RetrogeneDB ID: retro_chof_2023

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_457837:147..727(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPP1CB
• Ensembl ID: ENSCHOG00000000859
• Aliases: None
• Description: protein phosphatase 1, catalytic subunit, beta isozyme [Source:HGNC Symbol;Acc:9282]

Sequence

>retro_chof_2023
CTGTTATTTGCCTACAAAATCTAATATCCCGAAAATTTTTTTCTTCTCTGAGGAATCCATGAATGTGCCAGCATCAATAG
AATTTATGGAATTTATAATGAATGTAAAAGAAGATACAACATTAAACTATGGAAAACTTTTAACAGACTGCTTTAACTGT
ACCGATAGCAGCCATCGTGGATGAGAAAATATTCTGCTGTCATGGAGGTTTATCACCAGATCTTCAATCTATGGAACAGA
TTCCGTGAATAATGCGACCAACTGATGTAGGACTTCTTTGTTGCCTTTTGTGGTCTGACCCAATAAAGGTGTCTTAGGCT
GGGGTGGAAAATGACAGACGAGTGTCTTTCATATTTGGTGCAGAAGTGGTTGCCAAATTTCTCCATAAGCATGGTTTGGA
TCTTACATGTAGAGCCCATCAGGTGGTTGAAGATGGATGTGAAATTTTGCCAAGAGTCAGTTGGTCACTCTGTTTTCTGC
ACCCAATTGTTGTGGAGAGTTTGACAGTGCAGATGCCATAATGACTGTGGATGAAATGCTAACGTGTTCTTTTCAGATTT
TAAAGCCTGCAGAGAAAAAG

Alignment

ORF - retro_chof_2023 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.28 %
• Parental protein coverage: 53.83 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  LLLAYKIKYPENFFLLRGNHECASINRIYGFYDECKRRFNIKLWKTF-TDCFNCLP-IAAIVDEKIFCCH
          LL.AYKI.YPENFFLL.G.HECASINRIYG.Y.ECKRR.NIKLWKTF.TDCFNC....A........C..
Retrocopy LLFAYKI*YPENFFLL*GIHECASINRIYGIYNECKRRYNIKLWKTF>TDCFNCTD>AAIVDEKIFCCHG

Parental  GGLSPDLQSMEQIRRIMRPTDVPDTGLLCDLLWSD-PDKDVQGWG-ENDRGVSFTFGADVVSKFLNRHDL
          G.LSPDLQSMEQI..IMRPTDV...GLLC.LLWSD.P.K.V.GWG.ENDR.VSF.FGA.VV.KFL..H.L
Retrocopy G-LSPDLQSMEQIP*IMRPTDV---GLLCCLLWSD<PNKGVLGWG>ENDRRVSFIFGAEVVAKFLHKHGL

Parental  DLICRAHQVVEDGYEF-FAKRQLVTLFSAPNYCGEFDNAGGMMSVDETLMCSFHILKPSEKK
          DL.CRAHQVVEDG.E..FAK.QLVTLFSAPN.CGEFD.A...M.VDE.L.CSF.ILKP.EKK
Retrocopy DLTCRAHQVVEDGCEI<FAKSQLVTLFSAPNCCGEFDSADAIMTVDEMLTCSFQILKPAEKK

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_2023 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 4 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000859	5 retrocopies	retro_chof_2023 , retro_chof_2063, retro_chof_2076, retro_chof_2154, retro_chof_539,
Echinops telfairi	ENSETEG00000015038	2 retrocopies	retro_etel_1223, retro_etel_1364,
Myotis lucifugus	ENSMLUG00000003785	1 retrocopy	retro_mluc_1907,
Rattus norvegicus	ENSRNOG00000004612	2 retrocopies	retro_rnor_1455, retro_rnor_2344,