RetrogeneDB ID: retro_ogar_2997

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873694.1:75213..76098(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: DBT
• Ensembl ID: ENSOGAG00000005625
• Aliases: None
• Description: dihydrolipoamide branched chain transacylase E2 [Source:HGNC Symbol;Acc:2698]

Sequence

>retro_ogar_2997
GTGAGTGAAGTTGTTGGCAAAGGAAAATATGGCAGAATTCTTAAAGAAGATATTCTAAACTATTTGGAAAAGCAGACAGG
AGCTATATTACCTCCTTCACAAAAAGCTGAAATTATGCCACTTCCACCAAAAGCAAAAGACATGACTAGTCCCATACCAG
TATCCAAATCTTCGGTATTCACAGGCAAAGACAAAACAGAACCCATAAAAGGCTTTCAAAAAGCAATGGTCAAGACAATG
TCTGCAGCCTTGAAGATACCTCACTTTGGATATTATGACGAGGTCAACCTTACTGCGCTGGCTAAGCTACGAGAAGAATT
AAAACCCATTGCTTTAGCTCATGGAGTTAAACTCACCTCTTTGCCGTTCTTCTTAAGGGCTGCATCCTTGGGATTACTAC
TGTTTCCCATCCTGAATGCTTCTGTGGATGAACACTGCCAAAACATAACATATAAGGCTTCTCATAACATTGGCGTAGCA
ATGGATACTGAGCAGGGTTTGATTGTCCCTAATGTGAAAAACGTTCAGGTCTGCTCTGTACTGGACATCGCCACTGAATT
GGATCGCCTCCAGAAACTGGGCTCTGCAGGTCAGCTCAGCACTGCTGATCTTACAGGAGGGACATTTCCCCTATCCAACA
TTGGATCGATTGGTGGCACCTATGCCAAACCACTGATGTTGCCACCTGAAGTAGCCATTGGAGCTTTGGGATCAATTAAG
GCCCTTCCCCGATTTAACCAGAAAGGAGAAGTATATAAGGCACAGATAATGAATGTGAGCTGGTCAGCTGATCACAGAGT
TATTGATGGTGCAACAATGTCAAGCTTCTCTAATTTGTGGAAATGCTAATTAGAAAATCCAGCTCTGACGCTACTAAATC
TGAAA

Alignment

ORF - retro_ogar_2997 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.86 %
• Parental protein coverage: 61.2 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LSEVVGTGKDGRILKEDILNYLEKQTGAILPPSPKAEIMPPPPKPKDMTIPIPVSKSPVFTGKDKTEPIK
          .SEVVG.GK.GRILKEDILNYLEKQTGAILPPS.KAEIMP.PPK.KDMT.PIPVSKS.VFTGKDKTEPIK
Retrocopy VSEVVGKGKYGRILKEDILNYLEKQTGAILPPSQKAEIMPLPPKAKDMTSPIPVSKSSVFTGKDKTEPIK

Parental  GFQKAMVKTMSAALKIPHFGYCDEVDLTALVKLREELKPIALARGVKLTFLPFFLKAASLGLLQFPILNA
          GFQKAMVKTMSAALKIPHFGY.DEV.LTAL.KLREELKPIALA.GVKLT.LPFFL.AASLGLL.FPILNA
Retrocopy GFQKAMVKTMSAALKIPHFGYYDEVNLTALAKLREELKPIALAHGVKLTSLPFFLRAASLGLLLFPILNA

Parental  SVDENCQNITYKASHNIGIAMDTEQGLIVPNVKNVQVCSVFDIATELDRLQKLGSAGQLSTADLTGGTFT
          SVDE.CQNITYKASHNIG.AMDTEQGLIVPNVKNVQVCSV.DIATELDRLQKLGSAGQLSTADLTGGTF.
Retrocopy SVDEHCQNITYKASHNIGVAMDTEQGLIVPNVKNVQVCSVLDIATELDRLQKLGSAGQLSTADLTGGTFP

Parental  LSNIGSIGGTYAKPLILPPEVAIGALGSIKALPRFNQKGEVYKAQIMNVSWSADHRVIDGATMSRFSNLW
          LSNIGSIGGTYAKPL.LPPEVAIGALGSIKALPRFNQKGEVYKAQIMNVSWSADHRVIDGATMS.FSNLW
Retrocopy LSNIGSIGGTYAKPLMLPPEVAIGALGSIKALPRFNQKGEVYKAQIMNVSWSADHRVIDGATMSSFSNLW

Parental  KSYLENPALMLLNLK
          K..LENPAL.LLNLK
Retrocopy KC*LENPALTLLNLK

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_2997 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013258	2 retrocopies	retro_chof_52, retro_chof_655,
Microcebus murinus	ENSMICG00000006218	1 retrocopy	retro_mmur_1089,
Oryctolagus cuniculus	ENSOCUG00000014244	1 retrocopy	retro_ocun_952,
Otolemur garnettii	ENSOGAG00000005625	1 retrocopy	retro_ogar_2997 ,
Otolemur garnettii	ENSOGAG00000008559	1 retrocopy	retro_ogar_1946,