RetrogeneDB ID: | retro_sscr_868 | ||
Retrocopy location | Organism: | Pig (Sus scrofa) | |
| Coordinates: | 6:53557723..53558248(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | HSF2BP | ||
| Ensembl ID: | ENSSSCG00000022164 | ||
| Aliases: | None | ||
| Description: | heat shock transcription factor 2 binding protein [Source:HGNC Symbol;Acc:5226] |
Retrocopy-Parental alignment summary:
>retro_sscr_868
AAAAATCTGGAAAGGAAAGAGCAAGAATTAGAGCAACTGCGAATGGATTGTGAGCCCTTCAAAGCCCGCCTGGAGTCTGT
GCAAGAGGACAGCGTGCGAGAGAAGGACAAGCCGGCTCTCCGACAGCAGTGGAATGAAGCAAAGCAGCAGCTCCTGCAGC
AGACAGAGTGTTGCACAGAAATGGGTGCGGCAGCCTGTACCATTTTGTGGGGCGTCTCCAGCAGCGAGGAAGTGGTCAAA
GCCATCCTGGGAAGAGATAAAGCTTTGAAGTTTTTCAACATCATTGGTCAAACAATGCAGAGTTTTGTGAAGTACCTGGA
TGGGGTCGTCAAGGAGCTGGATTCTGATGAAAATCAGTTTGTTTTTGCTTTGGCTGGAATGGTAACAAAAGTTGCTGCCA
TCGCTTGTGGTGGTGAATTCCTGGTTACCTCAAGTCGGGTCCTCCTGAACACCATACTGCAGCTTCTGGGACACCTGAGA
CCCGGGCAGTGTACCAGACTCAAAGTGTGAATGCTGATGTCTCTA
ORF - retro_sscr_868 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 86.36 % |
| Parental protein coverage: | 57.14 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | KNLERKEQELEQLRMDCEHFKARLESVQADSVREKKEKLALRQQLNEAKQQLLQQAEYCTEMGAAACTIL |
| KNLERKEQELEQLRMDCE.FKARLESVQ.DSVREK..K.ALRQQ.NEAKQQLLQQ.E.CTEMGAAACTIL | |
| Retrocopy | KNLERKEQELEQLRMDCEPFKARLESVQEDSVREK-DKPALRQQWNEAKQQLLQQTECCTEMGAAACTIL |
| Parental | WGVSSSEEVVKAILGGDKAVKFFSITGQTMESFVKSLDGDAKELDSDENQFVFALAGIVTNVAAIACGRE |
| WGVSSSEEVVKAILG.DKA.KFF.I.GQTM.SFVK.LDG..KELDSDENQFVFALAG.VT.VAAIACG.E | |
| Retrocopy | WGVSSSEEVVKAILGRDKALKFFNIIGQTMQSFVKYLDGVVKELDSDENQFVFALAGMVTKVAAIACGGE |
| Parental | FLVTSSRVLLDTILQLLGDLKPGQCTRLKVLMLMAL |
| FLVTSSRVLL.TILQLLG.L.PGQCTRLKV.MLM.L | |
| Retrocopy | FLVTSSRVLLNTILQLLGHLRPGQCTRLKV*MLMSL |
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 | 12 .21 RPM |
| SRP014902_testis | 1 .70 RPM | 26 .17 RPM |
| SRP018288_heart | 0 .05 RPM | 7 .28 RPM |
| SRP018288_kidney | 0 .00 RPM | 10 .93 RPM |
| SRP018288_liver | 0 .00 RPM | 5 .12 RPM |
| SRP018288_lung | 0 .20 RPM | 8 .04 RPM |
| SRP018856_adipose | 0 .91 RPM | 41 .87 RPM |
| SRP035408_brain | 0 .41 RPM | 27 .95 RPM |
| SRP035408_liver | 0 .06 RPM | 21 .05 RPM |
Sus scrofa was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_sscr_868 retrocopy.
Sus scrofa was not studied using FANTOM5 data.
retro_sscr_868 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_sscr_868 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Otolemur garnettii | ENSOGAG00000009866 | 1 retrocopy | |
| Sus scrofa | ENSSSCG00000022164 | 1 retrocopy |
retro_sscr_868 ,
|
| Ictidomys tridecemlineatus | ENSSTOG00000011783 | 1 retrocopy |