RetrogeneDB ID: retro_rnor_1377

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 18:1454602..1455049(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000030649
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Polr2h
• Ensembl ID: ENSRNOG00000001748
• Aliases: None
• Description: polymerase (RNA) II (DNA directed) polypeptide H [Source:RefSeq peptide;Acc:NP_001128261]

Sequence

>retro_rnor_1377
GCGGGCATCCTGTTCGAGGATATTTTCGACGTGAAAGACATTGACCCAGAAGGCAAGAAATTTGACCGAGTATCCCAACT
GCATTGTGAGAGTGAATCTTTCAAGGTGGACCTCATCTTAGATATAAACATTCAGATTTACCCTGTAGACTTAGGTGACA
AGTTCCGGTTGGTTATAGCTAGTACTTTGTATGACGATGATACCTTGGATGATGGTGAATACAACCCCACAGATGGCAGA
CCTTCCAGGGCTGACCAGTTTGAGTATGTAATGTATGGGAAAGTGTACAGGATCGAAGGGGATGAGAGCTCAACTGAAGC
AGCCACATGTCTCTCTGCGTGTGTGTCCTATGGCGGCCTGCTCATGAGGCCTCAGGGCGACGCCAACAACCTACATGAAT
TTGAGGTGGACTCCCGAGTCTATCTGCTGAAGAAGAAGCTGGCGTTC

Alignment

ORF - retro_rnor_1377 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.95 %
• Parental protein coverage: 99.33 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AGILFEDIFDVKDIDPEGKKFDRVSRLHCESESFKMDLILDVNIQIYPVDLGDKFRLVIASTLYEDGTLD
          AGILFEDIFDVKDIDPEGKKFDRVS.LHCESESFK.DLILD.NIQIYPVDLGDKFRLVIASTLY.D.TLD
Retrocopy AGILFEDIFDVKDIDPEGKKFDRVSQLHCESESFKVDLILDINIQIYPVDLGDKFRLVIASTLYDDDTLD

Parental  DGEYNPTDDRPSRADQFEYVMYGKVYRIEGDETSTEAATRLSAYVSYGGLLMRLQGDANNLHGFEVDSRV
          DGEYNPTD.RPSRADQFEYVMYGKVYRIEGDE.STEAAT.LSA.VSYGGLLMR.QGDANNLH.FEVDSRV
Retrocopy DGEYNPTDGRPSRADQFEYVMYGKVYRIEGDESSTEAATCLSACVSYGGLLMRPQGDANNLHEFEVDSRV

Parental  YLLMKKLAF
          YLL.KKLAF
Retrocopy YLLKKKLAF

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
SRP017611_brain	0.00 RPM	0.00 RPM
SRP017611_kidney	0.00 RPM	0.00 RPM
SRP017611_liver	0.00 RPM	0.00 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1377 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1377 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1377 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000005751	1 retrocopy	retro_dnov_709,
Microcebus murinus	ENSMICG00000011294	1 retrocopy	retro_mmur_537,
Myotis lucifugus	ENSMLUG00000022295	2 retrocopies	retro_mluc_2322, retro_mluc_552,
Monodelphis domestica	ENSMODG00000002570	2 retrocopies	retro_mdom_1394, retro_mdom_1450,
Mus musculus	ENSMUSG00000021018	2 retrocopies	retro_mmus_3549, retro_mmus_936,
Otolemur garnettii	ENSOGAG00000001599	1 retrocopy	retro_ogar_3073,
Rattus norvegicus	ENSRNOG00000001748	2 retrocopies	retro_rnor_1377 , retro_rnor_773,