RetrogeneDB ID: | retro_pabe_1653 | ||
Retrocopy location | Organism: | Orangutan (Pongo abelii) | |
| Coordinates: | 19:59220170..59221482(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | PTCD3 | ||
| Ensembl ID: | ENSPPYG00000012216 | ||
| Aliases: | PTCD3, MRP-S39 | ||
| Description: | pentatricopeptide repeat-containing protein 3, mitochondrial precursor [Source:RefSeq peptide;Acc:NP_001126041] |
Retrocopy-Parental alignment summary:
>retro_pabe_1653
ATGGCAGCTGTAGCTGCTGTTCACTGGCTGGGGCTCTGCAGCAGGCTTGACCAGCCATTGACGGGTCAGCCGGCAGGTCT
GTGTGAACAGGCACATAGCTGCAGATTTTATTCTGGAAGTGCAACCCTCTCAAATATTGAAGGAACTGATATAACAGGGA
TTGAAGCAGTAGTAATTCCAAAAAAGAAAACTTGGGATAAAGTAGCCATTCTTCAGGCTCTTGCATTCACAGTAAACAGG
GTTCCCATGGCTGTACCTAGCGCATTTCAAGATAATCCTTACCTCATACCAACATCCTCTTCAGAATCTCGTTCATTTTT
ACTGGCAAAGAAATCTGGGGAGAATATGGCCAAGGTCATTATTAATTCATACACCAAATATTTTCAGAAGGACATAGCTG
AACCTCATATACTATGTTTAATGCCTGAGTACTTTGAACCTCAGATCAAAGACATAAGTGAAGCCACCCTCAAGGAACGA
ATCAAGCTCAGATAAGTCAAAGCCTCTGTGGACATGTTTGATCAGCTTTTGCAAGCAGGAACCACGGTGTCTCTTGGAAC
AACATATAGTCTCTCAGATTTATTGTGTTACTATGGTGACCAGGAGCCCTCAACTGATTATCATTTTCAACAAACTGAAC
AGTCAAAAGAATTGGAAGAGGAAAATAATAAGCGGTCTAGGAGGAAAGCTGGTCATCAGTTTGGAGTTACCTGGTGAGCA
AAAAATAACGCTGAGAGAATCTTTTCTCTGATGCCAGAGAAAAATGCACATTCCTATTGCACAGTGATCCGAGGAATGGT
GAAGCACCAAGCTTATGAGCAGGCATTAAACCTGTACACTGAGTTACTAAACAACAGACTCTGTGCTGGTGTATACACAT
TTAATGCAGTGATTGAAGCAACAGTATTGGTGATAAATAAGAAATTTGAGGAAGAATGGAATAATATACTGGAGCTGCTA
AGACAAATGGTTGCACAGAAGGTGAAACCAAATCTACAGACTTTTAATACCATTCTGAAATGTCTCTGAAGATTTTATGT
ACTTGCAGGATTGCCAGCCTTACAGATTCTACGTGAAATGAAAGCCATCAGAATAGAACCCTCGCTTGCAACATATCACC
ATATTATTCAGCTGTTTTATCAGCCTGGAAGCCCTTCAAAGGGATCATCTTTCATCATCTATGATATAATGAATGAATTA
AAGGGAAAGAGATTTTCCTCCAAAGGACCTGGATGATGATAAGTTTTTTCAGTCAGCCATGAGAGTATCCTCATCTCTCA
GAGATCTAGAACTTGCCTAGCAAATACACGGC
ORF - retro_pabe_1653 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 82.88 % |
| Parental protein coverage: | 63.43 % |
| Number of stop codons detected: | 4 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MAGVSAVRWLGLRSRLGQPLTGRRAGLCKQARSCRFYSGSATLSKVEGTDITGIEEVVIPKKKTWDKVAV |
| MA.V.AV.WLGL.SRL.QPLTG..AGLC.QA.SCRFYSGSATLS..EGTDITGIE.VVIPKKKTWDKVA. | |
| Retrocopy | MAAVAAVHWLGLCSRLDQPLTGQPAGLCEQAHSCRFYSGSATLSNIEGTDITGIEAVVIPKKKTWDKVAI |
