RetrogeneDB ID: retro_chof_897

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_164815:3710..4276(-)
• 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_897
TATGATTTGGACATAGAGAATCATGATGCCACCAATGACCAGGGCACCAAGGATGCTGCAGAAGCTATAAAGAGGTATAA
CATTGGCATCAAGTGTGCTACCTTCATGCCCAATGAGAATAGAGTTGAGGAATTCAAGTTGAAACAAATGTGGAAATCAC
CAAATGGTATCATCTGAAATATTCTGTATGGCACTGTCTTCAGGGAAGCTATTATCTGCAAAAATATCCCCTGGCTTGTG
AGTGGATGAGTAAAACTCATCATCATAGGTCAACACATTTATGGGGGATCAATACAGAGCTACCGATTTTGTTGGTCCCA
GACCTGGCAAAGTAGAGATGATCTACACGTCGAGTGATGGAACCCAAAAGGTGACACACTTAATACATCACTTTGAAGAG
TGTGGTGGCGTTGTCATGGGGATGTACACTCAGGATAAGTCCATTGAAGATTTTGCTCACAGTTCTTTCCAGAAGGCTCT
TTCTAAGGTTTGGCCCTTTTTATCTGAGCACTAAAAACACTATTCTGAAGAAATACGATGGGAGTTTTAAAGACATCTTT
CAGGAG

Alignment

ORF - retro_chof_897 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.84 %
• Parental protein coverage: 52.96 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  YDLGIENRDATNDQVTKDAAEAIKKYNVGVKCATITPDEKRVEEFKLKQMWKSPNGTIRNILGGTVFREA
          YDL.IEN.DATNDQ.TKDAAEAIK.YN.G.KCAT..P.E.RVEEFKLKQMWKSPNG.I.NIL.GTVFREA
Retrocopy YDLDIENHDATNDQGTKDAAEAIKRYNIGIKCATFMPNENRVEEFKLKQMWKSPNGII*NILYGTVFREA

Parental  IICKNIPRLVSGWVKPIIIGRHAY-GDQYRATDFVVPGPGKVEMIYTPSDGTQKVTYLVHNFEECGGVAM
          IICKNIP.LVSG.VK.IIIG.H.Y.GDQYRATDFV.P.PGKVEMIYT.SDGTQKVT.L.H.FEECGGV.M
Retrocopy IICKNIPWLVSG*VKLIIIGQHIY>GDQYRATDFVGPRPGKVEMIYTSSDGTQKVTHLIHHFEECGGVVM

Parental  GMYNQDKSIEDFAHSSFLMALSKGW-PLYLSTKNRIQYKSQFEAQKIWYE
          GMY.QDKSIEDFAHSSF..ALSK.W.P.YLSTKN.I..K.......I..E
Retrocopy GMYTQDKSIEDFAHSSFQKALSKVW>PFYLSTKNTILKKYDGSFKDIFQE

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_897 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,