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


Retrocopy-Parental alignment summary:






>retro_hsap_382
TGCTCAGTGAGGTGGAAGACCATATCTGCTAAACAGAAAGGAAAATCTGAAGATATGGCAAAGGCAAACAAGGCCCGTTA
TGAAAGAGAAATGAAAATCTATATCCCCCCTAAAGGGGAGACAAAAAAGAAGTTCAAGTCCAATGCACCCAAGTGGCCTC
CTGCAGCCTGTTTCGTGTTCTGTTCTGAGTGTTGCCCCAAATCAAAGAACATCTTGGCCTGTCCATTGGTGATGTTGCAA
AGAAACTGGGAGACATGTGGAATAGCACTGCTGCAGATGACAAGCAGCCTTATGAAAAGACAGCTGTGAAGCTGAAGGAA
AAATACAAAAAGGATCTTGCTGCATATTGAACTAAAGGAAAGCCTGATGCAGCAAAAAAGGGAGTCATCAAGGCTGAAAA
AAGC

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:

ParentalCSERWKTMSAKEKGKFEDMAKADKARYEREMKTYIPPKGETKKKFKDPNAPKRPPSAFFLFCSEYRPK-I
CS.RWKT.SAK.KGK.EDMAKA.KARYEREMK.YIPPKGETKKKFK..NAPK.PP.A.F.FCSE..PK.I
RetrocopyCSVRWKTISAKQKGKSEDMAKANKARYEREMKIYIPPKGETKKKFKS-NAPKWPPAACFVFCSECCPK<I
ParentalKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYRAKGKPDAAKKGVVKAEKS
K.EH.GLSIGDVAKKLG.MWN.TAADDKQPYEK.A.KLKEKY.KD.AAY..KGKPDAAKKGV.KAEKS
RetrocopyK-EHLGLSIGDVAKKLGDMWNSTAADDKQPYEKTAVKLKEKYKKDLAAY*TKGKPDAAKKGVIKAEKS

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






(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

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
RNA Polymerase II actvity near the 5' end of retro_hsap_382 was not detected
No EST(s) were mapped for retro_hsap_382 retrocopy.
No TSS is located nearby retro_hsap_382 retrocopy 5' end.
retro_hsap_382 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_382 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_388

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

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000088807 retrocopies
Bos taurus ENSBTAG000000181032 retrocopies
Canis familiaris ENSCAFG0000000659713 retrocopies
Callithrix jacchus ENSCJAG0000002161511 retrocopies
Cavia porcellus ENSCPOG000000039851 retrocopy
Equus caballus ENSECAG000000084392 retrocopies
Echinops telfairi ENSETEG0000000404818 retrocopies
Felis catus ENSFCAG0000000020010 retrocopies
Homo sapiens ENSG000000299938 retrocopies
Homo sapiens ENSG000001641041 retrocopy
Homo sapiens ENSG00000189403 37 retrocopies
Gorilla gorilla ENSGGOG0000002676423 retrocopies
Macropus eugenii ENSMEUG000000013802 retrocopies
Microcebus murinus ENSMICG000000005731 retrocopy
Microcebus murinus ENSMICG000000071447 retrocopies
Myotis lucifugus ENSMLUG0000002597917 retrocopies
Macaca mulatta ENSMMUG000000233993 retrocopies
Monodelphis domestica ENSMODG0000000923814 retrocopies
Mus musculus ENSMUSG00000066551129 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 ENSNLEG0000000072033 retrocopies
Oryctolagus cuniculus ENSOCUG0000002133516 retrocopies
Otolemur garnettii ENSOGAG00000003205104 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 ENSOGAG000000321471 retrocopy
Ochotona princeps ENSOPRG000000035078 retrocopies
Procavia capensis ENSPCAG000000022012 retrocopies
Pongo abelii ENSPPYG0000000554635 retrocopies
Pteropus vampyrus ENSPVAG000000014316 retrocopies
Rattus norvegicus ENSRNOG000000298131 retrocopy
Sorex araneus ENSSARG0000000447014 retrocopies
Sus scrofa ENSSSCG000000093273 retrocopies
Ictidomys tridecemlineatus ENSSTOG0000000044319 retrocopies
Tarsius syrichta ENSTSYG000000063287 retrocopies
Tursiops truncatus ENSTTRG000000103278 retrocopies

Expression level across human populations :
image/svg+xml GBR_HG00142 GBR_HG00099 GBR_HG00114 GBR_HG00143 GBR_HG00131 GBR_HG00137 GBR_HG00133 GBR_HG00119 GBR_HG00111 GBR_HG00134 FIN_HG00378 FIN_HG00338 FIN_HG00349 FIN_HG00375 FIN_HG00315 FIN_HG00277 FIN_HG00328 FIN_HG00321 FIN_HG00377 FIN_HG00183 TSI_NA20756 TSI_NA20538 TSI_NA20798 TSI_NA20532 TSI_NA20765 TSI_NA20518 TSI_NA20513 TSI_NA20512 TSI_NA20771 TSI_NA20786 YRI_NA19114 YRI_NA19099 YRI_NA18870 YRI_NA18907 YRI_NA19223 YRI_NA19214 YRI_NA18916 YRI_NA19093 YRI_NA19118 YRI_NA19213 Toscaniin Italia: Finnish inFinland: British in England and Scotland: Utah Residents (CEPH) with Northernand Western European Ancestry: Yoruba in Ibadan, Nigeria: CEU_NA12760 CEU_NA12827 CEU_NA12872 CEU_NA12751 CEU_NA12873 CEU_NA12400 CEU_NA11930 CEU_NA12004 CEU_NA11831 CEU_NA11843 No expression ( = 0 RPM ) > 0 RPM = 0.03 RPM Legend:


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


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


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

image/svg+xml Mexican Ancestryfrom Los Angeles USA MXL 100 % Puerto Ricansfrom Puerto Rico PUR 99.09 % Colombians fromMedellin, Colombia CLM 100 % Americans of AfricanAncestry in SW USA ASW 100 % Yoruba in Ibadan,Nigeria YRI 100 % Luhya in Webuye,Kenya LWK 100 % Utah Residents (CEPH)with Northern andWestern European Ancestry CEU 100 % Iberian Populationin Spain IBS 100 % British in Englandand Scotland GBR 100 % Finnish in Finland FIN 100 % Toscani in Italia TSI 100 % Han Chinese in Bejing,China CHB 100 % Japanese in Tokyo,Japan 100 % Southern Han Chinese CHS 100 % JPT EUROPE AMERICAS AFRICA EAST ASIA





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