RetrogeneDB ID: retro_chof_85

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: GeneScaffold_1623:117851..118299(-)
• Located in intron of: ENSCHOG00000006848

Retrocopy information

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

Parental gene information

• Parental gene symbol: DAZAP2
• Ensembl ID: ENSCHOG00000000298
• Aliases: None
• Description: DAZ associated protein 2 [Source:HGNC Symbol;Acc:2684]

Sequence

>retro_chof_85
CAATATTCAACACTGCCAGTCTACCCTGTGCAGCCTCCTGGGAATCTAGTGTACCCTCAGACCTTGCATCTTCCTCAGGC
ACCACCCTATGCTCCATCTGCTTACTCAGAGCTGTACTGTCCAAGTTTTGAGCACCAAGGGGCTGCTACAGTCCCTACTA
TGTCAATTGCATTCCCTGGCACCTCACTGTATCTTCCCATGGCGCAGTCTGTGGTGGTTGGACCTTTAGGTTCCACAATC
CCCATGGCCTATTAGTCAGTTGGTCCCATCTATCCACCCGGTTCAGCATTGCTGGTAGAAGGAGGATATGTATGACGCAG
GTGCCAGATTTAGCGCTGGGGCTACTGCAGGCAACATTCCTCTTCCACCCCCTGGATGCCCTACCAAAGCTGCTCAGCTT
GCAGTCTTTCAGGGAGCCAATGTCCTTGTAACTCACCAGAAGGGAAAC

Alignment

ORF - retro_chof_85 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.05 %
• Parental protein coverage: 92.02 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QYPTQPTYPVQPPGNPVYPQTLHLPQAPPYTDAPPAYSELYRPSFVHPGAATVPTMSAAFPGASLYLPMA
          QY.T.P.YPVQPPGN.VYPQTLHLPQAPPY..AP.AYSELY.PSF.H.GAATVPTMS.AFPG.SLYLPMA
Retrocopy QYSTLPVYPVQPPGNLVYPQTLHLPQAPPY--APSAYSELYCPSFEHQGAATVPTMSIAFPGTSLYLPMA

Parental  QSMAVGPLGST-TPMAYYPISP-IYPPGSAVLVEGVYAASARFGAGGTAGNIPPPPPGCPPNAAQLAVMQ
          QS..VGPLGST..P.......P.I.P.......E..Y.A.ARF.AG.TAGNIP.PPPGCP..AAQLAV.Q
Retrocopy QSVVVGPLGST>SPWPISQLVPSIHPVQHCW*KEDMYDAGARFSAGATAGNIPLPPPGCPTKAAQLAVFQ

Parental  GANVLVTQRKGN
          GANVLVT..KGN
Retrocopy GANVLVTHQKGN

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_85 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 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000298	1 retrocopy	retro_chof_85 ,
Dasypus novemcinctus	ENSDNOG00000009306	1 retrocopy	retro_dnov_1772,
Equus caballus	ENSECAG00000007313	1 retrocopy	retro_ecab_286,
Myotis lucifugus	ENSMLUG00000009959	1 retrocopy	retro_mluc_351,
Mus musculus	ENSMUSG00000000346	1 retrocopy	retro_mmus_1073,
Sorex araneus	ENSSARG00000003823	1 retrocopy	retro_sara_632,
Tupaia belangeri	ENSTBEG00000013232	1 retrocopy	retro_tbel_3228,
Vicugna pacos	ENSVPAG00000001156	2 retrocopies	retro_vpac_314, retro_vpac_568,