RetrogeneDB ID: | retro_pabe_3814 | ||
Retrocopy location | Organism: | Orangutan (Pongo abelii) | |
| Coordinates: | X:134977252..134978010(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | WDR4 | ||
| Ensembl ID: | ENSPPYG00000011458 | ||
| Aliases: | None | ||
| Description: | WD repeat domain 4 [Source:HGNC Symbol;Acc:12756] |
Retrocopy-Parental alignment summary:
>retro_pabe_3814
GCCACCTCTGCTGCAAACAATGATGACAACAACCTCTTCATCTATGACTGCAGTGCTGCAGAATAGTCACAAGAAAATAA
AGGGGAGGATGGGCTACCCTTGGTCTGGGGGAGTGGCATGATTCTGGCATCCACCTCCAAGTCTGGCAGCTATTTTGCTT
TAACAGATGACCACAAGCGTCTGATTCTTTTCCATACAAAACCATGGCAATGTCTGAGTGTCAGGACCATGGCAAGGAGG
TGTATGGCCCTGACCTTACAGCCTCTGTGGAGAAGGTCTTGGTGGCCGACAAATCTGGAGATGTGTACTCCTTTTTGGTT
TCAGAGCCACACAGATGCGGCAGACTTGACCTGGCACACCTGTCAATGTTGTTAGAGGTGACTGTGAGTGCTGATAACTG
CTTCATCCTCATTGCCAACCAGGATGAGAAGATCCAGGTCAGCTAGGCCACAGCACCTCACAGTATCGAGTCCTTCTGCC
TCGGGCACAGAGAATTCGTGAGCCGCATCTCTGTGGTGCCCACTCAGCCCGAACTGTTTCTTGTCCTCCTCCAGGGACTG
CACTCTTAGGCTCTAGGAGTACAGAAGTGGCCATCAACTGCACTTCTGTCACCTGGCCAGTCTGCAAGGGCTGATGGGCC
TCTGGGACACCAGAAGTTTGTCACATCCGGGATCACGTTCTGGTGCTAGGAGAACTGCATGACGCTTCTGTGCAACTGTA
TTCCCGTAATCTACATCTTCCAGCTTGATGCTCTCAGA
ORF - retro_pabe_3814 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 75.19 % |
| Parental protein coverage: | 61.65 % |
| Number of stop codons detected: | 4 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | ATSTASSDDDSLFIYDCSAAEKKSQENKGEDA-PLDQGSGAILASTFSKSGSYFALTDDSKRLILFRTKP |
| ATS.A..DD..LFIYDCSAAE..SQENKGED..PL..GSG.ILAST.SKSGSYFALTDD.KRLILF.TKP | |
| Retrocopy | ATSAANNDDNNLFIYDCSAAE*-SQENKGEDGLPLVWGSGMILAST-SKSGSYFALTDDHKRLILFHTKP |
| Parental | WQCLSVRTVARRCTALTF-TASEEKVLVADKSGDVYSFSVLEPHRCGRLELGHLSMLLDVAVSPDDCFIL |
| WQCLSVRT.ARRC.ALT..TAS.EKVLVADKSGDVYSF.V.EPHRCGRL.L.HLSMLL.V.VS.D.CFIL | |
| Retrocopy | WQCLSVRTMARRCMALTL<TASVEKVLVADKSGDVYSFLVSEPHRCGRLDLAHLSMLLEVTVSADNCFIL |
| Parental | TADRDEKIRVSWAAAPHSIESFCLGHTEFVSRISLVPTQPGL-LLSSSGDGTLRLWEYRSGRQLHCCHLA |
| .A..DEKI.VS.A.APHSIESFCLGH.EFVSRIS.VPTQP.L..LSSS.D.TLRL.EYRSG.QLH.CHLA | |
| Retrocopy | IANQDEKIQVS*ATAPHSIESFCLGHREFVSRISVVPTQPEL>FLSSSRDCTLRL*EYRSGHQLHFCHLA |
| Parental | SLQELV-DPQAPQRFAASRIAFWCQENCVALLCDGTPVVYIFQLDAHR |
| SLQ.L...P...Q.F..S.I.FWC.ENC..LLC...PV.YIFQLDA.R | |
| Retrocopy | SLQGLM<GPLGHQKFVTSGITFWC*ENCMTLLCNCIPVIYIFQLDALR |
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 | 3 .04 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 1 .46 RPM |
| SRP007412_heart | 0 .00 RPM | 0 .69 RPM |
| SRP007412_kidney | 0 .00 RPM | 3 .45 RPM |
| SRP007412_liver | 0 .00 RPM | 1 .10 RPM |
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_3814 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_3814 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_pabe_3814 has 2 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Homo sapiens | retro_hsap_4905 |
| Gorilla gorilla | retro_ggor_3063 |
Parental genes homology:
Parental genes homology involve 4 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Homo sapiens | ENSG00000160193 | 1 retrocopy | |
| Gorilla gorilla | ENSGGOG00000016652 | 1 retrocopy | |
| Nomascus leucogenys | ENSNLEG00000014641 | 1 retrocopy | |
| Pongo abelii | ENSPPYG00000011458 | 1 retrocopy |
retro_pabe_3814 ,
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