RetrogeneDB ID: retro_ogar_2020

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873581.1:9423623..9424078(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AGPAT1
• Ensembl ID: ENSOGAG00000010187
• Aliases: None
• Description: 1-acylglycerol-3-phosphate O-acyltransferase 1 [Source:HGNC Symbol;Acc:324]

Sequence

>retro_ogar_2020
AAAATCTTGCATCTAATGCTGCTCCATATCAAATACCTGTATGGGATCCGAGTAGAGGTGTGAGGGGCTCACCACTTCCC
TCCTTCGCAGACCTATGTTGTCTCCAACCACCAGAGCTCCCTCTACCAGCTTGGGATGATGGAGGTACTGTCAGGCCACT
GTGTGCCCATTGCCAAGCATGAGCTACTGTGGGCCGGCTCTACTGGGCTGGCCTGCTCACTAGCAGGTGTCCTCTTCATT
GAACGGAAGCATATGGGGGATGCCATCGGTGTCATGTCTAAGGTTGCTCAGACCCTGCTCACCCAGGATGTAGGGTCTGG
GTTTTTCCTGAGGGAACAAGAAACCATAACAGCTCCATGCTGCCCTTCAAACATGGCATTTTCCATCTTGCAGTGCAAGC
TCAGGTTCCCATTGTCCCAATAGTCATGTCCTCCTATCAAGACTTCTACTGCAGG

Alignment

ORF - retro_ogar_2020 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.71 %
• Parental protein coverage: 53.31 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KILRLMLLHIKYLYGIRVEVRGAHHFPPSQPYVVVSNHQSSLDLLGMMEVLPGRCVPIAKRELLWAGSAG
          KIL.LMLLHIKYLYGIRVEV.GAHHFPPSQ.YVV.SNHQSSL..LGMMEVL.G.CVPIAK.ELLWAGS.G
Retrocopy KILHLMLLHIKYLYGIRVEV*GAHHFPPSQTYVV-SNHQSSLYQLGMMEVLSGHCVPIAKHELLWAGSTG

Parental  LACWLAGVIFIDRKRTGDAISVMSEVAQTLLTQDV-RVWVFPEGTRNHNGSMLPFKRGAFHLAVQAQVPI
          LAC.LAGV.FI.RK..GDAI.VMS.VAQTLLTQDV.RVWVFPEGTRNHN.SMLPFK.G.FHLAVQAQVPI
Retrocopy LACSLAGVLFIERKHMGDAIGVMSKVAQTLLTQDV<RVWVFPEGTRNHNSSMLPFKHGIFHLAVQAQVPI

Parental  VPIVMSSYQDFYCK
          VPIVMSSYQDFYC.
Retrocopy VPIVMSSYQDFYCR

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_2020 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Otolemur garnettii	ENSOGAG00000010187	1 retrocopy	retro_ogar_2020 ,