RetrogeneDB ID: retro_ogar_2324

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873611.1:1391046..1391674(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MALSU1
• Ensembl ID: ENSOGAG00000017157
• Aliases: None
• Description: mitochondrial assembly of ribosomal large subunit 1 [Source:HGNC Symbol;Acc:21721]

Sequence

>retro_ogar_2324
ATGGGGCCAGGCAGCTATGTATCTGGGCGGCTCTGGCCACTTTTGTGGCATGCGTCCTGTCCCAAGTAGCAGCTGGAACT
GGGCTCTGGCTTCAGCTGCTGGCAGTGGAACTGCTTTCTGCAGGACCAGCCTTCCGCTGGACCTGCCTCACCCCTGACTC
CTTGCACAGCAAGCCCCAGCTGGAGGAGCAGGTGAAGGGGATGCCGGTCAAAAAACACCCAAACTCTAGCCCAGCAGTTC
ATATTGGTCCCAAGTTTGACATCAATATGATGGTTTCACTACTGAGGCAAGAAAATGCAGGAGACATTTGTGCAATCAAG
GTTCCTCCAGAAATGAAATACACAGATTACTTTATGATTAGTAGCGGAACTTTTACCAGACTCTTGCATGCCATAGCATA
TACATCACGAAAACGTACAAATAACTGAAATGTAAGAGTGGGCCTTATGTTAAGATCGAAGGAAAGGACACTGATGACTG
GATATGTGTGGGTTTTGGCAGCATGATGCTTCATTTGATGCTTCCAGAAACCAGAGAGATCTATGAATTAGAGAAATTAT
GGTCTCTCCATTCTTATGATGACCAGTCAGCTCAAATAGCACCAGAGACATTACCTAAAGACTTCATT

Alignment

ORF - retro_ogar_2324 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.95 %
• Parental protein coverage: 92.21 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MGPGGCVAGRLWPLLWRG-VRSRVGAGTGPRLWLPAVERLSAGPAFSWAYLTPDPVRGLHSGPQLEEQAE
          MGPG..V.GRLWPLLW...V.S.V.AGTG..L.L.AVE.LSAGPAF.W..LTPD....LHS.PQLEEQ..
Retrocopy MGPGSYVSGRLWPLLWHA<VLSQVAAGTGLWLQLLAVELLSAGPAFRWTCLTPD---SLHSKPQLEEQVK

Parental  GAPVEGRPESSAVDHIGPKFDIDMLVSLLRQENARDICVIKVPPEMKYTDYFVISSGTSTRHLHAMAY-Y
          G.PV...P.SS...HIGPKFDI.M.VSLLRQENA.DIC.IKVPPEMKYTDYF.ISSGT.TR.LHA.AY.Y
Retrocopy GMPVKKHPNSSPAVHIGPKFDINMMVSLLRQENAGDICAIKVPPEMKYTDYFMISSGTFTRLLHAIAY<Y

Parental  IVKMYKYLKRKSESHVKIEGKDTDDWLCVDFGSMVLHLMLPETREIYELEKLWTLRSYDDQLAQIAPETI
          I.K.YK.LK.KS...VKIEGKDTDDW.CV.FGSM.LHLMLPETREIYELEKLW.L.SYDDQ.AQIAPET.
Retrocopy ITKTYK*LKCKSGPYVKIEGKDTDDWICVGFGSMMLHLMLPETREIYELEKLWSLHSYDDQSAQIAPETL

Parental  PEDFI
          P.DFI
Retrocopy PKDFI

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_2324 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 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002338	1 retrocopy	retro_chof_1878,
Equus caballus	ENSECAG00000016105	1 retrocopy	retro_ecab_884,
Echinops telfairi	ENSETEG00000015566	1 retrocopy	retro_etel_574,
Loxodonta africana	ENSLAFG00000011921	1 retrocopy	retro_lafr_538,
Oryctolagus cuniculus	ENSOCUG00000008972	1 retrocopy	retro_ocun_621,
Otolemur garnettii	ENSOGAG00000017157	1 retrocopy	retro_ogar_2324 ,
Tursiops truncatus	ENSTTRG00000008920	1 retrocopy	retro_ttru_1715,