RetrogeneDB ID: retro_ogar_1105

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873536.1:2067502..2068184(+)
• Located in intron of: ENSOGAG00000013434

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDUFAF7
• Ensembl ID: ENSOGAG00000002568
• Aliases: None
• Description: NADH dehydrogenase (ubiquinone) complex I, assembly factor 7 [Source:HGNC Symbol;Acc:28816]

Sequence

>retro_ogar_1105
TACAGCTTTTATCTTACACGTGAATTTTTTGATGTTCTTCCTGTGCATAAGTTTCTGAAAACACAAGGGTGGCAAGAAGT
ATTCATTGATGTTGATGATAAACTGAGGTTTATTTTGGCATCTTATTTCACCCCGGTAGCAGCTTTCATACAACATAACG
AAATGAGGGATCGTGTTGAGGGTGTCCTGGTGCTGGTGTTATCATTCAGGAGCTTTCTCAACACGCTGCACTAGCTGGGG
TGCCGCGCTGATTGCTGATTCTGGTCAGGATGGAACAAAGACAGATACCGTCAGAAGGTTTTGTGGCCACAAGCTTCATG
GTGTGTTAATTGGCCAGGGAACAGTAGACCTAACAGCTGATGTAGACTTCAGTTATTTGTACAGAATGGCAAAGGGAAAA
GTAGCCTCCCTCAGTCCAATAAAAGAACAAGCATTTTTTTTAAATGTGGGTATTGCTGTTTGGCTCAGGGTTCTTTTAGT
TAAATCAGATGAGCCATCAGTAAGGCAGCTATTACTTCATGGGTGTAACATGTTAATGAATCCTAAGAACTAGGGAGAAA
GTTTTCACTTTTCTGCTTTGCTACCTCATCGTAGACTTCATGGTGGAAGGCACCAGATGAACCCCTGTCAGTCAAAACCC
TCTGCATCCCCTATGGCTGGGTTTAGTGAACTTGCTTGGCAG

Alignment

ORF - retro_ogar_1105 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.89 %
• Parental protein coverage: 52.71 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  YSFYLAHEFFDVLPVHKFQKTPQGWREVFIDVDPQIPDKLRFVLAPCVTPATAFIQHDETRDHVEV-CPD
          YSFYL..EFFDVLPVHKF.KT.QGW.EVFIDVD....DKLRF.LA...TP..AFIQH.E.RD.VE..CP.
Retrocopy YSFYLTREFFDVLPVHKFLKT-QGWQEVFIDVD----DKLRFILASYFTPVAAFIQHNEMRDRVEG<CPG

Parental  AGVIIQELSQRIALTG-GAALIADYGHDGTKTDTFRGFCGHKLHDVLIAPGTADLTADVDFSYLRRMAKG
          AGVIIQELSQ..AL.G.GAALIAD.G.DGTKTDT.R.FCGHKLH.VLI..GT.DLTADVDFSYL.RMAKG
Retrocopy AGVIIQELSQHAALAG<GAALIADSGQDGTKTDTVRRFCGHKLHGVLIGQGTVDLTADVDFSYLYRMAKG

Parental  KVASLGPIKQQTFLKNMGIDVRLKVLLDKSDEPSVRQQLLHGYDMLMNPKKMGDRFNFFALLPHQRLHGG
          KVASL.PIK.Q....N.GI.V.L.VLL.KSDEPSVRQ.LLHG..MLMNPK..G..F.F.ALLPH.RLHGG
Retrocopy KVASLSPIKEQAXXXNVGIAVWLRVLLVKSDEPSVRQLLLHGCNMLMNPKN*GESFHFSALLPHRRLHGG

Parental  MHQKNTCQSKPSASPVAGFSELAWQ
          .HQ.N.CQSKPSASP.AGFSELAWQ
Retrocopy RHQMNPCQSKPSASPMAGFSELAWQ

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_1105 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryctolagus cuniculus	ENSOCUG00000007239	1 retrocopy	retro_ocun_824,
Otolemur garnettii	ENSOGAG00000002568	1 retrocopy	retro_ogar_1105 ,
Rattus norvegicus	ENSRNOG00000005279	1 retrocopy	retro_rnor_1231,