RetrogeneDB ID: retro_chof_183

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: GeneScaffold_4064:24794..25483(+)
• Located in intron of: ENSCHOG00000001126

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPP6C
• Ensembl ID: ENSCHOG00000012357
• Aliases: None
• Description: protein phosphatase 6, catalytic subunit [Source:HGNC Symbol;Acc:9323]

Sequence

>retro_chof_183
TACCTGCCAGAGAACAACCTAAAGCAGTTTGTGACTATGTTTGTGACCTCTTCTTGGAAGAGTCAAATGTTCAGCCGATA
TCAACACCAGTTACAGTGTGTGGAGACACACATGGACAGTTTTATGATCTTTGTGAACTATTCAGAATTGGAGGTCAGGT
TTCTGACACAAACTACATATTTTTGGGTGACTTTGTAGACAGAGGTTACTATAGTTTGGAGACTTGCACTTCCCTTCTTG
CAATAAAGGCTAAATTGGCCTGATCGTATTTCACTTTTGCAAGGAAATCATTAGAGTAGACAGATAACACAGGTGTATGG
ATTTTATGATGAGTGCCAAACCAAATATGGAAATGCTAATAATGCCTGTAGATATTGTACCAAAGTTTCTTACATGCTCA
CAGTAGCAGCTTTAATAGATGAGCAGATTTTGTGTGTTCATGGTGGTTTCTCTCTCAATATGAAAACACTGGATCAAATT
CGAACTATTGAATGGAATCAGGAAATTTCTCATACAGGAGCATTTTGTGACCTGCTTTGGCCAGTCCTGATGTGGATACT
TGGGCAGTCAGTCCCTGAGGAGCAGGTTGGCTTTTTGGAGCAAAGGTCACAAATGAGTTTGTTCACATCAACAACTTGAA
ACTCATCCGCAGAGCACACCAACTAGTGCACGAAGGCTATAAATGTATG

Alignment

ORF - retro_chof_183 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.91 %
• Parental protein coverage: 75.66 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  YLPENDLKR-LCDYVCDLLLEESNVQPVSTPVTVCGDIHGQFYDLCELFRTGGQVPDTNYIFMGDFVDRG
          YLPEN.LK...CDYVCDL.LEESNVQP.STPVTVCGD.HGQFYDLCELFR.GGQV.DTNYIF.GDFVDRG
Retrocopy YLPENNLKQ<VCDYVCDLFLEESNVQPISTPVTVCGDTHGQFYDLCELFRIGGQVSDTNYIFLGDFVDRG

Parental  YYSLETFTYLLALKAK-WPDRITLLRGNHESRQITQVYGFYDECQTKYGNA-NAWRYCTKVFDMLTVAAL
          YYSLET.T.LLA.KAK.WPDRI.LL.GNH.SRQITQVYGFYDECQTKYGNA.NA.RYCTKV..MLTVAAL
Retrocopy YYSLETCTSLLAIKAK>WPDRISLLQGNH*SRQITQVYGFYDECQTKYGNANNACRYCTKVSYMLTVAAL

Parental  IDEQILCVHGGLSPDIKTLDQIRTIERNQEIPHKGAFCDLVW-SDPEDVDTWAISPRGAGWLFGAKVTNE
          IDEQILCVHGG.S...KTLDQIRTIE.NQEI.H.GAFCDL.W...P.DVDTWA.SP.GAGWLFGAKVTNE
Retrocopy IDEQILCVHGGFSLNMKTLDQIRTIEWNQEISHTGAFCDLLW<ASP-DVDTWAVSP*GAGWLFGAKVTNE

Parental  FVHINNLKLICRAHQPMYEGYKFM
          FVHINNLKLI.RAHQ...EGYK.M
Retrocopy FVHINNLKLIRRAHQLVHEGYKCM

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_183 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 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012357	3 retrocopies	retro_chof_1759, retro_chof_183 , retro_chof_608,
Dasypus novemcinctus	ENSDNOG00000015319	1 retrocopy	retro_dnov_1700,
Erinaceus europaeus	ENSEEUG00000010197	1 retrocopy	retro_eeur_706,
Macaca mulatta	ENSMMUG00000020549	1 retrocopy	retro_mmul_698,
Rattus norvegicus	ENSRNOG00000015145	1 retrocopy	retro_rnor_2074,
Sarcophilus harrisii	ENSSHAG00000008282	1 retrocopy	retro_shar_146,
Sus scrofa	ENSSSCG00000005600	1 retrocopy	retro_sscr_243,