RetrogeneDB ID: | retro_sscr_547 | ||
Retrocopy location | Organism: | Pig (Sus scrofa) | |
| Coordinates: | 16:37234746..37235543(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | POLR2M | ||
| Ensembl ID: | ENSSSCG00000030605 | ||
| Aliases: | None | ||
| Description: | polymerase (RNA) II (DNA directed) polypeptide M [Source:HGNC Symbol;Acc:14862] |
Retrocopy-Parental alignment summary:
>retro_sscr_547
ATGTCCTCGCTGCCTCGCGGCTTTGAGCCCCAAGCCCCCGAGGACTTGGGCCAGCGGAGTTTGGCAGAGCTGCTGGAGAC
GTTGAAGGCGCCAGGTGAGACTTTTGCACAATGTAAAATTCATCTGCAAATTGCCCGACAAAGGTAAAAAGATCATAGAC
TCTGTTGCCAAACTGAAAGTTGCCATTGAAGAACATGAAGAAGTTAGAGGAGGTAGTGACCTCTTTCATCCTGTTAGTTT
AGACTGTAAGCAGAGGACAAAAGCAATTACAGGTTATTGATGTGGACACAGATACAGCCCAGAATTCTGACCAGATACTT
GGTACTTCATCACTAGTTCCTGGCTGCTCCTCTATAGCTACCATCACCTCATCTCAGACAACCTCACAGCAGGACCTGGT
CCATGCTACTCCTGGAGGCAATGCTGAGGCCCCTGAGCCTGAACACTCAGTGAGCAAGTGCCCACCTTCCAGCAGTAGAG
CCGCTGTGCCTTCCGCATCCGAAGCCAGTGAGTGCCTCCCTCAGCATCACATTTCAAGTCAAGCAGAGAATCATTCTAGC
AGCTTGGACAACCTGTTTATTGATAGATTGCAAAGGATCACTATTACAGACCCTGGTGAACACCACTCGGAAGGAAACCC
AAGTCCGGAGAATTTGACTGGCCTTTGGCGTGAGTCGCAGAAGAAGCCTCATTACATGGAAGTGTCAGAAATGCTAGCCA
AAGATCCTCTGCCTCCACCACATAAAGTTAAAACCAATGTGTAAGTACCATCGGAAACAGGCTTGTCACAGGAGCAT
ORF - retro_sscr_547 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 85.02 % |
| Parental protein coverage: | 71.54 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | MSSLPRGFEPQPPEDLGQRSLAELRETLK-RQERLLRNVKFICKLPDKGRKIIDSVAKLKAAIEEHEEVR |
| MSSLPRGFEPQ.PEDLGQRSLAEL.ETLK.RQ.RLL.NVKFICKLPDKG.KIIDSVAKLK.AIEEHEEVR | |
| Retrocopy | MSSLPRGFEPQAPEDLGQRSLAELLETLK>RQVRLLHNVKFICKLPDKGKKIIDSVAKLKVAIEEHEEVR |
| Parental | GGSDLFHPVNLDCKWRTKAST-VVDVATDTAQNSDQILDTSSLVPGCSSIATITSSQTTSQRGLVHPTHG |
| GGSDLFHPV.LDCK.RTKA.T.V.DV.TDTAQNSDQIL.TSSLVPGCSSIATITSSQTTSQ..LVH.T.G | |
| Retrocopy | GGSDLFHPVSLDCKQRTKAIT>VIDVDTDTAQNSDQILGTSSLVPGCSSIATITSSQTTSQQDLVHATPG |
| Parental | GNAEAPEPEHSVSKCPPSSSRAAVPSSSEASERLPQHHISSQVEDHSSSSENLFIDRLQRITITDPGEHH |
| GNAEAPEPEHSVSKCPPSSSRAAVPS.SEASE.LPQHHISSQ.E.HSSS..NLFIDRLQRITITDPGEHH | |
| Retrocopy | GNAEAPEPEHSVSKCPPSSSRAAVPSASEASECLPQHHISSQAENHSSSLDNLFIDRLQRITITDPGEHH |
| Parental | SEGNPSLENLTGLWRGPQKKPHYMEVLEMRAKNPLPLPHKFKTNV-LPSQQHDSVSH |
| SEGNPS.ENLTGLWR..QKKPHYMEV.EM.AK.PLP.PHK.KTNV..PS....S..H | |
| Retrocopy | SEGNPSPENLTGLWRESQKKPHYMEVSEMLAKDPLPPPHKVKTNV*VPSETGLSQEH |
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 | 18 .58 RPM |
| SRP014902_testis | 0 .00 RPM | 31 .26 RPM |
| SRP018288_heart | 0 .03 RPM | 40 .36 RPM |
| SRP018288_kidney | 0 .00 RPM | 44 .62 RPM |
| SRP018288_liver | 0 .00 RPM | 38 .70 RPM |
| SRP018288_lung | 0 .00 RPM | 45 .72 RPM |
| SRP018856_adipose | 0 .00 RPM | 30 .56 RPM |
| SRP035408_brain | 0 .00 RPM | 59 .52 RPM |
| SRP035408_liver | 0 .00 RPM | 41 .45 RPM |
Sus scrofa was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_sscr_547 retrocopy.
Sus scrofa was not studied using FANTOM5 data.
retro_sscr_547 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_sscr_547 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 | |
|---|---|---|---|
| Homo sapiens | ENSG00000255529 | 1 retrocopy | |
| Sus scrofa | ENSSSCG00000030605 | 1 retrocopy |
retro_sscr_547 ,
|
| Ictidomys tridecemlineatus | ENSSTOG00000026874 | 1 retrocopy |