RetrogeneDB ID: retro_chof_2112

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_50204:4339..4976(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPP2CB
• Ensembl ID: ENSCHOG00000003467
• Aliases: None
• Description: protein phosphatase 2, catalytic subunit, beta isozyme [Source:HGNC Symbol;Acc:9300]

Sequence

>retro_chof_2112
CTGAGGGAATGCGAACAAACTTGGAACAAAGTGCGAACACCGTGCGTAAACGCTGCGGAAATCTTAACAAAGAATCAAAT
GTGCGAGAGGTTCGTGTCTGTGGAGATGTTCATGTTCAATTCCTTGATTTTAGGGAACTCTTTAGAATTGGTGGGAAATC
TCCAGATAAAAATTGTCTACTCATGGGTGACTCGGTAGGTTATTATTCAGTGGAGACTATGACTCTCTTTGTAGCATCAG
AAGTGTCTTTTTGAGATCACATTACAGTACTGAGAAGAAACCAAAAAAGCCGACAAATGACCCAAGTACATGGCTTTTAT
GATGAATGACTATGAAAATATGGAAACGCCGATATTTGTAAATATTTTACACAGCTATTTGATTATCTTCCACTAACAGC
TTTAGTAGATGGACAGATACTCTGCCTCCATAGTGGTTTCTCTACATCTGTAGATACACTGGATCATATAAGAGCCCTAG
ATCTTTTACAAGAAATTCCACATGAGGGCCCAATGTGTCATCTGTTCCTGTCAGATCCAGATGATGATGGTAGATGGGAT
ATTTTTACATGTGGTGCAGGCTACACTTTGGACAAGACACTTCTGAAGCATTTAGCCAAGCCAGTGGCCTTACACTA

Alignment

ORF - retro_chof_2112 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.47 %
• Parental protein coverage: 71.66 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LKECKQFKENQVQTLCEKAKEILTK-ESNVQEVRCPVTVCGDVHGQFHDLMELFRIGGKSPDTNYLFMGD
          L.EC.Q...N.V.T.C..A.EILTK.ESNV.EVR....VCGDVH.QF.D..ELFRIGGKSPD.N.L.MGD
Retrocopy LRECEQ-TWNKVRTPCVNAAEILTK<ESNVREVR----VCGDVHVQFLDFRELFRIGGKSPDKNCLLMGD

Parental  YVDRGYYSVETVTLLVALKVRYPERITILRGNHESRQITQVYGFYDECLRKYGNANVWKYFTDLFDYLPL
          .V..GYYSVET.TL.VA..V.....IT.LR.N..SRQ.TQV.GFYDE.L.KYGNA...KYFT.LFDYLPL
Retrocopy SV--GYYSVETMTLFVASEVSF*DHITVLRRNQKSRQMTQVHGFYDE*L*KYGNADICKYFTQLFDYLPL

Parental  TALVDGQIFCLHGGLSPSIDTLDHIRALDRLQEVPHEGPMCDLLWSDPDDRGGWGISPRGAGYT-FGQDI
          TALVDGQI.CLH.G.S.S.DTLDHIRALD.LQE.PHEGPMC.L..SDPDD.G.W.I...GAGYT.FGQD.
Retrocopy TALVDGQILCLHSGFSTSVDTLDHIRALDLLQEIPHEGPMCHLFLSDPDDDGRWDIFTCGAGYT<FGQDT

Parental  SETFNHANGLTL
          SE.F..A.GLTL
Retrocopy SEAFSQASGLTL

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_2112 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 2 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003467	9 retrocopies	retro_chof_1247, retro_chof_1521, retro_chof_1556, retro_chof_2112 , retro_chof_2267, retro_chof_2502, retro_chof_251, retro_chof_273, retro_chof_446,
Monodelphis domestica	ENSMODG00000019001	2 retrocopies	retro_mdom_192, retro_mdom_632,