RetrogeneDB ID: retro_chof_305

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: GeneScaffold_6979:17035..17233(+)
• Located in intron of: ENSCHOG00000002676

Retrocopy information

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

Parental gene information

• Parental gene symbol: COX7A1
• Ensembl ID: ENSCHOG00000012840
• Aliases: None
• Description: cytochrome c oxidase subunit VIIa polypeptide 1 (muscle) [Source:HGNC Symbol;Acc:2287]

Sequence

>retro_chof_305
AGGACTGTAAGTACTGCTTCATGCAGGCAATTTGAAAATAAAGTTCCAGAAAAACAAAAGCTATTTCAGGATGGTAATGG
AATACCAGTGCACCTGAAGGGTGGGATAGCTGACGCCCTCCTGTATAGAGCCACTATGGTTCTTACAGTTGGTGGAACAA
TGTACGCTATGTATCAGCTGGGCATGGCTTCATTTCCC

Alignment

ORF - retro_chof_305 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.03 %
• Parental protein coverage: 88. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RSFGSTARHRFQNRVAEKQKLFQADNDLPVHLKGGGTDNILYRLTMGLCLGGSAYSVYCLGWASYP
          R.........F.N.V.EKQKLFQ..N..PVHLKGG..D..LYR.TM.L..GG..Y..Y.LG.AS.P
Retrocopy RTVSTASCRQFENKVPEKQKLFQDGNGIPVHLKGGIADALLYRATMVLTVGGTMYAMYQLGMASFP

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_305 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 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012840	1 retrocopy	retro_chof_305 ,
Echinops telfairi	ENSETEG00000007654	1 retrocopy	retro_etel_2078,
Myotis lucifugus	ENSMLUG00000012331	1 retrocopy	retro_mluc_187,
Macaca mulatta	ENSMMUG00000000250	3 retrocopies	retro_mmul_1665, retro_mmul_1968, retro_mmul_2489,
Monodelphis domestica	ENSMODG00000025577	1 retrocopy	retro_mdom_1288,
Pan troglodytes	ENSPTRG00000010888	1 retrocopy	retro_ptro_125,