RetrogeneDB ID: | retro_sscr_278 | ||
Retrocopy location | Organism: | Pig (Sus scrofa) | |
| Coordinates: | 11:23314064..23314375(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSSSCG00000022876 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | PDCD5 | ||
| Ensembl ID: | ENSSSCG00000002860 | ||
| Aliases: | None | ||
| Description: | programmed cell death 5 [Source:HGNC Symbol;Acc:8764] |
Retrocopy-Parental alignment summary:
>retro_sscr_278
CTTGAGGCACTGAGGAAGCTGAAGCTGGCCGAGCTGCAGAGGAAGCACAGAGATCCTGGCGATGCAGCAAAAGAAGAAGC
AAAGCACAGGGGAGCAGAAATGAGAAACAGTATCTCAGCCCAAGTTCTGGATCAGTCAGCCTGGGCCTGGTTAAGTAACT
TAGCACTTGCAAAGCCTGAGAAACTAAAGCAGGAGAGGACTACCTGATACAGATAGCACAGTATGGACAGCTAAGTGGGA
CGGTATCAGGACAAGGTTTAATAGAAATCCTCAAAAATGTAAGCCAAAAACCAGAAAACAACTGTTCCATT
ORF - retro_sscr_278 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 74.29 % |
| Parental protein coverage: | 83.2 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | LEALRKQRLAELQAKHGDPGDAAQQEAKHREAEMRNSILAQVLDQSARARLSNLALVKPEK-TKAVENYL |
| LEALRK..LAELQ.KH.DPGDAA..EAKHR.AEMRNSI.AQVLDQSA.A.LSNLAL.KPEK.TKA.E.YL | |
| Retrocopy | LEALRKLKLAELQRKHRDPGDAAKEEAKHRGAEMRNSISAQVLDQSAWAWLSNLALAKPEK<TKAGEDYL |
| Parental | IQMARYGQLSGKVSEQGLIEILEKVSQQTEKKTTV |
| IQ.A.YGQLSG.VS.QGLIEIL..VSQ..E..... | |
| Retrocopy | IQIAQYGQLSGTVSGQGLIEILKNVSQKPENNCSI |
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 | 0 .00 RPM | 13 .01 RPM |
| SRP014902_testis | 0 .00 RPM | 21 .64 RPM |
| SRP018288_heart | 0 .08 RPM | 67 .32 RPM |
| SRP018288_kidney | 0 .00 RPM | 36 .25 RPM |
| SRP018288_liver | 0 .00 RPM | 20 .79 RPM |
| SRP018288_lung | 0 .00 RPM | 9 .47 RPM |
| SRP018856_adipose | 0 .00 RPM | 54 .81 RPM |
| SRP035408_brain | 0 .00 RPM | 90 .07 RPM |
| SRP035408_liver | 0 .00 RPM | 32 .56 RPM |
Sus scrofa was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_sscr_278 retrocopy.
Sus scrofa was not studied using FANTOM5 data.
retro_sscr_278 was not experimentally validated.