RetrogeneDB ID: retro_ogar_742

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873526.1:33755606..33756079(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000033405
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RHOQ
• Ensembl ID: ENSOGAG00000033272
• Aliases: None
• Description: ras homolog family member Q [Source:HGNC Symbol;Acc:17736]

Sequence

>retro_ogar_742
GTCAGTGTCACCATGGGGGGCAAGCAGTACCTCCTGGGACTCTATGACACGGCCGGACAGGAAGACTATGACCGTCTGAG
GCCTTTATCTTACCCAATGACCGACATCTTCCTTATTTGCTTCTCTGTGGTAAATCCAGCCTCATTTCAAAATGTCAAAG
AGGAGTGGGTACCAGAGCTTAAGGAATACGCACCAAATGTACCCTTTTTATTAATAGGAACTCAGATTGATCTCCGAGAT
GACCCCAAATTTTAGCAAGACTGAATGATATGAAAGAAAAACCTATATGTGTGGAACAAGGACAGAAACTAGCAAAAGAG
ATAGGAGCATGCTGCTATGTGGAATGTTCAGCTTTAATCCAGAAGGGATTAAAGACTGTTTTTGATGAGGATATCATAGC
CATTTTAACTCCAAAGAAACACACAGTAAAAAAAAGAATAGGATCAAGATGTATAAACAGTTGTTTGATCACG

Alignment

ORF - retro_ogar_742 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.71 %
• Parental protein coverage: 77.07 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VSVTVGGKQYLLGLYDTAGQEDYDRLRPLSYPMTDVFLICFSVVNPASFQNVKEEWVPELKEYAPNVPFL
          VSVT.GGKQYLLGLYDTAGQEDYDRLRPLSYPMTD.FLICFSVVNPASFQNVKEEWVPELKEYAPNVPFL
Retrocopy VSVTMGGKQYLLGLYDTAGQEDYDRLRPLSYPMTDIFLICFSVVNPASFQNVKEEWVPELKEYAPNVPFL

Parental  LIGTQIDLRDDPK-TLARLNDMKEKPICVEQGQKLAKEIGACCYVECSALTQKGLKTVFDEAIIAILTPK
          LIGTQIDLRDDPK..LARLNDMKEKPICVEQGQKLAKEIGACCYVECSAL.QKGLKTVFDE.IIAILTPK
Retrocopy LIGTQIDLRDDPK<ILARLNDMKEKPICVEQGQKLAKEIGACCYVECSALIQKGLKTVFDEDIIAILTPK

Parental  KHTVKKRIGSRCINSCLIT
          KHT....IGSRCINSCLIT
Retrocopy KHTXXXXIGSRCINSCLIT

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_742 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 15 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000549	3 retrocopies	retro_chof_2030, retro_chof_457, retro_chof_914,
Callithrix jacchus	ENSCJAG00000000685	1 retrocopy	retro_cjac_2403,
Erinaceus europaeus	ENSEEUG00000015226	1 retrocopy	retro_eeur_129,
Homo sapiens	ENSG00000119729	3 retrocopies	retro_hsap_1333, retro_hsap_2158, retro_hsap_2316,
Loxodonta africana	ENSLAFG00000004327	1 retrocopy	retro_lafr_316,
Microcebus murinus	ENSMICG00000009124	1 retrocopy	retro_mmur_29,
Otolemur garnettii	ENSOGAG00000004138	1 retrocopy	retro_ogar_2977,
Otolemur garnettii	ENSOGAG00000012467	1 retrocopy	retro_ogar_2140,
Otolemur garnettii	ENSOGAG00000014261	1 retrocopy	retro_ogar_131,
Otolemur garnettii	ENSOGAG00000033272	1 retrocopy	retro_ogar_742 ,
Pongo abelii	ENSPPYG00000012439	2 retrocopies	retro_pabe_1107, retro_pabe_2195,
Pteropus vampyrus	ENSPVAG00000013691	1 retrocopy	retro_pvam_611,
Rattus norvegicus	ENSRNOG00000015415	1 retrocopy	retro_rnor_473,
Sus scrofa	ENSSSCG00000008439	1 retrocopy	retro_sscr_102,
Tarsius syrichta	ENSTSYG00000002837	1 retrocopy	retro_tsyr_1609,