RetrogeneDB ID: | retro_ptro_869 | ||
Retrocopy location | Organism: | Chimpanzee (Pan troglodytes) | |
| Coordinates: | 13:55667110..55667832(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | HNF4G | ||
| Ensembl ID: | ENSPTRG00000020357 | ||
| Aliases: | None | ||
| Description: | hepatocyte nuclear factor 4, gamma [Source:HGNC Symbol;Acc:5026] |
Retrocopy-Parental alignment summary:
>retro_ptro_869
ACTTCTGCCCCAGAGAGGACAAATATGAATACCCAGACAACAGTCTCATCTGTCTTTGTGCTATATGTGAGTCAAGGCAA
CAGGAAAACACTGTGGGGCATCGAGCTGTGGTGGGTGCAAGGGCTTCTTCAGATGCAGCATATGCAAGAGTAACGTTTAT
TCTTGCAGGTTCCGTCGGCAATGTTTTGTTGACAAGGCCAAAAGAAATCAATGTAGATACTGTCAATTAAGAAAGTGTTT
TAGAGCAGGAATGGAAAAAGAAGTTGTGCATAATGAATGCAATAGAACAAGCACCAGAAGAAGCACATGTGATGGCAGCA
ATATCCCCTCCATTAACACACTGGCACAAGCTGAAGTTCTGTCTTGCCAGATCTCAGTCTCAAGCCTTGGGGCAAGTACT
GATATACATGTTAAAAAAATAAAAAATAAAGGTGTTGGTGATGTCTGTGAATTTCTGAAACAGCAGCTCTTAGTCTTGGT
GGAATGGGCTAAATATATTCCTGCCTTCTGTCAGTTACCATTGGATGGTAAGGTGGCACTGTTGAGATCTCATGCAGGAG
GACACTTAACTGCCTGGAGCTATAAAGAGATCCATGATGTATAAAGATATTTTGCTTTTGGGAAACAACTATATTATTCA
CTGCAACAGCTGTGAATTTGAGATTAGCAGTGTAATCAGTCGGGTTCTAGATGAGCTGGTTCAACCATTTCAAGAAATCC
AA
ORF - retro_ptro_869 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 76.64 % |
| Parental protein coverage: | 53.48 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | SSAPE-TSMNTT-DNGVNCLCAICGDR-ATGKHYGASSCDGCKGFFRRSIRKSHVYSCRFSRQCVVDKDK |
| .SAPE.T.MNT..DN...CLCAIC..R.ATGKH.GASSC.GCKGFFR.SI.KS.VYSCRF.RQC.VDK.K | |
| Retrocopy | TSAPERTNMNTQ<DNSLICLCAICESR<ATGKHCGASSCGGCKGFFRCSICKSNVYSCRFRRQCFVDKAK |
| Parental | RNQCRYCRLRKCFRAGMKKEAVQNERDRISTRRSTFDGSNIPSINTLAQAEVRSRQISVSSPGSSTDINV |
| RNQCRYC.LRKCFRAGM.KE.V.NE..R.STRRST.DGSNIPSINTLAQAEV.S.QISVSS.G.STDI.V | |
| Retrocopy | RNQCRYCQLRKCFRAGMEKEVVHNECNRTSTRRSTCDGSNIPSINTLAQAEVLSCQISVSSLGASTDIHV |
| Parental | --KKIASIGDVCESMKQQLLVLVEWAKYIPAFCELPLDDQVALLRAHAGEHL-LLGATKRSMMYKDILLL |
| ........GDVCE..KQQLLVLVEWAKYIPAFC.LPLD..VALLR.HAG.HL.L.GA.KRSMMYKDILLL | |
| Retrocopy | XXXXXXGVGDVCEFLKQQLLVLVEWAKYIPAFCQLPLDGKVALLRSHAGGHL>LPGAIKRSMMYKDILLL |
| Parental | GNNYVIHRNSCEVEISRVANRVLDELVRPFQEIQ |
| GNNY.IH.NSCE.EIS.V..RVLDELV.PFQEIQ | |
| Retrocopy | GNNYIIHCNSCEFEISSVISRVLDELVQPFQEIQ |
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 | 0 .04 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 0 .18 RPM |
| SRP007412_heart | 0 .00 RPM | 0 .00 RPM |
| SRP007412_kidney | 0 .00 RPM | 14 .54 RPM |
| SRP007412_liver | 0 .00 RPM | 2 .62 RPM |
| SRP007412_testis | 0 .00 RPM | 7 .06 RPM |
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_869 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_869 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ptro_869 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 | |
|---|---|---|---|
| Choloepus hoffmanni | ENSCHOG00000000938 | 1 retrocopy | |
| Pan troglodytes | ENSPTRG00000010661 | 1 retrocopy | |
| Pan troglodytes | ENSPTRG00000020357 | 1 retrocopy |
retro_ptro_869 ,
|