RetrogeneDB ID: retro_ogar_3426

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873830.1:345148..345823(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TSN
• Ensembl ID: ENSOGAG00000030436
• Aliases: None
• Description: translin [Source:HGNC Symbol;Acc:12379]

Sequence

>retro_ogar_3426
GTGAGGGAAATCTTGATGAAGTTGTGGAGCTTTTTGGTTGCTGAGCAGTATATGGGAAGGAAAACTGAAGAGTTGTCCAG
CGTTTAGAACAAACTGCTTGTGAGATTTTAACTCTACTGCAAGGGGTCCATCTGGGACCTGGGTTTCAGGATATCTCAAA
CAGGTGTTTGAAAGATTGAGAACATTTTAGCACAGTAAAAACACATCTAACATCTTTGAATACCAAGTTCCTTGCTGAAC
AATATTACAGATTCTGTGACCACTGAAGGTTTGTGTTGCAGTACTTGGTCATCTTGACAATATTTGTTGTGTATTTGGAA
GCAGAAATACTGGTGACTCCAGAAGCAGTTGCAGAAATTCTTGGCATTGAGCCAGATCAGGAGAAAGGATTTCATATATA
TGTAGAAGATTACCTCTGAGGAGTTATAATTCTTGCTAATGAACTGTAGAACCTGTCTGTTAGTGCGACTGCTGGGGACT
ACTCTCGGCCTTTCCACATATTCACCTTCATCAGTGAGCTGGATTCTGGTTTCTGCCTTCTCAGTCTGAAAAAATGACTC
CCTCATGAAGTGCTATGATGGATTAAAGTACAACATGAAGAAAGTAGAAGAGGTGGTCTATGATCTCTCCACTTGGGGCT
TCAGTAAGGAGACAGCTGACACTTGTGTTGAAAAA

Alignment

ORF - retro_ogar_3426 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.37 %
• Parental protein coverage: 99.12 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VSEIFVELQGFLAAEQDIREEIR-KVVQSLEQTAREILTLLQGVHQGAGFQDIPKRCLKAREHFGTVKTH
          V.EI...L..FL.AEQ.........VVQ.LEQTA.EILTLLQGVH.G.GFQDI..RCLK..EHF.TVKTH
Retrocopy VREILMKLWSFLVAEQYMGRKTE<RVVQRLEQTACEILTLLQGVHLGPGFQDISNRCLKD*EHFSTVKTH

Parental  LTSLKTKFPAEQYYRFHEHWRFVLQRLVFLAAFVVYLETETLVTREAVTEILGIEPDREKGFHLDVEDYL
          LTSL.TKF.AEQYYRF..H.RFVLQ.LV.L..FVVYLE.E.LVT.EAV.EILGIEPD.EKGFH..VEDYL
Retrocopy LTSLNTKFLAEQYYRFCDH*RFVLQYLVILTIFVVYLEAEILVTPEAVAEILGIEPDQEKGFHIYVEDYL

Parental  SGVLILASELSRLSVNSVTAGDYSRPLHISTFINELDSGFRLLNL-KNDSLRKRYDGLKYDVKKVEEVVY
          .GV.ILA.EL..LSV.S.TAGDYSRP.HI.TFI.ELDSGF.LL.L.KNDSL.K.YDGLKY..KKVEEVVY
Retrocopy *GVIILANEL*NLSV-SATAGDYSRPFHIFTFISELDSGFCLLSL>KNDSLMKCYDGLKYNMKKVEEVVY

Parental  DLSIRGFNKETAAACVEK
          DLS..GF.KETA..CVEK
Retrocopy DLSTWGFSKETADTCVEK

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_3426 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 14 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006059	1 retrocopy	retro_btau_1598,
Dasypus novemcinctus	ENSDNOG00000025740	2 retrocopies	retro_dnov_1581, retro_dnov_907,
Felis catus	ENSFCAG00000027149	1 retrocopy	retro_fcat_1577,
Homo sapiens	ENSG00000211460	1 retrocopy	retro_hsap_3760,
Gorilla gorilla	ENSGGOG00000002216	2 retrocopies	retro_ggor_2528, retro_ggor_2610,
Myotis lucifugus	ENSMLUG00000012656	1 retrocopy	retro_mluc_1420,
Macaca mulatta	ENSMMUG00000021119	1 retrocopy	retro_mmul_1718,
Monodelphis domestica	ENSMODG00000000147	1 retrocopy	retro_mdom_1896,
Nomascus leucogenys	ENSNLEG00000001202	1 retrocopy	retro_nleu_170,
Ornithorhynchus anatinus	ENSOANG00000003457	1 retrocopy	retro_oana_120,
Oryctolagus cuniculus	ENSOCUG00000023529	1 retrocopy	retro_ocun_271,
Otolemur garnettii	ENSOGAG00000030436	3 retrocopies	retro_ogar_1221, retro_ogar_2875, retro_ogar_3426 ,
Pan troglodytes	ENSPTRG00000012420	1 retrocopy	retro_ptro_2551,
Tarsius syrichta	ENSTSYG00000004395	1 retrocopy	retro_tsyr_1593,