RetrogeneDB ID: retro_ogar_3069

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873709.1:1526421..1527152(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPP2R2B
• Ensembl ID: ENSOGAG00000010873
• Aliases: None
• Description: protein phosphatase 2, regulatory subunit B, beta [Source:HGNC Symbol;Acc:9305]

Sequence

>retro_ogar_3069
TGGAACTTTGAAATAAGCAATCAAAGTTTTAACATCGTGGACATCAAGCCTGCCGACATGGAGGAGCTCACGGAGGTGAT
CATGGCAGCCGAGTTCTACCCCATCACTGCAACACCTTCCTCTACAGCAGTAGCAAAGGGACAGTCCGGCTGTGTGACAT
GTGGGTGTCAGCCCTGTGTGACAGGCACACCAAGTTTTTTGAAGAGCTAGAATATCCAAGCAACAGATCGTTTTTCTCTG
AAATTATCTCTTCGGTTTCAGATGTGAAGTTCAGCCACAGTGGGAGGGACTGTGGGACCAGGGACTACCTTACTGTTAAA
GTGTGGGATCTCAACATGGAAAACTGCCCCATCAAGTCTTACCAGGTCCATGACTACCTCCACAGCAAGTTGTGTTCCCT
CTACGAAAATGATGGCATTTTTGATAAATTTGAGTGTGTCTGGAATAGGTCAGACAACGTCATCATGACAGGCTCCTACA
ACAACTTCTTCAGGATGTTTAACTGAAACACCAAGTGCGGTGTGACCCTTGAGGCCTCACGAGAAAACAGCAAACCCCGG
GCTATCCTCAAGCCCCGAAAAGTGTGGGGGGCCAAGCAGAGAAAAGACGAGATCAGTGTTGATAGTCTGGACTTTAGCAA
AAAGATCTTACATACAGCTTGACATCCTTCAGAAAATATTATAGCAGTGGCGGCTACAAGTAACCTATATATATTCTAGG
ACAAGATTAAC

Alignment

ORF - retro_ogar_3069 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.18 %
• Parental protein coverage: 55.3 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  WNFEITNQSFNIVDIKPANMEELTEVITAAEFHP-HHCNTFVYSSSKGTIRLCDMRASALCDRHTKFFEE
          WNFEI.NQSFNIVDIKPA.MEELTEVI.AAEF.P.HHCNTF.YSSSKGT.RLCDM..SALCDRHTKFFEE
Retrocopy WNFEISNQSFNIVDIKPADMEELTEVIMAAEFYP<HHCNTFLYSSSKGTVRLCDMWVSALCDRHTKFFEE

Parental  PEDPSNRSFFSEIISSISDVKFSHSGRYIMTRDYLTVKVWDLNMENRPIETYQVHDYLRSKLCSLYENDC
          .E.PSNRSFFSEIISS.SDVKFSHSGR...TRDYLTVKVWDLNMEN.PI..YQVHDYL.SKLCSLYEND.
Retrocopy LEYPSNRSFFSEIISSVSDVKFSHSGRDCGTRDYLTVKVWDLNMENCPIKSYQVHDYLHSKLCSLYENDG

Parental  IFDKFECVWNGSDSVIMTGSYNNFFRMFDRNTKRDVTLEASRENSKPRAILKPRKVCVGGKRRKDEISVD
          IFDKFECVWN.SD.VIMTGSYNNFFRMF..NTK..VTLEASRENSKPRAILKPRKV..G.K.RKDEISVD
Retrocopy IFDKFECVWNRSDNVIMTGSYNNFFRMFN*NTKCGVTLEASRENSKPRAILKPRKVW-GAKQRKDEISVD

Parental  SLDFSKKILHTAWHPSENIIAVAATNNLYIFQDKVN
          SLDFSKKILHTA.HPSENIIAVAAT.NLYIF.DK.N
Retrocopy SLDFSKKILHTA*HPSENIIAVAATSNLYIF*DKIN

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Otolemur garnettii was not studied using RNA-Seq expression data.

ChIP-Seq

Otolemur garnettii was not studied using ChIP-Seq data.

EST

Otolemur garnettii was not studied using EST data.

TSS

Otolemur garnettii was not studied using FANTOM5 data.

Lab

retro_ogar_3069 was not experimentally validated.

Homology

Retrocopy orthology:

Otolemur garnettii 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 ,