RetrogeneDB ID: retro_ogar_2279

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873608.1:3714882..3715682(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SEC61A2
• Ensembl ID: ENSOGAG00000005809
• Aliases: None
• Description: Sec61 alpha 2 subunit (S. cerevisiae) [Source:HGNC Symbol;Acc:17702]

Sequence

>retro_ogar_2279
GAAGGTGCAGTCATAGCTCGGTTTCATTTGTTGGCCACCAGGACAGACAAAGTCTGAGCTTTACAGGAAGCTTTTTACCA
GCAGAACTTACCCAATCTCATGAACCACATAGCTACAGTTTTTGCATTTGCTGTTGTTATATATTTTCAGGGATTTCGTG
TTGACTTGCCCATTAAGTCAGCCTGCTATCGAAGACGGTATAGCAGCTGTCCCGTCAAGCTGTTCTGCACCTCGAATAGT
CCCATTATTCTCCAGTCTGCCTTAATTTCAAACCTGTAGGTTATTTCCCAGATGCTGTCTGTTTGATTTAGTGGCAACTT
TTTAATCAAGTTACTAGGACAGTGGGCTGACGTCAGTGGGGGAAGACCTGCTCATTCTTACTCAGTTGGAGGCCTCTGCT
ACTACCTTTCTCCTCCTAAGTCTGGTGGGGGCCATGTTTGAGGATCCCGTCCATGTAGTTGTTTACATCATCTTTATGTT
GGGACCCTGTGCATTCTTTTCTAAGACATGGATAGAGGTGTATGGTTTCTCAGCCAAAGATGTAGCTAAGCAGCTTAAGG
AACAGCAGACAGTAATGAGGGGTCACAGAGACACCTCTGTGGTTCATGAGCTTAGCAGGTACATCCCACAGCAGTTGCAT
TTGGTGTCCTGTGGATTGGTGCCCTGTCGGTGTTGGTGGACTTCCTGGGGGCCACTGGATCTGGCACCACAATTCTGCTT
TCCATCACTATGATTGATTAGTATTTTGCAATATTTGTTAAGGAACAGGCTGAAGTTAGTGGATGGGTGCTTTGTTTTTC

Alignment

ORF - retro_ogar_2279 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.96 %
• Parental protein coverage: 59.07 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EGAVIALFHLLATRTDKVRALREAFYRQNLPNLMNLIATVFVFAVVIYFQGFRVDLPIKSARYRGQYSSY
          EGAVIA.FHLLATRTDKV.AL.EAFY.QNLPNLMN.IATVF.FAVVIYFQGFRVDLPIKSA.YR..YSS.
Retrocopy EGAVIARFHLLATRTDKV*ALQEAFYQQNLPNLMNHIATVFAFAVVIYFQGFRVDLPIKSACYRRRYSSC

Parental  PIKLFYTSNIPIILQSALVSNLYVISQMLSVRFSGNFLVNLLGQWADVSGGGPARSYPVGGLCYYLSPPE
          P.KLF.TSN.PIILQSAL.SNL.VISQMLSV.FSGNFL..LLGQWADVSGG.PA.SY.VGGLCYYLSPP.
Retrocopy PVKLFCTSNSPIILQSALISNL*VISQMLSV*FSGNFLIKLLGQWADVSGGRPAHSYSVGGLCYYLSPPK

Parental  S-MGAIFEDPVHVVVYIIFMLGSCAFFSKTWIEVSGSSAKDVAKQLKEQQMVMRGHRDTSMVHELNRYI-
          S..GA.FEDPVHVVVYIIFMLG.CAFFSKTWIEV.G.SAKDVAKQLKEQQ.VMRGHRDTS.VHEL.RYI.
Retrocopy S>VGAMFEDPVHVVVYIIFMLGPCAFFSKTWIEVYGFSAKDVAKQLKEQQTVMRGHRDTSVVHELSRYI<

Parental  PTAAAFGGLCIGALSVLADFLGAIGSGTGILLAVTIIYQYFEIFVKEQAEVGG-MGALFF
          PTA.AFG.L.IGALSVL.DFLGA.GSGT.ILL..T.I..YF.IFVKEQAEV.G.MGALFF
Retrocopy PTAVAFGVLWIGALSVLVDFLGATGSGTTILLSITMID*YFAIFVKEQAEVSG<MGALFF

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_2279 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Microcebus murinus	ENSMICG00000004906	1 retrocopy	retro_mmur_1258,
Otolemur garnettii	ENSOGAG00000005809	1 retrocopy	retro_ogar_2279 ,