RetrogeneDB ID:

retro_hsap_1164

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:12:130701351..130701702(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000242963
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RPS20
Ensembl ID:ENSG00000008988
Aliases:None
Description:ribosomal protein S20 [Source:HGNC Symbol;Acc:10405]


Retrocopy-Parental alignment summary:






>retro_hsap_1164
ATGGCTTTTAAAGACACCGGAAAACACCCACAGGGCCAGAGGTCGCAATTCACCAAGTTCAAGTCTCCCTAATGAGCCGC
AACATGCAATCCTTGGAGAAGGTGTGTACTGACTTGACCAGAGCCGCAAAGGAAGGTCATCTCCAAGTGAAAGGACTGGC
CCAGCTGCCTCCCGAGCCTTTGAGAAGCACTACAGGAAAAACTCCTTGTGGCGAAGGCTCTTGACATGGGCTTCCTTCCA
GAGGAGAATCCACCCGCAACCTACACACCTGCACAGCCCTCCTGAGACTGCCAAGTGGATTATTCTCATCAGTGTGAGCC
AGGAGTTGGGGTTGAAGTCACCATTGCAGAT

ORF - retro_hsap_1164 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 62.81 %
Parental protein coverage: 99.16 %
Number of stop codons detected: 0
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalMAFKDTGK-TPVEPEVAIHRIRITLTSRNVKSLEKVCADLIRGAKEKNLKVKGPVRMPTKTLRITTRKTP
MAFKDTGK.TP..PEVAIH.....L.SRN..SLEKVC.DL.R.AKE..L.VKG....P...LR.TT.KTP
RetrocopyMAFKDTGK<TPTGPEVAIHQVQVSLMSRNMQSLEKVCTDLTRAAKEGHLQVKGLAQLPPEPLRSTTGKTP
ParentalCGEGS-KTWDRFQMRIHKRLIDLHSPSEIVKQITSISI-EPGVEVEVTIAD
CGEGS..TW..FQ.RIH.....LHSP.E..K.I..IS..EPGV.VEVTIAD
RetrocopyCGEGS<LTWASFQRRIHPQPTHLHSPPETAKWIILISV<EPGVGVEVTIAD

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 967 .42 RPM
bodymap2_adrenal 0 .00 RPM 1126 .84 RPM
bodymap2_brain 0 .00 RPM 290 .40 RPM
bodymap2_breast 0 .00 RPM 1125 .69 RPM
bodymap2_colon 0 .00 RPM 1089 .88 RPM
bodymap2_heart 0 .00 RPM 203 .20 RPM
bodymap2_kidney 0 .00 RPM 360 .05 RPM
bodymap2_liver 0 .00 RPM 201 .31 RPM
bodymap2_lung 0 .00 RPM 798 .31 RPM
bodymap2_lymph_node 0 .00 RPM 898 .08 RPM
bodymap2_ovary 0 .00 RPM 1291 .38 RPM
bodymap2_prostate 0 .00 RPM 856 .24 RPM
bodymap2_skeletal_muscle 0 .00 RPM 315 .29 RPM
bodymap2_testis 0 .02 RPM 945 .45 RPM
bodymap2_thyroid 0 .00 RPM 527 .95 RPM
bodymap2_white_blood_cells 0 .00 RPM 860 .00 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_1164 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_1164 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_1164 retrocopy 5' end.

