RetrogeneDB ID: retro_hsap_382

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 1:50864611..50865015(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000229316
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: HMGB1
• Ensembl ID: ENSG00000189403
• Aliases: HMGB1, HMG1, HMG3, SBP-1
• Description: high mobility group box 1 [Source:HGNC Symbol;Acc:4983]

Sequence

>retro_hsap_382
TGCTCAGTGAGGTGGAAGACCATATCTGCTAAACAGAAAGGAAAATCTGAAGATATGGCAAAGGCAAACAAGGCCCGTTA
TGAAAGAGAAATGAAAATCTATATCCCCCCTAAAGGGGAGACAAAAAAGAAGTTCAAGTCCAATGCACCCAAGTGGCCTC
CTGCAGCCTGTTTCGTGTTCTGTTCTGAGTGTTGCCCCAAATCAAAGAACATCTTGGCCTGTCCATTGGTGATGTTGCAA
AGAAACTGGGAGACATGTGGAATAGCACTGCTGCAGATGACAAGCAGCCTTATGAAAAGACAGCTGTGAAGCTGAAGGAA
AAATACAAAAAGGATCTTGCTGCATATTGAACTAAAGGAAAGCCTGATGCAGCAAAAAAGGGAGTCATCAAGGCTGAAAA
AAGC

Alignment

ORF - retro_hsap_382 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.16 %
• Parental protein coverage: 63.72 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  CSERWKTMSAKEKGKFEDMAKADKARYEREMKTYIPPKGETKKKFKDPNAPKRPPSAFFLFCSEYRPK-I
          CS.RWKT.SAK.KGK.EDMAKA.KARYEREMK.YIPPKGETKKKFK..NAPK.PP.A.F.FCSE..PK.I
Retrocopy CSVRWKTISAKQKGKSEDMAKANKARYEREMKIYIPPKGETKKKFKS-NAPKWPPAACFVFCSECCPK<I

Parental  KGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYRAKGKPDAAKKGVVKAEKS
          K.EH.GLSIGDVAKKLG.MWN.TAADDKQPYEK.A.KLKEKY.KD.AAY..KGKPDAAKKGV.KAEKS
Retrocopy K-EHLGLSIGDVAKKLGDMWNSTAADDKQPYEKTAVKLKEKYKKDLAAY*TKGKPDAAKKGVIKAEKS

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
bodymap2_adipose	0.00 RPM	214.74 RPM
bodymap2_adrenal	0.00 RPM	211.82 RPM
bodymap2_brain	0.00 RPM	210.82 RPM
bodymap2_breast	0.00 RPM	194.48 RPM
bodymap2_colon	0.00 RPM	255.02 RPM
bodymap2_heart	0.00 RPM	90.20 RPM
bodymap2_kidney	0.00 RPM	153.20 RPM
bodymap2_liver	0.00 RPM	79.47 RPM
bodymap2_lung	0.00 RPM	233.53 RPM
bodymap2_lymph_node	0.00 RPM	212.78 RPM
bodymap2_ovary	0.00 RPM	222.71 RPM
bodymap2_prostate	0.00 RPM	222.60 RPM
bodymap2_skeletal_muscle	0.00 RPM	91.67 RPM
bodymap2_testis	0.00 RPM	195.45 RPM
bodymap2_thyroid	0.00 RPM	267.05 RPM
bodymap2_white_blood_cells	0.00 RPM	221.65 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_382 was not detected

EST

No EST(s) were mapped for retro_hsap_382 retrocopy.

TSS

No TSS is located nearby retro_hsap_382 retrocopy 5' end.

