RetrogeneDB ID: retro_ogar_1946

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873576.1:11354590..11355585(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DLAT
• Ensembl ID: ENSOGAG00000008559
• Aliases: None
• Description: dihydrolipoamide S-acetyltransferase [Source:HGNC Symbol;Acc:2896]

Sequence

>retro_ogar_1946
ATACTAGTATTAGAAGGTACCAGAAATGTTCCAGTTGGCGTGATCATCTGTATCACAGCTGCAAAACCTAAGGGTATTGA
GGCCTTTAAAAATTATACATGAATTCCTCAGCAGCACCTGCCCCGTGAGTAGCCCTACCACCAACCCCTGCTGCTGCTTT
GCCTCCTACATCTTCTGCTCAGGCTCCTGGTGTCTCATATTCCACACATATGCACATATTTCTTCTTGCCCTTTCTCCCA
CTGTGACCATGGGTACAGTTCAGAGATGGGAAAAAAAATGTGGCTGAGAAGCTAAGTGAAGGACACTTATTGGCAGAGAT
AGAGACTAACAAAGCCCTTAGAGGTTTTAAAGTATAGGGAGAAGGTTAACTGGCAAAAGTCTTGGTCCCTGAAGGCATAA
GAGATGTCCTTCTAGGAACTCCACCTTGTATCATTGTCGAAAAAGAGGCAGATAGAGCAGCATTTGCTAACTATAGGCCA
ACTGAAGTAACAGATTTAAAACCACAAGCACCACCACCTACTTCACCCCCAGGGACCACTGTTCCTCCAACTCCCCAACC
TTTAGCTCCTACTCCTTTAGCCCCCCTGCCCAGATACTCTTGCTGGACCCAAGGGAAGGGTGTTTGTTAGCCCTCTTGCA
AAGAAGTTGGTGGCAGAAGAAGGGATTGACCTTATCCAAGTGAAAGGGACAGGACCAGATGGTAGAATTATGAAGAAGGG
CATTGACTTTTGTGTGTCTGCTAAAGCTGTGCTGCCTCAGCAGCTGCTATGCCTCCTCTGGGTCTGGGAGTGGACCAGTT
CCTGTAGGAGTCTTCACAGTCATCCCAATCAGTAACATTCATTGAGTTATTACACAGTGATTAATGCAATCAAAGCAAAT
CATACTTCATTATCACCATTCTATTGATGTAAATATGGGAGAAATTTTGTTGGTACAGAAAGAACTTAATAAGATTTTAG
AAGGTGGGAAGGAGAGAACAAATGAATATTTGGTA

Alignment

ORF - retro_ogar_1946 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.27 %
• Parental protein coverage: 51.78 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  ILVAEGTRDVPVGAIICITVAKPEDIEAFKNYT-LDSSAVPAPQAVPAPTPAAASAPPTPSAQAPGSSYP
          ILV.EGTR.VPVG.IICIT.AKP..IEAFKNYT...SSA.PAP.....PTPAAA..PPT.SAQAPG.SY.
Retrocopy ILVLEGTRNVPVGVIICITAAKPKGIEAFKNYT<MNSSAAPAP*VALPPTPAAA-LPPTSSAQAPGVSYS

Parental  THMQVLLPALSPTMTMGTVQRWEKKVG-EKLSEGDLLAEIETDKATIGFEVQEEGYLAKILVPEGTRDVP
          THM...L.ALSPT.TMGTVQRW....G.EKLSEG.LLAEIET.KA..GF.V..EG.LAK.LVPEG.RDV.
Retrocopy THMHIFLLALSPTVTMGTVQRWXXXCG>EKLSEGHLLAEIETNKALRGFKV*GEG*LAKVLVPEGIRDVL

Parental  LGTPLCIIVEKEADIAAFADYRPTEVTDLKPQVPPPTPPPVAAVPPTPQPLAPAPSA-PCPATPAGPKGR
          LGTP.CIIVEKEAD.AAFA.YRPTEVTDLKPQ.PPPT.PP...VPPTPQPLAP.P.A.PCP.T.AGPKGR
Retrocopy LGTPPCIIVEKEADRAAFANYRPTEVTDLKPQAPPPTSPPGTTVPPTPQPLAPTPLA>PCPDTLAGPKGR

Parental  VFVSPLAKKLAAEKGIDLTQVKGTGPDGRITKKDIDSFVPAKA-APAPAAAVPPPGPGV-APVPTGVFTD
          VFVSPLAKKL.AE.GIDL.QVKGTGPDGRI.KK.ID..V.AKA...A.AAA.PP.G.GV..PVP.GVFT.
Retrocopy VFVSPLAKKLVAEEGIDLIQVKGTGPDGRIMKKGIDFCVSAKA<CAASAAAMPPLGLGV<GPVPVGVFTV

Parental  VPISNIRRVIAQRLMQSKQTIPHYYLSIDVNMGEVLLVRKELNKMLEGKSKISVNDFII
          .PISNI..VI.Q.LMQSKQ.I.HY..SIDVNMGE.LLV.KELNK.LEG..K...N....
Retrocopy IPISNIH*VITQ*LMQSKQIILHYHHSIDVNMGEILLVQKELNKILEG-GKERTNEYLV

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_1946 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
Macaca mulatta	ENSMMUG00000017568	1 retrocopy	retro_mmul_65,
Otolemur garnettii	ENSOGAG00000005625	1 retrocopy	retro_ogar_2997,
Otolemur garnettii	ENSOGAG00000008559	1 retrocopy	retro_ogar_1946 ,