RetrogeneDB ID: retro_ogar_3073

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873710.1:1064162..1064519(+)
• Located in intron of: ENSOGAG00000000141

Retrocopy information

• Ensembl ID: ENSOGAG00000000142
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: POLR2H
• Ensembl ID: ENSOGAG00000001599
• Aliases: None
• Description: polymerase (RNA) II (DNA directed) polypeptide H [Source:HGNC Symbol;Acc:9195]

Sequence

>retro_ogar_3073
ATAGGGGGCATCCTGTTTGAGGATAATTTCAATGTGAAAGATAGTGACCCAGAGAGCAAGACCTTTGACCACGTGTCTCC
GTTGCATTGTGAGAGTGAATTTTTCAAGATAGATTACATCTTAGATGGAAACATCCAGATTTACCCTGTAGACTTAGGTG
ACAATTTCTGGTTGGTCATAGCTAGTACCTTGTATGAAGACAGTACCCTGGATGATGGTGAATGCAACCCCACTGATGAC
AGGCCTTCCAGGGCTGATCAGTTTGAGTATGTAATGTATGGAACAGTGTACAGGATTGAGGGAGATGAAACTTCTACCGA
AGTAGCAACACCTCTCTGCCTCCGTGTCCTATGGGGG

Alignment

ORF - retro_ogar_3073 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.99 %
• Parental protein coverage: 79.33 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAGILFEDIFDVKDIDPEGKKFDRVSRLHCESESFKMDLILDVNIQIYPVDLGDKFRLVIASTLYEDGTL
          ..GILFED.F.VKD.DPE.K.FD.VS.LHCESE.FK.D.ILD.NIQIYPVDLGD.F.LVIASTLYED.TL
Retrocopy IGGILFEDNFNVKDSDPESKTFDHVSPLHCESEFFKIDYILDGNIQIYPVDLGDNFWLVIASTLYEDSTL

Parental  DDGEYNPTDDRPSRADQFEYVMYGKVYRIEGDETSTEAATRLSAYVSYG
          DDGE.NPTDDRPSRADQFEYVMYG.VYRIEGDETSTE.AT.L...V..G
Retrocopy DDGECNPTDDRPSRADQFEYVMYGTVYRIEGDETSTEVATPLCLRVLWG

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Otolemur garnettii was not studied using RNA-Seq expression data.

ChIP-Seq

Otolemur garnettii was not studied using ChIP-Seq data.

EST

Otolemur garnettii was not studied using EST data.

TSS

Otolemur garnettii was not studied using FANTOM5 data.

Lab

retro_ogar_3073 was not experimentally validated.

Homology

Retrocopy orthology:

Otolemur garnettii does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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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,