RetrogeneDB ID: retro_ogar_2558

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873634.1:6126917..6127531(+)
• Located in intron of: ENSOGAG00000034380

Retrocopy information

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

Parental gene information

• Parental gene symbol: TRA2A
• Ensembl ID: ENSOGAG00000009733
• Aliases: None
• Description: transformer 2 alpha homolog (Drosophila) [Source:HGNC Symbol;Acc:16645]

Sequence

>retro_ogar_2558
GGTTAAGTAAATGAGTCTTGCTCTCAGTCAAAATCTCGAACAGGAACTCCTGCTTGTGTAAAATTGGAGAGCAGGTCAGG
ATCTTGTGGTCCATCAGGGGTTTTGAAACACTCTGAATCCCATTCTCAATCAAGATCAAAATCCAGGTCAAGGTCAAGGA
GGAATTCTCATAGATGTTACACTCAATCCAGATCCCATTCTCACTCTCATAGGAGATGATCTCGGAGTAGGTGATATACA
CCAGAATACCGGTGGTGAAGGAGCCGAAGTCATTCTCCAATGTCAAACTGGAGAAGACCTACAGGCAGCAGGGCAAATCC
AGATCCAAACACATGTCTTGGAGTGTTAGGCTTCAGTTTGTATACAACAGAGAGAGATTTTCATGAAGTGTTTTCTCGAT
ATGGACCCTTAAGTGGTGTCAATGTGGTTTATGATCAGCGAACTGGACAATCTTGAGGATTGCTTTTGTGTATTTTGAGA
GAATAGATGATTCAAAAGAGGCTATGGAAAGGGCAAATGGAATGGAGCTGGATGGCAGAATAATTCATGCAGATTATTCT
ATCACCAAGAGAGCTCACACACCTACACCTGGCATCTACATGGGCAGACCAACT

Alignment

ORF - retro_ogar_2558 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.95 %
• Parental protein coverage: 72.44 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GTLNESRSQSKSPTGTPARVKSESRSGSRSPSRVSKHSESHSRSRSKSRSRSRRHSHRRYTRSRSHSHSH
          G..NES.SQSKS.TGTPA.VK.ESRSGS..PS.V.KHSESHS.SRSKSRSRSRR.SHR.YT.SRSHSHSH
Retrocopy G*VNESCSQSKSRTGTPACVKLESRSGSCGPSGVLKHSESHSQSRSKSRSRSRRNSHRCYTQSRSHSHSH

Parental  RRRSRSRSYTPEYRRRRSRSHSPMSNRRRHTGSRANPDPNTCLGVFGLSLYTTERDLREVFSRYGPLSGV
          RR.SRSR.YTPEYR..RSRSHSPMSN.RR.TGSRANPDPNTCLGV.G.SLYTTERD..EVFSRYGPLSGV
Retrocopy RR*SRSR*YTPEYRW*RSRSHSPMSNWRRPTGSRANPDPNTCLGVLGFSLYTTERDFHEVFSRYGPLSGV

Parental  NVVYDQRTGRSRG-FAFVYFERIDDSKEAMERANGMELDGRRIRVDYSITKRAHTPTPGIYMGRPT
          NVVYDQRTG.S.G..AFVYFERIDDSKEAMERANGMELDGR.I..DYSITKRAHTPTPGIYMGRPT
Retrocopy NVVYDQRTGQS*G<IAFVYFERIDDSKEAMERANGMELDGRIIHADYSITKRAHTPTPGIYMGRPT

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_2558 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 12 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001130	1 retrocopy	retro_chof_974,
Callithrix jacchus	ENSCJAG00000001509	1 retrocopy	retro_cjac_1759,
Echinops telfairi	ENSETEG00000007250	2 retrocopies	retro_etel_323, retro_etel_692,
Homo sapiens	ENSG00000164548	1 retrocopy	retro_hsap_386,
Gorilla gorilla	ENSGGOG00000009053	1 retrocopy	retro_ggor_391,
Mustela putorius furo	ENSMPUG00000013480	1 retrocopy	retro_mputfur_1442,
Nomascus leucogenys	ENSNLEG00000014794	1 retrocopy	retro_nleu_1481,
Otolemur garnettii	ENSOGAG00000007839	5 retrocopies	retro_ogar_1057, retro_ogar_137, retro_ogar_1586, retro_ogar_2445, retro_ogar_2584,
Otolemur garnettii	ENSOGAG00000009733	3 retrocopies	retro_ogar_1966, retro_ogar_2558 , retro_ogar_3027,
Pongo abelii	ENSPPYG00000017728	1 retrocopy	retro_pabe_324,
Pan troglodytes	ENSPTRG00000018988	1 retrocopy	retro_ptro_299,
Sorex araneus	ENSSARG00000012900	1 retrocopy	retro_sara_467,