RetrogeneDB ID: retro_ogar_2932

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873683.1:3470361..3471411(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000012530
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TRAM1
• Ensembl ID: ENSOGAG00000006379
• Aliases: None
• Description: translocation associated membrane protein 1 [Source:HGNC Symbol;Acc:20568]

Sequence

>retro_ogar_2932
ATGGGGCTCCGTAAGAAGAGCGCCAGGAACCCCCAGGTCCTGAGCCACGAATTCATCCTGCAGAATCATGCGGACATCGT
CGCCTGCGTGGGGATGTTCTTCGTGCTGGGGCTGATGTTCGAGGGAACGGCAGAAGTATCTATCGTTTTCCTTACTCTTC
AGCACGGCGTCATCGTCCCTGCCGCAGAAGAGCAAGGCGCGGGATCAAAGTCCCTTTATCATTACGGCGCCAAAGATTTG
GCGACGATTTTCTTCTACATGCTGGTGGCAATAATCGTTCACGCCTCAATTCAGGAGTATGTGTTGGATAAAATTAACAG
GAAAATGCACTTCACCAAAGCGAAACAAAACAAGTTTAATGAATCTGGGCAGTTTAGTGTCTTCTACTTCGTTTCTTGTA
TCTGGGGCACAATCCTTCTGATCTCTGAAAACTGCCTGTCAGACCCAACTCTCTTATGGAGGGCTCATCCCCATAACATG
ATGACATTTCAAATGAAGTTTTTCTACATATCACAGTTGGCTTATTGGTTTCATGCTTTTCCTGAACTCTACTTCCAGAG
AACCAAAAAACAAGATGTCCCTGGTCAACTGGTGTACATAGGGCTTCACCTCTTTCACATCATTGGAGCTTATCTCTTGT
ACTTGAACCATTTGGGATTACTTCTTTTGGTGCTGCATTATTTTGTTGAATTACTTTCCCACATGTGCGGCCTGTTTTAT
TTTAGTGATGAAAGGTACCAGAAAGGGATCTCTCTGTGGGCCATTGTGTTTATTTTGGGTAGACTTGTTACTTTAATTGT
TTCTGTCCTCACTGTTGGGTTTCACCTGGCTGGATCGCACAATCGGAATCCGGATTCCATTACTGGAAATGTGAATGTGT
TGGCAGCTAAAATTGCTGTTCTGTCGTCCAGTTGTTCTATCCAAGTATACATAACGTGGAACTTAATTACCCTCCGACTT
CAGAGGTGGGTAGAGGAGTCTAATTTTCAGACGTCATGTGTGAAGAAGAAACGGTCCAAGTCTAAAAAAGGAACGGAAAA
TGGAGTGGAA

Alignment

ORF - retro_ogar_2932 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.09 %
• Parental protein coverage: 93.85 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAIRKKSSKSPPVLSHEFVLQNHADIVSCVAMVFLLGLMFEITAKASIIFVTLQYNVTHPATEEQAAESV
          M..RKKS...P.VLSHEF.LQNHADIV.CV.M.F.LGLMFE.TA..SI.F.TLQ..V..PA.EEQ.A.S.
Retrocopy MGLRKKSARNPQVLSHEFILQNHADIVACVGMFFVLGLMFEGTAEVSIVFLTLQHGVIVPAAEEQGAGSK

Parental  SLYHYGVKDLATVFFYMLVAIIIHAIIQEYVLDKINRRMHFSKTKHSKFNESGQLSAFYLFACVWGTFIL
          SLYHYG.KDLAT.FFYMLVAII.HA.IQEYVLDKINR.MHF.K.K..KFNESGQ.S.FY...C.WGT..L
Retrocopy SLYHYGAKDLATIFFYMLVAIIVHASIQEYVLDKINRKMHFTKAKQNKFNESGQFSVFYFVSCIWGTILL

