RetrogeneDB ID: | retro_sscr_201 | ||
Retrocopy location | Organism: | Pig (Sus scrofa) | |
| Coordinates: | 1:275565346..275565908(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | RRAS | ||
| Ensembl ID: | ENSSSCG00000003183 | ||
| Aliases: | None | ||
| Description: | related RAS viral (r-ras) oncogene homolog [Source:HGNC Symbol;Acc:10447] |
Retrocopy-Parental alignment summary:
>retro_sscr_201
TACCGGCTCGTGGTGGTCTGTGGAGGCGGCGTGGGCAAGTCGGCGCTCACCATCCAGTTCATCCAGTCCTATGTTGTAAC
GGATTATGATCCAACCATCGAGGATTCCTACACAAAGCAATGTGTATTAGATGACCGGGCAGGCCGGCTAGATATTCTGG
ATACAGCAGGACAAGAGGAGTTTGGAGCTATGAGAGAACAGTATATGAGAACTGGCAAGGGTTTCCTGTTGGTCTTTTCA
GTCACAGATAGAGGCAGTTTTGAAGAAATCTCTAAGTTTCAAAGACAGATTCTCAGAGCAAAGGATCGTGAACGAGTTTC
TAATGATTTTAACTGGTAATAAAGTAGCTCTGGATCATCAAAGACAACGCAGGAAGGGACAGCAAGTGGCACGGCAGCTT
AAAGTAACATACATGGAGGCATCAGCAAAGATTAGGATGAATGTGGATCAAGCTATCCATGAACTTATCCTGGTTATAAG
GAAATTTCAAGAGCAGGAATGTCCTCCTTCACCAGAACCAATATGGAAAGAAAAAGACAAGAAAGGCTGCCATTGTGTCA
TT
ORF - retro_sscr_201 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 61.05 % |
| Parental protein coverage: | 86.24 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | HKLVVVGGGGVGKSALTIQFIQSYFVSDYDPTIEDSYTKICTVDGVPARLDILDTAGQEEFGAMREQYMR |
| ..LVVV.GGGVGKSALTIQFIQSY.V.DYDPTIEDSYTK.C..D....RLDILDTAGQEEFGAMREQYMR | |
| Retrocopy | YRLVVVCGGGVGKSALTIQFIQSYVVTDYDPTIEDSYTKQCVLDDRAGRLDILDTAGQEEFGAMREQYMR |
| Parental | AGHGFLLVFAINDRQSFNEVGKLFTQILRVKDRD-DFPIVLVGNKADLETQRQVPRSEASAFSNSHHVAY |
| .G.GFLLVF...DR.SF.E..K...QILR.KDR...F...L.GNK..L..QRQ..R...........V.Y | |
| Retrocopy | TGKGFLLVFSVTDRGSFEEISKFQRQILRAKDRE>EFLMILTGNKVALDHQRQ--RRKGQQVARQLKVTY |
| Parental | FEASAKLRLNVDEAFEQLVRAVRKFQEQELPPSPPSAPRKKD-RSCPCIL |
| .EASAK.R.NVD.A...L....RKFQEQE.PPSP......KD...C.C.. | |
| Retrocopy | MEASAKIRMNVDQAIHELILVIRKFQEQECPPSPEPIWKEKDKKGCHCVI |
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 |
|---|---|---|
| SRP014902_placenta | 43 .80 RPM | 61 .19 RPM |
| SRP014902_testis | 16 .55 RPM | 20 .51 RPM |
| SRP018288_heart | 14 .22 RPM | 30 .15 RPM |
| SRP018288_kidney | 6 .30 RPM | 16 .15 RPM |
| SRP018288_liver | 4 .48 RPM | 14 .39 RPM |
| SRP018288_lung | 9 .37 RPM | 57 .02 RPM |
| SRP018856_adipose | 16 .42 RPM | 171 .02 RPM |
| SRP035408_brain | 4 .10 RPM | 10 .42 RPM |
| SRP035408_liver | 4 .32 RPM | 21 .61 RPM |
Sus scrofa was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_sscr_201 retrocopy.
Sus scrofa was not studied using FANTOM5 data.
retro_sscr_201 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_sscr_201 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Otolemur garnettii | ENSOGAG00000010243 | 1 retrocopy | |
| Sus scrofa | ENSSSCG00000003183 | 2 retrocopies |
retro_sscr_201 , retro_sscr_570,
|
| Tursiops truncatus | ENSTTRG00000005524 | 1 retrocopy |