RetrogeneDB ID: retro_chof_539

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_119383:6516..7210(+)
• 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_539
GTGAGAAAAGGCCGAGCCACAGCTGCAGCCTCCGCTGCCAAGAAGCCCTTGTTCTCACTGTCTGGAGGGAAAGCCTGGTG
CCGACACGATGGCGGACAGGGAGCTGAACGTGGACAGTCTCATCCCCTGTGCCCTGGAGGTACCAGGATGTCATCCAGAA
AAGATTGTCCAGGCGACTGAAGCAGAAGTTAGGGGCTTATGTATCAAGTCTCAGGAGACCTTTCTCAGTCAGACTATTCT
TTTGGAATTGGAAGCACTGTTGAAACTTTGTAGAGATATTCATGGACAGTATACAGATTTACTGTGATTATTTGAATATG
GGGGTTTCCTACCAGAAGTCAACTCTCTTTCCTTAGGAGATTGTGTGGACAAAGGAAAGCAGTCTTTGGAAACCATTCGT
TTGTTATTGATTTAAAAAATCAAATATCCAGTGAATGTCTTTCTCTTAAGAGGAAACCATGTGTATGGTAGCATGAACAG
CACTTACGAAGTCTATGATGAATGCAAACGAAGGTTTAATATTAAATTACGGAAGACCTTCACCGTTTGTTTTAACTGTC
TGCCTGTAGCTGCCGTTGTGGTTGAAATCTGCTGTCATGGAGGACTGTCACCAGACCTACAATCAAGGGAGCAGATTCAG
AGAATTGTGACACCTGCTGATGTCCCTCATACAGGTTTGCTCTGTGATTTGCTG

Alignment

ORF - retro_chof_539 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.64 %
• Parental protein coverage: 63.66 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VREGRAVAAASAAEKPLFPLPGGRAC-ADKMADGELNVDSLITRLLEVRGCRPGKIVQMTEAEVRGLCIK
          VR.GRA.AAASAA.KPLF.L.GG.A..AD.MAD.ELNVDSLI...LEV.GC.P.KIVQ.TEAEVRGLCIK
Retrocopy VRKGRATAAASAAKKPLFSLSGGKAW>ADTMADRELNVDSLIPCALEVPGCHPEKIVQATEAEVRGLCIK

Parental  SREIFLSQPILLELEAPLKICGDIHGQYTDLLRLFEYGGFPPEANYLFLGDYVDRGKQSLETICLLLAYK
          S.E.FLSQ.ILLELEA.LK.C.DIHGQYTDLL.LFEYGGF.PE.N.L.LGD.VD.GKQSLETI.LLL..K
Retrocopy SQETFLSQTILLELEALLKLCRDIHGQYTDLL*LFEYGGFLPEVNSLSLGDCVDKGKQSLETIRLLLI*K

Parental  IKYPENFFLLRGNHECASINRIYGFYDECKRRFNIKLWKTFTDCFNCLPIAAIVDEKIFCCHGGLSPDLQ
          IKYP.N.FLLRGNH...S.N..Y..YDECKRRFNIKL.KTFT.CFNCLP.AA.V.E...CCHGGLSPDLQ
Retrocopy IKYPVNVFLLRGNHVYGSMNSTYEVYDECKRRFNIKLRKTFTVCFNCLPVAAVVVE--ICCHGGLSPDLQ

Parental  SMEQIRRIMRPTDVPDTGLLCDLL
          S.EQI.RI..P.DVP.TGLLCDLL
Retrocopy SREQIQRIVTPADVPHTGLLCDLL

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_539 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,