Parental  ISENYISDPTILWRAYPHNLMTFQMKFFYISQLAYWLHAFPELYFQKTKKEDIPRQLVYIGLYLFHIAGA
          ISEN..SDPT.LWRA.PHN.MTFQMKFFYISQLAYW.HAFPELYFQ.TKK.D.P.QLVYIGL.LFHI.GA
Retrocopy ISENCLSDPTLLWRAHPHNMMTFQMKFFYISQLAYWFHAFPELYFQRTKKQDVPGQLVYIGLHLFHIIGA

Parental  YLLNLNHLGLVLLVLHYFVEFLFHISRLFYFSDEKYQKGFSLWAVLFVLGRLLTLILSVLTVGFGLARAE
          YLL.LNHLGL.LLVLHYFVE.L.H...LFYFSDE.YQKG.SLWA..F.LGRL.TLI.SVLTVGF.LA...
Retrocopy YLLYLNHLGLLLLVLHYFVELLSHMCGLFYFSDERYQKGISLWAIVFILGRLVTLIVSVLTVGFHLAGSH

Parental  NQKLDFSTGNFNVLAVRIAVLASICITQAFMMWKFINFQLRRWREHSTYQAPAIKKKPTVTKSRSSRKGT
          N...D..TGN.NVLA..IAVL.S.C..Q....W..I...L.RW.E.S..Q....KKK....K......G.
Retrocopy NRNPDSITGNVNVLAAKIAVLSSSCSIQVYITWNLITLRLQRWVEESNFQTSCVKKKRSKSK-KGTENGV

Parental  E
          E
Retrocopy E

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_2932 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 24 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006325	1 retrocopy	retro_amel_78,
Bos taurus	ENSBTAG00000007562	1 retrocopy	retro_btau_24,
Canis familiaris	ENSCAFG00000007866	1 retrocopy	retro_cfam_15,
Callithrix jacchus	ENSCJAG00000007893	1 retrocopy	retro_cjac_168,
Dasypus novemcinctus	ENSDNOG00000009296	2 retrocopies	retro_dnov_27, retro_dnov_906,
Dipodomys ordii	ENSDORG00000001901	1 retrocopy	retro_dord_27,
Equus caballus	ENSECAG00000018378	1 retrocopy	retro_ecab_506,
Echinops telfairi	ENSETEG00000018447	1 retrocopy	retro_etel_674,
Felis catus	ENSFCAG00000028775	1 retrocopy	retro_fcat_136,
Homo sapiens	ENSG00000067167	1 retrocopy	retro_hsap_51,
Loxodonta africana	ENSLAFG00000011625	1 retrocopy	retro_lafr_9,
Macaca mulatta	ENSMMUG00000001516	1 retrocopy	retro_mmul_235,
Mustela putorius furo	ENSMPUG00000010616	1 retrocopy	retro_mputfur_558,
Mus musculus	ENSMUSG00000025935	1 retrocopy	retro_mmus_117,
Nomascus leucogenys	ENSNLEG00000011376	1 retrocopy	retro_nleu_73,
Oryctolagus cuniculus	ENSOCUG00000008734	1 retrocopy	retro_ocun_52,
Otolemur garnettii	ENSOGAG00000006379	1 retrocopy	retro_ogar_2932 ,
Pongo abelii	ENSPPYG00000018660	1 retrocopy	retro_pabe_169,
Pan troglodytes	ENSPTRG00000020334	1 retrocopy	retro_ptro_2081,
Rattus norvegicus	ENSRNOG00000007892	1 retrocopy	retro_rnor_287,
Sus scrofa	ENSSSCG00000006193	1 retrocopy	retro_sscr_980,
Ictidomys tridecemlineatus	ENSSTOG00000005537	1 retrocopy	retro_itri_38,
Tarsius syrichta	ENSTSYG00000013887	1 retrocopy	retro_tsyr_24,
Tursiops truncatus	ENSTTRG00000000328	1 retrocopy	retro_ttru_24,