RetrogeneDB ID: retro_ogar_921

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873530.1:12152929..12153713(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPP2CA
• Ensembl ID: ENSOGAG00000009695
• Aliases: None
• Description: protein phosphatase 2, catalytic subunit, alpha isozyme [Source:HGNC Symbol;Acc:9299]

Sequence

>retro_ogar_921
ATGGACCACAAGACCTTCACCAAGGAGCTGGACTAGTGGGTGGAGCCTCTGAACGAGTGTAAACAGCTTAAGGAAAACAA
GTGTGGATGCTGTGCAAATAGGCTAAAGAAATTCTAACAAAAGAATCAAATGTGCAAGAGGTTCATTGTTCTGTTACTGT
CTGTGGAGATGTGCACGGTCAATTTCATGATGTTATGGAACACTTTAGAATTGGTGGGAAATCACCAGACACAAACTATT
TATTCATGAGTGACTACGTGGACAGAGGTTATTATTCAGTAGAGACTGTCCCTCTTCCTGTAGCAGTAAAGGTGCGTTAT
CCAGAAGGCATTACAAGATTGAGAGGAAATCATGAAAGCGAACAAACTACCCAAGTATATGGCTTTTATGATGAATGTCT
ATGAAAGTATGGGAATGCCAATGTTTGGAAATATTTTACTGATCTATTTGATTATCTTCCACTTACAGCTTTAGTAGATG
GACAGATAATCTGCCTCCATGGTGGCCTCTCTCCATCTATAGACACACTGGATCATGTAAGAGGCCTGGATTGCTTACAG
GAAGTACCACGTGAGGGCCCAACATGGGATCTGTTACGGTCAGATCCAGATGATGTGGTGGGTGGGGTATTTCACCACGC
GGTGCTGGCTACACATTTGGACAAGACATTTCTGAAACATTTAACCAGGCCAGTGGCCTCACTCTGGTTTCTCATGCTCA
CCAGCTTGTAATGGAGGGATGCAATTGGTGTCGGGATCGGAATGTGGTTACAACTTTCAGTGCA

Alignment

ORF - retro_ogar_921 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.09 %
• Parental protein coverage: 84.79 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MDEKVFTKELDQWIEQLNECKQLSES-QVKSLCEKAKEILTKESNVQEVRCPVTVCGDVHGQFHDLMELF
          MD.K.FTKELD.W.E.LNECKQL.E..QV..LC..AKEILTKESNVQEV.C.VTVCGDVHGQFHD.ME.F
Retrocopy MDHKTFTKELD*WVEPLNECKQLKEN<QVWMLCK*AKEILTKESNVQEVHCSVTVCGDVHGQFHDVMEHF

Parental  RIGGKSPDTNYLFMGDYVDRGYYSVETVTLLVALKVRYRERITILRGNHESRQITQVYGFYDECLRKYGN
          RIGGKSPDTNYLFM.DYVDRGYYSVETV.L.VA.KVRY.E.IT.LRGNHES.Q.TQVYGFYDECL.KYGN
Retrocopy RIGGKSPDTNYLFMSDYVDRGYYSVETVPLPVAVKVRYPEGITRLRGNHESEQTTQVYGFYDECL*KYGN

Parental  ANVWKYFTDLFDYLPLTALVDGQIFCLHGGLSPSIDTLDHIRALDRLQEVPHEGPMCDLLWSDPDD-RGG
          ANVWKYFTDLFDYLPLTALVDGQI.CLHGGLSPSIDTLDH.R.LD.LQEVP.EGP..DLL.SDPDD..GG
Retrocopy ANVWKYFTDLFDYLPLTALVDGQIICLHGGLSPSIDTLDHVRGLDCLQEVPREGPTWDLLRSDPDD<CGG

Parental  WGISPRGAGYTFGQDISETFNHANGLTLVSRAHQLVMEGYNWCHDRNVVTIFSA
          WGISPRGAGYTFGQDISETFN.A.GLTLVS.AHQLVMEG.NWC.DRNVVT.FSA
Retrocopy WGISPRGAGYTFGQDISETFNQASGLTLVSHAHQLVMEGCNWCRDRNVVTTFSA

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_921 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 9 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000002653	1 retrocopy	retro_acar_69,
Callithrix jacchus	ENSCJAG00000013634	2 retrocopies	retro_cjac_1346, retro_cjac_4113,
Homo sapiens	ENSG00000113575	1 retrocopy	retro_hsap_369,
Nomascus leucogenys	ENSNLEG00000026729	1 retrocopy	retro_nleu_2441,
Otolemur garnettii	ENSOGAG00000002488	1 retrocopy	retro_ogar_3188,
Otolemur garnettii	ENSOGAG00000009695	2 retrocopies	retro_ogar_3414, retro_ogar_921 ,
Rattus norvegicus	ENSRNOG00000005389	5 retrocopies	retro_rnor_1263, retro_rnor_1264, retro_rnor_1265, retro_rnor_1266, retro_rnor_817,
Sarcophilus harrisii	ENSSHAG00000016632	3 retrocopies	retro_shar_313, retro_shar_428, retro_shar_471,
Ictidomys tridecemlineatus	ENSSTOG00000010560	1 retrocopy	retro_itri_258,