RetrogeneDB ID: retro_ogar_1233

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873540.1:2399428..2400031(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000028736
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RRAS
• Ensembl ID: ENSOGAG00000010243
• Aliases: None
• Description: related RAS viral (r-ras) oncogene homolog [Source:HGNC Symbol;Acc:10447]

Sequence

>retro_ogar_1233
GGGCCAGGACCCGGGGACCCCCCACCCAGCGAGACACACAAGCTGGTGGTCATGGGCGGCGGCGGCATGGGCAAGAGCAT
GCTGAACATCCAATTCATCCAGTCCTACTTTGTGTCTGAATACAATCCCACTATCAAGGACTCCCACACAAAGATCTGCA
CTGTGGATGGCATCCCAGCCCGGCTGGACATTCTGGACACCGCGGGCCAGGAGGAATTCAGGGCCATGCAGGAGCAGTAT
ATGCGCACTGGCCACAGCTTCCTGCTGGTATATGCCATTAACAACTGGCAGAGTTTCAACGAGGTGGACAAGCTCTTCAC
ACAGATCCTCCAAGTCAAGCACCAGGATGACTTCCCTGTCATGCTGGTTGAGAACAATGCAGACCTGGAGACACAGCACC
AGGTCCCCCAATCTTGAAGCACTGGCCTTCAGCGCCTCCCACCATGTGGCTTACTTTGAGGCCTCAGCCAACTGCGCCTC
AATGTGGATGAGGCCTTCGAGCAGCTGGTTGTTAGCTGTCTGGAAATTCCAAGACAGGAGCTCCCACCCAGTCCCCCCAG
TGCCCCCAGGAAGAAGGGTGGGGGCTGCCCCTGCGTCCTCCTA

Alignment

ORF - retro_ogar_1233 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.34 %
• Parental protein coverage: 83.4 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GPGPGDPPPSETHKLVVVGGGGVGKSALTIQFIQSYFVSDYDPTIEDSYTKICTVDGIPARLDILDTAGQ
          GPGPGDPPPSETHKLVV.GGGG.GKS.L.IQFIQSYFVS.Y.PTI.DS.TKICTVDGIPARLDILDTAGQ
Retrocopy GPGPGDPPPSETHKLVVMGGGGMGKSMLNIQFIQSYFVSEYNPTIKDSHTKICTVDGIPARLDILDTAGQ

Parental  EEFGAMREQYMRAGHGFLLVFAINDRQSFNEVGKLFTQILRVKDRDDYPVVLVGNKADLETQRQVPRS-E
          EEF.AM.EQYMR.GH.FLLV.AIN..QSFNEV.KLFTQIL.VK..DD.PV.LV.N.ADLETQ.QVP.S.E
Retrocopy EEFRAMQEQYMRTGHSFLLVYAINNWQSFNEVDKLFTQILQVKHQDDFPVMLVENNADLETQHQVPQS>E

Parental  ALAFSASHHVAYFEASA-KLRLNVDEAFEQLVRAVRKFQEQELPPSPPSAPKKKGGGCPCVLL
          ALAFSASHHVAYFEASA..LRLNVDEAFEQLV........QE..........KKGGGCPCVLL
Retrocopy ALAFSASHHVAYFEASA<QLRLNVDEAFEQLVVSCLEIPRQEXXXXXXXXXXKKGGGCPCVLL

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_1233 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 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Otolemur garnettii	ENSOGAG00000010243	1 retrocopy	retro_ogar_1233 ,
Otolemur garnettii	ENSOGAG00000027655	1 retrocopy	retro_ogar_1081,
Sus scrofa	ENSSSCG00000003183	2 retrocopies	retro_sscr_201, retro_sscr_570,
Tursiops truncatus	ENSTTRG00000005524	1 retrocopy	retro_ttru_771,