RetrogeneDB ID: retro_hsap_3974

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 8:74894359..74894706(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000244295
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPS20
• Ensembl ID: ENSG00000008988
• Aliases: None
• Description: ribosomal protein S20 [Source:HGNC Symbol;Acc:10405]

Sequence

>retro_hsap_3974
ATGGCTTTTAAACATACCAGAAAAACACCCGTGGAGTCAGAGGTGGCAATTCACCGAATTCATATCACTCTAACGAGTTG
CAACGTAAAATCCCTGGATAAGGTGTGTGCTGACTTGATCTGAGGAGCAAAGGAAAAGAATCAGTGAAAGGACCAGTTTG
AATGCCTACCAAGACTTTGAGAATCACTACAAGAAAAACTTACGGTGAAGGTTCTAAGGCATGGGATCGTTTCCAGATGA
GAATCCACAAGCGACTCATTGACTTGCGCAGTCCTCAGATAGTTAAGCAGATTACTTCCATCAGTATTGAGCCAGGAGTT
GAGATGGAAGTCACCATTGCAAATGCT

Alignment

ORF - retro_hsap_3974 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.5 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAFKDTGKTPVEPEVAIHRIRITLTSRNVKSLEKVCADLIRGA-KEKNLKVKGPVRMPTKTLRITTRKTP
          MAFK.T.KTPVE.EVAIHRI.ITLTS.NVKSL.KVCADLI.GA.K.K...VKGPV.MPTKTLRITTRKT.
Retrocopy MAFKHTRKTPVESEVAIHRIHITLTSCNVKSLDKVCADLI*GA<KGKE-SVKGPV*MPTKTLRITTRKT-

Parental  CGEGSKTWDRFQMRIHKRLIDLHSPSEIVKQITSISIEPGVEVEVTIADA
          .GEGSK.WDRFQMRIHKRLIDL.SP..IVKQITSISIEPGVE.EVTIA.A
Retrocopy YGEGSKAWDRFQMRIHKRLIDLRSP-QIVKQITSISIEPGVEMEVTIANA

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	0.58 RPM	967.42 RPM
bodymap2_adrenal	11.36 RPM	1126.84 RPM
bodymap2_brain	3.70 RPM	290.40 RPM
bodymap2_breast	1.65 RPM	1125.69 RPM
bodymap2_colon	0.95 RPM	1089.88 RPM
bodymap2_heart	0.79 RPM	203.20 RPM
bodymap2_kidney	0.74 RPM	360.05 RPM
bodymap2_liver	1.10 RPM	201.31 RPM
bodymap2_lung	1.55 RPM	798.31 RPM
bodymap2_lymph_node	0.46 RPM	898.08 RPM
bodymap2_ovary	5.03 RPM	1291.38 RPM
bodymap2_prostate	1.25 RPM	856.24 RPM
bodymap2_skeletal_muscle	0.53 RPM	315.29 RPM
bodymap2_testis	1.70 RPM	945.45 RPM
bodymap2_thyroid	7.23 RPM	527.95 RPM
bodymap2_white_blood_cells	1.67 RPM	860.00 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_3974 was not detected

EST

No EST(s) were mapped for retro_hsap_3974 retrocopy.

TSS

No TSS is located nearby retro_hsap_3974 retrocopy 5' end.

Lab

retro_hsap_3974 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3974 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 22 parental genes, and 304 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000019147	11 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	ENSCAFG00000029884	20 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	ENSCJAG00000016631	4 retrocopies	retro_cjac_3017, retro_cjac_319, retro_cjac_667, retro_cjac_749,
Dipodomys ordii	ENSDORG00000005794	2 retrocopies	retro_dord_252, retro_dord_653,
Echinops telfairi	ENSETEG00000003394	3 retrocopies	retro_etel_16, retro_etel_1814, retro_etel_2067,
Felis catus	ENSFCAG00000029233	22 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	ENSGGOG00000001837	21 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	ENSMEUG00000014171	21 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	ENSMODG00000009114	6 retrocopies	retro_mdom_1701, retro_mdom_1735, retro_mdom_1738, retro_mdom_1814, retro_mdom_1817, retro_mdom_1943,
Mustela putorius furo	ENSMPUG00000010452	15 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	ENSMUSG00000028234	7 retrocopies	retro_mmus_1442, retro_mmus_2796, retro_mmus_3138, retro_mmus_3159, retro_mmus_3321, retro_mmus_3627, retro_mmus_3718,
Nomascus leucogenys	ENSNLEG00000001214	19 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	ENSOCUG00000003068	17 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	ENSOGAG00000007760	10 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	ENSOPRG00000011042	11 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	ENSPCAG00000004300	3 retrocopies	retro_pcap_244, retro_pcap_427, retro_pcap_438,
Pongo abelii	ENSPPYG00000018600	30 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	ENSPTRG00000020264	27 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	ENSRNOG00000008555	7 retrocopies	retro_rnor_142, retro_rnor_155, retro_rnor_192, retro_rnor_288, retro_rnor_381, retro_rnor_401, retro_rnor_58,
Sarcophilus harrisii	ENSSHAG00000011200	10 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	ENSSSCG00000006249	12 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,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.71 RPM
CEU_NA11843	0.82 RPM
CEU_NA11930	0.75 RPM
CEU_NA12004	0.72 RPM
CEU_NA12400	0.60 RPM
CEU_NA12751	0.49 RPM
CEU_NA12760	0.27 RPM
CEU_NA12827	0.85 RPM
CEU_NA12872	0.33 RPM
CEU_NA12873	0.38 RPM
FIN_HG00183	0.44 RPM
FIN_HG00277	0.37 RPM
FIN_HG00315	0.88 RPM
FIN_HG00321	0.57 RPM
FIN_HG00328	0.64 RPM
FIN_HG00338	0.96 RPM
FIN_HG00349	1.22 RPM
FIN_HG00375	0.49 RPM
FIN_HG00377	1.01 RPM
FIN_HG00378	0.85 RPM
GBR_HG00099	1.13 RPM
GBR_HG00111	0.64 RPM
GBR_HG00114	0.84 RPM
GBR_HG00119	0.57 RPM
GBR_HG00131	0.32 RPM
GBR_HG00133	0.68 RPM
GBR_HG00134	0.76 RPM
GBR_HG00137	0.36 RPM
GBR_HG00142	0.42 RPM
GBR_HG00143	1.05 RPM
TSI_NA20512	0.82 RPM
TSI_NA20513	0.70 RPM
TSI_NA20518	1.11 RPM
TSI_NA20532	0.61 RPM
TSI_NA20538	0.55 RPM
TSI_NA20756	0.70 RPM
TSI_NA20765	0.75 RPM
TSI_NA20771	0.57 RPM
TSI_NA20786	0.44 RPM
TSI_NA20798	0.31 RPM
YRI_NA18870	0.44 RPM
YRI_NA18907	0.80 RPM
YRI_NA18916	0.76 RPM
YRI_NA19093	0.42 RPM
YRI_NA19099	0.69 RPM
YRI_NA19114	0.45 RPM
YRI_NA19118	0.70 RPM
YRI_NA19213	0.48 RPM
YRI_NA19214	1.21 RPM
YRI_NA19223	0.88 RPM

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Indel association:

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