RetrogeneDB ID: retro_chof_1899

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_41857:144..555(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCHOG00000007730
• Aliases: None
• Description: None

Sequence

>retro_chof_1899
GCTGAAGGGTATGTGATTGGCAGCTGTATTAAGCACATTCCAATCGCAGAACGAGATATAACGTATTTTATTCAGCAACT
GCTGAGAGACCAAGAAGTAGGAATCCCCCCAGAGCAATCCTTGGAAACAGCTAAGGCAGTAAAAGAGTGTTATAGTTATG
TCTGCCCAGATTTAGTAAAATAATTTAACAACTATGACACAGATGGGTCAAAGTGGATTAAGCAGTATACTGGAATCAAT
GCTATCTCAAAGAAAGAATTTTCCATTTATGTCAGTTATGAGAGATTCTTGGGACCTGAAATCTTTTTTCACCCAGCGTT
TGCTAATCTAGACTTCACACAACCTATCTCAGAAGCAGTAGATGAGGTAATTCAGAATTGTCCTATTGATGTCAGGCATC
CTCTCTACAAG

Alignment

ORF - retro_chof_1899 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.1 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AEGYVIGSCIKHIPIAGRDITYFIQQLLKEREVGIPPEQSLETAKAISEKYCYICPDIVKEFAKYDVDPR
          AEGYVIGSCIKHIPIA.RDITYFIQQLL...EVGIPPEQSLETAKA..E.Y.Y.CPD.VK.F..YD.D..
Retrocopy AEGYVIGSCIKHIPIAERDITYFIQQLLRDQEVGIPPEQSLETAKAVKECYSYVCPDLVK*FNNYDTDGS

Parental  KWIKQYTGINAINQKKFIIDVGYERFLGPEIFFHPEFANPDFMESISDVVDEVIQNCPIDVRRPLYK
          KWIKQYTGINAI..K.F.I.V.YERFLGPEIFFHP.FAN.DF...IS..VDEVIQNCPIDVR.PLYK
Retrocopy KWIKQYTGINAISKKEFSIYVSYERFLGPEIFFHPAFANLDFTQPISEAVDEVIQNCPIDVRHPLYK

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_1899 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 36 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007730	5 retrocopies	retro_chof_1134, retro_chof_1204, retro_chof_1899 , retro_chof_208, retro_chof_2171,
Dasypus novemcinctus	ENSDNOG00000019288	2 retrocopies	retro_dnov_1143, retro_dnov_2539,
Homo sapiens	ENSG00000133627	7 retrocopies	retro_hsap_1676, retro_hsap_2126, retro_hsap_2540, retro_hsap_2966, retro_hsap_4334, retro_hsap_4921, retro_hsap_561,
Macropus eugenii	ENSMEUG00000004885	5 retrocopies	retro_meug_1340, retro_meug_1477, retro_meug_2105, retro_meug_330, retro_meug_899,
Nomascus leucogenys	ENSNLEG00000015688	1 retrocopy	retro_nleu_733,
Oryctolagus cuniculus	ENSOCUG00000000459	1 retrocopy	retro_ocun_320,
Otolemur garnettii	ENSOGAG00000003249	2 retrocopies	retro_ogar_1307, retro_ogar_3388,
Pongo abelii	ENSPPYG00000018206	1 retrocopy	retro_pabe_2460,
Pan troglodytes	ENSPTRG00000019897	8 retrocopies	retro_ptro_1137, retro_ptro_1479, retro_ptro_2007, retro_ptro_2952, retro_ptro_2961, retro_ptro_3052, retro_ptro_3281, retro_ptro_420,
Tupaia belangeri	ENSTBEG00000011647	2 retrocopies	retro_tbel_2820, retro_tbel_932,
Tursiops truncatus	ENSTTRG00000016334	2 retrocopies	retro_ttru_471, retro_ttru_93,