RetrogeneDB ID: retro_ogar_1909

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873573.1:8054348..8054739(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000031328
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: UBXN2A
• Ensembl ID: ENSOGAG00000000025
• Aliases: None
• Description: UBX domain protein 2A [Source:HGNC Symbol;Acc:27265]

Sequence

>retro_ogar_1909
GAAAGTATAAAAGAATGGGCCTGTGAAACAGGATCTGACAATCAACTTCTTGGTGATAATCAACAAACAATTGTAAATAT
TTTGTTGACAGCCTTTTTGAGGAAGCTCAGAAAGTTGGTACCAAATGCTTGTCCCCCACAGAACAGAAGAAACAGGCAGG
TTTAAGTATAAAGTTATGGAAAATGTATTCGCAGTCAACGATTCCAGAAGCTCTTCTGATGGTACAACTCAGCAGTTTCT
GAACGCTATCCAAAGGGGGAATTACCTTCAGAATTACAGGGAATTTTTGATAAAGAGGAGGTAGATGCTAAAGTTGAAGA
TAACAAAATGAAGTACATGCATCTACGAAACTGTATTTTAGCCCTTTTCAGGACAAGGCCACAGACTAGGA

Alignment

ORF - retro_ogar_1909 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.58 %
• Parental protein coverage: 51.54 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  ESIKEEWDCETGSDHQPLSDNQQT-NCEYFVDSLFEEAQKVGTKCLSPTGQKKQVDLSIKLWK-NGFTVN
          ESIKE.W.CETGSD.Q.L.DNQQT.NC.YFVDSLFEEAQKVGTKCLSPT.QKKQ..LSIKLWK.N.F.VN
Retrocopy ESIKE-WACETGSDNQLLGDNQQT<NCKYFVDSLFEEAQKVGTKCLSPTEQKKQAGLSIKLWK<NVFAVN

Parental  DDFRSYSDGASQQFLNAIK-KGELPSELQGIFDKEEVDAKVEDKK-NEICASTK-PVFQPFSGQGHRLG
          D..RS.SDG..QQFLNAI..KGELPSELQGIFDKEEVDAKVED.K.NE..ASTK..VF.PFSGQGHRLG
Retrocopy DS-RSSSDGTTQQFLNAIQ<KGELPSELQGIFDKEEVDAKVEDNK<NEVHASTK<TVF*PFSGQGHRLG

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_1909 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 19 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001640	5 retrocopies	retro_chof_1096, retro_chof_1171, retro_chof_2641, retro_chof_961, retro_chof_964,
Callithrix jacchus	ENSCJAG00000007665	1 retrocopy	retro_cjac_2085,
Equus caballus	ENSECAG00000020144	1 retrocopy	retro_ecab_569,
Echinops telfairi	ENSETEG00000002623	1 retrocopy	retro_etel_1116,
Homo sapiens	ENSG00000173960	1 retrocopy	retro_hsap_2025,
Gorilla gorilla	ENSGGOG00000002445	1 retrocopy	retro_ggor_1463,
Myotis lucifugus	ENSMLUG00000015640	1 retrocopy	retro_mluc_1195,
Macaca mulatta	ENSMMUG00000006487	1 retrocopy	retro_mmul_2068,
Mus musculus	ENSMUSG00000020634	1 retrocopy	retro_mmus_1007,
Nomascus leucogenys	ENSNLEG00000000751	1 retrocopy	retro_nleu_2612,
Oryctolagus cuniculus	ENSOCUG00000008783	1 retrocopy	retro_ocun_207,
Otolemur garnettii	ENSOGAG00000000025	1 retrocopy	retro_ogar_1909 ,
Otolemur garnettii	ENSOGAG00000002630	2 retrocopies	retro_ogar_1144, retro_ogar_1609,
Procavia capensis	ENSPCAG00000011502	4 retrocopies	retro_pcap_169, retro_pcap_255, retro_pcap_271, retro_pcap_323,
Pan troglodytes	ENSPTRG00000011705	1 retrocopy	retro_ptro_1347,
Rattus norvegicus	ENSRNOG00000004950	2 retrocopies	retro_rnor_1746, retro_rnor_2966,
Sorex araneus	ENSSARG00000010108	1 retrocopy	retro_sara_272,
Sus scrofa	ENSSSCG00000026283	1 retrocopy	retro_sscr_537,
Tupaia belangeri	ENSTBEG00000012158	1 retrocopy	retro_tbel_3887,