RetrogeneDB ID: | retro_pabe_2115 | ||
Retrocopylocation | Organism: | Orangutan (Pongo abelii) | |
| Coordinates: | 2b:47633131..47634178(-) | ||
| Located in intron of: | None | ||
Retrocopyinformation | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental geneinformation | Parental gene summary: | ||
| Parental gene symbol: | MTA2 | ||
| Ensembl ID: | ENSPPYG00000003161 | ||
| Aliases: | None | ||
| Description: | metastasis associated 1 family, member 2 [Source:HGNC Symbol;Acc:7411] |
Retrocopy-Parental alignment summary:
>retro_pabe_2115
ATGGCGGCCAGCATGTACCAGGTAGGAGATTTTGTCTACTTTGAGAATTCCTCCAGCAACCCATAAATAATCAGGATAGA
AAAACTCGACAAGACTGCAAGTGGCAACATGGAAGCAAAAGTAGTATGCTTTTACAGGTTACATGATATTTCCAACACAC
TGATAATGCTTGTGGACATGCATGCTAAAGAAATTGAGGAAGAATCTGAAACAATATTTGACCCTTACTTGACCAATACT
CAGAAACATCAATCGAAACATAAGTTACTTTCTTTGTCACCCCAATATGAATCTTTGCCTTCAACACATATTAGGGGAAA
TTGCAGTGTTGCCTTATGAATGAGACAGAATCAGTATTGTCATATCTTCATAAAAAGGATAATTTCTTCTACTTATTGAT
CCTGACCCCTCATCGAAAACACTATTAGCTGATGAAGGTGAATTCAGAATGGGACCTAGATATCAAGTAGACGTCCCAGA
AATGCTCATAGAAGGAGAATAAGATGAGAGGGAACAGTGAAAATGGAAAGTTAAAGTTTGGGGATCCAAATGGCCCACTG
AAAGATTGATCAATTAACCAGTTTTTAATTGTAGCAAGTACTATTGGGACACTCCCTAGACCTCTCTATTGCAGCAGTTC
TTTGAGGCAGCCTAATTTGCATATGAGTGCTGCTGCAGCTTCCCAAGACATCACCTTCTTTCATGCTATCGATACATTGT
GTAGACACAGCTATGATTTGAGCAGTGCAATTAGTGTCTCAGTACCACTTGAAGAAGCTGTTTTATGCAGAGATAAATTG
GAAGAATGGTCAGCCTCTTAAGCTAGCTTATTTGAAGAGGTACTGGAAAAAATACGGCAAAGACTTCAACGACATACACC
AAAACTTTTTCCCTTGGAAATCATTGACTAGCATCACTGAATGTTATTTCTTGTGGAGAACTACTGACAGATATGTGCAA
CAGAAATGGTTAAAAGCAGCAGAAACTGAGAGTAAGCTGAAACAAGTATATATCCCAATTTACAGCAAACCAAATCCCAA
CCAAATA
ATGGCGGCCAGCATGTACCAGGTAGGAGATTTTGTCTACTTTGAGAATTCCTCCAGCAACCCATAAATAATCAGGATAGA
AAAACTCGACAAGACTGCAAGTGGCAACATGGAAGCAAAAGTAGTATGCTTTTACAGGTTACATGATATTTCCAACACAC
TGATAATGCTTGTGGACATGCATGCTAAAGAAATTGAGGAAGAATCTGAAACAATATTTGACCCTTACTTGACCAATACT
CAGAAACATCAATCGAAACATAAGTTACTTTCTTTGTCACCCCAATATGAATCTTTGCCTTCAACACATATTAGGGGAAA
TTGCAGTGTTGCCTTATGAATGAGACAGAATCAGTATTGTCATATCTTCATAAAAAGGATAATTTCTTCTACTTATTGAT
CCTGACCCCTCATCGAAAACACTATTAGCTGATGAAGGTGAATTCAGAATGGGACCTAGATATCAAGTAGACGTCCCAGA
AATGCTCATAGAAGGAGAATAAGATGAGAGGGAACAGTGAAAATGGAAAGTTAAAGTTTGGGGATCCAAATGGCCCACTG
AAAGATTGATCAATTAACCAGTTTTTAATTGTAGCAAGTACTATTGGGACACTCCCTAGACCTCTCTATTGCAGCAGTTC
TTTGAGGCAGCCTAATTTGCATATGAGTGCTGCTGCAGCTTCCCAAGACATCACCTTCTTTCATGCTATCGATACATTGT
GTAGACACAGCTATGATTTGAGCAGTGCAATTAGTGTCTCAGTACCACTTGAAGAAGCTGTTTTATGCAGAGATAAATTG
GAAGAATGGTCAGCCTCTTAAGCTAGCTTATTTGAAGAGGTACTGGAAAAAATACGGCAAAGACTTCAACGACATACACC
