RetrogeneDB ID: retro_chof_1922

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_424039:217..598(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDUFAF2
• Ensembl ID: ENSCHOG00000013975
• Aliases: None
• Description: NADH dehydrogenase (ubiquinone) complex I, assembly factor 2 [Source:HGNC Symbol;Acc:28086]

Sequence

>retro_chof_1922
GGACAAACTATTCGAGAGAAAAGAATTGTAGAAGCAGCAATTATCAAAGAAGTAGGCTATGAAATACAGGATATTCCAAC
AGAGTGGGAAGCTTGGATTAGAAGAACAAGAAAGACTCCACCTACTATGGAGGAAATACTAAAGAATGAAAAATATAGAG
AAGAAGTGAAGATCGAAAGCAAAGAACTTTATGAAAAAGAAAAACTGCTAAGTAAAGAGAGCAAAGAGGAACTCTTGGCT
CCGCTGGTTCAAACTCAAATTAAAGGGCATGCCTCTGCTCCATGCCATGGAAAGGAAGAACACTCAGAGGATCCCAGTAG
CACTGGTAAAACCTTTCAGCCAGGATCCTGGATGCCACAAGATGGCAAGAGCCGAAATGAA

Alignment

ORF - retro_chof_1922 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.4 %
• Parental protein coverage: 75. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GQTIREK-IVEAANIKEVGYEIQDIPTEWEAWIRRTRKIPPTMEEILKNEKHREEMKIKSKELNEKEKLL
          GQTIREK.IVEAA.IKEVGYEIQDIPTEWEAWIRRTRK.PPTMEEILKNEK.REE.KI.SKEL.EKEKLL
Retrocopy GQTIREKRIVEAAIIKEVGYEIQDIPTEWEAWIRRTRKTPPTMEEILKNEKYREEVKIESKELYEKEKLL

Parental  NKESKEELLALPVQTQIKGHASAPYYGKEEPSEDPTSTGKTFQPGSWMPQDGKSQNK
          .KESKEELLA..VQTQIKGHASAP..GKEE.SEDP.STGKTFQPGSWMPQDGKS.N.
Retrocopy SKESKEELLAPLVQTQIKGHASAPCHGKEEHSEDPSSTGKTFQPGSWMPQDGKSRNE

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_1922 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013975	2 retrocopies	retro_chof_1922 , retro_chof_733,
Callithrix jacchus	ENSCJAG00000015375	1 retrocopy	retro_cjac_3153,
Homo sapiens	ENSG00000164182	1 retrocopy	retro_hsap_2232,