RetrogeneDB ID: retro_chof_339

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: GeneScaffold_7672:63745..64206(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NSMCE1
• Ensembl ID: ENSCHOG00000011003
• Aliases: None
• Description: non-SMC element 1 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:29897]

Sequence

>retro_chof_339
AGTACAACAACAACAGGCATCATGACTGATGTCCATTGGTGATTCCTCCAGTTGCTGATGACTCCTGGAGTGCTAGAGAA
ATGGGATGTTAAGTCCTTGCTGAAGCATTTTTATAAGGTCTGTGACTGCAGTGCTCCTGTAGAGAAGTTGGAAGACTTTT
TTTAACGGTATTTAACAGTGTCTTGGAGTCCTTGTATATTGAGATAAAGAAAGGAGTCCTAACAGATGGCAGGAGACCCA
GCTACACACTGATGAATCTTGTAACTACATCAGTTTCCAAAATGATATTGGATTTTGCAGAGAATGAACTTGATCTGTTC
ACAAAAGTTTTAGGACTGATTTTTAACTCAGAAACTGGCTTTGCACCTTCCATAAACATTTTAAACCTTAAAGGCAAGAA
AATGAGGAATAAGGAAGCTGAACACGTTACAAAATTTGTTCAGAACAAATGGCTGATTGAG

Alignment

ORF - retro_chof_339 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.88 %
• Parental protein coverage: 98.14 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  STRRMGIMTDVHRRFLQLLMTHGVLEERDVKHLQKHCYKVHDRNATVEKLEDFI-NNI-NSVLESLYIEI
          ST...GIMTDVH..FLQLLMT.GVLE..DVK.L.KH.YKV.D..A.VEKLEDF..N.I.NSVLESLYIEI
Retrocopy STTTTGIMTDVHW*FLQLLMTPGVLEKWDVKSLLKHFYKVCDCSAPVEKLEDFF>NGI>NSVLESLYIEI

Parental  KKGVTEDDGRPIYALVNLATTSISKMASDFAENELDLFRKALELIIDSETGFASSTNILNLVDQLKGKKM
          KKGV..D..RP.Y.L.NL.TTS.SKM..DFAENELDLF.K.L.LI..SETGFA.S.NILNL....KGKKM
Retrocopy KKGVLTDGRRPSYTLMNLVTTSVSKMILDFAENELDLFTKVLGLIFNSETGFAPSINILNL----KGKKM

Parental  KKKEAEHVLQKFVQNKWLIE
          ..KEAEHV..KFVQNKWLIE
Retrocopy RNKEAEHV-TKFVQNKWLIE

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_339 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 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000011003	2 retrocopies	retro_chof_1394, retro_chof_339 ,
Callithrix jacchus	ENSCJAG00000020515	1 retrocopy	retro_cjac_2191,
Dasypus novemcinctus	ENSDNOG00000013271	1 retrocopy	retro_dnov_641,
Mus musculus	ENSMUSG00000030750	2 retrocopies	retro_mmus_1564, retro_mmus_2488,
Ochotona princeps	ENSOPRG00000011452	1 retrocopy	retro_opri_732,