RetrogeneDB ID: retro_ogar_2726

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873655.1:3763762..3764262(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAD1
• Ensembl ID: ENSOGAG00000014822
• Aliases: None
• Description: RAD1 homolog (S. pombe) [Source:HGNC Symbol;Acc:9806]

Sequence

>retro_ogar_2726
ATGCCTCTCCCATGGCAGCACACCCAAGACGAGAGTGGTCGGTAGGCTTGGTGGCCAGCTCCACAATGTCAGGGGTCTCC
ACCATCTTGGGAGCTATTTGTTTCCAAGACTGTGCCCCAGTTTCACTACCACAAGTAGAATCAAGGTTACCTTAGAAAAT
GCAAAGTGTGTGCAAGCAAATGCTTATTCAGGCTGGAATGTTTCAAGAGTTTTACAGGCCAGGAAGAGTCTGGTACTTTT
TGAATTAATTAACTCTCCTTATAGCTGTTTATCTGCTTTTGGATCAAATCCCACACCGGGGAATTTAACTGCATTTCTGA
TGTTGTTACCAAGACTGTGGCTACCCTTTGATGCTGTTCTTGGAAGAAGGAGGCGTGGTGATGGTCTGCAAAATCAATAC
TCAGGAGCCAGTGGAGACTCTGGAGTTTGATTTCTGGAGCACCAATGTTATTAATAAAATGATTCTGCAGTCAGAGGGGC
TCTGAGAAGCATTTTCCAAA

Alignment

ORF - retro_ogar_2726 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.86 %
• Parental protein coverage: 59.93 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  MPLLTQHIEDENDQ-YSLVASLDNVRNLSTILKAIHFQDYATC-FATKNGIKVTVENAKCVQANAF-IQA
          MPL..QH..DE......LVAS.......STIL.AI.FQD.A...F.T...IKVT.ENAKCVQANA.....
Retrocopy MPLPWQHTQDESGR<VGLVAS-STMSGVSTILGAICFQDCAPV<FTTTSRIKVTLENAKCVQANAY<FRL

Parental  GIFQEFTVQEESITFRIN-LTVLL-DCLSIFGSSPTPGTLTALRM-CYQDYGYPLMLFLEEGGVVTVCKI
          ..F..FT.QEES.TF.IN.LT.L...CLS.FGS.PTPG.LTA..M.CYQD.GYPLMLFLEEGGVV.VCKI
Retrocopy ECFKSFTGQEESGTF*IN<LTLLI<SCLSAFGSNPTPGNLTAFLM>CYQDCGYPLMLFLEEGGVVMVCKI

Parental  NTQEPVETLDFDFCSTNVINKIILQSEGLREAFSE
          NTQEPVETL.FDF.STNVINK.ILQSEGL.EAFS.
Retrocopy NTQEPVETLEFDFWSTNVINKMILQSEGL*EAFSK

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_2726 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 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018514	1 retrocopy	retro_cjac_1004,
Homo sapiens	ENSG00000113456	1 retrocopy	retro_hsap_634,
Gorilla gorilla	ENSGGOG00000004219	1 retrocopy	retro_ggor_555,
Macaca mulatta	ENSMMUG00000030184	1 retrocopy	retro_mmul_54,
Nomascus leucogenys	ENSNLEG00000014437	1 retrocopy	retro_nleu_455,
Otolemur garnettii	ENSOGAG00000014822	2 retrocopies	retro_ogar_2296, retro_ogar_2726 ,
Pongo abelii	ENSPPYG00000015389	1 retrocopy	retro_pabe_564,
Pan troglodytes	ENSPTRG00000016783	1 retrocopy	retro_ptro_462,
Tarsius syrichta	ENSTSYG00000002894	1 retrocopy	retro_tsyr_738,