RetrogeneDB ID: retro_ogar_3117

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873721.1:433563..434116(+)
• Located in intron of: ENSOGAG00000009684

Retrocopy information

• Ensembl ID: ENSOGAG00000009692
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: HMGB2
• Ensembl ID: ENSOGAG00000017149
• Aliases: None
• Description: high mobility group box 2 [Source:HGNC Symbol;Acc:5000]

Sequence

>retro_ogar_3117
ATGGGCAAAGGAGACCCCAACAAGCCGTGGGGCAAGATGTCATCGTACACCTTCTTCATGCAGACGTGCCACGAAGAGCA
CAAGAAGAAGCACCGGACTCCTCCGTCAACTTCGCCGAGTTCTCAAAGAAGTGCTCAGAGTGGTGGAAGACCATGTCTGC
AAAGGAAAAGTCCAAGTTTGAAGATATGGCCAAAAATGACAAAGCTCACTATGACAGGGAGATGAAGAACTACGTTCCTC
CCAAAGGCGGCAAGAAAGGAAAGAAAAAGATCCCAATGCTCCTAAAAGGCCCCCGTCTGCCTTTTTCCTGTTTTGTTCAG
AACGCCCAAAGATCAAAAGTGAATACCCCGGCCTATCCATTGCGGATACTGCAAAAAAATTGAGTGAAATGTGGTCTGAG
CAGTCAGCCAAAGATAAACAGCCATACGAACAGAAAGCAGCAAAGCTAAAGGAAAAATATGGAAAGGATATTGCTGCATA
CCATGCCAAGGACAAAAGTGAAGCAGGGAAGAAAGGCCCTGGCAGGCCAACAGGTTCAAAGAAGAATGAACCT

Alignment

ORF - retro_ogar_3117 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.01 %
• Parental protein coverage: 89.47 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MGKGDPNKPRGKMSSYAFFVQTCREEHKKKH-PDSSVNFAEFSKKCSERWKTMSAKEKSKFEDMAKNDKA
          MGKGDPNKP.GKMSSY.FF.QTC.EEHKKKH.PDSSVNFAEFSKKCSE.WKTMSAKEKSKFEDMAKNDKA
Retrocopy MGKGDPNKPWGKMSSYTFFMQTCHEEHKKKH<PDSSVNFAEFSKKCSEWWKTMSAKEKSKFEDMAKNDKA

Parental  RYDREMKNYVPPKGDKKGKKK-DPNAPKRPPSAFFLFCSEHRPKIKSEHPGLSIGDTAKKLGEMWSEQSA
          .YDREMKNYVPPKG.KKGKKK.DPNAPKRPPSAFFLFCSE.RPKIKSE.PGLSI.DTAKKL.EMWSEQSA
Retrocopy HYDREMKNYVPPKGGKKGKKK<DPNAPKRPPSAFFLFCSE-RPKIKSEYPGLSIADTAKKLSEMWSEQSA

Parental  KDKQPYEQKAAKLKEKYEKDIAAYRAKGKSEAGKKGPGRPTGSKKKNEP
          KDKQPYEQKAAKLKEKY.KDIAAY.AK.KSEAGKKGPGRPTGS.KKNEP
Retrocopy KDKQPYEQKAAKLKEKYGKDIAAYHAKDKSEAGKKGPGRPTGS-KKNEP

