RetrogeneDB ID: retro_chof_1495

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_30810:117..1368(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPP2R2B
• Ensembl ID: ENSCHOG00000001182
• Aliases: None
• Description: protein phosphatase 2, regulatory subunit B, beta [Source:HGNC Symbol;Acc:9305]

Sequence

>retro_chof_1495
AATATAATTTCTACAGTAGAATTCACTCATTTTGGAGAATTACTGGCAACAGGAGATAAAGGTGTAGAGTTGTCATCTTT
CAACAGGAGCAGGAGAACAAAATCCAGTCTCATAGCAGAGGAGAATATAATGTTTACAGCACCTTCCAGAGCCATGAGCC
AGAATTTGACTACTCAAAAAGTTTAGAAATAGAAGATCAACAAAAGTAGGTGGTTGCCCCAGGAAAATGCTGCTCAGTTT
TTATTGTCTACCAATGATAAAACAATAAAATTATGGAAATCAGTGAAAGGGACAAAAGACCAGAAGGGTATAACTTGAAA
GAGGAAGATGGAAAGTATAGAGATCCTACTACAGTTACTACACTACATGTACCAGTCTTTAGGCCCATGGATCTAATGGT
TGAAACCAGCCATGAAGAATATTTGCCAGAGCTCATACGTATCACATCAACTCTATTTCTATAAATAGTAATTATGAAAC
ACTTAATCTGCAGATGATTTGTGGGTTAATCTTTGGCATCTGGAAATTACAGACAGAAGTTTTAATATTGTGGATATCAA
GCCTGCTAATATGGAAGAACTAACAGAGGTGATTACAGCAGCAGAATTTCATCCAAACAGCTGTAACACATTTGTACACA
GCAGCAGTAAAGGAACTATTCGGTTATGTGACATGAGAGCATCTGCCCTCTGTAATAGACATTCTAAACTGTTTGAAGAA
CCTGAAGATCCCAGTTTAACAGGTCATTTTTTTTCTGAAATCATCTCCTCTATTTCTGATGTAAAATTCAGCCATAGTGG
TCAATATATGATGACAAGAGACTATTTGTCAGTCAAAATTTGGGACTTAAATATGGAAAATAGGCCTGTGGAAACCTATC
AGGTTCATGAATACCTCAGAAGTAAATTTTGTTCACTGTATGAAAATGACTGCTTATTTGACAAATTTGAATTTTGTTGG
AATGGATCTGACAGTGTTGTTATGACTGGATCTTATAATAATTTCTTCAGAATGTTTGACAGGAACACAAAGCGAGCCAT
AACCCTAGAAGCATCATGGGAAAATAATATACCTCACATGGTTTTGAAGTCACACAAAGTCTGTGCAAGTGGCAAACAAA
AGAAAGATGAAATAAGTGTTGACAGTCTAGATTTCAACAAGAAAATACTTCATACAGCCTGGCACCCCAAGGAAAACATC
ATTGCTGTAGCAACTACAAACAATCTGTATATATTTCAAGACGAAGTGAAT

Alignment

ORF - retro_chof_1495 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.12 %
• Parental protein coverage: 82.32 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  DIISTVEFNHTGELLATGDKGG-RVVIFQREQESKNQVHRRG-EYNVYSTFQSHEPEFDYLKSLEIEEKI
          .IISTVEF.H.GELLATGDKG..RVVIFQ..QE..N.......E.N...T..S...............KI
Retrocopy NIISTVEFTHFGELLATGDKGV<RVVIFQ--QEQENKIQSHS>EENIMFTAPSRAMSQNLTTQKV*K*KI

Parental  NKIRWLPQQNAAYFLLSTNDKTVKLWK-VSERDKRPEGYNLKDEEGRLRDPATITTLRVPVLRPMDLMVE
          NK.RWLPQ.NAA.FLLSTNDKT.KLWK..SERDKRPEGYNLK.E.G..RDP.T.TTL.VPV.RPMDLMVE
Retrocopy NKSRWLPQENAAQFLLSTNDKTIKLWK<ISERDKRPEGYNLKEEDGKYRDPTTVTTLHVPVFRPMDLMVE

Parental  AT-PRRVFANAHTYHINSISVNSDYETYM-SADDLRINLWNFEITNQSFNIVDIKPANMEELTEVITAAE
          ...P.R.FA.AHTYHINSIS.NS.YET...SADDL..NLW..EIT..SFNIVDIKPANMEELTEVITAAE
Retrocopy TS<P*RIFARAHTYHINSISINSNYETLN<SADDLWVNLWHLEITDRSFNIVDIKPANMEELTEVITAAE

Parental  FHPHHCNTFVYSSSKGTIRLCDMRASALCDRHTKFFEEPEDPS-NRSFFSEIISSISDVKFSHSGRYIMT
          FHP..CNTFV.SSSKGTIRLCDMRASALC.RH.K.FEEPEDPS.......EIISSISDVKFSHSG.Y.MT
Retrocopy FHPNSCNTFVHSSSKGTIRLCDMRASALCNRHSKLFEEPEDPSLTGXXXXEIISSISDVKFSHSGQYMMT

Parental  RDYLTVKVWDLNMENRPIETYQVHDYLRSKLCSLYENDCIFDKFECVWNGSDSVIMTGSYNNFFRMFDRN
          RDYL.VK.WDLNMENRP.ETYQVH.YLRSK.CSLYENDC.FDKFE..WNGSDSV.MTGSYNNFFRMFDRN
Retrocopy RDYLSVKIWDLNMENRPVETYQVHEYLRSKFCSLYENDCLFDKFEFCWNGSDSVVMTGSYNNFFRMFDRN

Parental  TKRDVTLEASRENSKPRAILKPRKVCVGGKRRKDEISVDSLDFSKKILHTAWHPSENIIAVAATNNLYIF
          TKR..TLEAS.EN..P...LK..KVC..GK..KDEISVDSLDF.KKILHTAWHP.ENIIAVA.TNNLYIF
Retrocopy TKRAITLEASWENNIPHMVLKSHKVCASGKQKKDEISVDSLDFNKKILHTAWHPKENIIAVATTNNLYIF

Parental  QDKVN
          QD.VN
Retrocopy QDEVN

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_1495 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001182	2 retrocopies	retro_chof_1495 , retro_chof_2033,
Otolemur garnettii	ENSOGAG00000010873	1 retrocopy	retro_ogar_3069,