RetrogeneDB ID: retro_hsap_107

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 19:24009963..24010851(+)
• Located in intron of: ENSG00000233836

Retrocopy information

• Ensembl ID: ENSG00000205246
• Aliases: RPSAP58, RPSA_30_1642
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: RPSA
• Ensembl ID: ENSG00000168028
• Aliases: RPSA, 37LRP, 67LR, ICAS, LAMBR, LAMR1, LBP, LBP/p40, LRP, LRP/LR, NEM/1CHD4, SA, lamR, p40
• Description: ribosomal protein SA [Source:HGNC Symbol;Acc:6502]

Sequence

>retro_hsap_107
ATGTCCGGAGCCCTTGATGTCCTGCAAATGAAGGAGGAGGATGTCCTTAAGTTCCTTGCAGCAGGAACCCACTTAGGTGG
CACCAATCTTGACTTCCAGATGGAACACTACATCTATAAAAGGAAAAGTGATGGCATCTATATCATAAATCTCAAGAGGA
CCTGGGAGAAGCTTCTGCTGGCAGCTCGTGCTATTGTTGCCATTGAAAACCCTGCTGATGTCAGTGTTATATCCTCCAGG
AATACTGGCCAGAGGGCTGTGCTGAAGTTTGCTGCTGCCACTGGAGCCACTCCAATTGCTGGCCGCTTCACTCCTGGAAC
CTTCACTAACCAGATCCAGGCAGCCTTCTGGGAGCCACGGCTTCTTGTGGTTACTGACCCCAGGGCTGACCACCAGCCTC
TCACGGAGGCATCTTATGTTAACCTACCTACCATTGCGCTGTGTAACACAGATTCTCCTCTGCGCTATGTGGACATTGCC
ATCCCATGCAACAACAAGGGAGCTCACTCAGTGGGTTTGATGTGGTGGATGCTGGCTCGGGAAGTTCTGCGCATGCGTGG
CACCATTTCCCGTGAACACCCATGGGAGGTCATGCCTGATCTGTACTTCTACAGAGATCCTGAAGAGATTGAAAAAGAAG
AGCAGGCTGCTGCTGAGAAGGCAGTGACCAAGGAGGAATTTCAGGGTGAATGGACTGCTCCCTCTCCTGAGTTCACTGCT
ACTCAGCCTGAGGTTGCAGACTGGTCTGAAGGTGTACAGGTGCCCTCTGTGCCTATTCAGCAATTCCCTACTGAAGACTG
GAGCGCTCAGCCTGCCACGGAAGACTGGTCTGCAGCTCCCACTGCTCAGGCCACTGAATGGGTAGGAGCAACCACTGACT
GGTCTTAA

Alignment

ORF - retro_hsap_107 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.98 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSGALDVLQMKEEDVLKFLAAGTHLGGTNLDFQMEQYIYKRKSDGIYIINLKRTWEKLLLAARAIVAIEN
          MSGALDVLQMKEEDVLKFLAAGTHLGGTNLDFQME.YIYKRKSDGIYIINLKRTWEKLLLAARAIVAIEN
Retrocopy MSGALDVLQMKEEDVLKFLAAGTHLGGTNLDFQMEHYIYKRKSDGIYIINLKRTWEKLLLAARAIVAIEN

Parental  PADVSVISSRNTGQRAVLKFAAATGATPIAGRFTPGTFTNQIQAAFREPRLLVVTDPRADHQPLTEASYV
          PADVSVISSRNTGQRAVLKFAAATGATPIAGRFTPGTFTNQIQAAF.EPRLLVVTDPRADHQPLTEASYV
Retrocopy PADVSVISSRNTGQRAVLKFAAATGATPIAGRFTPGTFTNQIQAAFWEPRLLVVTDPRADHQPLTEASYV

Parental  NLPTIALCNTDSPLRYVDIAIPCNNKGAHSVGLMWWMLAREVLRMRGTISREHPWEVMPDLYFYRDPEEI
          NLPTIALCNTDSPLRYVDIAIPCNNKGAHSVGLMWWMLAREVLRMRGTISREHPWEVMPDLYFYRDPEEI
Retrocopy NLPTIALCNTDSPLRYVDIAIPCNNKGAHSVGLMWWMLAREVLRMRGTISREHPWEVMPDLYFYRDPEEI

Parental  EKEEQAAAEKAVTKEEFQGEWTAPAPEFTATQPEVADWSEGVQVPSVPIQQFPTEDWSAQPATEDWSAAP
          EKEEQAAAEKAVTKEEFQGEWTAP.PEFTATQPEVADWSEGVQVPSVPIQQFPTEDWSAQPATEDWSAAP
Retrocopy EKEEQAAAEKAVTKEEFQGEWTAPSPEFTATQPEVADWSEGVQVPSVPIQQFPTEDWSAQPATEDWSAAP