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_3117 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 18 parental genes, and 158 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000015101	1 retrocopy	retro_btau_58,
Dasypus novemcinctus	ENSDNOG00000019440	4 retrocopies	retro_dnov_1142, retro_dnov_1457, retro_dnov_454, retro_dnov_532,
Echinops telfairi	ENSETEG00000010379	3 retrocopies	retro_etel_1474, retro_etel_1841, retro_etel_2023,
Echinops telfairi	ENSETEG00000016379	1 retrocopy	retro_etel_414,
Felis catus	ENSFCAG00000004218	2 retrocopies	retro_fcat_279, retro_fcat_52,
Homo sapiens	ENSG00000164104	1 retrocopy	retro_hsap_3663,
Gorilla gorilla	ENSGGOG00000015882	1 retrocopy	retro_ggor_2474,
Macropus eugenii	ENSMEUG00000002256	3 retrocopies	retro_meug_1920, retro_meug_1989, retro_meug_550,
Monodelphis domestica	ENSMODG00000003527	3 retrocopies	retro_mdom_1160, retro_mdom_1919, retro_mdom_69,
Nomascus leucogenys	ENSNLEG00000006662	3 retrocopies	retro_nleu_113, retro_nleu_517, retro_nleu_550,
Otolemur garnettii	ENSOGAG00000001773	19 retrocopies	retro_ogar_1318, retro_ogar_1647, retro_ogar_1728, retro_ogar_187, retro_ogar_1930, retro_ogar_204, retro_ogar_2076, retro_ogar_2530, retro_ogar_2591, retro_ogar_2678, retro_ogar_2743, retro_ogar_2983, retro_ogar_3127, retro_ogar_3371, retro_ogar_343, retro_ogar_3433, retro_ogar_3479, retro_ogar_3513, retro_ogar_65,
Otolemur garnettii	ENSOGAG00000003205	104 retrocopies	retro_ogar_1008, retro_ogar_1043, retro_ogar_106, retro_ogar_1133, retro_ogar_123, retro_ogar_1232, retro_ogar_1296, retro_ogar_1299, retro_ogar_1330, retro_ogar_1386, retro_ogar_1398, retro_ogar_1399, retro_ogar_1421, retro_ogar_1423, retro_ogar_1424, retro_ogar_1431, retro_ogar_1461, retro_ogar_1560, retro_ogar_1571, retro_ogar_1585, retro_ogar_1597, retro_ogar_1600, retro_ogar_1607, retro_ogar_1628, retro_ogar_163, retro_ogar_1664, retro_ogar_1698, retro_ogar_17, retro_ogar_172, retro_ogar_1738, retro_ogar_1758, retro_ogar_1781, retro_ogar_1843, retro_ogar_1844, retro_ogar_1861, retro_ogar_1867, retro_ogar_1878, retro_ogar_1894, retro_ogar_1896, retro_ogar_198, retro_ogar_1991, retro_ogar_2136, retro_ogar_2165, retro_ogar_219, retro_ogar_2282, retro_ogar_2318, retro_ogar_2319, retro_ogar_2352, retro_ogar_2385, retro_ogar_2403, retro_ogar_2429, retro_ogar_2436, retro_ogar_2458, retro_ogar_250, retro_ogar_2559, retro_ogar_2598, retro_ogar_2615, retro_ogar_2618, retro_ogar_2730, retro_ogar_2777, retro_ogar_2778, retro_ogar_2814, retro_ogar_2824, retro_ogar_2836, retro_ogar_284, retro_ogar_2845, retro_ogar_2891, retro_ogar_2894, retro_ogar_2906, retro_ogar_2961, retro_ogar_3008, retro_ogar_3018, retro_ogar_3028, retro_ogar_304, retro_ogar_311, retro_ogar_3136, retro_ogar_317, retro_ogar_320, retro_ogar_3208, retro_ogar_3230, retro_ogar_3325, retro_ogar_3330, retro_ogar_3355, retro_ogar_3374, retro_ogar_3500, retro_ogar_422, retro_ogar_435, retro_ogar_511, retro_ogar_542, retro_ogar_547, retro_ogar_634, retro_ogar_663, retro_ogar_698, retro_ogar_716, retro_ogar_772, retro_ogar_778, retro_ogar_8, retro_ogar_835, retro_ogar_890, retro_ogar_904, retro_ogar_912, retro_ogar_918, retro_ogar_92, retro_ogar_933,
Otolemur garnettii	ENSOGAG00000017149	3 retrocopies	retro_ogar_3117 , retro_ogar_3323, retro_ogar_3336,
Otolemur garnettii	ENSOGAG00000032147	1 retrocopy	retro_ogar_1712,
Pongo abelii	ENSPPYG00000015204	3 retrocopies	retro_pabe_297, retro_pabe_3005, retro_pabe_3380,
Pan troglodytes	ENSPTRG00000016597	3 retrocopies	retro_ptro_19, retro_ptro_2484, retro_ptro_2789,
Rattus norvegicus	ENSRNOG00000013167	2 retrocopies	retro_rnor_173, retro_rnor_54,
Tursiops truncatus	ENSTTRG00000015650	1 retrocopy	retro_ttru_1640,