RetrogeneDB ID: | retro_ptro_1373 | ||
Retrocopy location | Organism: | Chimpanzee (Pan troglodytes) | |
| Coordinates: | 19:45206432..45207861(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | PATL1 | ||
| Ensembl ID: | ENSPTRG00000003697 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_ptro_1373
AAGATTCTGCGTTCAAAGCCTGTCCATGTTCGGCCCCCAATGCCACCGTGTTATCCTGGTCCCTATGATGAGAGGATGCC
TCCAAATCAGCTCTACAGTGTCCTGAACTCTTCCTTCCTGGGTCACCCTTTTCCTCCTAGTGTTCCTCCTGTTCTCAGCC
CCCTTTAGAGAGCACAGCTTCTTGGAGGAGCACAGCTACAGCCTGGACAGATGTCTCCCAGCCAGTTTGCATGGGTCCCT
GGATTTGTTGGTAGTCCACATGCTGCTATGAATCCCAAGTTGCTACAAGGGCAAGTTGGGCAGATGCTTCCCCCAGCACC
AGGCTTCCATGCCTTCTTTAGTGCTCCACCCTCTGCTACACCACCTCCACAGCAGTGCCCTCCTGGCCCAGGACCTCACT
TGCAAAACTTAAGATCTCAAGTCCCAGTGTTTAGACTGGACGCAACTCCCCTCCATCCACAGCACCATTGACTCTTGCAT
CAGAGACAGCAACAGAATAGAAATCAGCATCAGAATCTCAGTGGTGCAGGAGATAGAGGAAGTCACTGGAGCAGTCATCA
AGATCATCTCCGAAAGGATCCATATGCCAGTCTCATGTTGCTGTGGGAAAAGGATTGGGCCTCTAAAATTCAGATGATGC
AACTGCAAAGCAATGATCCCCACCTGGATGATTTTTATTACCAGAATTACTTTGAAAAACTGGAGAAACCATCAGCTGCT
GAAGAAATACGAGGTGATGGCCCTAAAAAGGAGCATAACAAGCTTATTACCCCTCAAGTGGCCAAACTGGAGTGCACCTA
TAAGCCAGTACAATTTGTGGGCTCTTTGGGAAAGCTTACTGTTTCTAGTGTGAATAATCCCTGAAAAATGATTGATGCTG
TTGTGACATCTTGGAGTGAGGATGATGAGATAAAAGAAAAACAAATTCGAGACAAGAGGAGAAAAACCCGTCATAATTAA
GAAAACCTACAGTTTACTCCTTGATGTGGAGGACTATGAAAGACGTTATCTCCTAAGTCTAAGACAGCGACCTGCTCTAA
TGGATGAGCGAAAGTACGGATTTTGTAGCATGTATGACAACTTAAGAGGGAAACAGCCTGGACAAGAGAGGCCTAGTGAT
GACCGCTTTGTACAGATCATGTGTATCCAAAAAGGGAAGACAATGGTTGCCCGTATTCTTCCTTTCCTCTCCACAGAGCA
AGCAGCTGACATTTTCATGACAACAGCCAGGGACCTCCCTTTCCTTATCAAGAAAGATGCACAAGATGAGGTGCTGCCAT
GTTTACTGAGTCCCTTCTCTCTCCTCCTCTATCATCTTCCAACAGTGACTATCACCAGCCTTTTGCAACAGCTAATGAAC
CTACCTCAAAGTGCAGCTACACCAGCTCCCTCCAATCCTCACTTCACTGCTGTGCTCCAGAACAAATTC
ORF - retro_ptro_1373 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 85.8 % |
| Parental protein coverage: | 62.08 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | QILCPKPVHVRPPMPPRYPAPYGERMSPNQLCSVPNSSLLGHPFPPSVPPVLSPLQRAQLLGGAQLQPGR |
| .IL..KPVHVRPPMPP.YP.PY.ERM.PNQL.SV.NSS.LGHPFPPSVPPVLSPL.RAQLLGGAQLQPG. | |
| Retrocopy | KILRSKPVHVRPPMPPCYPGPYDERMPPNQLYSVLNSSFLGHPFPPSVPPVLSPL*RAQLLGGAQLQPGQ |
| Parental | MSPSQFARVPGFVGSPLAAMNPKLLQGRVGQMLPPAPGFRAFFSAPPSTAPPPQQHPPGPGPHLQNLRSQ |
