RetrogeneDB ID: retro_chof_2692

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_97846:557..893(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SWI5
• Ensembl ID: ENSCHOG00000008548
• Aliases: None
• Description: SWI5 recombination repair homolog (yeast) [Source:HGNC Symbol;Acc:31412]

Sequence

>retro_chof_2692
CTCAGGAGGTCTCAAACAGGACTTTTCAAAAGTTACTGCATAATCTTCTGATCCCCTTGGCCGTCTCCCAAGTCTGGCCT
AGTCAATGGAGCCAGTGAGGATTCCTTGCAGCTTGACATTCAGAAACCAAAAGAGAAGAGAGATATGCTGGACACAGAGT
TCTCCCAATTAATATCTGAAGCCTACATTATGGATTAATTGGAGGACCATATCTCCCAGCTCCACAAATATAATGATATC
AAGGATGTAGGCCAGATGCTTGTGGGCAAACTAGCTGTGATCCAGGGTGTCACCATCAGAAAGCTGAATCCAGAATTTGA
TAAGAACATGGATGAC

Alignment

ORF - retro_chof_2692 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.64 %
• Parental protein coverage: 75.68 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LSRTQPGLFKSCRGTSLSPLPSPKSGQIDGAGEDSLQLDIQKLKEKSDMLDKEISQLIAEGYSVDELEDH
          L.R.Q.GLFKS......SP.PSPKSG...GA.EDSLQLDIQK.KEK.DMLD.E.SQLI.E.Y..D.LEDH
Retrocopy LRRSQTGLFKSYCIIF*SPWPSPKSGLVNGASEDSLQLDIQKPKEKRDMLDTEFSQLISEAYIMD*LEDH

Parental  ISQLHEYNDIKDVGQMLLGKLAVIPGVTTKELCPEFDLDMGE
          ISQLH.YNDIKDVGQML.GKLAVI.GVT...L.PEFD..M..
Retrocopy ISQLHKYNDIKDVGQMLVGKLAVIQGVTIRKLNPEFDKNMDD

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_2692 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 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008548	1 retrocopy	retro_chof_2692 ,
Mus musculus	ENSMUSG00000044627	2 retrocopies	retro_mmus_317, retro_mmus_980,
Oryctolagus cuniculus	ENSOCUG00000005318	4 retrocopies	retro_ocun_1628, retro_ocun_1809, retro_ocun_1826, retro_ocun_1836,