RetrogeneDB ID: retro_ogar_2369

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873615.1:7617072..7617761(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: OXA1L
• Ensembl ID: ENSOGAG00000000631
• Aliases: None
• Description: oxidase (cytochrome c) assembly 1-like [Source:HGNC Symbol;Acc:8526]

Sequence

>retro_ogar_2369
CTGCAACACCCTCCTGTTGTTTTTGCAATGCCCTCACCTGCAGCAGTACCTGAGGTGGCTTCTAGAGAGACTGCAGACAT
AGTCCATAGTTCTCTGCTGCAGAACAGAGCTTTACTGAACTGGGACTGAAGTCATACACCAAGGAGGACTGATCCAGAAC
TTCCTGGAATTTATGTCTCCTGACCTGGGCCTACCTTGGTGAGGGGCCATTGCTGCAAGTACAGTCCTTGCCTGCTGCCT
GGTTTTTCCTCTCATCGTGAAGGGTCAGTGAGAGGCAGCCAAGATCCACACCACTTGCCAGAGATGCAGAAGTATTTCAC
TCTAATCAGAGACGCCATGTTGGCAGGAGACCATGCTGAGTTTTCCAGGGCCTCCTCAGAGATGACACTTTACCAGAAAA
AGCATGATATCAAACTCTTTAATCTCTCATTCTACCTCTGACTCAGGCTCCAGTCTTCATCTGTTTCATTGCTTTGAGAG
AGACGGCCAACCTTCCTGAGCCCAGCCTGCAGACAGGTGGCCTCTGGTGGTTCCAGGATCTCACAATATCTGATCCCACC
TACATGTTAGTTCTAGTAGTCACTGCTCCAATGTGGGGTCTCCTTGAGCCAGGTGCTGAGACAGCAGTGCAAAGTTCTGA
CCTTCAGTAGATGAGAAATGTGATCAGAGTGATACCTCTGGCAGCCTTG

Alignment

ORF - retro_ogar_2369 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.07 %
• Parental protein coverage: 53.24 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VQAPPVVPATPSPTAVPEVASGETADVVQAAAEQSFTELGLG-SYTP-VGLIQNFLEFMHVDLGLPWWGA
          .Q.PPVV.A.PSP.AVPEVAS.ETAD.V.....Q....L....S.TP..GLIQNFLEFM..DLGLPW.GA
Retrocopy LQHPPVVFAMPSPAAVPEVASRETADIVHSSLLQNRALLNWD*SHTP>GGLIQNFLEFMSPDLGLPW*GA

Parental  IAACTVLARCLVFPLIVKGQREAAKIH-NHLPEIQKYATQIREAKLAGDNTEFYRASSEMALYQKKHDIK
          IAA.TVLA.CLVFPLIVKGQ.EAAKIH..HLPE.QKY.T.IR.A.LAGD..EF.RASSEM.LYQKKHDIK
Retrocopy IAASTVLACCLVFPLIVKGQ*EAAKIH<HHLPEMQKYFTLIRDAMLAGDHAEFSRASSEMTLYQKKHDIK

Parental  LFR-PLILPLTQAPVFISFFIALREMANLPVPSLQTGGLWWFQDLTISDPTYMLPLVVTATMWGVLELGA
          LF...LILPLTQAPVFI..FIALRE.ANLP.PSLQTGGLWWFQDLTISDPTYML.LVVTA.MWG.LE.GA
Retrocopy LFN<SLILPLTQAPVFIC-FIALRETANLPEPSLQTGGLWWFQDLTISDPTYMLVLVVTAPMWGLLEPGA

Parental  ETGVQSSDLQWMRNVIRVMPLVVL
          ET.VQSSDLQ.MRNVIRV.PL..L
Retrocopy ETAVQSSDLQ*MRNVIRVIPLAAL

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_2369 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 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Myotis lucifugus	ENSMLUG00000012893	1 retrocopy	retro_mluc_2461,
Monodelphis domestica	ENSMODG00000005347	1 retrocopy	retro_mdom_1308,
Oryctolagus cuniculus	ENSOCUG00000000720	1 retrocopy	retro_ocun_367,
Otolemur garnettii	ENSOGAG00000000631	1 retrocopy	retro_ogar_2369 ,
Ictidomys tridecemlineatus	ENSSTOG00000003318	1 retrocopy	retro_itri_352,