..NH..K.LQSI.QA......KELKLLC | |
| Retrocopy | KEGHGNLPIQA<TISDTIADLKKYINTQSIYCVKANEYVSPVN>NHANKMLQSIDQANNDTAKKELKLLC |
| Parental | SNSAFLRVVRCRSLAEEYGLDTINKDEIISSMDNPDNEIVLYLMLRAVDRFHKQHGRYPG |
| SNS.FLRV.RC.S..EEYGLDTINK..I.SSM...DNEIVLYL.L...DRF..Q..R.PG | |
| Retrocopy | SNSSFLRVLRCESFTEEYGLDTINKNKIFSSMGTADNEIVLYLILWTIDRFYMQQYRCPG |
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 .63 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 18 .60 RPM |
| SRP007412_heart | 0 .00 RPM | 7 .80 RPM |
| SRP007412_kidney | 0 .00 RPM | 6 .03 RPM |
| SRP007412_liver | 0 .00 RPM | 5 .39 RPM |
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_759 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_759 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_pabe_759 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 | |
|---|---|---|---|
| Equus caballus | ENSECAG00000021954 | 1 retrocopy | |
| Nomascus leucogenys | ENSNLEG00000004047 | 1 retrocopy | |
| Otolemur garnettii | ENSOGAG00000014645 | 1 retrocopy | |
| Pongo abelii | ENSPPYG00000007428 | 2 retrocopies |
retro_pabe_3596, retro_pabe_759 ,
|