RetrogeneDB ID: retro_chof_1925

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_42443:2867..3267(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCHOG00000000013
• Aliases: None
• Description: None

Sequence

>retro_chof_1925
GCTCAAGTGTCCCTCTCTGGCTCCTTCAGCGCGAGCCACCGGCTCCACAGCAAATCTCTGAGTCATGAAGAAAACTTGAA
ACTGTTTGGATATGCAACCATCCAAATGGCCATGGGAACAACTACAAAGTTGCGGTGACAGTACATAGAGAGATTGCTCC
TGTTACAGGGATGGTTATGAACTTGACTGAACTCAAAGAGTATATGGAGGAGACAATTAGAAGCCCCTTGATCACAAGAA
TCTGGACCTGGGTGTATCATACTTCACTGATGTTGTGAGCATGACAGAAAATGTGGCTGTATATAAGTGGGAAAACCTTC
CAAAATGTCTTCCTGTGGGAATTCCTTATAAAGTAAAAGTGCATGAAACTGACAACAATATTGTAGTCTTTAACAGAGAA

Alignment

ORF - retro_chof_1925 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.59 %
• Parental protein coverage: 91.78 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AQLSRLVSFSATHRLHSKSLSNEENLKLFGK-CNNPNGHGHNYRXXXXXXXXIDPVTGMVMNLTDLKECM
          AQ.S...SFSA.HRLHSKSLS.EENLKLFG..CN.PNGHG.NY.........I.PVTGMVMNLT.LKE.M
Retrocopy AQVSLSGSFSASHRLHSKSLSHEENLKLFGY<CNHPNGHGNNYKVAVTVHREIAPVTGMVMNLTELKEYM

Parental  EQAIM-KPLDHKNLDLDVSYFPDVVSRTEDVAVYIWENLQKFLPVGVLHKVKVYETDNNIVVYKGE
          E..I..KPLDHKNLDL.VSYF.DVVS.TE.VAVY.WENL.K.LPVG...KVKV.ETDNNIVV...E
Retrocopy EETIR<KPLDHKNLDLGVSYFTDVVSMTENVAVYKWENLPKCLPVGIPYKVKVHETDNNIVVFNRE

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_1925 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 11 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000013	2 retrocopies	retro_chof_1925 , retro_chof_2556,
Callithrix jacchus	ENSCJAG00000012437	2 retrocopies	retro_cjac_2534, retro_cjac_2853,
Dasypus novemcinctus	ENSDNOG00000014823	1 retrocopy	retro_dnov_1747,
Echinops telfairi	ENSETEG00000008145	2 retrocopies	retro_etel_1924, retro_etel_2039,
Homo sapiens	ENSG00000150787	1 retrocopy	retro_hsap_3408,
Macaca mulatta	ENSMMUG00000015255	1 retrocopy	retro_mmul_995,
Nomascus leucogenys	ENSNLEG00000007299	1 retrocopy	retro_nleu_1856,
Otolemur garnettii	ENSOGAG00000017191	3 retrocopies	retro_ogar_1718, retro_ogar_2790, retro_ogar_609,
Pongo abelii	ENSPPYG00000003880	1 retrocopy	retro_pabe_432,
Pan troglodytes	ENSPTRG00000004288	3 retrocopies	retro_ptro_2315, retro_ptro_2979, retro_ptro_337,
Ictidomys tridecemlineatus	ENSSTOG00000013277	1 retrocopy	retro_itri_1096,