RetrogeneDB ID: retro_ogar_71

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873705.1:2753379..2754528(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000006882
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: PABPC4
• Ensembl ID: ENSOGAG00000004067
• Aliases: None
• Description: poly(A) binding protein, cytoplasmic 4 (inducible form) [Source:HGNC Symbol;Acc:8557]

Sequence

>retro_ogar_71
ATGGGGAGCGGGGAGCCTAAGCCTGCTGGCAAGAAAAAGAAGTATCTCAAGGCCGCCCTGTACGTGGGTGACTTGGACCC
AGATGTCACTGAGGACATGCTCTATAAGAAATTCAGGCCTGCCGGTCCTCTGCGATTCACCAGAATCTGCCGTGACCCGG
TGACCCACAGCCCTCTGGGCTATGGCTATGTTAACTTTCGTTTCCCTGCAGATGCTGAATGGGCCCTGAACACCATGAAT
TTTGATTTGCTTAATGGCAAACCATTCCGCCTCATGTGGTCTCAGCCAGATGACCGCTTAAGAAAGTCTGGAGTTGGAAA
TATATTCATCAAAAACCTGGACAAATCCATAGACAACAGGGCCCTGTTTTACTTATTTTCTGCTTTTGGAAACATTCTTT
CTTGCAAAGTAGTATGCGATGACAATGGTTCTAAGGGTTATGCCTACGTGCACTTCGACAGCCTGGCCGCTGCCAATAGG
GCCATCTGGCACATGAATGGAGTGCGGCTCAACAACCGCCAGGTATATGTTGGCCGATTCAAATTCCCGGAAGAGCGGGC
AGCAGAGGTCAGAACTAGAGATCGAGCAACTTTCACTAATGTTTTTGTTAAAAACTTGGGAGATGACATGGATGACGAAA
AACTAAAGGAACTTTTCAGTGAATATGGGCCAACTGAGAGTGTTAAGGTAATCAGAGATGCCAGTGGGAAATCGAAGGGC
TTTGGATTTGTGAGATATGAGACACATGAGGCTGCCCAAAAGGCTGTGCTAGACCTGCATGGAAAGTCCATCGATGGCAA
GATTCTATATGTAGGGCGAGCACAGAAGAAAATCGAACGCTTGGCTGAGTTGAGGCGGAGATTTGAACGGCTGAGATTAA
AAGACAAAAGTCGGCCTCCAGGGGTGCCTATCTATATTAAGAACCTGGATGAGACCATAGATGATGAAAAACTTAAGGAG
GAATTTTCTCCATTTGGATCAATTAGCCGAGCCAAAGTGATGATGGAAGTGGGGCAAGGCAAAGGGTTTGGTGTTGTCTG
TTTTTCCTCTTTTGAAGAGGCTGCCAAAGCAGTGGATGAGATGAATGGTCGCACAGTAGGTTCCAAGCCCCTGCATGTCA
CCCTGGGCCAGGCCCGGCGCAGGTGGTGA

Alignment

ORF - retro_ogar_71 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.58 %
• Parental protein coverage: 56.26 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YPMASLYVGDLHSDVTEAMLYEKFSPAGPVLSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVI
          Y..A.LYVGDL..DVTE.MLY.KF.PAGP....R.CRD..T...LGY.YVNF..PADAE.AL.TMNFD..
Retrocopy YLKAALYVGDLDPDVTEDMLYKKFRPAGPLRFTRICRDPVTHSPLGYGYVNFRFPADAEWALNTMNFDLL

Parental  KGKPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYAFVHFET
          .GKP.R.MWSQ.D..LRKSGVGN.FIKNLDKSIDN.AL...FSAFGNILSCKVVCD.NGSKGYA.VHF..
Retrocopy NGKPFRLMWSQPDDRLRKSGVGNIFIKNLDKSIDNRALFYLFSAFGNILSCKVVCDDNGSKGYAYVHFDS

