RetrogeneDB ID: retro_chof_733

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_14174:734..1234(-)
• 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_733
GGTTGGTCTCAGAGTTTGTTCCACGGCTTGTGGAGAGCGCTGTCAAAGGAAGTGAAGCAGCACGTGGGCACGGACCAATT
TGGGAACAAGTACTATTATATCTCGGAGCACAAGAACTGGAGAGGACAAACTATTCAAGAGAAAAGAATTGTAGAAGCGG
CAAATATCAAAGAAGTAGGCTATGAAATACAGGATATTCCAACAGAGTGGGAAGCTTGGATTAGAAGAACAAGAAAGGTT
CCACCTATGGAGGAAGTACTAAAGAAGGAAAAATATAGAGAAGAAATGAAGATCAAAAGGAAAGAACTTTATGAAAAAGA
AAAACTGCTAAGTAAGAGAGCAAAGAGGAACTCTTCGCCCCACCGGTTCAAACTCAAATTAAAGGGCATGTCTCTGCTCC
ATCCTGCGGAAAGGAAAAACCCTCAGAGGATCCCACTAGCACTGGTAAAACCTTTCAGCCAGGATCCTGGATGCCACAAG
ATGTCAAGAGCCGAAATAAA

Alignment

ORF - retro_chof_733 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.57 %
• Parental protein coverage: 99.4 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GWFQSLFRGLWRALSKEVKQHVGTDQFGNKYYYISEHKNWRGQTIREK-IVEAANIKEVGYEIQDIPTEW
          GW.QSLF.GLWRALSKEVKQHVGTDQFGNKYYYISEHKNWRGQTI.EK.IVEAANIKEVGYEIQDIPTEW
Retrocopy GWSQSLFHGLWRALSKEVKQHVGTDQFGNKYYYISEHKNWRGQTIQEKRIVEAANIKEVGYEIQDIPTEW

Parental  EAWIRRTRKIPPTMEEILKNEKHREEMKIKSKELNEKEKLLNK-ESKEELLALPVQTQIKGHASAPYYGK
          EAWIRRTRK.PP.MEE.LK.EK.REEMKIK.KEL.EKEKLL.K.ESKEEL.A.PVQTQIKGH.SAP..GK
Retrocopy EAWIRRTRKVPP-MEEVLKKEKYREEMKIKRKELYEKEKLLSK<ESKEELFAPPVQTQIKGHVSAPSCGK

Parental  EEPSEDPTSTGKTFQPGSWMPQDGKSQNK
          E.PSEDPTSTGKTFQPGSWMPQD.KS.NK
Retrocopy EKPSEDPTSTGKTFQPGSWMPQDVKSRNK

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_733 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,