RetrogeneDB ID: retro_ogar_987

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873532.1:22380023..22381182(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PAPOLA
• Ensembl ID: ENSOGAG00000004611
• Aliases: None
• Description: poly(A) polymerase alpha [Source:HGNC Symbol;Acc:14981]

Sequence

>retro_ogar_987
CAGACTTTGCTGAGTAAGGTAGAGTAGTCCAAACTTTTTGAAGCTCCAATCTTCTTTCAAAAGTACAAGGATTATATTGT
ACTTCTAGCAGGTGCACCGACAGAAAAACAACGTTTAGAGTGGGTGGGCTTGGTGGAATCAAAAATTTGAATCCTAATTG
GAAGCTTGGAAAAGAATGAATTTATTACATTGGCTCATGTCAATCCCCAGGCATTTCCGGCACCCAAAGAAAATCCTGAC
AAGAAAGAATTTTGCACAGTGTGGGTGATTTGGGTTAGTGTTTAAAAAAACAGAAAACTACAAAAACCTGAGTGTCAATC
TCCCCATGACATTCAGGCTTTCACAGACACAGTGTATAGGCAAAGCAAGAAACAGCAAGATGTTTGAGGTGGATATGAGA
ATTGCTGCAACGCATGTAAAAAGAAAGCAACTCCATCAACTACTACCTAAGCATGTGCTTTAGAAAAAGAAAAAGCATTC
AGCAGAAGGTGTCAGATTCACAGCTCTGAATGGCAGTAGGCTTGACTTGTCTGCGGACAGTGATAGCAGCGTGTCTGTGC
CTTCATCTACGAGTGCTATGAGGACCAGTCCCGGCAGCTCTCGGGGCAGAAACAGTCCTGCTCCAGCTGCAACAGCAGCA
TCTGTGACCAACACACAGGCTACCGAAGTTTCTGTGCCACAAGTAAATTCCAGTGAAAGCTCAGGGGTTACATCGAGGGA
AAGCGTTCCTCAAACTGCCACACAACCAGCCATTTCTCTACCACCAAAGCCTGTGGTCTCCAGAGTTGTTTGTTCAATGT
GTCTGGTAAATCCGCCACCTAGACCTTCAGAAAATGCAGCAACAAAAGTATCTAATCCTGTAGAGGGAGTCACGAGGACA
TCGCCACCTCATAAAGAAGCTAGTTCCAAGAAAACTAAAACAGAAGAGGACGAAACAAGTGAAGATGCTAACTGTCTTGC
TTTGAGTGGATGTGAAAAAACAGAAACAAAGGAACAACTTGATCCAGAGACAAGTACAGCTCATTCAGAAGCCATCCAGA
CAGCCGCTTCTCTGTTGGTGTCTCAGAAAACACCCAGTATGGACCTTTCTGATATCCCTGCTGTCCCCGCAAATCCTATT
CCTGTTATCAGGAATTCAATAAAACTGAGATTGAATCAG

Alignment

ORF - retro_ogar_987 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.46 %
• Parental protein coverage: 52.84 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EILLSKAEWSKLFEAPNFFQKYKHYIVLLASAPTEKQRLEWVGLVESKIRILVGSLEKNEFITLAHVNPQ
          ..LLSK.E.SKLFEAP.FFQKYK.YIVLLA.APTEKQRLEWVGLVESKI.IL.GSLEKNEFITLAHVNPQ
Retrocopy QTLLSKVE*SKLFEAPIFFQKYKDYIVLLAGAPTEKQRLEWVGLVESKI*ILIGSLEKNEFITLAHVNPQ

Parental  SFPAPKENPDKEEFRTMWVI-GLVFKKTENSENLSVDLT-YDIQSFTDTVYRQ-AINSKMFEVDMKIAAM
          .FPAPKENPDK.EF.T.WVI.GLVF........LSV.L...DIQ.FTDTVYRQ.A.NSKMFEVDM.IAA.
Retrocopy AFPAPKENPDKKEFCTVWVI>GLVFXXXXXXXXLSVNLP<HDIQAFTDTVYRQ>ARNSKMFEVDMRIAAT

