RetrogeneDB ID: retro_chof_160

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: GeneScaffold_3606:68571..68901(+)
• Located in intron of: ENSCHOG00000010422

Retrocopy information

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

Parental gene information

• Parental gene symbol: RRP36
• Ensembl ID: ENSCHOG00000012525
• Aliases: None
• Description: ribosomal RNA processing 36 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:21374]

Sequence

>retro_chof_160
TCCCTCCGCTGGGCCTGGGATGGTGGGGAGAATGGAGGGGACTTGGAGCCCGGGGCTGTGACCTGTGACTCGCAAAAGGA
CACATCCAACATGTCATTTGAAGAGCTGTCGGAATTGCAGAGCCAAGTGGGGAATAAGGTGTGCAAACATTTGGTAGCTG
GAAACAGCACTAGGAAACAAGGTTCTAGACCACTTGTCCAAAACGCATGTGTTGCCGATAAGCACAGGCCTCTGGAAATA
TCAGCCAAGGTCCAAGTGCCATATTTCTGTCAGGTTGTCCCCCATCAGTAAAGAAGGTGTTCCGTGACCCCTGCTTTTGA
TGATCTGTCA

Alignment

ORF - retro_chof_160 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.36 %
• Parental protein coverage: 58.38 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SAEGARHGGEDGGVLEPRTATCDSQKDTSNMSFEELLELQSQMGNKTCKHLVAGNSTRKQDFRPPVQNAC
          S...A..GGE.GG.LEP...TCDSQKDTSNMSFEEL.ELQSQ.GNK.CKHLVAGNSTRKQ..RP.VQNAC
Retrocopy SLRWAWDGGENGGDLEPGAVTCDSQKDTSNMSFEELSELQSQVGNKVCKHLVAGNSTRKQGSRPLVQNAC

Parental  AADKH-PLEMSARSRVPFLRQVVPII-KKVFLNPRLNDLS
          .ADKH.PLE.SA...VP...QVVP.........P...DLS
Retrocopy VADKHRPLEISAKVQVPYFCQVVPHQ*RRCSVTPAFDDLS

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_160 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012525	1 retrocopy	retro_chof_160 ,
Otolemur garnettii	ENSOGAG00000012699	1 retrocopy	retro_ogar_3139,
Ictidomys tridecemlineatus	ENSSTOG00000009511	1 retrocopy	retro_itri_1520,