Lab

retro_hsap_382 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_382 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_388

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Parental genes homology:

Parental genes homology involve 33 parental genes, and 563 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008880	7 retrocopies	retro_amel_1130, retro_amel_1216, retro_amel_1299, retro_amel_1389, retro_amel_1545, retro_amel_1629, retro_amel_1767,
Bos taurus	ENSBTAG00000018103	2 retrocopies	retro_btau_1551, retro_btau_224,
Canis familiaris	ENSCAFG00000006597	13 retrocopies	retro_cfam_1088, retro_cfam_1102, retro_cfam_1387, retro_cfam_1628, retro_cfam_1765, retro_cfam_1831, retro_cfam_1980, retro_cfam_242, retro_cfam_280, retro_cfam_467, retro_cfam_495, retro_cfam_521, retro_cfam_528,
Callithrix jacchus	ENSCJAG00000021615	11 retrocopies	retro_cjac_1042, retro_cjac_1546, retro_cjac_1819, retro_cjac_1842, retro_cjac_1934, retro_cjac_2269, retro_cjac_2901, retro_cjac_2934, retro_cjac_3090, retro_cjac_718, retro_cjac_895,
Cavia porcellus	ENSCPOG00000003985	1 retrocopy	retro_cpor_69,
Equus caballus	ENSECAG00000008439	2 retrocopies	retro_ecab_101, retro_ecab_64,
Echinops telfairi	ENSETEG00000004048	18 retrocopies	retro_etel_1092, retro_etel_111, retro_etel_1146, retro_etel_1290, retro_etel_1293, retro_etel_146, retro_etel_1481, retro_etel_1587, retro_etel_1892, retro_etel_1943, retro_etel_2015, retro_etel_453, retro_etel_498, retro_etel_508, retro_etel_577, retro_etel_826, retro_etel_827, retro_etel_871,
Felis catus	ENSFCAG00000000200	10 retrocopies	retro_fcat_1046, retro_fcat_1271, retro_fcat_1306, retro_fcat_1330, retro_fcat_1759, retro_fcat_693, retro_fcat_728, retro_fcat_762, retro_fcat_770, retro_fcat_821,
Homo sapiens	ENSG00000029993	8 retrocopies	retro_hsap_1461, retro_hsap_1873, retro_hsap_2621, retro_hsap_3064, retro_hsap_3683, retro_hsap_4251, retro_hsap_4904, retro_hsap_627,
Homo sapiens	ENSG00000164104	1 retrocopy	retro_hsap_3663,
Homo sapiens	ENSG00000189403	37 retrocopies	retro_hsap_1230, retro_hsap_1357, retro_hsap_1504, retro_hsap_1589, retro_hsap_1608, retro_hsap_176, retro_hsap_1832, retro_hsap_1954, retro_hsap_2103, retro_hsap_2192, retro_hsap_2219, retro_hsap_2228, retro_hsap_2340, retro_hsap_2490, retro_hsap_2552, retro_hsap_2613, retro_hsap_2660, retro_hsap_2858, retro_hsap_2947, retro_hsap_3317, retro_hsap_3340, retro_hsap_3592, retro_hsap_3615, retro_hsap_3666, retro_hsap_382 , retro_hsap_3942, retro_hsap_4003, retro_hsap_4109, retro_hsap_4309, retro_hsap_4669, retro_hsap_470, retro_hsap_4738, retro_hsap_4832, retro_hsap_525, retro_hsap_554, retro_hsap_758, retro_hsap_933,
