RetrogeneDB ID: retro_chof_2158

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_54203:7515..8054(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: IDH1
• Ensembl ID: ENSCHOG00000004574
• Aliases: None
• Description: isocitrate dehydrogenase 1 (NADP+), soluble [Source:HGNC Symbol;Acc:5382]

Sequence

>retro_chof_2158
CAGTATAAATCCCAATTTGAAGCCCAGAAGATCTGGTATGAACATAGGCTCATCAATGACATGGTGGCCCAAGCCATGAA
ATTAGAAGGAGGCTTCACCTGGGCATGTGAAAACCATGATGGTGACGTACAGTTGGACTCCGTGGCCCAAGGTTTTGGCT
CTCTTGGCATGATGACCAGTGTGCTGATTTGTCCAGATGGCAAGACAGTAGAAGCAGAGGCTGCCCATGGGACTGTGACA
CGTCACTGCCGCATGCACCAGAAAGCACAGGAGACATCCACCAACACCATCACTTTCATTTTTTGCCTGGACCAGAGGGT
TAGCCCACAGAGCTAAGCTAGATAACAACAAAGAGCCTGGCTCCTTTGCAAAGGCTTTTGAAGAAGTCTGTTTTGAGACC
ATCGAGGCTGGCTTCATGACCAAGGGCTTGGCTGCTTGCGTTAAAGTTTATCCAACATGCAACATTCTGACCGCCTGAAT
CCACAACTCATGGACAAACCTGGAGAAACTTGAAAATCAAACTAGCTCAGGTCAAACTT

Alignment

ORF - retro_chof_2158 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.07 %
• Parental protein coverage: 50.99 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  QYKSQFEAQKIWYEHRLIDDMVAQAMKSEGGFIWACKNYDGDVQSDSVAQGFGSLGMMTSVLICPDNKTV
          QYKSQFEAQKIWYEHRLI.DMVAQAMK.EGGF.WAC.N.DGDVQ.DSVAQGFGSLGMMTSVLICPD.KTV
Retrocopy QYKSQFEAQKIWYEHRLINDMVAQAMKLEGGFTWACENHDGDVQLDSVAQGFGSLGMMTSVLICPDGKTV

Parental  EAEAAHGTVTRHYRMHQKGQETSTN-PIASIFAWTRGLAHRAKLDNNKELDYFAKALEEVCVETIEAGFM
          EAEAAHGTVTRH.RMHQK.QETSTN.P..S.FAWTRGLAHRAKLDNNKE...FAKA.EEVC.ETIEAGFM
Retrocopy EAEAAHGTVTRHCRMHQKAQETSTN>PSLSFFAWTRGLAHRAKLDNNKEPGSFAKAFEEVCFETIEAGFM

Parental  TKDLAACIK-GLPNVQRSDYLNTFEFMDKLGE-NLKIKLAQAKL
          TK.LAAC.K..L.N.Q.SD.LN....MDK.GE.NLKIKLAQ.KL
Retrocopy TKGLAACVK<SLSNMQHSDRLNP-QLMDKPGE<NLKIKLAQVKL

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_2158 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 12 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020527	1 retrocopy	retro_btau_1235,
Choloepus hoffmanni	ENSCHOG00000004574	2 retrocopies	retro_chof_2158 , retro_chof_897,
Cavia porcellus	ENSCPOG00000013587	1 retrocopy	retro_cpor_1010,
Homo sapiens	ENSG00000138413	1 retrocopy	retro_hsap_3554,
Gorilla gorilla	ENSGGOG00000012619	1 retrocopy	retro_ggor_2400,
Microcebus murinus	ENSMICG00000009797	1 retrocopy	retro_mmur_1364,
Macaca mulatta	ENSMMUG00000016077	1 retrocopy	retro_mmul_1817,
Nomascus leucogenys	ENSNLEG00000007143	3 retrocopies	retro_nleu_1169, retro_nleu_2328, retro_nleu_3117,
Otolemur garnettii	ENSOGAG00000014848	4 retrocopies	retro_ogar_1488, retro_ogar_2270, retro_ogar_2925, retro_ogar_3057,
Pongo abelii	ENSPPYG00000013125	2 retrocopies	retro_pabe_2935, retro_pabe_926,
Pan troglodytes	ENSPTRG00000012865	1 retrocopy	retro_ptro_2415,
Sus scrofa	ENSSSCG00000023264	1 retrocopy	retro_sscr_549,