RetrogeneDB ID: | retro_sscr_281 | ||
Retrocopy location | Organism: | Pig (Sus scrofa) | |
| Coordinates: | 11:37257612..37258294(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | PDHA1 | ||
| Ensembl ID: | ENSSSCG00000023643 | ||
| Aliases: | None | ||
| Description: | pyruvate dehydrogenase (lipoamide) alpha 1 [Source:HGNC Symbol;Acc:8806] |
Retrocopy-Parental alignment summary:
>retro_sscr_281
CATGGTTTTCACTTTACTCATGGACTTTCTGTGAAAGAAATTCTTGCAGAGTTTATAAGATGAATAGGAGGTTGTGCTAA
AGGAAAAGAAAGATCCATACACATATACGCCAAGAATTTCTATGGGAGCAATGGCATCTTGGGAGCTCAGGTGACTCTGG
GGGCTGGGCTTGCTTTGGCCTGTAAGTATAATGGAAAAAATGAGGTCTGTTTGACTTCGTATGGCAATGGCACTGCTAAT
GAGGATCAGGTATACAAAGCTGACAATATGGCAGCTTTGTGGAAATTACCTTGTGTTTTCAACTTTGAGAATAACCACTG
TGGGATGGAAACATCTGTGGAGAGAGCAGCAGCCATCACTGACTACTACAAGAGAGACAACTTCATTCTGGGCTGAGAGT
AGATGGAATGGATATCCTGAGTGTCTGGGAGGCCACAGGGTTTGCAGCTTCCTATTGTAGATCAGGAAAGGGGAACATAC
TGACGGAGCTGCAGACTTACCATTACCATGGGCATATGAGTGATCCTGGTGTCAGTTATGGTACCTGAGAAGAAATTCAG
GAAATAGGAAGAGGGACCCTATCATTGTTCTCAAGGATAGGATGGTGAACAGCAGTCTTATCAGTGTTGAAGAATTAAAC
AAAATTGATGTTGAAGTGAGGAAAGAAATTGAGGATGCTGCG
ORF - retro_sscr_281 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 74.14 % |
| Parental protein coverage: | 58.97 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | HGFTFTRGLSVREILAELTGRRGGCGKGKGGSMHMYAKNFYGGNGIVGAQVPLGAGIALACKYNGKDEVC |
| HGF.FT.GLSV.EILAE.....GGC.KGK..S.H.YAKNFYG.NGI.GAQV.LGAG.ALACKYNGK.EVC | |
| Retrocopy | HGFHFTHGLSVKEILAEFIR*IGGCAKGKERSIHIYAKNFYGSNGILGAQVTLGAGLALACKYNGKNEVC |
| Parental | LTLYGDGAANQGQIFEAYNMAALWKLPCVFICENNRYGMGTSVERAAASTDYYKRGDFI-PGLRVDGMDI |
| LT.YG.G.AN..Q...A.NMAALWKLPCVF..ENN..GM.TSVERAAA.TDYYKR..FI..GLRVDGMDI | |
| Retrocopy | LTSYGNGTANEDQVYKADNMAALWKLPCVFNFENNHCGMETSVERAAAITDYYKRDNFI<SGLRVDGMDI |
| Parental | LCVREATRFAAAYCRSGKGPILMELQTYRYHGHSMSDPGVSYRTREEIQEV-RSKSDPIMLLKDRMVNSN |
| L.V.EAT.FAA.YCRSGKG.IL.ELQTY.YHGH.MSDPGVSY.T.EEIQE..R.....I..LKDRMVNS. | |
| Retrocopy | LSVWEATGFAASYCRSGKGNILTELQTYHYHGH-MSDPGVSYGT*EEIQEI<RKRDPIIV-LKDRMVNSS |
| Parental | LASVEELKEIDVEVRKEIEDAA |
| L.SVEEL..IDVEVRKEIEDAA | |
| Retrocopy | LISVEELNKIDVEVRKEIEDAA |
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 | 28 .67 RPM |
| SRP014902_testis | 0 .00 RPM | 69 .87 RPM |
| SRP018288_heart | 0 .00 RPM | 888 .93 RPM |
| SRP018288_kidney | 0 .00 RPM | 1343 .52 RPM |
| SRP018288_liver | 0 .00 RPM | 173 .34 RPM |
| SRP018288_lung | 0 .00 RPM | 86 .35 RPM |
| SRP018856_adipose | 0 .00 RPM | 671 .62 RPM |
| SRP035408_brain | 0 .00 RPM | 105 .06 RPM |
| SRP035408_liver | 0 .00 RPM | 161 .16 RPM |
Sus scrofa was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_sscr_281 retrocopy.
Sus scrofa was not studied using FANTOM5 data.
retro_sscr_281 was not experimentally validated.