RetrogeneDB ID: retro_ogar_1783

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873565.1:13086277..13087185(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000027141
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: EIF3M
• Ensembl ID: ENSOGAG00000015913
• Aliases: None
• Description: eukaryotic translation initiation factor 3, subunit M [Source:HGNC Symbol;Acc:24460]

Sequence

>retro_ogar_1783
ATGAGCGTCCCGGCCTTCATCGACATCAGCGAGGAAGACCAGGCTGCTGAACTTCATGCTTATCTGAAATCTAAAGGAGC
TGAGATCTCAGAAGAGAACTCAGAAGGTGGACTTCATGTAGATTTAGCTCAAATTATTGAAGCCTGTGATGTGTGTCTGA
AGGAAGATGATAAAGATGTTGAAAGTGTGATGAACAGCGTGGTATCCCTCCTCTTGATCTTGGAACCAGACAAGCAAGAA
GCTTTGATTGAAAGCCTATGCGGAAAAACTGGTCAAATTTTGTGAAGGTGAACGCCCATCTCTGAGACTGCAGTTGCTAA
GCAACCTTTTCCATGGAATGGACAAGAACACTCCTGTAAGATATACAGTGTATTGCAGCCTTATTAAAGTGGCAGCAGCT
TGTGGGGCCATCCAGTACATTCCGACTGAGCTGGATCAAGTTAGAAAATGGATTTCTGACTGGAATCTCACCACTGAAAA
AAAAACACACCCTTTTAAGACTACTTTATGAGTCACTTGTGGACTGTAAAAAAAGTGATGCTGCTTCAAAAGTTATGGTG
GAATTGCTTGGAAGTTACACAGAGGACAATGCTTCCCAGGCTCGAGTTGATGCCCACAGGTGTATTGTACGAGCATTGAA
AGATCCAAATGCATTTCTTTTTGACCACCTTCTTACTTTAAAACCAGTCAAGTTTTTGGAAGGCAAGCTTATTCATGACC
TTTTAACCATTTTTGTGAGTGCTAAATTGGCATCATATGTCAAGTTTTATCAGAATAATAAAGACTTCATTGATTCACTT
GGCCTATTACATGAACAGAATATGGCAAAGATGAGATTACTTACCTTTATGGGAATGGCGGTGGAAAATAAAGAAATTTC
TTTTGATACAATGCAGCAGGAACTTCAA

Alignment

ORF - retro_ogar_1783 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.04 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSVPAFIDISEEDQAAELRAYLKSKGAEISEENSEGGLHVDLAQIIEACDVCLKEDDKDVESVMNSVVSL
          MSVPAFIDISEEDQAAEL.AYLKSKGAEISEENSEGGLHVDLAQIIEACDVCLKEDDKDVESVMNSVVSL
Retrocopy MSVPAFIDISEEDQAAELHAYLKSKGAEISEENSEGGLHVDLAQIIEACDVCLKEDDKDVESVMNSVVSL

Parental  LLILEPDKQEALIESLC-EKLVKFREGERPSLRLQLLSNLFHGMDKNTPVRYTVYCSLIKVAASCGAIQY
          LLILEPDKQEALIESLC.EKLVKF.EGERPSLRLQLLSNLFHGMDKNTPVRYTVYCSLIKVAA.CGAIQY
Retrocopy LLILEPDKQEALIESLC>EKLVKFCEGERPSLRLQLLSNLFHGMDKNTPVRYTVYCSLIKVAAACGAIQY

Parental  IPTELDQVRKWISDWNLTTEKK-HTLLRLLYESLVDCKKSDAASKVMVELLGSYTEDNASQARVDAHRCI
          IPTELDQVRKWISDWNLTT....HTLLRLLYESLVDCKKSDAASKVMVELLGSYTEDNASQARVDAHRCI
Retrocopy IPTELDQVRKWISDWNLTTXXX>HTLLRLLYESLVDCKKSDAASKVMVELLGSYTEDNASQARVDAHRCI

Parental  VRALKDPNAFLFDHLLTLKPVKFLEGELIHDLLTIFVSAKLASYVKFYQNNKDFIDSLGLLHEQNMAKMR
          VRALKDPNAFLFDHLLTLKPVKFLEG.LIHDLLTIFVSAKLASYVKFYQNNKDFIDSLGLLHEQNMAKMR
Retrocopy VRALKDPNAFLFDHLLTLKPVKFLEGKLIHDLLTIFVSAKLASYVKFYQNNKDFIDSLGLLHEQNMAKMR

Parental  LLTFMGMAVENKEISFDTMQQELQ
          LLTFMGMAVENKEISFDTMQQELQ
Retrocopy LLTFMGMAVENKEISFDTMQQELQ

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_1783 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 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005338	2 retrocopies	retro_btau_1736, retro_btau_812,
Echinops telfairi	ENSETEG00000013437	1 retrocopy	retro_etel_120,
Myotis lucifugus	ENSMLUG00000014727	2 retrocopies	retro_mluc_1982, retro_mluc_431,
Mus musculus	ENSMUSG00000027170	1 retrocopy	retro_mmus_421,
Oryctolagus cuniculus	ENSOCUG00000004483	1 retrocopy	retro_ocun_282,
Otolemur garnettii	ENSOGAG00000015913	1 retrocopy	retro_ogar_1783 ,
Pteropus vampyrus	ENSPVAG00000015083	1 retrocopy	retro_pvam_1134,
Vicugna pacos	ENSVPAG00000007791	1 retrocopy	retro_vpac_342,