| MSPSQFA.VPGFVGSP.AAMNPKLLQG.VGQMLPPAPGF.AFFSAPPS..PPPQQ.PPGPGPHLQNLRSQ | |
| Retrocopy | MSPSQFAWVPGFVGSPHAAMNPKLLQGQVGQMLPPAPGFHAFFSAPPSATPPPQQCPPGPGPHLQNLRSQ |
| Parental | APMFRPDTTHLHPQHRRLLHQRQQQNRNQHRNLNGAGDRGSHRSSHQDHLRKDPYANLMLQREKDWVSKI |
| .P.FR.D.T.LHPQH..LLHQRQQQNRNQH.NL.GAGDRGSH.SSHQDHLRKDPYA.LML..EKDW.SKI | |
| Retrocopy | VPVFRLDATPLHPQHH*LLHQRQQQNRNQHQNLSGAGDRGSHWSSHQDHLRKDPYASLMLLWEKDWASKI |
| Parental | QMMQLQSTDPYLDDFYYQNYFEKLEKLSAAEEIQGDGPKKERTKLITPQVAKLEHAYKPVQFEGSLGKLT |
| QMMQLQS.DP.LDDFYYQNYFEKLEK.SAAEEI.GDGPKKE..KLITPQVAKLE..YKPVQF.GSLGKLT | |
| Retrocopy | QMMQLQSNDPHLDDFYYQNYFEKLEKPSAAEEIRGDGPKKEHNKLITPQVAKLECTYKPVQFVGSLGKLT |
| Parental | VSSVNNPRKMIDAVVTSRSEDDETKEKQVRDKRRKT-LVIIEKTYSLLLDVEDYERRYLLSLEEERPALM |
| VSSVNNP.KMIDAVVTS.SEDDE.KEKQ.RDKRRKT...I..KTYSLLLDVEDYERRYLLSL...RPALM | |
| Retrocopy | VSSVNNP*KMIDAVVTSWSEDDEIKEKQIRDKRRKT>VII-KKTYSLLLDVEDYERRYLLSL-RQRPALM |
| Parental | DDRKHKICSMYDNLRGKLPGQERPSDDHFVQIMCIRKGKRMVARILPFLSTEQAADILMTTARNLPFLIK |
| D.RK...CSMYDNLRGK.PGQERPSDD.FVQIMCI.KGK.MVARILPFLSTEQAADI.MTTAR.LPFLIK | |
| Retrocopy | DERKYGFCSMYDNLRGKQPGQERPSDDRFVQIMCIQKGKTMVARILPFLSTEQAADIFMTTARDLPFLIK |
| Parental | KDAQDEVLPCLLSPFSLLLYHLPSVSITSLLRQLMNLPQSAATPAPSNPHLTAVLQNKF |
| KDAQDEVLPCLLSPFSLLLYHLP.V.ITSLL.QLMNLPQSAATPAPSNPH.TAVLQNKF | |
| Retrocopy | KDAQDEVLPCLLSPFSLLLYHLPTVTITSLLQQLMNLPQSAATPAPSNPHFTAVLQNKF |
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 | 2 .56 RPM | 18 .55 RPM |
| SRP007412_cerebellum | 1 .94 RPM | 47 .54 RPM |
| SRP007412_heart | 0 .35 RPM | 36 .20 RPM |
| SRP007412_kidney | 0 .81 RPM | 53 .95 RPM |
| SRP007412_liver | 0 .07 RPM | 62 .75 RPM |
| SRP007412_testis | 2 .95 RPM | 85 .57 RPM |
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_1373 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_1373 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ptro_1373 has 1 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Homo sapiens | retro_hsap_2059 |
Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Homo sapiens | ENSG00000166889 | 1 retrocopy | |
| Pan troglodytes | ENSPTRG00000003697 | 1 retrocopy |
retro_ptro_1373 ,
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