RetrogeneDB ID:

retro_hsap_3683

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:6:154259630..154260136(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000217085
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:HMGB3
Ensembl ID:ENSG00000029993
Aliases:HMGB3, HMG-2a, HMG-4, HMG2A, HMG4
Description:high mobility group box 3 [Source:HGNC Symbol;Acc:5004]


Retrocopy-Parental alignment summary:






>retro_hsap_3683
AAGGGCAACATGTCTGCTTATGCCTTCTTTGGGCAGATGTGCAGAGAAGAACATAAGAAGAAAAACCCAGAGGTCTCCCT
GTCAATTTTACAGAATTTTCCAAGAAGCGCTCTGAGAGGTAGAAGACAGAGTCTGGGAAAGAGAAGCCTAAATTTGGTGA
AGTGGCAAAGGCGGATAAAGTATGCTATGATTGGGAAATGAAGGATTATGGACCAGCTAAGTGAGACAAGAAGAAGGACC
CTAATGCCCCCAAAAGGCCATCGACTGCATTCTTCCTGTTCTGTTAAGAATTCAGCCCCAAGATAAAATCCACAAACCCT
GGCAACTCTTTTGGTGACATGGCAAAAAAAAGAAAACTGGGTGAGATGTGGAATAACCTAAGTGACAATGAAAAGCAGCC
TTACATCCCTAAGATGGCCAAGCTGAAGGAGAAGTATGAGAAGAATGCTGCTGACTATAAGTTTCAAGGAAAGTTTGCTG
GTGCAAAGGATCCTGCTAAAGTTGCC

ORF - retro_hsap_3683 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 74.27 %
Parental protein coverage: 83.5 %
Number of stop codons detected: 3
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalKGKMSAYAFFVQTCREEHKK-KNPE-VPVNFAEFSKKCSERWKTMSGKEKSKFDEMAKADKVRYDREMKD
KG.MSAYAFF.Q.CREEHKK...P...PVNF.EFSKK.SER.KT.SGKEK.KF.E.AKADKV.YD.EMKD
RetrocopyKGNMSAYAFFGQMCREEHKK<EKPRGLPVNFTEFSKKRSER*KTESGKEKPKFGEVAKADKVCYDWEMKD
ParentalYGPAKGGKKKKDPNAPKRPPSGFFLFCSEFRPKIKSTNPGISIGDVAKK--LGEMWNNLNDSEKQPYITK
YGPAK..KKK.DPNAPKRP...FFLFC.EF.PKIKSTNPG.S.GD......LGEMWNNL.D.EKQPYI.K
RetrocopyYGPAK*DKKK-DPNAPKRPSTAFFLFC*EFSPKIKSTNPGNSFGDMXXXXXLGEMWNNLSDNEKQPYIPK
ParentalAAKLKEKYEKDVADYKSKGKFDGAKGPAKVA
.AKLKEKYEK..ADYK..GKF.GAK.PAKVA
RetrocopyMAKLKEKYEKNAADYKFQGKFAGAKDPAKVA