AAAACTTTTTCCCTTGGAAATCATTGACTAGCATCACTGAATGTTATTTCTTGTGGAGAACTACTGACAGATATGTGCAA
CAGAAATGGTTAAAAGCAGCAGAAACTGAGAGTAAGCTGAAACAAGTATATATCCCAATTTACAGCAAACCAAATCCCAA
CCAAATA
ORF - retro_pabe_2115 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 62.71 % |
| Parental protein coverage: | 51.95 % |
| Number of stop codons detected: | 5 |
| Number of frameshifts detected | 4 |
Retrocopy - Parental Gene Alignment:
| Parental | MAANMYRVGDYVYFENSSSNPYLVRRIEELNKTANGNVEAKVVCLFRRRDISSSLNSLADSNAREFEEES |
| MAA.MY.VGD.VYFENSSSNP...R.IE.L.KTA.GN.EAKVVC..R..DIS..L..L.D..A.E.EEES | |
| Retrocopy | MAASMYQVGDFVYFENSSSNP*IIR-IEKLDKTASGNMEAKVVCFYRLHDISNTLIMLVDMHAKEIEEES |
| Parental | K---QPGVSEQQRHQLKHRELFLSRQFESLPATHIRGKCSVTL-LNETDILSQYLEKEDCFFYSLVF-DP |
| .....P.....Q.HQ.KH..L.LS.Q.ESLP.THIRG.CSV.L..NET.....YL.K.D.FFY.L...DP | |
| Retrocopy | ETIFDPYLTNTQKHQSKHKLLSLSPQYESLPSTHIRGNCSVAL<MNETESVLSYLHKKDNFFYLLIL<DP |
| Parental | VQKTLLADQGEIRVGCKYQAEIPDRLAEGESDHRNQQKMEMKVW-DPDNPLTDRQIDQFLVVARAVGTFA |
| ..KTLLAD.GE.R.G..YQ...P..L.EGE.D.R.Q.K...KVW.DP..PL.D..I.QFL.VA...GT.. | |
| Retrocopy | SSKTLLADEGEFRMGPRYQVDVPEMLIEGE*DEREQ*KWKVKVW>DPNGPLKD*SINQFLIVASTIGTLP |
| Parental | RALDCSSSIRQPSLHMSAAAASRDITLFHAMDTLQRNGYDLAKAMSTLVPQGGPVLCRDEMEEWSASEAM |
| R.L.CSSS.RQP.LHMSAAAAS.DIT.FHA.DTL.R..YDL..A.S..VP....VLCRD..EEWSAS.A. | |
| Retrocopy | RPLYCSSSLRQPNLHMSAAAASQDITFFHAIDTLCRHSYDLSSAISVSVPLEEAVLCRDKLEEWSAS*AS |
| Parental | LFEEALE-KYGKDFNDIRQDFLPWKSLASIVQFYYMWKTTDRYIQQKRLKAAEADSKLKQVYIPTYTKPN |
| LFEE.LE.KYGKDFNDI.Q.F.PWKSL.SI...Y..W.TTDRY.QQK.LKAAE..SKLKQVYIP.Y.KPN | |
| Retrocopy | LFEEVLE>KYGKDFNDIHQNFFPWKSLTSITECYFLWRTTDRYVQQKWLKAAETESKLKQVYIPIYSKPN |
| Parental | PNQI |
| PNQI | |
| Retrocopy | PNQI |
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 | 17 .53 RPM |
| SRP007412_cerebellum | 0 .24 RPM | 25 .29 RPM |
| SRP007412_heart | 0 .03 RPM | 7 .44 RPM |
| SRP007412_kidney | 0 .00 RPM | 26 .25 RPM |
| SRP007412_liver | 0 .00 RPM | 14 .99 RPM |
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_2115 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_2115 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_pabe_2115 has 3 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Homo sapiens | retro_hsap_2337 |
| Pan troglodytes | retro_ptro_1708 |
| Gorilla gorilla | retro_ggor_1773 |
Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Pongo abelii | ENSPPYG00000003161 | 1 retrocopy |
retro_pabe_2115 ,
|