RetrogeneDB ID: retro_ttru_1371

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_111542:159003..159982(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LIAS
• Ensembl ID: ENSTTRG00000014293
• Aliases: None
• Description: lipoic acid synthetase [Source:HGNC Symbol;Acc:16429]

Sequence

>retro_ttru_1371
GAATTTTTACAGAATGGACCAGACCTTCAAGATTTTGTATCTGGTGATCTAGCAGACAAGAGCACCTGGGATGAGTATAA
AGGAGGCATAAAACGCCAGAAAGGAGAACAGTTAAGACTACCTCCATGGCTAAAGACGGAGATTCCCATGGGGAAAAAAT
TACACTAAACTGAAAAATACAATGCAGAATTTAAATCTCCATACAGGGTGTGAGGAAGCTCGGTGTCCCAATATTGGAGA
GTGTTGGGGCGGCAGAGAATATGCCACTGCCCCAATCATGTTGATGGGTGACACATGTACAAGAGGTTGTAGGTTTTGTT
CTGCTAAGACTGCAAGAAATCCACCTCCACTGCATGCCAAGGAGCCCTACAATACTGCAAAGGCAATTGCAGAGTGGGGT
CTGGATTATGTAGTCCTGACGTCTGTGGATCGAGAAGATATGCCTGATGGAGGAGCTGAGCACTTTGCAAAGACGGTGCC
TTACTTAAAGGAAAGGAATCCGAAAATCCTTGTGGAATGTCTCGCCCCTGATTTCTGAGATCTTAAAGCAACAGAAAAAG
TTGCTCTGTCGGGATCAGATGTGTATGCACATAACGTAGAAACAGTTCCAGAACTACAGAGGAAAGTTCGCGATCCCCGG
GCCAGTTTGGACCAGTCTCTACGTGCACTGAAACACGCCAAGGAAGTTCGACCTGATGTTATTCTAAAACACCTATAATG
TTGGGTTTAGGTGAGGATGACGAGCAAGTATATGCAACGATGAAAGTACTTCGTGAGGCACATGTGGACTGTCTGACTTT
GGGACAATATATGCAGCCAACAAAGCGCCACCTTAAGGTTGAAGAATACATTACTCCTGAAAAGTTCAAATACTGGGAAA
AAAGCAGGAAATGAACTTGGATTTCATTAGACTGCAAGTGGCCCTCTGGTGTGTTCTTCACATAAAGCAGGTGAATTTTT
CCTGAAAAATCTAGTAGCT

Alignment

ORF - retro_ttru_1371 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.25 %
• Parental protein coverage: 88.44 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KFLQNGPDLQDFVSGDLADKSTWDEYKGDLKRQKGERLRLPPWLKTEIPMGK-NYNKLKNTLRNLNLHTV
          .FLQNGPDLQDFVSGDLADKSTWDEYKG..KRQKGE.LRLPPWLKTEIPMGK.NY.KLKNT..NLNLHT.
Retrocopy EFLQNGPDLQDFVSGDLADKSTWDEYKGGIKRQKGEQLRLPPWLKTEIPMGK>NYTKLKNTMQNLNLHTG

Parental  CEEARCPNIGECWGGGEHATATATIMLMGDTCTRGCRFCSVKTARNPPPLDANEPYNTAKAIAEWGLDYV
          CEEARCPNIGECWGG.E.ATA...IMLMGDTCTRGCRFCS.KTARNPPPL.A.EPYNTAKAIAEWGLDYV
Retrocopy CEEARCPNIGECWGGREYATAP--IMLMGDTCTRGCRFCSAKTARNPPPLHAKEPYNTAKAIAEWGLDYV

Parental  VLTSVDRDDMPDGGAEHFAKTVSYLKERNPKILVECLTPDFRGDLKAIEKVALSGLDVYAHNVETVPELQ
          VLTSVDR.DMPDGGAEHFAKTV.YLKERNPKILVECL.PDF..DLKA.EKVALSG.DVYAHNVETVPELQ
Retrocopy VLTSVDREDMPDGGAEHFAKTVPYLKERNPKILVECLAPDF-*DLKATEKVALSGSDVYAHNVETVPELQ

Parental  RKVRDPRANFDQSLRILKHAKKVRPDVI-SKTSIMLGLGENDEQVYAMMKVLREADVDCLTLGQYMQPTK
          RKVRDPRA..DQSLR.LKHAK.VRPDVI.SKT.IMLGLGE.DEQVYA.MKVLREA.VDCLTLGQYMQPTK
Retrocopy RKVRDPRASLDQSLRALKHAKEVRPDVI<SKTPIMLGLGEDDEQVYATMKVLREAHVDCLTLGQYMQPTK

Parental  RHLKVEEYITPEKFKYWE-KVGNELGFHYTASGPLVRSSYKAGEFFLKSLVA
          RHLKVEEYITPEKFKYWE.K.GNELGFH.TASGPLV.SS.KAGEFFLK.LVA
Retrocopy RHLKVEEYITPEKFKYWE>KAGNELGFH*TASGPLVCSSHKAGEFFLKNLVA

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Tursiops truncatus was not studied using RNA-Seq expression data.

ChIP-Seq

Tursiops truncatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ttru_1371 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1371 was not experimentally validated.

Homology

Retrocopy orthology:

Tursiops truncatus 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 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012946	2 retrocopies	retro_chof_1942, retro_chof_2555,
Dasypus novemcinctus	ENSDNOG00000007417	1 retrocopy	retro_dnov_266,
Myotis lucifugus	ENSMLUG00000004602	2 retrocopies	retro_mluc_1985, retro_mluc_347,
Mus musculus	ENSMUSG00000029199	1 retrocopy	retro_mmus_3029,
Tursiops truncatus	ENSTTRG00000014293	1 retrocopy	retro_ttru_1371 ,