RetrogeneDB ID: retro_ogar_2296

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873610.1:1681936..1682368(+)
• 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_2296
AAAATCAATACTCAAGAACCTGCGAAGGCTCTGGATTCTGATTTCTGCAACACCAATATTGTGAATCAAATTATTCTGTA
GTCAGAGGGACTCTGTGAAGCATTCTCCAAATTGAATGTGACGAGTGAGATCCGACAGATTATCATGTCTCTTGACAAGC
TTTGTTTCAGTATATCTACCATTGGAAATGCCGGAAGCTCCTACCTTGACTGTTTCAAAAATTCTGATTTGATGGAAGTA
TTTCATTATAAGCAGGCTCATGTCAACAGATACAGGATTTCCTTACTGAGAACCTTTATGAAGACATTATTCCTACCTTA
CACGGTATCTATTTAGAGAGATAACTGAATATTCCTCTTATTATAGATTTTGATTGGAAATGAAAATGGAGAAATATACT
TTGCAACATGATGCTGCTTCCATGATGAAGTC

Alignment

ORF - retro_ogar_2296 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.64 %
• Parental protein coverage: 51.06 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KINTQEPVETLDFDFCSTNVINKIILQSEGLREAFSELDMTSEVLQITMSPEKPYFRLSTFGNAGSSHLD
          KINTQEP...LD.DFC.TN..N.IIL.SEGL.EAFS.L..TSE..QI.MS..K..F..ST.GNAGSS.LD
Retrocopy KINTQEPAKALDSDFCNTNIVNQIIL*SEGLCEAFSKLNVTSEIRQIIMSLDKLCFSISTIGNAGSSYLD

Parental  YPKDSDLMEAFHCNETQVNRYKISLLKPSTKALVLSCKVSIRTDNRGFLSLQYMIRNEDGQICFVEYYCC
          ..K.SDLME.FH.....VNRY.ISLL....K.L.L...VSI..DN..FL.L...I.NE.G.I.F....C.
Retrocopy CFKNSDLMEVFHYKQAHVNRYRISLLRTFMKTLFLPYTVSI*RDN*IFLLL*ILIGNENGEIYFAT*CCF

Parental  PDEV
          .DEV
Retrocopy HDEV

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_2296 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,