Parental  TAQATEWVGATTDWS
          TAQATEWVGATTDWS
Retrocopy TAQATEWVGATTDWS

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	1.89 RPM	169.00 RPM
bodymap2_adrenal	4.44 RPM	492.13 RPM
bodymap2_brain	5.20 RPM	88.16 RPM
bodymap2_breast	0.86 RPM	154.22 RPM
bodymap2_colon	2.22 RPM	419.88 RPM
bodymap2_heart	1.81 RPM	82.37 RPM
bodymap2_kidney	0.72 RPM	231.62 RPM
bodymap2_liver	9.21 RPM	157.12 RPM
bodymap2_lung	29.03 RPM	253.01 RPM
bodymap2_lymph_node	67.39 RPM	347.77 RPM
bodymap2_ovary	4.47 RPM	397.06 RPM
bodymap2_prostate	24.63 RPM	425.43 RPM
bodymap2_skeletal_muscle	0.22 RPM	81.10 RPM
bodymap2_testis	0.81 RPM	256.27 RPM
bodymap2_thyroid	1.21 RPM	262.21 RPM
bodymap2_white_blood_cells	50.13 RPM	630.62 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_107 was not detected

EST

No EST(s) were mapped for retro_hsap_107 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_72276	1479 libraries	331 libraries	19 libraries	0 libraries	0 libraries