Gorilla gorilla	ENSGGOG00000026764	23 retrocopies	retro_ggor_1057, retro_ggor_1212, retro_ggor_1421, retro_ggor_1596, retro_ggor_1637, retro_ggor_1662, retro_ggor_1735, retro_ggor_1777, retro_ggor_1856, retro_ggor_1951, retro_ggor_1977, retro_ggor_213, retro_ggor_2422, retro_ggor_2441, retro_ggor_2478, retro_ggor_259, retro_ggor_2897, retro_ggor_3013, retro_ggor_388, retro_ggor_448, retro_ggor_483, retro_ggor_753, retro_ggor_964,
Macropus eugenii	ENSMEUG00000001380	2 retrocopies	retro_meug_1591, retro_meug_825,
Microcebus murinus	ENSMICG00000000573	1 retrocopy	retro_mmur_1529,
Microcebus murinus	ENSMICG00000007144	7 retrocopies	retro_mmur_11, retro_mmur_1452, retro_mmur_154, retro_mmur_182, retro_mmur_40, retro_mmur_428, retro_mmur_664,
Myotis lucifugus	ENSMLUG00000025979	17 retrocopies	retro_mluc_1062, retro_mluc_1103, retro_mluc_1446, retro_mluc_1584, retro_mluc_1591, retro_mluc_1608, retro_mluc_1615, retro_mluc_1773, retro_mluc_1798, retro_mluc_2013, retro_mluc_2201, retro_mluc_2460, retro_mluc_506, retro_mluc_551, retro_mluc_800, retro_mluc_809, retro_mluc_953,
Macaca mulatta	ENSMMUG00000023399	3 retrocopies	retro_mmul_2079, retro_mmul_320, retro_mmul_385,
Monodelphis domestica	ENSMODG00000009238	14 retrocopies	retro_mdom_1088, retro_mdom_1144, retro_mdom_1228, retro_mdom_1689, retro_mdom_1727, retro_mdom_1819, retro_mdom_2007, retro_mdom_2024, retro_mdom_3, retro_mdom_434, retro_mdom_548, retro_mdom_72, retro_mdom_760, retro_mdom_958,
Mus musculus	ENSMUSG00000066551	129 retrocopies	retro_mmus_1025, retro_mmus_1037, retro_mmus_1047, retro_mmus_1065, retro_mmus_1094, retro_mmus_1112, retro_mmus_1113, retro_mmus_1114, retro_mmus_1115, retro_mmus_1128, retro_mmus_1135, retro_mmus_1140, retro_mmus_1178, retro_mmus_1181, retro_mmus_1209, retro_mmus_1284, retro_mmus_1302, retro_mmus_1351, retro_mmus_1407, retro_mmus_1423, retro_mmus_1508, retro_mmus_1553, retro_mmus_1554, retro_mmus_1584, retro_mmus_1672, retro_mmus_1705, retro_mmus_1706, retro_mmus_1712, retro_mmus_1716, retro_mmus_1725, retro_mmus_1775, retro_mmus_1794, retro_mmus_1800, retro_mmus_1822, retro_mmus_1845, retro_mmus_1871, retro_mmus_1989, retro_mmus_2015, retro_mmus_2077, retro_mmus_2080, retro_mmus_2096, retro_mmus_2191, retro_mmus_2194, retro_mmus_2199, retro_mmus_2209, retro_mmus_2224, retro_mmus_2229, retro_mmus_2280, retro_mmus_2300, retro_mmus_2324, retro_mmus_2404, retro_mmus_2407, retro_mmus_2409, retro_mmus_2414, retro_mmus_2420, retro_mmus_2425, retro_mmus_2467, retro_mmus_2469, retro_mmus_2524, retro_mmus_2532, retro_mmus_2627, retro_mmus_2670, retro_mmus_2682, retro_mmus_2702, retro_mmus_2719, retro_mmus_2754, retro_mmus_2789, retro_mmus_2815, retro_mmus_2823, retro_mmus_2866, retro_mmus_2877, retro_mmus_2886, retro_mmus_292, retro_mmus_2923, retro_mmus_2936, retro_mmus_2940, retro_mmus_2954, retro_mmus_2965, retro_mmus_2977, retro_mmus_303, retro_mmus_3046, retro_mmus_3056, retro_mmus_3059, retro_mmus_3067, retro_mmus_3070, retro_mmus_3075, retro_mmus_3102, retro_mmus_3106, retro_mmus_3121, retro_mmus_3169, retro_mmus_3175, retro_mmus_319, retro_mmus_3190, retro_mmus_3199, retro_mmus_3207, retro_mmus_3239, retro_mmus_3289, retro_mmus_3322, retro_mmus_3353, retro_mmus_3375, retro_mmus_3476, retro_mmus_3494, retro_mmus_3533, retro_mmus_359, retro_mmus_3612, retro_mmus_3676, retro_mmus_3692, retro_mmus_3715, retro_mmus_418, retro_mmus_515, retro_mmus_530, retro_mmus_574, retro_mmus_599, retro_mmus_618, retro_mmus_623, retro_mmus_624, retro_mmus_634, retro_mmus_704, retro_mmus_705, retro_mmus_785, retro_mmus_813, retro_mmus_839, retro_mmus_855, retro_mmus_881, retro_mmus_903, retro_mmus_906, retro_mmus_930, retro_mmus_965, retro_mmus_981,
Nomascus leucogenys	ENSNLEG00000000720	33 retrocopies	retro_nleu_1148, retro_nleu_1165, retro_nleu_1241, retro_nleu_1271, retro_nleu_1393, retro_nleu_1461, retro_nleu_1633, retro_nleu_1746, retro_nleu_1932, retro_nleu_2160, retro_nleu_2210, retro_nleu_2377, retro_nleu_2512, retro_nleu_2517, retro_nleu_2637, retro_nleu_2681, retro_nleu_2708, retro_nleu_2752, retro_nleu_278, retro_nleu_2798, retro_nleu_2859, retro_nleu_292, retro_nleu_301, retro_nleu_322, retro_nleu_345, retro_nleu_393, retro_nleu_520, retro_nleu_576, retro_nleu_602, retro_nleu_875, retro_nleu_885, retro_nleu_968, retro_nleu_984,
Oryctolagus cuniculus	ENSOCUG00000021335	16 retrocopies	retro_ocun_1039, retro_ocun_1112, retro_ocun_1368, retro_ocun_1407, retro_ocun_1554, retro_ocun_1658, retro_ocun_1739, retro_ocun_1882, retro_ocun_1937, retro_ocun_285, retro_ocun_36, retro_ocun_471, retro_ocun_616, retro_ocun_633, retro_ocun_737, retro_ocun_825,
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	ENSOGAG00000032147	1 retrocopy	retro_ogar_1712,
Ochotona princeps	ENSOPRG00000003507	8 retrocopies	retro_opri_1030, retro_opri_1150, retro_opri_1209, retro_opri_140, retro_opri_279, retro_opri_42, retro_opri_553, retro_opri_706,
Procavia capensis	ENSPCAG00000002201	2 retrocopies	retro_pcap_256, retro_pcap_432,
Pongo abelii	ENSPPYG00000005546	35 retrocopies	retro_pabe_1023, retro_pabe_1125, retro_pabe_1254, retro_pabe_1334, retro_pabe_1500, retro_pabe_159, retro_pabe_1724, retro_pabe_1831, retro_pabe_1973, retro_pabe_1997, retro_pabe_2070, retro_pabe_2089, retro_pabe_2194, retro_pabe_222, retro_pabe_2313, retro_pabe_2362, retro_pabe_2406, retro_pabe_2444, retro_pabe_264, retro_pabe_2732, retro_pabe_2751, retro_pabe_2752, retro_pabe_2777, retro_pabe_2953, retro_pabe_2966, retro_pabe_3008, retro_pabe_3365, retro_pabe_3523, retro_pabe_3684, retro_pabe_3757, retro_pabe_452, retro_pabe_511, retro_pabe_522, retro_pabe_761, retro_pabe_762,
Pteropus vampyrus	ENSPVAG00000001431	6 retrocopies	retro_pvam_1156, retro_pvam_154, retro_pvam_429, retro_pvam_508, retro_pvam_774, retro_pvam_960,
Rattus norvegicus	ENSRNOG00000029813	1 retrocopy	retro_rnor_421,