Lab - click to see more details

retro_hsap_1164 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1164 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_797
Gorilla gorilla retro_ggor_909
Pongo abelii retro_pabe_968
Parental genes homology:
Parental genes homology involve 22 parental genes, and 304 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG0000001914711 retrocopies
retro_btau_1082, retro_btau_1086, retro_btau_1250, retro_btau_1272, retro_btau_1274, retro_btau_1419, retro_btau_1526, retro_btau_1789, retro_btau_1818, retro_btau_454, retro_btau_632,
Canis familiaris ENSCAFG0000002988420 retrocopies
retro_cfam_1144, retro_cfam_1247, retro_cfam_1287, retro_cfam_1367, retro_cfam_1409, retro_cfam_1472, retro_cfam_1633, retro_cfam_1646, retro_cfam_1688, retro_cfam_1719, retro_cfam_1810, retro_cfam_1964, retro_cfam_1978, retro_cfam_1992, retro_cfam_2008, retro_cfam_2193, retro_cfam_559, retro_cfam_666, retro_cfam_672, retro_cfam_949,
Callithrix jacchus ENSCJAG000000166314 retrocopies
retro_cjac_3017, retro_cjac_319, retro_cjac_667, retro_cjac_749,
Dipodomys ordii ENSDORG000000057942 retrocopies
retro_dord_252, retro_dord_653,
Echinops telfairi ENSETEG000000033943 retrocopies
retro_etel_16, retro_etel_1814, retro_etel_2067,
Felis catus ENSFCAG0000002923322 retrocopies
retro_fcat_1077, retro_fcat_1079, retro_fcat_1164, retro_fcat_1247, retro_fcat_1351, retro_fcat_1433, retro_fcat_1476, retro_fcat_1503, retro_fcat_1537, retro_fcat_1646, retro_fcat_1647, retro_fcat_1724, retro_fcat_174, retro_fcat_1849, retro_fcat_1899, retro_fcat_2006, retro_fcat_312, retro_fcat_486, retro_fcat_646, retro_fcat_696, retro_fcat_957, retro_fcat_967,
Homo sapiens ENSG00000008988 26 retrocopies
retro_hsap_1062, retro_hsap_1078, retro_hsap_1164 , retro_hsap_1247, retro_hsap_1383, retro_hsap_1497, retro_hsap_197, retro_hsap_2111, retro_hsap_2223, retro_hsap_2308, retro_hsap_2329, retro_hsap_2527, retro_hsap_2739, retro_hsap_3219, retro_hsap_3225, retro_hsap_3272, retro_hsap_3921, retro_hsap_393, retro_hsap_3974, retro_hsap_4045, retro_hsap_4099, retro_hsap_416, retro_hsap_4185, retro_hsap_4271, retro_hsap_870, retro_hsap_899,
Gorilla gorilla ENSGGOG0000000183721 retrocopies
retro_ggor_1074, retro_ggor_1149, retro_ggor_1581, retro_ggor_1640, retro_ggor_1751, retro_ggor_1768, retro_ggor_1908, retro_ggor_2193, retro_ggor_2227, retro_ggor_2639, retro_ggor_2712, retro_ggor_2751, retro_ggor_2809, retro_ggor_2857, retro_ggor_410, retro_ggor_707, retro_ggor_727, retro_ggor_838, retro_ggor_851, retro_ggor_909, retro_ggor_977,
Macropus eugenii ENSMEUG0000001417121 retrocopies
retro_meug_100, retro_meug_1015, retro_meug_1058, retro_meug_1170, retro_meug_1313, retro_meug_1614, retro_meug_1702, retro_meug_1761, retro_meug_1777, retro_meug_1831, retro_meug_1911, retro_meug_1951, retro_meug_2065, retro_meug_2110, retro_meug_2187, retro_meug_659, retro_meug_710, retro_meug_723, retro_meug_818, retro_meug_892, retro_meug_928,
Monodelphis domestica ENSMODG000000091146 retrocopies
retro_mdom_1701, retro_mdom_1735, retro_mdom_1738, retro_mdom_1814, retro_mdom_1817, retro_mdom_1943,
Mustela putorius furoENSMPUG0000001045215 retrocopies
retro_mputfur_1094, retro_mputfur_1188, retro_mputfur_1313, retro_mputfur_1366, retro_mputfur_1374, retro_mputfur_1432, retro_mputfur_238, retro_mputfur_249, retro_mputfur_320, retro_mputfur_418, retro_mputfur_424, retro_mputfur_433, retro_mputfur_620, retro_mputfur_77, retro_mputfur_819,
