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 symbol: POLR2M
• Ensembl ID: ENSSSCG00000030605
• Aliases: None
• Description: polymerase (RNA) II (DNA directed) polypeptide M [Source:HGNC Symbol;Acc:14862]

Sequence

>retro_sscr_547
ATGTCCTCGCTGCCTCGCGGCTTTGAGCCCCAAGCCCCCGAGGACTTGGGCCAGCGGAGTTTGGCAGAGCTGCTGGAGAC
GTTGAAGGCGCCAGGTGAGACTTTTGCACAATGTAAAATTCATCTGCAAATTGCCCGACAAAGGTAAAAAGATCATAGAC
TCTGTTGCCAAACTGAAAGTTGCCATTGAAGAACATGAAGAAGTTAGAGGAGGTAGTGACCTCTTTCATCCTGTTAGTTT
AGACTGTAAGCAGAGGACAAAAGCAATTACAGGTTATTGATGTGGACACAGATACAGCCCAGAATTCTGACCAGATACTT
GGTACTTCATCACTAGTTCCTGGCTGCTCCTCTATAGCTACCATCACCTCATCTCAGACAACCTCACAGCAGGACCTGGT
CCATGCTACTCCTGGAGGCAATGCTGAGGCCCCTGAGCCTGAACACTCAGTGAGCAAGTGCCCACCTTCCAGCAGTAGAG
CCGCTGTGCCTTCCGCATCCGAAGCCAGTGAGTGCCTCCCTCAGCATCACATTTCAAGTCAAGCAGAGAATCATTCTAGC
AGCTTGGACAACCTGTTTATTGATAGATTGCAAAGGATCACTATTACAGACCCTGGTGAACACCACTCGGAAGGAAACCC
AAGTCCGGAGAATTTGACTGGCCTTTGGCGTGAGTCGCAGAAGAAGCCTCATTACATGGAAGTGTCAGAAATGCTAGCCA
AAGATCCTCTGCCTCCACCACATAAAGTTAAAACCAATGTGTAAGTACCATCGGAAACAGGCTTGTCACAGGAGCAT

Alignment

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

Expression

RNA-Seq

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

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_547 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_547 was not experimentally validated.

Homology

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	retro_hsap_2941,
Sus scrofa	ENSSSCG00000030605	1 retrocopy	retro_sscr_547 ,
Ictidomys tridecemlineatus	ENSSTOG00000026874	1 retrocopy	retro_itri_80,