RetrogeneDB ID: | retro_ptro_1700 | ||
Retrocopy location | Organism: | Chimpanzee (Pan troglodytes) | |
| Coordinates: | 2B:146997178..146997870(-) | ||
| Located in intron of: | ENSPTRG00000012509 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | SFXN4 | ||
| Ensembl ID: | ENSPTRG00000002990 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_ptro_1700
TTTCTTCAGTGGACACAATTATTAGATCTTAAAAATCTGGTCATTTCAATTGAGAAAATAGAGGCAACTACTCTTTGTAA
ATAAAGAGGCATCCAGGCCTGACTTGGAGGACCCAATGATACAAGAAACTTTGAAGAGCAGTCTCTCAACAGGGCATCAT
GACAGCAGCAAACTGAACCCTGCCTTTTTCAGCCTATAGCTATATTGCCTTTCATGATGCCCATGGTATTTCTGTAGATG
ATGCCAGCAAAAGGGAGAAAGTCCATGGTTTTACCCCAGGTTTCTTATAAACTTACATATAATTATAGCACACAGCATTA
TCAGCAGAAATGCAAACTGTAATCATTGCCAAAGAGTATATTACTAGGGGAAGGAGTAATTGCTTCTTCAATCTTCTTTG
GAATAATCCCTCATTTGGGCCCAAATGAAGTATGCCCAGGATAATCTTTAGATGAAAAAAACCTGACCTATCATCTTTCT
CAACCAAGTCAATGGAATGAATGTTTTTGCATTCCAAAGTTTTGGGCCCATTCAAGGGATCAAGGTAATGGGCAAGGAAG
GCAATGTCATGGACCATCTCAGAAGAGCTGGGAAAAAGGCTGTTAAAGAAACAGCAATATCCAGGGAAGCGCTGTTTGGG
ACATTAGCTTTTATTCCGATGTCTTCAACTATTTTTTAAAAAGACACAGTAC
ORF - retro_ptro_1700 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 51.24 % |
| Parental protein coverage: | 69.44 % |
| Number of stop codons detected: | 4 |
| Number of frameshifts detected: | 5 |
Retrocopy - Parental Gene Alignment:
| Parental | FLQWTELLDPTNVFISVESIENS-RQLLCTNEDASSPASADQRIQEAWKRSLATVHPDSSNLIPK-LFRP |
| FLQWT.LLD..N....V.SIE...RQLL..N..AS.P...D..IQE..K.SL.T.H.DSS.L.P..LF.P | |
| Retrocopy | FLQWTQLLDLKNL---VISIEKI>RQLLFVNKEASRPDLEDPMIQETLKSSLSTGHHDSSKLNPA<LFQP |
| Parental | AAFLPFMAPTVFLSMTPLKGIKSVILPQVFLCAYMAAFNSINGNRSYTCK--PLERSLLMA-GAVASSTF |
| .A.LPFM.P.VFL.M.P.KG.KS..LPQV....Y....N.........CK...L..S.L...G..ASS.F | |
| Retrocopy | IAILPFMMPMVFL*MMPAKGRKSMVLPQV---SYKLTYNYSTQHYQQKCKL*SLPKSILLGEGVIASSIF |
| Parental | LGVIPQ-FVQMKYGLTGPWIKRLLPVIFLVQASGMNVYMSRSLESIKGIAVMDKEGNVLGHSRIAGTKAV |
| .G.IP....QMKY.......K...P.IFL.Q..GMNV....S...I.GI.VM.KEGNV..H.R.AG.KAV | |
| Retrocopy | FGIIPH>WAQMKYAQDNL*MKKT*PIIFLNQVNGMNVFAFQSFGPIQGIKVMGKEGNVMDHLRRAGKKAV |
| Parental | RETLASRIVLFGTSALIP-EVFTY-FFKRTQY |
| .ET..SR..LFGT.A.IP..VF.Y.FFK.TQY | |
| Retrocopy | KETAISREALFGTLAFIP<DVFNY<FFKKTQY |
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 | 8 .26 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 10 .58 RPM |
| SRP007412_heart | 0 .03 RPM | 14 .98 RPM |
| SRP007412_kidney | 0 .00 RPM | 17 .23 RPM |
| SRP007412_liver | 0 .10 RPM | 10 .77 RPM |
| SRP007412_testis | 0 .00 RPM | 18 .44 RPM |
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_1700 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_1700 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ptro_1700 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Dipodomys ordii | ENSDORG00000004492 | 1 retrocopy | |
| Pan troglodytes | ENSPTRG00000002990 | 1 retrocopy |
retro_ptro_1700 ,
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