Mus musculus ENSMUSG000000282347 retrocopies
retro_mmus_1442, retro_mmus_2796, retro_mmus_3138, retro_mmus_3159, retro_mmus_3321, retro_mmus_3627, retro_mmus_3718,
Nomascus leucogenys ENSNLEG0000000121419 retrocopies
retro_nleu_1013, retro_nleu_1343, retro_nleu_1447, retro_nleu_1566, retro_nleu_1794, retro_nleu_1798, retro_nleu_1805, retro_nleu_1818, retro_nleu_2059, retro_nleu_2159, retro_nleu_2654, retro_nleu_2659, retro_nleu_2750, retro_nleu_2786, retro_nleu_2819, retro_nleu_2843, retro_nleu_3066, retro_nleu_382, retro_nleu_41,
Oryctolagus cuniculus ENSOCUG0000000306817 retrocopies
retro_ocun_1006, retro_ocun_1076, retro_ocun_1218, retro_ocun_1438, retro_ocun_1467, retro_ocun_1526, retro_ocun_1585, retro_ocun_1586, retro_ocun_1609, retro_ocun_286, retro_ocun_299, retro_ocun_332, retro_ocun_682, retro_ocun_707, retro_ocun_783, retro_ocun_827, retro_ocun_948,
Otolemur garnettii ENSOGAG0000000776010 retrocopies
retro_ogar_1337, retro_ogar_1759, retro_ogar_177, retro_ogar_1927, retro_ogar_2203, retro_ogar_2286, retro_ogar_2576, retro_ogar_309, retro_ogar_310, retro_ogar_900,
Ochotona princeps ENSOPRG0000001104211 retrocopies
retro_opri_1022, retro_opri_1024, retro_opri_1156, retro_opri_1206, retro_opri_164, retro_opri_402, retro_opri_41, retro_opri_53, retro_opri_592, retro_opri_906, retro_opri_980,
Procavia capensis ENSPCAG000000043003 retrocopies
retro_pcap_244, retro_pcap_427, retro_pcap_438,
Pongo abelii ENSPPYG0000001860030 retrocopies
retro_pabe_1038, retro_pabe_1148, retro_pabe_1248, retro_pabe_1508, retro_pabe_1860, retro_pabe_1981, retro_pabe_1992, retro_pabe_2176, retro_pabe_2180, retro_pabe_2667, retro_pabe_2674, retro_pabe_2692, retro_pabe_2708, retro_pabe_2815, retro_pabe_2950, retro_pabe_306, retro_pabe_319, retro_pabe_3193, retro_pabe_3317, retro_pabe_3356, retro_pabe_3424, retro_pabe_3485, retro_pabe_422, retro_pabe_440, retro_pabe_681, retro_pabe_776, retro_pabe_885, retro_pabe_897, retro_pabe_902, retro_pabe_968,
Pan troglodytes ENSPTRG0000002026427 retrocopies
retro_ptro_1016, retro_ptro_1472, retro_ptro_1548, retro_ptro_1632, retro_ptro_1684, retro_ptro_1702, retro_ptro_176, retro_ptro_1853, retro_ptro_2169, retro_ptro_2177, retro_ptro_2213, retro_ptro_2665, retro_ptro_2699, retro_ptro_2739, retro_ptro_2780, retro_ptro_2839, retro_ptro_2897, retro_ptro_2946, retro_ptro_303, retro_ptro_318, retro_ptro_605, retro_ptro_620, retro_ptro_723, retro_ptro_732, retro_ptro_797, retro_ptro_858, retro_ptro_949,
Rattus norvegicus ENSRNOG000000085557 retrocopies
retro_rnor_142, retro_rnor_155, retro_rnor_192, retro_rnor_288, retro_rnor_381, retro_rnor_401, retro_rnor_58,
Sarcophilus harrisii ENSSHAG0000001120010 retrocopies
retro_shar_135, retro_shar_228, retro_shar_418, retro_shar_436, retro_shar_441, retro_shar_443, retro_shar_450, retro_shar_504, retro_shar_544, retro_shar_785,
Sus scrofa ENSSSCG0000000624912 retrocopies
retro_sscr_1123, retro_sscr_30, retro_sscr_567, retro_sscr_575, retro_sscr_577, retro_sscr_585, retro_sscr_611, retro_sscr_646, retro_sscr_691, retro_sscr_708, retro_sscr_724, retro_sscr_838,

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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