Sorex araneus	ENSSARG00000004470	14 retrocopies	retro_sara_131, retro_sara_182, retro_sara_259, retro_sara_293, retro_sara_302, retro_sara_342, retro_sara_378, retro_sara_402, retro_sara_47, retro_sara_564, retro_sara_576, retro_sara_613, retro_sara_655, retro_sara_765,
Sus scrofa	ENSSSCG00000009327	3 retrocopies	retro_sscr_1222, retro_sscr_304, retro_sscr_649,
Ictidomys tridecemlineatus	ENSSTOG00000000443	19 retrocopies	retro_itri_1060, retro_itri_1220, retro_itri_127, retro_itri_1489, retro_itri_1531, retro_itri_1580, retro_itri_1644, retro_itri_1852, retro_itri_233, retro_itri_238, retro_itri_444, retro_itri_518, retro_itri_553, retro_itri_584, retro_itri_712, retro_itri_754, retro_itri_792, retro_itri_825, retro_itri_991,
Tarsius syrichta	ENSTSYG00000006328	7 retrocopies	retro_tsyr_1405, retro_tsyr_1621, retro_tsyr_1744, retro_tsyr_1937, retro_tsyr_1945, retro_tsyr_632, retro_tsyr_76,
Tursiops truncatus	ENSTTRG00000010327	8 retrocopies	retro_ttru_102, retro_ttru_1143, retro_ttru_119, retro_ttru_1382, retro_ttru_256, retro_ttru_723, retro_ttru_757, retro_ttru_956,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.00 RPM
CEU_NA11843	0.00 RPM
CEU_NA11930	0.00 RPM
CEU_NA12004	0.00 RPM
CEU_NA12400	0.00 RPM
CEU_NA12751	0.00 RPM
CEU_NA12760	0.00 RPM
CEU_NA12827	0.00 RPM
CEU_NA12872	0.00 RPM
CEU_NA12873	0.00 RPM
FIN_HG00183	0.00 RPM
FIN_HG00277	0.00 RPM
FIN_HG00315	0.00 RPM
FIN_HG00321	0.00 RPM
FIN_HG00328	0.00 RPM
FIN_HG00338	0.00 RPM
FIN_HG00349	0.00 RPM
FIN_HG00375	0.00 RPM
FIN_HG00377	0.03 RPM
FIN_HG00378	0.00 RPM
GBR_HG00099	0.00 RPM
GBR_HG00111	0.00 RPM
GBR_HG00114	0.00 RPM
GBR_HG00119	0.00 RPM
GBR_HG00131	0.00 RPM
GBR_HG00133	0.00 RPM
GBR_HG00134	0.00 RPM
GBR_HG00137	0.00 RPM
GBR_HG00142	0.00 RPM
GBR_HG00143	0.00 RPM
TSI_NA20512	0.00 RPM
TSI_NA20513	0.00 RPM
TSI_NA20518	0.00 RPM
TSI_NA20532	0.00 RPM
TSI_NA20538	0.00 RPM
TSI_NA20756	0.00 RPM
TSI_NA20765	0.00 RPM
TSI_NA20771	0.00 RPM
TSI_NA20786	0.00 RPM
TSI_NA20798	0.00 RPM
YRI_NA18870	0.00 RPM
YRI_NA18907	0.00 RPM
YRI_NA18916	0.00 RPM
YRI_NA19093	0.00 RPM
YRI_NA19099	0.00 RPM
YRI_NA19114	0.00 RPM
YRI_NA19118	0.00 RPM
YRI_NA19213	0.00 RPM
YRI_NA19214	0.00 RPM
YRI_NA19223	0.00 RPM

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Indel association:

The presence of retro_hsap_382 across human populations is associated with 1 indel. The percentage values indicate the frequencies of retro_hsap_382 presence in various populations. Based on Kabza et al. 2015 (PubMed).

#	Indel coordinates	AFR, African			AMR, Ad Mixed American			EUR, European					EAS, East Asian
		ASW	YRI	LWK	MXL	PUR	CLM	CEU	IBS	GBR	FIN	TSI	JPT	CHB	CHS
1.	1:50861088..50877200	100	100	100	100	99.09	100	100	100	100	100	100	100	100	100

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Indel #1, located at the genomic coordinates 1:50861088..50877200.