RetrogeneDB ID: retro_chof_2555

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_85935:5145..6014(+)
• 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_2555
CGCACACTTGGGCCTGCATGTTTGGAAGGTATTTATACAGCCCAGCCAGAGCATTGAGATCCATGCCAGAAGAAAAAAAA
AGAATTTTCATGGAATGGACCAGAACGTCAAGATTTTGTATCTGGTGACCTTGCAAAGAGTCCTTGGGTTGAATATAAAG
GAAACATAAAATGACAGAAAGAAGAAAGGTTAAGACTACCTCCATGGTTAAAGACAGAGGTTTCCATGGGGAAAAATTAA
AATTAGCTGGAAAATACATTGCAAAATTTAAATCTCCATACAGTGTGTGAGGAATGTCCCAGTATTGTGGACTGTTGGGG
AGGTAGAGAATATGCCACAGCCACAGCTACGATCATGCTGATGGGTGACATATGTACAAGAGGTTGTAGATTTTGCTCTG
TTAAAATTGTAAGAAATCCCCCTCCACTGGATGCCAATGAGCCCTACCATACTGCAAAGGCAATTGCAGACTGGGGTCTG
GATTATGTTGCCTGACATCGTGGCTCGAGATGATATGCCTGATGGGGGAGCTGAGCATCTTGCAAAAACCATGTCATGTT
TAAAGGAAAGGAATCCAAAAATTCTTGTGGAATGCCTCACCCCTGATTTGTGAGGATATCTTAAAGCAATAGAGAAAGTT
GCTCTTTCAGGATTAGATGTGTATGCACATAATGTGGAAACAGTTCCAGAATTACAGAAGAAAGTTTGTGATTGGTGAGC
CAATTTTGACCAGTCTCTATGTGTACTGAAAACATGCCAAGGAGGTACAGCCTAATTTTATTTCTAAAACATCTATAATG
TTGGGTTTAAGTGAGAATGAATAGCAAGTATATGCAACAATGAAAGCACTTTGAGAGGCAGATGTGGAC

Alignment

ORF - retro_chof_2555 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.86 %
• Parental protein coverage: 78.76 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  RTLGPR-VFGRYLCSPVRALSSLPEEKK-EFLQNGPDLQDFVSGDLADKSTWVEYKGNLKRQKGERLRLP
          RTLGP...FGRYL.SP.RAL.S.PE....EF..NGP..QDFVSGDLA.KS.WVEYKGN.K.QK.ERLRLP
Retrocopy RTLGPA<MFGRYLYSPARALRSMPEXXX>EFSWNGPERQDFVSGDLA-KSPWVEYKGNIK*QKEERLRLP

Parental  PWLKTEIPMGKNYNKLKNTLRNLNLHTVCEEARCPNIGECWGGGEHATATATIMLMGDTCTRGCRFCSVK
          PWLKTE..MGKN.N.L.NTL.NLNLHTVCEE..CP.I..CWGG.E.ATATATIMLMGD.CTRGCRFCSVK
Retrocopy PWLKTEVSMGKN*N*LENTLQNLNLHTVCEE--CPSIVDCWGGREYATATATIMLMGDICTRGCRFCSVK

Parental  TARNPPPLDANEPYNTARAIAEWGLDYVV-LTS-VDRDDMPDGGAEHFAKTVSCLKERNPKILVECLTPD
          ..RNPPPLDANEPY.TA.AIA.WGLDYV..LTS.V.RDDMPDGGAEH.AKT.SCLKERNPKILVECLTPD
Retrocopy IVRNPPPLDANEPYHTAKAIADWGLDYVA<LTS<VARDDMPDGGAEHLAKTMSCLKERNPKILVECLTPD

Parental  FRGDFKAVEKVALSGLDVYAHNVETVPEFQRKVRDPRANFDQSLRVL-KHAKEVQPDVISKTSIMLGLGE
          ..G..KA.EKVALSGLDVYAHNVETVPE.Q.KV.D..ANFDQSL.VL.KHAKEVQP..ISKTSIMLGL.E
Retrocopy L*GYLKAIEKVALSGLDVYAHNVETVPELQKKVCDW*ANFDQSLCVL>KHAKEVQPNFISKTSIMLGLSE

Parental  NDEQVYATMKALREADVD
          N..QVYATMKAL.EADVD
Retrocopy NE*QVYATMKAL*EADVD

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_2555 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,