RetrogeneDB ID: retro_ogar_3159

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873731.1:1095695..1096299(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000025820
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MRPL11
• Ensembl ID: ENSOGAG00000010448
• Aliases: None
• Description: mitochondrial ribosomal protein L11 [Source:HGNC Symbol;Acc:14042]

Sequence

>retro_ogar_3159
ATGTCGAAGCTAAGCCGGGCCACTCTGGGCCTCAAGAAGCCCAAGGCCGGCGGCGTGATCTGGACCATCGTTCGAGCAGG
CCAGGCCATGTCTGGGCCCCCATTAGGTCCCATCCTGGGTCAGCGAGGTGTTTCCATCAATCAGTTCTGCAAGGAGTTCA
ATGAGAAGACAAAGGACATAAAAGAAGGTATTCCTCTGCCTACCAAGATTTTTGTGAAGCCTGACAGGACATTTGAAATA
AAGATTGGACAACCCACTGTTTCCTGTTTCCTGAAGGCAGCTGCTGGCATTGAGAAGGGGGCCCGGCAGACAGGGAAAGA
GGTGGCAGGCCTGGTGACCTTGAAGCATGTGTACGAGATTGCCCGTGTCAAAGGTCAGGATGAGGCCTTCGCTTTGCAAG
ATGTACCCATGTCCTCTGTTGTCCGCTCCGTCATTGGGTCTGCCTGGTCTCTGGGCATTCGGGTGGTGACAGACCTCAGT
GCAGAAGAGCTGGCAGCTTTCCAGAGGGAACGAGCTAGATTCCTGGCTGCTCAGAAAAAGGCAGACTGGGCAGCCCAGGC
AGAAGCTGACAAGAAGTGATCCTTCACACTCCCAAGATTATAAA

Alignment

ORF - retro_ogar_3159 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.08 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSKLSRATRGLKKPEAGGVIRTIVRAGQAMSGPPLGPILGQRGVSINQFCKEFNEKTKDIKEGIPLPTKI
          MSKLSRAT.GLKKP.AGGVI.TIVRAGQAMSGPPLGPILGQRGVSINQFCKEFNEKTKDIKEGIPLPTKI
Retrocopy MSKLSRATLGLKKPKAGGVIWTIVRAGQAMSGPPLGPILGQRGVSINQFCKEFNEKTKDIKEGIPLPTKI

Parental  FVKPDRTFEIKIGQPTVSYFLKAAAGIEKGARQTGKEVAGLVTLKHVYEIARVKAQDEAFALQDVPMSSV
          FVKPDRTFEIKIGQPTVS.FLKAAAGIEKGARQTGKEVAGLVTLKHVYEIARVK.QDEAFALQDVPMSSV
Retrocopy FVKPDRTFEIKIGQPTVSCFLKAAAGIEKGARQTGKEVAGLVTLKHVYEIARVKGQDEAFALQDVPMSSV

Parental  VRSIIGSARSLGIQVVTDLSAEELAAFQRERAIFLAAQRQT-W-RPRQKLTRSDPSHSQDFK
          VRS.IGSA.SLGI.VVTDLSAEELAAFQRERA.FLAAQ....W..PRQKLTRSDPSHSQD.K
Retrocopy VRSVIGSAWSLGIRVVTDLSAEELAAFQRERARFLAAQKKADW>QPRQKLTRSDPSHSQDYK

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_3159 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 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000012706	1 retrocopy	retro_cfam_761,
Callithrix jacchus	ENSCJAG00000001470	1 retrocopy	retro_cjac_803,
Dasypus novemcinctus	ENSDNOG00000004111	2 retrocopies	retro_dnov_1607, retro_dnov_566,
Echinops telfairi	ENSETEG00000015216	2 retrocopies	retro_etel_1754, retro_etel_333,
Homo sapiens	ENSG00000174547	1 retrocopy	retro_hsap_3390,
Gorilla gorilla	ENSGGOG00000001300	1 retrocopy	retro_ggor_2296,
Myotis lucifugus	ENSMLUG00000004047	1 retrocopy	retro_mluc_2131,
Mus musculus	ENSMUSG00000024902	1 retrocopy	retro_mmus_2118,
Nomascus leucogenys	ENSNLEG00000006111	1 retrocopy	retro_nleu_1705,
Otolemur garnettii	ENSOGAG00000010448	2 retrocopies	retro_ogar_1143, retro_ogar_3159 ,
Pongo abelii	ENSPPYG00000003025	1 retrocopy	retro_pabe_2786,
Pan troglodytes	ENSPTRG00000003924	1 retrocopy	retro_ptro_2305,
Ictidomys tridecemlineatus	ENSSTOG00000025971	1 retrocopy	retro_itri_941,
Tarsius syrichta	ENSTSYG00000008712	1 retrocopy	retro_tsyr_1095,
Tursiops truncatus	ENSTTRG00000002678	1 retrocopy	retro_ttru_431,