Parental  QEAADKAIEKMNGMLLNDRKVFVGRFKSRKEREAELGAKAKE-FTNVYIKNFGEEVDDESLKELFSQFGK
          ..AA..AI..MNG..LN.R.V.VGRFK...ER.AE........FTNV..KN.G...DDE.LKELFS..G.
Retrocopy LAAANRAIWHMNGVRLNNRQVYVGRFKFPEERAAEVRTRDRATFTNVFVKNLGDDMDDEKLKELFSEYGP

Parental  TLSVKVMRDPSGKSKGFGFVSYEKHEDANKAVEEMNGKEISGKVIFVGRAQKKVERQAELKRKFEQLKQE
          T.SVKV.RD.SGKSKGFGFV.YE.HE.A.KAV....GK.I.GK...VGRAQKK.ER.AEL.R.FE.L...
Retrocopy TESVKVIRDASGKSKGFGFVRYETHEAAQKAVLDLHGKSIDGKILYVGRAQKKIERLAELRRRFERLRLK

Parental  RISRYQGVNLYIKNLDDTIDDEKLRKEFSPFGSITSAKVMLEDGRSKGFGFVCFSSPEEATKAVTEMNGR
          ..SR..GV..YIKNLD.TIDDEKL..EFSPFGSI..AKVM.E.G..KGFG.VCFSS.EEA.KAV.EMNGR
Retrocopy DKSRPPGVPIYIKNLDETIDDEKLKEEFSPFGSISRAKVMMEVGQGKGFGVVCFSSFEEAAKAVDEMNGR

Parental  IVGSKPLYVALAQRK
          .VGSKPL.V.L.Q..
Retrocopy TVGSKPLHVTLGQAR

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_71 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 20 parental genes, and 42 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011535	2 retrocopies	retro_amel_107, retro_amel_676,
Callithrix jacchus	ENSCJAG00000002512	3 retrocopies	retro_cjac_214, retro_cjac_2722, retro_cjac_284,
Cavia porcellus	ENSCPOG00000009552	2 retrocopies	retro_cpor_1330, retro_cpor_77,
Felis catus	ENSFCAG00000015254	2 retrocopies	retro_fcat_116, retro_fcat_545,
Homo sapiens	ENSG00000090621	2 retrocopies	retro_hsap_109, retro_hsap_74,
Gorilla gorilla	ENSGGOG00000004002	3 retrocopies	retro_ggor_2127, retro_ggor_87, retro_ggor_916,
Microcebus murinus	ENSMICG00000016633	1 retrocopy	retro_mmur_675,
Macaca mulatta	ENSMMUG00000007497	1 retrocopy	retro_mmul_178,
Monodelphis domestica	ENSMODG00000017657	2 retrocopies	retro_mdom_1090, retro_mdom_1805,
Mustela putorius furo	ENSMPUG00000014414	2 retrocopies	retro_mputfur_152, retro_mputfur_546,
Mus musculus	ENSMUSG00000011257	7 retrocopies	retro_mmus_2006, retro_mmus_2326, retro_mmus_2327, retro_mmus_798, retro_mmus_801, retro_mmus_803, retro_mmus_805,
Nomascus leucogenys	ENSNLEG00000011928	2 retrocopies	retro_nleu_1517, retro_nleu_62,
Oryctolagus cuniculus	ENSOCUG00000000562	2 retrocopies	retro_ocun_153, retro_ocun_792,
Otolemur garnettii	ENSOGAG00000004067	1 retrocopy	retro_ogar_71 ,
Otolemur garnettii	ENSOGAG00000016228	1 retrocopy	retro_ogar_2755,
Ochotona princeps	ENSOPRG00000011984	1 retrocopy	retro_opri_1133,
Pongo abelii	ENSPPYG00000001506	2 retrocopies	retro_pabe_190, retro_pabe_2563,
Pan troglodytes	ENSPTRG00000000573	3 retrocopies	retro_ptro_101, retro_ptro_2093, retro_ptro_8,
Rattus norvegicus	ENSRNOG00000015642	2 retrocopies	retro_rnor_175, retro_rnor_92,
Sarcophilus harrisii	ENSSHAG00000018139	1 retrocopy	retro_shar_823,