RetrogeneDB ID: retro_chof_1279

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_246973:219..568(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF4H
• Ensembl ID: ENSCHOG00000002525
• Aliases: None
• Description: eukaryotic translation initiation factor 4H [Source:HGNC Symbol;Acc:12741]

Sequence

>retro_chof_1279
TCCCCCGGCATTGCTGGTGGCCATGGTTCGCGGAGCCAGAAGGAGCTGTCCACAGAGCCCCTTACACAGCCTATGTAGGA
AATCTACCTTTTAATACACTTCAGGGCGACATCGAGGCTCTCTTTAAGGATCTCAGCATAAGGAGTGTACGGTAGTCTGA
GACAAAGGCACAGACAAATATAAGAGATTCTGCTAGGCAGAATTTGATGAGGTGGATTCCCTTAAAGAAGCTTTGTCATG
TGATGGTGCATTGTTGGGTGATCGGTCACTGCGTGTGGACATCCCAGAAGGCAGAAAACAAGACAAAGGCAGCTTTGGAT
TCAGGAAAGGTGGACCAGACGACAGAGGA

Alignment

ORF - retro_chof_1279 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.03 %
• Parental protein coverage: 51.32 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SRGSAGGHGSRSQKELPTEP-PYTAYVGNLPFNTVQGDIDAIFKDLSIRSVR-LVRDKDTDKFKGFCYVE
          S.G.AGGHGSRSQKEL.TEP.PYTAYVGNLPFNT.QGDI.A.FKDLSIRSVR..V.DK.TDK.K.FC..E
Retrocopy SPGIAGGHGSRSQKELSTEP<PYTAYVGNLPFNTLQGDIEALFKDLSIRSVR<VV*DKGTDKYKRFC*AE

Parental  FDEVDSLKEALTYDGALLGDRSLRVDIAEGRKQDKGGFGFRKGGPDDRG
          FDEVDSLKEAL..DGALLGDRSLRVDI.EGRKQDKG.FGFRKGGPDDRG
Retrocopy FDEVDSLKEALSCDGALLGDRSLRVDIPEGRKQDKGSFGFRKGGPDDRG

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_1279 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 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001608	2 retrocopies	retro_chof_1310, retro_chof_366,
Choloepus hoffmanni	ENSCHOG00000002525	2 retrocopies	retro_chof_1279 , retro_chof_1903,
Felis catus	ENSFCAG00000029386	1 retrocopy	retro_fcat_580,
Gorilla gorilla	ENSGGOG00000005284	1 retrocopy	retro_ggor_1598,
Macaca mulatta	ENSMMUG00000006205	2 retrocopies	retro_mmul_2634, retro_mmul_619,
Mus musculus	ENSMUSG00000040731	1 retrocopy	retro_mmus_3659,
Oryctolagus cuniculus	ENSOCUG00000017685	1 retrocopy	retro_ocun_1475,
Otolemur garnettii	ENSOGAG00000028051	1 retrocopy	retro_ogar_2796,
Pongo abelii	ENSPPYG00000017489	2 retrocopies	retro_pabe_1879, retro_pabe_1988,
Pan troglodytes	ENSPTRG00000019287	1 retrocopy	retro_ptro_1489,
Rattus norvegicus	ENSRNOG00000001454	1 retrocopy	retro_rnor_2924,
Tupaia belangeri	ENSTBEG00000009558	2 retrocopies	retro_tbel_1636, retro_tbel_2470,