RetrogeneDB ID: retro_chof_1942

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_428032:26..948(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LIAS
• Ensembl ID: ENSCHOG00000012946
• Aliases: None
• Description: lipoic acid synthetase [Source:HGNC Symbol;Acc:16429]

Sequence

>retro_chof_1942
GCAGACAAGTGCACCTGGGTTGAATATAAAGAAAACTTAATACGCCAGAAAGTTGAAAGTTTAAGACTACCTCCATGTAA
AGACAGAGATTCACATGGGGAAAAATTACAATAAGCTGAAAAATACATTGCAAATTTAAACTCTCCATACAGTGTGCAAG
GACTCTTGATGTCCCAATATTGGGGAGGGTTGGGGAGGTAGAAATATGCCACAGCAAGAGTTATGTTGATGGATGACACA
TGTACAAGAGGTTGTAGATTTTGTTCTGTTAAAACTGTAAGAAATCCACCTCTTCTGGATGCCAATGAGCTCTACAATAC
TGCAAAGCAATTGCAGAGTGGGATATGGGTTATGTTGTCCTGACCTCTGTGGATCGAGATGATATGCTTGATGGGGGGCA
CTTTGCAAAAACTGTGTCATGCCTAAAAGAAAGGAATCTAAAAATTCTTGTGGAATGCTCACCCCTGATTCTGAGGACAT
CTTAAAGCAATAGAGAACATTGCTCTGACAGGATTAGATGTGTACGCACATAACGTAGAAACAGTTTCAGAATTACATAG
AAAAGTTTGTGGTCCCTCGGCCTACTTTGCCCAGTCTCCGTGTGTACTGAAACATGGCAAGGAGGTTTCAGCCTGATCTT
ATTTCTAAAACATCTATAATGTTGGGTTTAGGTGAGAATGATGAGCAAGTATATGCAACAATGAAAGCACTTCGTGAGGC
AGATGTGGACTGTTTGACTTTAGGACAATATATGCAGCCAACAAAGTGCCACCTTAAGGTTGAAGAATACGTTACTCCTG
AAAAGTTCAAATACTGGGAAAAAGTAGGAAATGAACTTGGCTTTCATTATACTGCAAGTGGCCCTCTGGTGCGTTCCTCA
TATAGAGCAGTTGAATTTTTCCTGAAAAATTTAGTGGCCAAA

Alignment

ORF - retro_chof_1942 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.86 %
• Parental protein coverage: 84.14 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  ADKSTWVEYKGNLKRQKGERLRLPPWLKTEIPMGKNYNKLKNTLRNLN-LHTVCEEARCPNIGECWGGG-
          ADK.TWVEYK.NL.RQK.E.LRLPP..K.....G...........NLN.LHTVC....CPNIGE.WGG..
Retrocopy ADKCTWVEYKENLIRQKVESLRLPP-CKDRDSHGEKLQ*AEKYIANLN>LHTVCKDS*CPNIGEGWGGR<

Parental  EHATATATIMLMGDTCTRGCRFCSVKTARNPPPLDANEPYNTA-RAIAEWGLDYVVLTSVDRDDMPDGGA
          ..AT..A..MLM.DTCTRGCRFCSVKT.RNPP.LDANE.YNTA..AIAEW...YVVLTSVDRDDM.DGG.
Retrocopy KYAT--ARVMLMDDTCTRGCRFCSVKTVRNPPLLDANELYNTA<KAIAEWDMGYVVLTSVDRDDMLDGG-

Parental  EHFAKTVSCLKERNPKILVEC-LTPD-FRGDFKAVEKVALSGLDVYAHNVETVPEFQRKVRDPRANFDQS
          .HFAKTVSCLKERN.KILVEC.LTPD.F.G..KA.E..AL.GLDVYAHNVETV.E..RKV..P.A.F.QS
Retrocopy -HFAKTVSCLKERNLKILVEC<LTPD<F*GHLKAIENIALTGLDVYAHNVETVSELHRKVCGPSAYFAQS

Parental  LRVLKHAKEV-QPDVISKTSIMLGLGENDEQVYATMKALREADVDCWTLGQYMQPTKRHFKVEEYVTPEK
          ..VLKH.KEV.QPD.ISKTSIMLGLGENDEQVYATMKALREADVDC.TLGQYMQPTK.H.KVEEYVTPEK
Retrocopy PCVLKHGKEV>QPDLISKTSIMLGLGENDEQVYATMKALREADVDCLTLGQYMQPTKCHLKVEEYVTPEK

Parental  FKYWEKVGNELGFHYTASGPLVRSSYKAGEFFLKNLVAK
          FKYWEKVGNELGFHYTASGPLVRSSY.A.EFFLKNLVAK
Retrocopy FKYWEKVGNELGFHYTASGPLVRSSYRAVEFFLKNLVAK

Legend:

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

Expression

RNA-Seq

Choloepus hoffmanni was not studied using RNA-Seq expression data.

ChIP-Seq

Choloepus hoffmanni was not studied using ChIP-Seq data.

EST

Choloepus hoffmanni was not studied using EST data.

TSS

Choloepus hoffmanni was not studied using FANTOM5 data.

Lab

retro_chof_1942 was not experimentally validated.

Homology

Retrocopy orthology:

Choloepus hoffmanni 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,