RetrogeneDB ID: retro_ogar_2135

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873595.1:1896538..1897290(+)
• 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_2135
GACATACAGTGTAATAATGTGGTTGATGGAAGTCCCAGTGCGCAGGTAATTCAGTTTAAGCCTCTGTTATACAGATGGCA
GTACCAATTCATTAAAGATTCAGTGGATCTCATGAACTCAAGAAGGTTGCAGCCCTGGGATATGGTGATACTTTGCTCAT
CAGCACTTAAAAGTGTTTCCATGCATTGAATTGCTTGTTGGAGCAGACAAGGATGGGGATAAATTACCATGGAAAGGGGG
AAAGTTGGCTCCCATCCTGGGGCATTTTCTGTAACCCCAGGAGCTGGATTTGACTATTACATTGTATGTGGCTCTGTTGT
GGAGAGAGACTCTCTTTTGCTTAGACAACTTGATAATGTGTATTGAATTAATAGAACATTTGGATTCAGACAATCTGGCA
GATTTCCTGAAGTGGTGTTTGGGTACCCATCTCCGTCCATGGTCATTGTCAGCACGCCAAATTCTGAATTCAATCCCTCA
TTTCCAGCAGTGACCTTAAGAGATTCAGATCATAAATCTGAGTGGATTAGAATGGAATTTCAGAACTGGGTTCACACGCG
GCAAATCTCCGTAAGTCCTCCGTGGCGTTCCCCTGGATGGGAGCACCACCAGCTGCTGCTGAGAGTGTTAGATTCTGCAC
ACAGGCAGGCGTCTACTGGAAAAGTAGTGGAAAGGCAGCTGAACTGTGTGTCTCAGAGCAGCTTGTTCAGCGCACTTATA
AAGCTGTTTTTACGGCCTCATACCCAAGTTTA

Alignment

ORF - retro_ogar_2135 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.82 %
• Parental protein coverage: 64.77 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  NFQCDNVVDGSASAPVIQFKPPLYRQRYQFVKDLVDL-HQPKKVADLGCGDTSLI-RQLKVFPCIELLIG
          ..QC.NVVDGS.SA.VIQFKP.LYR..YQF.KD.VDL.H..KKVA.LG.GDT.LI...LKVFPCIELL.G
Retrocopy DIQCNNVVDGSPSAQVIQFKPLLYRWQYQFIKDSVDL<HELKKVAALGYGDTLLI<QHLKVFPCIELLVG

Parental  VDIDGDKLRWKGEKLAPVLGHFLQPRELNLTITLYCGSVVERDSRLLGLDLITCIELIEHLDSDDLA-RF
          .D.DGDKL.WKG.KLAP.LGHFL.P.EL.LTITLY......R........LI.CIELIEHLDSD.LA.RF
Retrocopy ADKDGDKLPWKGGKLAPILGHFL*PQELDLTITLYV-ALLWRETLFCLDNLIMCIELIEHLDSDNLA<RF

Parental  PEVVFGYLSPSMVVISTPNSEFNPLFPAVTLRDSDHKFEWTRMEFQNW-ASHAANLYNYSVEFTGVGAPP
          PEVVFGY.SPSMV..STPNSEFNP.FPAVTLRDSDHK.EW.RMEFQNW..SHAANL...SV.F...GAPP
Retrocopy PEVVFGYPSPSMVIVSTPNSEFNPSFPAVTLRDSDHKSEWIRMEFQNW<GSHAANLRKSSVAFPWMGAPP

Parental  AGAESVGFCTQIGVFRKNGGKAAESCVLEQ---HAYKVVFTASYPSL
          A.AESV.FCTQ.GV..K..GKAAE.CV.EQ.....YK.VFTASYPSL
Retrocopy AAAESVRFCTQAGVYWKSSGKAAELCVSEQLVQRTYKAVFTASYPSL

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_2135 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,