RetrogeneDB ID: | retro_sscr_334 | ||
Retrocopy location | Organism: | Pig (Sus scrofa) | |
| Coordinates: | 13:126746090..126746597(+) | ||
| Located in intron of: | ENSSSCG00000011763 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | HLCS | ||
| Ensembl ID: | ENSSSCG00000012059 | ||
| Aliases: | None | ||
| Description: | holocarboxylase synthetase (biotin-(proprionyl-CoA-carboxylase (ATP-hydrolysing)) ligase) [Source:HGNC Symbol;Acc:4976] |
Retrocopy-Parental alignment summary:
>retro_sscr_334
CAGTACCAGGACATCAACTTATGGGTGAAGTGGCCCAATGATATTTATTACAGTGACCTCATGAATCTCAGTGGCATTCT
GGTTAACTCGACACTTATGGGAGAAACATTTTATATACTTATTGGCTGTGGCTTTAACGTGACTAACAGTAACCCTACCA
TATGCATCAACGGCCTCATCACAGGATACAATAAGAAACACAGTGCAGGACTGAGGCCCTTAAGAGCTGATTATCTCATT
GCTTGAACTGTGACTGTGCTGGAGAAACTGATCGATACACTTCAGGAGGAGGGGCGCAAGAGCGTTCTTCCTCTGTATTA
TAAATATTGGGTACACAGTGCTCAGCAATTCCACCTGGGAAGCGCGGAGGGACCAAAGCTGTGGATAATTGGCCTCGATG
ATTCTGGGTTCCTTCTGGTTCACCAGGAGAACGGCGAAGCGGTCACTATGCATCCTGATGGCAACTCCTTCAACATGCTG
AGAAACCTCACTGTGCCCAAGCGGCCT
ORF - retro_sscr_334 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 84.62 % |
| Parental protein coverage: | 68.15 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | QYQDINLRVKWPNDIYYNDLMKLGGVLVNSTLMGETFYILVGCGFNVTNSNPTICINDLITEYNKQHSAG |
| QYQDINL.VKWPNDIYY.DLM.L.G.LVNSTLMGETFYIL.GCGFNVTNSNPTICIN.LIT.YNK.HSAG | |
| Retrocopy | QYQDINLWVKWPNDIYYSDLMNLSGILVNSTLMGETFYILIGCGFNVTNSNPTICINGLITGYNKKHSAG |
| Parental | LKPLRADYLIARTVTVLEKLIDTFQEEGPNGVLPLYYKYWIHSAQQVRLGSTEGPKVWIVGLDDAGFLLV |
| L.PLRADYLIA.TVTVLEKLIDT.QEEG...VLPLYYKYW.HSAQQ..LGS.EGPK.WI.GLDD.GFLLV | |
| Retrocopy | LRPLRADYLIA*TVTVLEKLIDTLQEEGRKSVLPLYYKYWVHSAQQFHLGSAEGPKLWIIGLDDSGFLLV |
| Parental | HQENGEVVTVHPDGNSFDMLRNLIVPKRP |
| HQENGE.VT.HPDGNSF.MLRNL.VPKRP | |
| Retrocopy | HQENGEAVTMHPDGNSFNMLRNLTVPKRP |
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 | 19 .51 RPM |
| SRP014902_testis | 0 .00 RPM | 51 .06 RPM |
| SRP018288_heart | 0 .00 RPM | 19 .59 RPM |
| SRP018288_kidney | 0 .00 RPM | 40 .98 RPM |
| SRP018288_liver | 0 .00 RPM | 42 .54 RPM |
| SRP018288_lung | 0 .00 RPM | 99 .48 RPM |
| SRP018856_adipose | 0 .02 RPM | 166 .01 RPM |
| SRP035408_brain | 0 .00 RPM | 14 .99 RPM |
| SRP035408_liver | 0 .00 RPM | 19 .35 RPM |
Sus scrofa was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_sscr_334 retrocopy.
Sus scrofa was not studied using FANTOM5 data.
retro_sscr_334 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_sscr_334 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Sus scrofa | ENSSSCG00000012059 | 1 retrocopy |
retro_sscr_334 ,
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