| Parental | LQALASTVNRDTTSVPYVFQDDPYLIPASSLESRLFLLAKKSGENVAKFIINSYPKYFQKDIAEPHIPCL |
| LQALA.TVNR....VP..FQD.PYLIP.SS.ESR.FLLAKKSGEN.AK.IINSY.KYFQKDIAEPHI.CL | |
| Retrocopy | LQALAFTVNRVPMAVPSAFQDNPYLIPTSSSESRSFLLAKKSGENMAKVIINSYTKYFQKDIAEPHILCL |
| Parental | MPEYFEPQIKDISEAALKERIELRKVKASVDMFDQLLQAGTTVSLETTNSLLDLLCYFGDQEPSTDYHFQ |
| MPEYFEPQIKDISEA.LKERI.LR.VKASVDMFDQLLQAGTTVSL.TT.SL.DLLCY.GDQEPSTDYHFQ | |
| Retrocopy | MPEYFEPQIKDISEATLKERIKLR*VKASVDMFDQLLQAGTTVSLGTTYSLSDLLCYYGDQEPSTDYHFQ |
| Parental | QTEQSEALEVENDETSRRKAGHQFGVTWQAKNNAERIFSLMPEKNAHSYCTMIRGMVKHRAYEQALNLYT |
| QTEQS..LE.EN...SRRKAGHQFGVTW.AKNNAERIFSLMPEKNAHSYCT.IRGMVKH.AYEQALNLYT | |
| Retrocopy | QTEQSKELEEENNKRSRRKAGHQFGVTW*AKNNAERIFSLMPEKNAHSYCTVIRGMVKHQAYEQALNLYT |
| Parental | ELLNNRLHADVYTFNALTEATVCVINEKFEEKWSKIQELLRHMVAQKVKPNLQTFNTILKCLRRFHVFAR |
| ELLNNRL.A.VYTFNA..EATV.VIN.KFEE.W..I.ELLR.MVAQKVKPNLQTFNTILKCL.RF.V.A. | |
| Retrocopy | ELLNNRLCAGVYTFNAVIEATVLVINKKFEEEWNNILELLRQMVAQKVKPNLQTFNTILKCL*RFYVLAG |
| Parental | SPALQILREMKAIGIEPSLATYHHIIHVFDQPGDPLKRSSFIIYDIMNELMGKRFS-PKDPDDDKFFQSA |
| .PALQILREMKAI.IEPSLATYHHII..F.QPG.P.K.SSFIIYDIMNEL.GKRFS.PKD.DDDKFFQSA | |
| Retrocopy | LPALQILREMKAIRIEPSLATYHHIIQLFYQPGSPSKGSSFIIYDIMNELKGKRFS>PKDLDDDKFFQSA |
| Parental | MSICSSLRDLELAYQVHG |
| M...SSLRDLELA.Q.HG | |
| Retrocopy | MRVSSSLRDLELA*QIHG |
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 | 54 .85 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 132 .42 RPM |
| SRP007412_heart | 0 .00 RPM | 65 .75 RPM |
| SRP007412_kidney | 0 .00 RPM | 82 .44 RPM |
| SRP007412_liver | 0 .03 RPM | 80 .54 RPM |
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_1653 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_1653 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_pabe_1653 has 2 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Homo sapiens | retro_hsap_2017 |
| Gorilla gorilla | retro_ggor_1461 |
Parental genes homology:
Parental genes homology involve 4 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Homo sapiens | ENSG00000132300 | 1 retrocopy | |
| Gorilla gorilla | ENSGGOG00000001793 | 1 retrocopy | |
| Nomascus leucogenys | ENSNLEG00000002493 | 1 retrocopy | |
| Pongo abelii | ENSPPYG00000012216 | 1 retrocopy |
retro_pabe_1653 ,
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