RetrogeneDB ID: retro_chof_2154

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_53840:2805..3710(-)
• 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_2154
ATGGCAGATATAGATAAACTCAATATCGACAGTATCATCCAATTGCTGCTGGAAGTGAGAGGGTCCAGCCTGGTAAGAAT
GTCCAGCTACAGGAGAATGAAATCAGAGGATTGTGCTTTAAGTCTCATGAGATCTTCCTCAGTCAGCCTATCCTACTAGA
ACTTGAAGCACCACTCAAAATATGTGGTGATATCCATGGGCAATACTATGATTTGCTTCGACTTTTTGAGTACGGTGGTT
TTCCACCAGAAAGCAACTATCTGTTTCTTGGGGACTATGTGGACAGAGGGAATCAGTCATTGGAGACTATATGCCTCTTA
CTGGCCTACAAAATCAAATATTCTGAGAATTTTTTTCTTCTCCAAGGAAACCACGAATGTGCCAGCATCAGTAGAATTTA
TGGATTTTATGATGAATGTAAAAGAAGATACAACACTAAACTATGGAAAACTTTCACAGACTGCTTTAACTGTTTACTGA
TAGCAGCCATCGTTGGTGAGAAAATATTCTGCTGTCATGGAAGTTTATCACCAGATCTTCAATCTATGGAGCAGATACGG
CGAATTATGAGACCAACTGATGTACCAGATCAAGGTCTTCTTTGTGATCTTTTGTAGTCTGACCCCGATGAACATGTCTT
AGGCTGGGATGAAATTGACAGAGGAGTGTCCTTCACATTTGGTGCAGAAGTGGTTGCAAAATTTCTCCATAAGCATGATT
TGGATCTTATATGTAGAGCCCATCAGATGGCGGAAGATGGATATGAATTTTTTGCCAAGAGGCAGTTGGTCACTCTGTTT
TCTGCACCCAATTATTGTGGAGAGTTTGACAATGCAGGTGCCGTGATGAGTGTGGATGAAATGCTAATGTGATCTTTTCA
GATTTTAAAGCCTGCAGAGAAAAAG

Alignment

ORF - retro_chof_2154 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.49 %
• Parental protein coverage: 82.24 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAD-GELNVDSLITRLLEVRGC-RPGKIVQMTEAEVRGLCIKSREIFLSQPILLELEAPLKICGDIHGQY
          MAD...LN.DS.I..LLEVRG...PGK.VQ..E.E.RGLC.KS.EIFLSQPILLELEAPLKICGDIHGQY
Retrocopy MADIDKLNIDSIIQLLLEVRGS<QPGKNVQLQENEIRGLCFKSHEIFLSQPILLELEAPLKICGDIHGQY

Parental  TDLLRLFEYGGFPPEANYLFLGDYVDRGKQSLETICLLLAYKIKYPENFFLLRGNHECASINRIYGFYDE
          .DLLRLFEYGGFPPE.NYLFLGDYVDRG.QSLETICLLLAYKIKY.ENFFLL.GNHECASI.RIYGFYDE
Retrocopy YDLLRLFEYGGFPPESNYLFLGDYVDRGNQSLETICLLLAYKIKYSENFFLLQGNHECASISRIYGFYDE

Parental  CKRRFNIKLWKTFTDCFNCLPIAAIVDEKIFCCHGGLSPDLQSMEQIRRIMRPTDVPDTGLLCDLLWSDP
          CKRR.N.KLWKTFTDCFNCL.IAAIV.EKIFCCHG.LSPDLQSMEQIRRIMRPTDVPD.GLLCDLL.SDP
Retrocopy CKRRYNTKLWKTFTDCFNCLLIAAIVGEKIFCCHGSLSPDLQSMEQIRRIMRPTDVPDQGLLCDLL*SDP

Parental  DKDVQGWGENDRGVSFTFGADVVSKFLNRHDLDLICRAHQVVEDGYEFFAKRQLVTLFSAPNYCGEFDNA
          D..V.GW.E.DRGVSFTFGA.VV.KFL..HDLDLICRAHQ..EDGYEFFAKRQLVTLFSAPNYCGEFDNA
Retrocopy DEHVLGWDEIDRGVSFTFGAEVVAKFLHKHDLDLICRAHQMAEDGYEFFAKRQLVTLFSAPNYCGEFDNA

Parental  GGMMSVDETLMCSFHILKPSEKK
          G..MSVDE.LM.SF.ILKP.EKK
Retrocopy GAVMSVDEMLM*SFQILKPAEKK

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_2154 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,