RetrogeneDB ID: retro_chof_10

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_212729:3368..3845(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCHOG00000007166
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCHOG00000000258
• Aliases: None
• Description: None

Sequence

>retro_chof_10
ATGGCGGCCGCTCCACTGGTTAGAAGACTGCGGCGGTTTGTCCCTGAACTGCTGTTGGGAGGAAGAGTCCGGGAACTGTT
CCAGCCGCGACATGGAGCGGGCGCCCTCGGTCCGGAGCGCAACTTCAGCCTCTCTTCCAATCTGGGCACGGTCATCGTAG
AGCGCTGGTGGAAGGTGCCGCTGGCCGGGGAAGGCCGGAAGCCGCACCTCCACCGGAGACATCGCGTCTACAAGCTGGTG
GAGGACACGAAACACCGGCCCAAAGACAACCTGGAGCTCATTCTTACGCAGTCTGTGGAGGAACTTGGAGTCCGGGGTGA
CTTGGTCTCAGTGAAGAAATCTGTGGGCCGTAATCAACTACTTCCTCAAGGACTGGCTGTATACGCATCCCCCGAAAACA
AGAAGCTGTTTGAAGAGGAGAAATTGCTGAGACAAGAAGGAAAATTAGAGAAGATCCAGACCAAGGCAGGTGAGGCG

Alignment

ORF - retro_chof_10 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.57 %
• Parental protein coverage: 71.56 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAAPLVRRLRRFVPELLLGGRVRELLKPRHGGVAFGPERNFXXXXXX-TVIVERWWKVPLAGEARKPHL
          MAAAPLVRRLRRFVPELLLGGRVREL..PRHG..A.GPERNF.......TVIVERWWKVPLAGE.RKPHL
Retrocopy MAAAPLVRRLRRFVPELLLGGRVRELFQPRHGAGALGPERNFSLSSNLGTVIVERWWKVPLAGEGRKPHL

Parental  HRRHRVY-LVEDTKHRPKDNLELI-TQSVEELGVRGDLVSVKKSVGRNQLLPQGLAVYASPENKKLFEEE
          HRRHRVY.LVEDTKHRPKDNLELI.TQSVEELGVRGDLVSVKKSVGRNQLLPQGLAVYASPENKKLFEEE
Retrocopy HRRHRVYKLVEDTKHRPKDNLELILTQSVEELGVRGDLVSVKKSVGRNQLLPQGLAVYASPENKKLFEEE

Parental  KLLRQEGKLEKIQTKAGEA
          KLLRQEGKLEKIQTKAGEA
Retrocopy KLLRQEGKLEKIQTKAGEA

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_10 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 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000258	1 retrocopy	retro_chof_10 ,
Dasypus novemcinctus	ENSDNOG00000011403	1 retrocopy	retro_dnov_1989,
Homo sapiens	ENSG00000143436	1 retrocopy	retro_hsap_4078,
Gorilla gorilla	ENSGGOG00000001902	1 retrocopy	retro_ggor_2735,
Loxodonta africana	ENSLAFG00000006271	2 retrocopies	retro_lafr_498, retro_lafr_563,
Nomascus leucogenys	ENSNLEG00000010275	1 retrocopy	retro_nleu_2045,
Oryctolagus cuniculus	ENSOCUG00000001383	1 retrocopy	retro_ocun_725,
Otolemur garnettii	ENSOGAG00000030456	1 retrocopy	retro_ogar_159,
Pongo abelii	ENSPPYG00000000857	1 retrocopy	retro_pabe_3347,
Pan troglodytes	ENSPTRG00000001295	2 retrocopies	retro_ptro_2765, retro_ptro_2996,
Vicugna pacos	ENSVPAG00000000664	1 retrocopy	retro_vpac_123,