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






RNA-Seq - click to see more details

(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 13 .14 RPM
bodymap2_adrenal 0 .00 RPM 11 .38 RPM
bodymap2_brain 0 .00 RPM 31 .13 RPM
bodymap2_breast 0 .00 RPM 9 .24 RPM
bodymap2_colon 0 .00 RPM 9 .32 RPM
bodymap2_heart 0 .00 RPM 3 .99 RPM
bodymap2_kidney 0 .00 RPM 13 .09 RPM
bodymap2_liver 0 .00 RPM 45 .12 RPM
bodymap2_lung 0 .00 RPM 11 .67 RPM
bodymap2_lymph_node 0 .00 RPM 8 .17 RPM
bodymap2_ovary 0 .00 RPM 8 .56 RPM
bodymap2_prostate 0 .00 RPM 6 .18 RPM
bodymap2_skeletal_muscle 0 .00 RPM 27 .32 RPM
bodymap2_testis 0 .00 RPM 35 .12 RPM
bodymap2_thyroid 0 .00 RPM 38 .51 RPM
bodymap2_white_blood_cells 0 .00 RPM 2 .80 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3683 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3683 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3683 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3683 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3683 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2497
Gorilla gorilla retro_ggor_2490
Parental genes homology:
Parental genes homology involve 27 parental genes, and 230 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000051502 retrocopies
retro_btau_190, retro_btau_38,
Choloepus hoffmanni ENSCHOG000000050052 retrocopies
retro_chof_1891, retro_chof_2010,
Callithrix jacchus ENSCJAG000000039369 retrocopies
retro_cjac_1596, retro_cjac_1950, retro_cjac_2343, retro_cjac_2469, retro_cjac_2470, retro_cjac_2738, retro_cjac_2900, retro_cjac_688, retro_cjac_965,
Dipodomys ordii ENSDORG000000108264 retrocopies
retro_dord_214, retro_dord_337, retro_dord_454, retro_dord_609,
Echinops telfairi ENSETEG000000156894 retrocopies
retro_etel_104, retro_etel_1272, retro_etel_385, retro_etel_465,
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 ENSG000001641041 retrocopy
retro_hsap_3663,
Homo sapiens ENSG0000018940337 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 ENSGGOG0000002716416 retrocopies
retro_ggor_1371, retro_ggor_1538, retro_ggor_1540, retro_ggor_1651, retro_ggor_1834, retro_ggor_2104, retro_ggor_2250, retro_ggor_2469, retro_ggor_2490, retro_ggor_2580, retro_ggor_272, retro_ggor_2944, retro_ggor_301, retro_ggor_414, retro_ggor_549, retro_ggor_618,
Myotis lucifugus ENSMLUG000000109264 retrocopies
retro_mluc_1055, retro_mluc_1989, retro_mluc_215, retro_mluc_529,
Macaca mulatta ENSMMUG0000000463320 retrocopies
retro_mmul_1003, retro_mmul_1115, retro_mmul_1143, retro_mmul_1303, retro_mmul_1341, retro_mmul_1482, retro_mmul_1568, retro_mmul_1624, retro_mmul_1799, retro_mmul_1957, retro_mmul_2106, retro_mmul_2425, retro_mmul_2451, retro_mmul_2469, retro_mmul_2484, retro_mmul_2526, retro_mmul_267, retro_mmul_399, retro_mmul_514, retro_mmul_597,
Monodelphis domestica ENSMODG000000057357 retrocopies
retro_mdom_1257, retro_mdom_1508, retro_mdom_1883, retro_mdom_1952, retro_mdom_587, retro_mdom_698, retro_mdom_831,
Mustela putorius furoENSMPUG000000116062 retrocopies
retro_mputfur_138, retro_mputfur_26,
Mus musculus ENSMUSG000000152171 retrocopy
retro_mmus_273,
Oryctolagus cuniculus ENSOCUG000000059867 retrocopies
retro_ocun_1033, retro_ocun_1913, retro_ocun_1914, retro_ocun_534, retro_ocun_568, retro_ocun_891, retro_ocun_931,
Otolemur garnettii ENSOGAG0000000177319 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,
Pongo abelii ENSPPYG0000002081822 retrocopies
retro_pabe_1207, retro_pabe_1411, retro_pabe_1505, retro_pabe_1580, retro_pabe_1823, retro_pabe_1825, retro_pabe_1927, retro_pabe_2339, retro_pabe_2538, retro_pabe_2712, retro_pabe_2816, retro_pabe_3000, retro_pabe_3041, retro_pabe_3144, retro_pabe_3387, retro_pabe_3685, retro_pabe_3813, retro_pabe_410, retro_pabe_442, retro_pabe_560, retro_pabe_632, retro_pabe_784,
Pan troglodytes ENSPTRG0000002237122 retrocopies
retro_ptro_1115, retro_ptro_1211, retro_ptro_1276, retro_ptro_1429, retro_ptro_1432, retro_ptro_1561, retro_ptro_174, retro_ptro_1766, retro_ptro_2066, retro_ptro_213, retro_ptro_2218, retro_ptro_2296, retro_ptro_2477, retro_ptro_2497, retro_ptro_2608, retro_ptro_2891, retro_ptro_2944, retro_ptro_3154, retro_ptro_3271, retro_ptro_456, retro_ptro_522, retro_ptro_629,
Pteropus vampyrus ENSPVAG000000002191 retrocopy
retro_pvam_356,
Rattus norvegicus ENSRNOG000000110964 retrocopies
retro_rnor_1049, retro_rnor_2303, retro_rnor_2359, retro_rnor_2363,
Rattus norvegicus ENSRNOG000000509105 retrocopies
retro_rnor_1956, retro_rnor_2516, retro_rnor_2625, retro_rnor_720, retro_rnor_954,
Sarcophilus harrisii ENSSHAG000000029162 retrocopies
retro_shar_139, retro_shar_316,
Sus scrofa ENSSSCG000000127453 retrocopies
retro_sscr_1094, retro_sscr_466, retro_sscr_467,
Ictidomys tridecemlineatus ENSSTOG000000239086 retrocopies
retro_itri_1366, retro_itri_1527, retro_itri_1655, retro_itri_1749, retro_itri_777, retro_itri_909,
Tupaia belangeri ENSTBEG0000000306818 retrocopies
retro_tbel_1002, retro_tbel_1230, retro_tbel_1579, retro_tbel_1700, retro_tbel_1819, retro_tbel_2543, retro_tbel_2730, retro_tbel_3261, retro_tbel_3476, retro_tbel_3623, retro_tbel_3781, retro_tbel_408, retro_tbel_410, retro_tbel_4203, retro_tbel_4209, retro_tbel_4299, retro_tbel_605, retro_tbel_698,
Tursiops truncatus ENSTTRG000000002052 retrocopies
retro_ttru_1187, retro_ttru_372,
Vicugna pacos ENSVPAG000000000962 retrocopies
retro_vpac_245, retro_vpac_434,

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 ) 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 .00 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:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).



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