RetrogeneDB ID: retro_chof_2076

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_4775:15615..16500(+)
• 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_2076
CTCAACATCAAAAGCATCATCCAATGGCTGCTGGAAATGAGAGGGTCCAAACCTGGTAAGAATGCCCAGCTGCAGGAGAA
TGAAATTGGAGGTTTGTGCTTAAAGTCTCATGAGATTTTTCTCAGTCAGCCCATCCTACTAGCACTTGAAGCACCACTCA
AAATATGTGGTGCTGTCCATAGGCAATACTATGATTTGCTTCAACTTTTTGAGTAGGGTGGTTTCCCACCAGAAAGCAGC
CAACTGTTTCTTGAGGACTATGTGGACAGAAGGAAGCGGTCATCGGAGACTATCTGCCTCTTATTGGCTACAAAATCAAA
TATCCCACAAATTTTTTTCTTCTCTGAGGAAACCACAAATGTACCAGCATCAATAGAATTTGTGGATTTGATGATGAATG
TAAAAGAAGATATAACATTAAACTATGGAAAATTTTCACAGACTGCTTTAACTTTTTACTGATAGCAGCCATTGTGGATA
AAAAAATATTCTGCTTTCATGGAGGTTTATCACCAGATTTCCAATCTATGGAGAAGATGCAGCAAATTATGTGACCAACT
GATGTACCATATCAAGGTCTTCTTTGGGATCTTTTGTGGTCAGACTCCAATAAAGATGTCTGAGGCTGGCGTGAAAATGA
CAGAGAAGCATCCTTCACATTTGGTGCAGAAGTGGTTGCAAAATTCTCCATAAGCATGTTTTGGATCTTATATGTAGACC
CCATCAGGTGATTGAAGATGGATATAAAATTTTGGCAAGAGGCAGTTGGTCACTCTGTTTTCTGCACCCAATTGTTGTGG
AGAGTTTGACAGTGCAGGTGCTATGATGAGTGCAGATGAAACACTAATGTGTTCTTTTCAGATTTTAAAGCCTGCAGAGA
AAAAG

Alignment

ORF - retro_chof_2076 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.25 %
• Parental protein coverage: 80.87 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LNVDSLITRLLEVRGCRPGKIVQMTEAEVRGLCIKSREIFLSQPILLELEAPLKICGDIHGQYTDLLRLF
          LN..S.I..LLE.RG..PGK..Q..E.E..GLC.KS.EIFLSQPILL.LEAPLKICG..H.QY.DLL.LF
Retrocopy LNIKSIIQWLLEMRGSKPGKNAQLQENEIGGLCLKSHEIFLSQPILLALEAPLKICGAVHRQYYDLLQLF

Parental  EYGGFPPEANYLFLGDYVDRGKQSLETICLLLA-YKIKYPENFFLLRGNHECASINRIYGFYDECKRRFN
          E.GGFPPE...LFL.DYVDR.K.S.ETICLLLA.YKIKYP.NFFLL.GNH.C.SINRI.GF.DECKRR.N
Retrocopy E*GGFPPESSQLFLEDYVDRRKRSSETICLLLA<YKIKYPTNFFLL*GNHKCTSINRICGFDDECKRRYN

Parental  IKLWKTFTDCFNCLPIAAIVDEKIFCCHGGLSPDLQSMEQIRRIMRPTDVPDTGLLCDLLWSDPDKDVQG
          IKLWK.FTDCFN.L.IAAIVD.KIFC.HGGLSPD.QSME....IM.PTDVP..GLL.DLLWSD..KDV.G
Retrocopy IKLWKIFTDCFNFLLIAAIVDKKIFCFHGGLSPDFQSMEKMQQIM*PTDVPYQGLLWDLLWSDSNKDV*G

Parental  WGENDRGVSFTFGADVVSKF-LNRHDLDLICRAHQVVEDGYEF-FAKRQLVTLFSAPNYCGEFDNAGGMM
          W.ENDR..SFTFGA.VV.KF.L..H.LDLICR.HQV.EDGY...F.KRQLVTLFSAPN.CGEFD.AG.MM
Retrocopy WRENDREASFTFGAEVVAKF<LHKHVLDLICRPHQVIEDGYKI<FGKRQLVTLFSAPNCCGEFDSAGAMM

Parental  SVDETLMCSFHILKPSEKK
          S.DETLMCSF.ILKP.EKK
Retrocopy SADETLMCSFQILKPAEKK

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_2076 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,