RetrogeneDB ID: retro_ogar_2013

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873580.1:875868..876449(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HENMT1
• Ensembl ID: ENSOGAG00000013441
• Aliases: None
• Description: HEN1 methyltransferase homolog 1 (Arabidopsis) [Source:HGNC Symbol;Acc:26400]

Sequence

>retro_ogar_2013
ATGGACATGCAGTGTAATAGTGCGGTTGATGGAAGTCCCAGCGTGCTGGTAATTCAATTCAGACCTCCGTTATACAGAAA
GTGGTATCAGTTCATTAAAGACTTAGTGGATCTACATGAACCCAAGAAGCTTGCAGCCCTGGGATGTGGTGCTACTTCGC
TCGTAAGGCAGTTAAAAGTGTTTCCATGCATTCAATTGGTCGTTGAAGTAGATATTGATGGGGACAAATTATGACGGAAA
GGGGAAAAGTTGCCTCCTGTCCTGGGGCATTTTCTGCAACCCCAGGAACTGGATTTGACTATTACCTTGTATGTGGCTCT
GTTGTGGAGAGAGACTGTTGTTTGCTTGGATTCGACTTGATAATGTGCACTGAATTAATAGAACATTTGGGTTCAGACGA
TCTGGCCAGATTTCCTGAAGTGGTGTTTGGGTTCCCATCTCCATCCATGGTCCTCATCAGCACACCAAACTCTGGATTCA
ATCCCTTGTTTCCAGCAGTGACTGTGAAAGAATCAGATCATAAATTTGAGTGGACTAGAAAGGAATTTCAGAACTGGGTT
TTATTTGTGACAAATCTATTC

Alignment

ORF - retro_ogar_2013 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.38 %
• Parental protein coverage: 50.26 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VNFQCDNVVDGSASAPVIQFKPPLYRQRYQFVKDLVDLHQPKKVADLGCGDTSLIRQLKVFPCIELLIGV
          ...QC...VDGS.S..VIQF.PPLYR..YQF.KDLVDLH.PKK.A.LGCG.TSL.RQLKVFPCI.L...V
Retrocopy MDMQCNSAVDGSPSVLVIQFRPPLYRKWYQFIKDLVDLHEPKKLAALGCGATSLVRQLKVFPCIQLVVEV

Parental  DIDGDKLRWKGEKLAPVLGHFLQPRELNLTITLY-CGSVVERDSRLLGLDLITCIELIEHLDSDDLARFP
          DIDGDKL..KGEKL.PVLGHFLQP.EL.LTITLY.CGSVVERD..LLG.DLI.C.ELIEHL.SDDLARFP
Retrocopy DIDGDKL*RKGEKLPPVLGHFLQPQELDLTITLY<CGSVVERDCCLLGFDLIMCTELIEHLGSDDLARFP

Parental  EVVFGYLSPSMVVISTPNSEFNPLFPAVTLRDSDHKFEWTRMEFQNWASHAANLY
          EVVFG..SPSMV.ISTPNS.FNPLFPAVT...SDHKFEWTR.EFQNW.....NL.
Retrocopy EVVFGFPSPSMVLISTPNSGFNPLFPAVTVKESDHKFEWTRKEFQNWVLFVTNLF

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_2013 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 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004357	1 retrocopy	retro_amel_532,
Otolemur garnettii	ENSOGAG00000013441	4 retrocopies	retro_ogar_1961, retro_ogar_2013 , retro_ogar_2135, retro_ogar_562,
Sus scrofa	ENSSSCG00000006846	1 retrocopy	retro_sscr_80,