RetrogeneDB ID: retro_chof_1307

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_256971:0..596(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPUSD4
• Ensembl ID: ENSCHOG00000010249
• Aliases: None
• Description: RNA pseudouridylate synthase domain containing 4 [Source:HGNC Symbol;Acc:25898]

Sequence

>retro_chof_1307
CTGAGACGAGGGATTCTTCAACAGGACAACGACCTTGTGGTCATCAATAAGCCCTACAGTCTCCCTGTCATTGGTGGCCC
TGGGGTCCAGCTCTGCATCAGGGATGTGCTGCCTATCCTGGCAAGGATGTTGCTTGACCACAAGGCAGAGCCCCTGCATC
GGTGCCACCGGCTGGACAAGGAAACTACGGGCTTGATGGTGTTGGCTCGGGAGATGGAAGTGGCACATCAAGTCCAAGAG
TTGTTTAGAACCTGTCAGGTGGCAAAGAAGTAATGGGCAAACACTGTGTGCATCCCAATTCCCCCAGGAGGAGTCGTAGA
CATCCCCATCATTGAGAAGGAAGTGCAAGGGCAGCAGCACCACCACAAGATGATGCTGTCCCCGAGCTACCACATGGACA
GTGGGAAAATAGTGAAAGTGCATACCAACTGGCATGCACACATGACCATGACCTGGTACCAGGTGCTCAGCAGCACACTG
TCCTCTGCCCTGCTGGAGCTCCAGCTTGTGACCAGAATAAACATCAGCTTTGAGTTCACCTGTCTTTTGGTTTGGATTGT
CCCATCCTTGGTGATCACAAATACTCAGACTGGAAT

Alignment

ORF - retro_chof_1307 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.5 %
• Parental protein coverage: 70.32 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LRRGILHQDNDLVVINKPYGLPVHGGPGVQLCISDVLPILAKMLLGPKAEPLHLCHRLDKETTGVMVLAR
          LRRGIL.QDNDLVVINKPY.LPV.GGPGVQLCI.DVLPILA.MLL..KAEPLH.CHRLDKETTG.MVLAR
Retrocopy LRRGILQQDNDLVVINKPYSLPVIGGPGVQLCIRDVLPILARMLLDHKAEPLHRCHRLDKETTGLMVLAR

Parental  EKEVAHQVQELFRTRQVTKKYWAITVRVPMPPAGVVDIPIIEKEVQGQQRHHKMTLSPSYHMDNGKMVKM
          E.EVAHQVQELFRT.QV.KK.WA.TV..P.PP.GVVDIPIIEKEVQGQQ.HHKM.LSPSYHMD.GK.VK.
Retrocopy EMEVAHQVQELFRTCQVAKK*WANTVCIPIPPGGVVDIPIIEKEVQGQQHHHKMMLSPSYHMDSGKIVKV

Parental  RTNRHAHVAVTRYQVLSSTLSSALLELQPVTGI-KHQLRVHLSFGLDCPILGDHKYSDWN
          .TN.HAH...T.YQVLSSTLSSALLELQ.VT.I.KHQL.VHLSFGLDCPILGDHKYSDWN
Retrocopy HTNWHAHMTMTWYQVLSSTLSSALLELQLVTRI<KHQL*VHLSFGLDCPILGDHKYSDWN

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_1307 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010249	1 retrocopy	retro_chof_1307 ,