RetrogeneDB ID: | retro_ptro_2385 | ||
Retrocopy location | Organism: | Chimpanzee (Pan troglodytes) | |
| Coordinates: | 6:119734404..119734970(+) | ||
| Located in intron of: | ENSPTRG00000018549 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | SSX9 | ||
| Ensembl ID: | ENSPTRG00000021857 | ||
| Aliases: | None | ||
| Description: | synovial sarcoma, X breakpoint 9 [Source:HGNC Symbol;Acc:19655] |
Retrocopy-Parental alignment summary:
>retro_ptro_2385
ATGAACGGAGACAGCACCTTTGCAAAGAGACCCAGGGATGATGCTCAGATATCAGAGAAGAGACACAAGGCCTTCAATGA
TATTGCCAGATACTTATCTAATAAAGAGTGGGGAAAGCTGAAAAACTCAGAGAAAATCACCCATGTGTATATGAAGAGAA
ACTATGAGACCATGACTAAACTAGGTCTCTAGGCCACCCTCCCAACTTTCATGTATAATACATGGGCTGCAGAATTCCAG
GGGAATGATTCTGATATAGACTAAAACTGCAGGAATCAGGATGAATATCCTCAGATGGCTTTCGGCATGCTACAAGGGAA
CTTTCCAAAGATGATGCCCAAGAAGCCAGCAGAGGAAGGAAATGATTTGAAGGGAGTGCCAGAAGCATCTGGCTCACAAA
ACAATGGGAAACAGCGGTGTCCCCTGGGAAAAGAAAGTACCTCTGAGAAGACTAACAAGACATCTAGACCCAAGAAAAGG
GGGAACATGTCTGGACCCACAGACTGCGAGAGAGAAAGTATCTAGTGATTTATGAAGAGATCAGAGACCCTGAGGAAGAT
GACAAA
ORF - retro_ptro_2385 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 70.0 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MNGDDAFARRPKAGAQIPEKIQKAFDDIAKYFSKKEWEKMKSSEKISYVYMKRKYEAMTKLGFKATLPPF |
| MNGD..FA.RP...AQI.EK..KAF.DIA.Y.S.KEW.K.K.SEKI..VYMKR.YE.MTKLG..ATLP.F | |
| Retrocopy | MNGDSTFAKRPRDDAQISEKRHKAFNDIARYLSNKEWGKLKNSEKITHVYMKRNYETMTKLGL*ATLPTF |
| Parental | MRNTGATDLQGNDFDNDRNHRNQVERPQMTFGRLQGIFPKIMPKKPAEVGNDSK-VPEASGSQNNGKQLC |
| M.NT.A...QGND.D.D.N.RNQ.E.PQM.FG.LQG.FPK.MPKKPAE.GND.K.VPEASGSQNNGKQ.C | |
| Retrocopy | MYNTWAAEFQGNDSDID*NCRNQDEYPQMAFGMLQGNFPKMMPKKPAEEGNDLKGVPEASGSQNNGKQRC |
| Parental | PPGKRTTSEKINKASGP-KRG-KHAWTHRLSERKQLVIYEEISDPEEDNE |
| P.GK..TSEK.NK.S.P.KRG..H.WTHRL.ERK.LVIYEEI.DPEED.. | |
| Retrocopy | PLGKESTSEKTNKTSRPKKRG<EHVWTHRLRERKYLVIYEEIRDPEEDDK |
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 .07 RPM | 0 .00 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 0 .00 RPM |
| SRP007412_heart | 0 .12 RPM | 0 .00 RPM |
| SRP007412_kidney | 1 .31 RPM | 0 .00 RPM |
| SRP007412_liver | 0 .16 RPM | 0 .00 RPM |
| SRP007412_testis | 0 .00 RPM | 1 .05 RPM |
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_2385 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_2385 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ptro_2385 has 5 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Homo sapiens | retro_hsap_3512 |
| Gorilla gorilla | retro_ggor_2374 |
| Pongo abelii | retro_pabe_2903 |
| Macaca mulatta | retro_mmul_1862 |
| Callithrix jacchus | retro_cjac_2373 |
Parental genes homology:
Parental genes homology involve 3 parental genes, and 5 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000014776 | 1 retrocopy | |
| Pan troglodytes | ENSPTRG00000021857 | 1 retrocopy |
retro_ptro_2385 ,
|
| Ictidomys tridecemlineatus | ENSSTOG00000015375 | 3 retrocopies |