Parental  HVKRKQLHQLLPNHVLQKKKKHSTEGVRLTALNDSSLDLSMDSDNSMSVPSPTSAMKTSPLNSSGSSQGR
          HVKRKQLHQLLP.HVL.KKKKHS.EGVR.TALN.S.LDLS.DSD.S.SVPS.TSAM.TSP....GSS.GR
Retrocopy HVKRKQLHQLLPKHVL*KKKKHSAEGVRFTALNGSRLDLSADSDSSVSVPSSTSAMRTSP----GSSRGR

Parental  NSPAPAVTAASVTNTQATEVSVPQVNSSESSGGTSSESIPQTATQPAISPPPKPTVSRVVGSTRLVNPPP
          NSPAPA.TAASVTNTQATEVSVPQVNSSESSG.TS.ES.PQTATQPAIS.PPKP.VSRVV.S..LVNPPP
Retrocopy NSPAPAATAASVTNTQATEVSVPQVNSSESSGVTSRESVPQTATQPAISLPPKPVVSRVVCSMCLVNPPP

Parental  PRPSGNAATKVPNPIVGVKRTSSPHKEESPKKTKTEEDETSEDANCLALSGHDKTETKEQLDTETSTTQS
          .RPS.NAATKV.NP..GV.RTS.PHKE.S.KKTKTEEDETSEDANCLALSG..KTETKEQLD.ETST..S
Retrocopy -RPSENAATKVSNPVEGVTRTSPPHKEASSKKTKTEEDETSEDANCLALSGCEKTETKEQLDPETSTAHS

Parental  ETIQTAASLLASQKTSSTDLSDIPALPANPIPVIKNSIKLRLNR
          E.IQTAASLL.SQKT.S.DLSDIPA.PANPIPVI.NSIKLRLN.
Retrocopy EAIQTAASLLVSQKTPSMDLSDIPAVPANPIPVIRNSIKLRLNQ

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_987 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 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014142	1 retrocopy	retro_amel_517,
Bos taurus	ENSBTAG00000004054	1 retrocopy	retro_btau_1078,
Canis familiaris	ENSCAFG00000017783	1 retrocopy	retro_cfam_1783,
Callithrix jacchus	ENSCJAG00000006512	2 retrocopies	retro_cjac_1763, retro_cjac_543,
Homo sapiens	ENSG00000090060	1 retrocopy	retro_hsap_30,
Gorilla gorilla	ENSGGOG00000006287	1 retrocopy	retro_ggor_202,
Loxodonta africana	ENSLAFG00000000946	1 retrocopy	retro_lafr_895,
Myotis lucifugus	ENSMLUG00000010922	1 retrocopy	retro_mluc_1396,
Macaca mulatta	ENSMMUG00000018610	1 retrocopy	retro_mmul_1675,
Monodelphis domestica	ENSMODG00000012887	2 retrocopies	retro_mdom_1714, retro_mdom_1916,
Mustela putorius furo	ENSMPUG00000003054	1 retrocopy	retro_mputfur_1375,
Mus musculus	ENSMUSG00000021111	1 retrocopy	retro_mmus_37,
Nomascus leucogenys	ENSNLEG00000000625	1 retrocopy	retro_nleu_2771,
Otolemur garnettii	ENSOGAG00000004611	1 retrocopy	retro_ogar_987 ,
Procavia capensis	ENSPCAG00000004199	1 retrocopy	retro_pcap_91,
Pongo abelii	ENSPPYG00000006128	1 retrocopy	retro_pabe_3113,
Pan troglodytes	ENSPTRG00000006704	1 retrocopy	retro_ptro_2595,
Pteropus vampyrus	ENSPVAG00000013925	1 retrocopy	retro_pvam_360,
Rattus norvegicus	ENSRNOG00000004827	1 retrocopy	retro_rnor_863,
Vicugna pacos	ENSVPAG00000006464	1 retrocopy	retro_vpac_378,