RetrogeneDB ID: retro_ogar_3414

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873823.1:290839..291531(-)
• 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_3414
TGGGGCTAGTGGGTAGACCAGAGTAAACAGCTTAACAGAAACCAACTGCGAATGCTGTGGGAAAAGGCTAAAGAAATTTT
AACCAAAGAATCAACATGCAAGAGGTTTGCTGTGCTCTTCAGTCTGTGGAGATGTGCATGGTCAATTTCATGTTCTTACC
AAACTCTTTAGAATTGGTGGGAAATGACCAGATACAAACTATTTATTCGTGGGTACTATGGAGACAGAGGTTATTATTCA
GTGGAGACTGTGACTCTTCTTGTAGTGTTGAAGGTGCATTATTCAGAATGCTTTACAATATTGAGAGGAAATCATGACAC
CCAACAAATTACCCAAGTAATGGCTTTTATGATGAATGTCTACAAAGGTACGGGATAGCCGATGTTTGGAAATATTTTAC
AGATCTATTTGATTATCTTCTACTTACAGCTTAGGTAGATGGATAGATACCCTGCCTCCACGGTGGCCTCTTTCCATCCC
TAGGCACACTGGATCAGGTAAGAACCTTGGATCACTTACAAGAAGTTCCACATGAAGGCCCAACATGTGATCTGTTATGG
TCAGATCCAAATGATCGCAGTGGGTGAGATATTTCACCACTTGGTGCTGGCTACACATTTGGACAAGACATTTACGAAAC
GTTTATCCATGCCAATGGCCTCACAGCTTGTAATGGAAGGATGCAATTGGTG

Alignment

ORF - retro_ogar_3414 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.19 %
• Parental protein coverage: 75.08 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  WIEQLNECKQLSESQVKSLCEKAKEILTKES-NVQEVRCPV-TVCGDVHGQFHDLMELFRIGGKSPDTNY
          W.......KQL...Q...L.EKAKEILTKES.N.QEV.C....VCGDVHGQFH.L..LFRIGGK.PDTNY
Retrocopy WG*WVDQSKQLNRNQLRMLWEKAKEILTKES<NMQEVCCAL<SVCGDVHGQFHVLTKLFRIGGK*PDTNY

Parental  LFMGD-YVDRGYYSVETVTLLVALKVRYRERITILRGNHESRQITQVY-GFYDECLRKYGNANVWKYFTD
          LF.G..Y.DRGYYSVETVTLLV.LKV.Y.E..TILRGNH...QITQV..GFYDECL..YG.A.VWKYFTD
Retrocopy LFVGT<YGDRGYYSVETVTLLVVLKVHYSECFTILRGNHDTQQITQVM<GFYDECLQRYGIADVWKYFTD

Parental  LFDYLPLTALVDGQIFCLHGGLSPSIDTLDHIRALDRLQEVPHEGPMCDLLWSDPDDRGGWGISPRGAGY
          LFDYL.LTA.VDG.I.CLHGGL.PS..TLD..R.LD.LQEVPHEGP.CDLLWSDP.DR.G..ISP.GAGY
Retrocopy LFDYLLLTA*VDG*IPCLHGGLFPSLGTLDQVRTLDHLQEVPHEGPTCDLLWSDPNDRSG*DISPLGAGY

Parental  TFGQDISETFNHANGLTLVSRAHQLV
          TFGQDI.ETF.HANGLT......QLV
Retrocopy TFGQDIYETFIHANGLTACNGRMQLV

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_3414 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,