RetrogeneDB ID: | retro_sscr_55 | ||
Retrocopy location | Organism: | Pig (Sus scrofa) | |
| Coordinates: | 7:22072660..22073326(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSSSCG00000001137 | |
| Aliases: | None | ||
| Status: | KNOWN_PROTEIN_CODING | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | HIST1H1B | ||
| Ensembl ID: | ENSSSCG00000030023 | ||
| Aliases: | None | ||
| Description: | histone cluster 1, H1b [Source:HGNC Symbol;Acc:4719] |
Retrocopy-Parental alignment summary:
>retro_sscr_55
ATGTCGGAGACCGCTCCAGTGGCTCCTGCTGCTCCCGCGCCTGCAGAGAAAACACCTGTAAAGAAAAAGGCGAAGAAGAC
GGGCGCAGCTGCTGGGAAACGCAAAGCGTCCGGGCCTCCGGTGTCCGAGCTCATCACCAAGGCTGTCGCCGCCTCCAAGG
AGCGCAACGGCGTGTCTCTGGCCGCGCTCAAGAAGGCGCTGGCTGCCGCCGGCTACGATGTGGAAAAGAACAACAGCCGG
ATCAAGCTGGGGCTTAAAAGCTTGGTGAGCAAGGGCACCCTGGTGCAGACTAAAGGCACTGGCGCTTCGGGCTCCTTCAA
ACTCAACAAGAAGGCGGCCACCGGGGAAGCCAAGCCCAAAGCTAAGAAAGCGGGAGCAGCTAAGCCTAAGAAGTCTGCTG
GGGCAGCCAAGAAGCCCAAGAAGGCTACCGGAACAGCCACCCCAAAGAAGACCGCCAAGAAGACCCCCAAGAAAGCCAAG
AAGCCGGCAGCGGCAGCTGGCACCAAGAAGGTGGCCAAGAGCCCGAAGAAGGCGAAGGCAGCCAAGCCGAAAAAGGCCGC
TAAGAGCCCGGCCAAGGCCAAAGCCCCCAAGCCCAAGGCAGCCAAGCCTAAAGCCGCAAAACCCAAGGCTACAAAGGCCA
AGAAAGCCGTCTCCAAGAAGAAGTAA
ORF - retro_sscr_55 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 77.51 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MSETAPAETAAPAPVEKSPAKKKATKKPASGGAAKRKATGPPVSELITKAVAASKERNGLSLAALKKALA |
| MSETAP...AAPAP.EK.P.KKKA.K..A..G..KRKA.GPPVSELITKAVAASKERNG.SLAALKKALA | |
| Retrocopy | MSETAPVAPAAPAPAEKTPVKKKAKKTGAAAG--KRKASGPPVSELITKAVAASKERNGVSLAALKKALA |
| Parental | AGGYDVEKNNSRIKLGLKSLVSKGTLVQTKGTGASGSFKLNKKAATGEAKPKTKKAGAAKAKKPAGSTTE |
| A.GYDVEKNNSRIKLGLKSLVSKGTLVQTKGTGASGSFKLNKKAATGEAKPK.KKAGAAK.KK.AG.... | |
| Retrocopy | AAGYDVEKNNSRIKLGLKSLVSKGTLVQTKGTGASGSFKLNKKAATGEAKPKAKKAGAAKPKKSAGA-AK |
| Parental | KPKKAAG---PRKAVKKTPKKAKK-SAAAGVKKVAKSPK--KAVKPKAAKPKAAKPKAAKPTAAKATKA |
| KPKKA.G...P.K..KKTPKKAKK..AAAG.KKVAKSPK..KA.KPK.A....AK.KA.KP.AAK...A | |
| Retrocopy | KPKKATGTATPKKTAKKTPKKAKKPAAAAGTKKVAKSPKKAKAAKPKKAAKSPAKAKAPKPKAAKPKAA |
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 | 9 .16 RPM | 0 .00 RPM |
| SRP014902_testis | 5 .94 RPM | 0 .57 RPM |
| SRP018288_heart | 2 .65 RPM | 0 .03 RPM |
| SRP018288_kidney | 5 .32 RPM | 0 .00 RPM |
| SRP018288_liver | 10 .71 RPM | 0 .00 RPM |
| SRP018288_lung | 26 .47 RPM | 0 .20 RPM |
| SRP018856_adipose | 9 .55 RPM | 0 .00 RPM |
| SRP035408_brain | 1 .59 RPM | 0 .00 RPM |
| SRP035408_liver | 31 .73 RPM | 0 .44 RPM |
Sus scrofa was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_sscr_55 retrocopy.
Sus scrofa was not studied using FANTOM5 data.
retro_sscr_55 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_sscr_55 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 | ENSSSCG00000030023 | 1 retrocopy |
retro_sscr_55 ,
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