The graphical summary, for retro_hsap_107 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1829 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_hsap_107 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_107 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 27 parental genes, and 426 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000004183	1 retrocopy	retro_acar_140,
Ailuropoda melanoleuca	ENSAMEG00000008962	13 retrocopies	retro_amel_1091, retro_amel_1276, retro_amel_1357, retro_amel_1432, retro_amel_1446, retro_amel_1497, retro_amel_1634, retro_amel_1817, retro_amel_1857, retro_amel_196, retro_amel_430, retro_amel_808, retro_amel_943,
Bos taurus	ENSBTAG00000009757	19 retrocopies	retro_btau_1037, retro_btau_1063, retro_btau_1091, retro_btau_1107, retro_btau_1158, retro_btau_1234, retro_btau_1288, retro_btau_1580, retro_btau_1633, retro_btau_1669, retro_btau_1716, retro_btau_1756, retro_btau_1770, retro_btau_416, retro_btau_848, retro_btau_871, retro_btau_896, retro_btau_964, retro_btau_990,
Canis familiaris	ENSCAFG00000005101	27 retrocopies	retro_cfam_1046, retro_cfam_1109, retro_cfam_1173, retro_cfam_1189, retro_cfam_1263, retro_cfam_1288, retro_cfam_1366, retro_cfam_1373, retro_cfam_1435, retro_cfam_1511, retro_cfam_1534, retro_cfam_1545, retro_cfam_1555, retro_cfam_1679, retro_cfam_1770, retro_cfam_1814, retro_cfam_1957, retro_cfam_1990, retro_cfam_2140, retro_cfam_512, retro_cfam_820, retro_cfam_828, retro_cfam_854, retro_cfam_928, retro_cfam_957, retro_cfam_980, retro_cfam_994,
Callithrix jacchus	ENSCJAG00000009675	15 retrocopies	retro_cjac_1113, retro_cjac_1572, retro_cjac_1595, retro_cjac_2265, retro_cjac_2438, retro_cjac_2500, retro_cjac_2502, retro_cjac_2750, retro_cjac_2897, retro_cjac_305, retro_cjac_3160, retro_cjac_4124, retro_cjac_53, retro_cjac_732, retro_cjac_958,
Dasypus novemcinctus	ENSDNOG00000004048	27 retrocopies	retro_dnov_1022, retro_dnov_108, retro_dnov_1099, retro_dnov_1219, retro_dnov_1372, retro_dnov_1431, retro_dnov_1614, retro_dnov_184, retro_dnov_1913, retro_dnov_1974, retro_dnov_1987, retro_dnov_1988, retro_dnov_2067, retro_dnov_2200, retro_dnov_2224, retro_dnov_2309, retro_dnov_2339, retro_dnov_2469, retro_dnov_2480, retro_dnov_375, retro_dnov_42, retro_dnov_456, retro_dnov_465, retro_dnov_663, retro_dnov_800, retro_dnov_895, retro_dnov_940,
Dipodomys ordii	ENSDORG00000008267	1 retrocopy	retro_dord_548,
Equus caballus	ENSECAG00000013062	5 retrocopies	retro_ecab_193, retro_ecab_453, retro_ecab_46, retro_ecab_592, retro_ecab_71,
Echinops telfairi	ENSETEG00000018160	4 retrocopies	retro_etel_1399, retro_etel_1665, retro_etel_1960, retro_etel_92,
Felis catus	ENSFCAG00000002739	22 retrocopies	retro_fcat_1119, retro_fcat_1127, retro_fcat_1239, retro_fcat_1353, retro_fcat_1595, retro_fcat_1668, retro_fcat_1694, retro_fcat_1720, retro_fcat_1758, retro_fcat_1804, retro_fcat_1807, retro_fcat_1861, retro_fcat_1970, retro_fcat_239, retro_fcat_258, retro_fcat_384, retro_fcat_391, retro_fcat_551, retro_fcat_682, retro_fcat_722, retro_fcat_793, retro_fcat_906,
Homo sapiens	ENSG00000168028	2 retrocopies	retro_hsap_107 , retro_hsap_3015,
Loxodonta africana	ENSLAFG00000032009	5 retrocopies	retro_lafr_1234, retro_lafr_367, retro_lafr_806, retro_lafr_863, retro_lafr_997,
Macropus eugenii	ENSMEUG00000008169	14 retrocopies	retro_meug_1123, retro_meug_1137, retro_meug_1643, retro_meug_1722, retro_meug_1923, retro_meug_1933, retro_meug_1936, retro_meug_343, retro_meug_429, retro_meug_684, retro_meug_810, retro_meug_847, retro_meug_957, retro_meug_990,
Microcebus murinus	ENSMICG00000004518	32 retrocopies	retro_mmur_1031, retro_mmur_1042, retro_mmur_1120, retro_mmur_1310, retro_mmur_1357, retro_mmur_136, retro_mmur_1432, retro_mmur_1482, retro_mmur_1513, retro_mmur_1522, retro_mmur_1593, retro_mmur_1596, retro_mmur_1607, retro_mmur_1628, retro_mmur_196, retro_mmur_219, retro_mmur_284, retro_mmur_302, retro_mmur_367, retro_mmur_477, retro_mmur_522, retro_mmur_532, retro_mmur_559, retro_mmur_561, retro_mmur_604, retro_mmur_620, retro_mmur_714, retro_mmur_727, retro_mmur_753, retro_mmur_756, retro_mmur_821, retro_mmur_933,
Macaca mulatta	ENSMMUG00000022965	19 retrocopies	retro_mmul_1008, retro_mmul_1167, retro_mmul_120, retro_mmul_1237, retro_mmul_136, retro_mmul_1527, retro_mmul_1678, retro_mmul_1755, retro_mmul_1879, retro_mmul_1909, retro_mmul_2274, retro_mmul_2388, retro_mmul_2538, retro_mmul_2541, retro_mmul_2622, retro_mmul_378, retro_mmul_789, retro_mmul_876, retro_mmul_911,
Monodelphis domestica	ENSMODG00000010967	2 retrocopies	retro_mdom_1244, retro_mdom_1726,
Mustela putorius furo	ENSMPUG00000002463	21 retrocopies	retro_mputfur_1045, retro_mputfur_1143, retro_mputfur_1194, retro_mputfur_1227, retro_mputfur_1311, retro_mputfur_1318, retro_mputfur_1427, retro_mputfur_1502, retro_mputfur_1558, retro_mputfur_1584, retro_mputfur_288, retro_mputfur_358, retro_mputfur_423, retro_mputfur_477, retro_mputfur_515, retro_mputfur_560, retro_mputfur_576, retro_mputfur_712, retro_mputfur_733, retro_mputfur_932, retro_mputfur_953,
Mus musculus	ENSMUSG00000032518	1 retrocopy	retro_mmus_219,
Nomascus leucogenys	ENSNLEG00000005626	49 retrocopies	retro_nleu_1204, retro_nleu_1277, retro_nleu_1278, retro_nleu_1462, retro_nleu_1564, retro_nleu_1607, retro_nleu_1635, retro_nleu_1719, retro_nleu_1769, retro_nleu_1837, retro_nleu_1885, retro_nleu_1924, retro_nleu_1983, retro_nleu_2020, retro_nleu_2035, retro_nleu_2036, retro_nleu_2172, retro_nleu_2289, retro_nleu_2298, retro_nleu_2343, retro_nleu_2450, retro_nleu_254, retro_nleu_2579, retro_nleu_2624, retro_nleu_2650, retro_nleu_2662, retro_nleu_2693, retro_nleu_275, retro_nleu_2837, retro_nleu_2849, retro_nleu_2912, retro_nleu_3057, retro_nleu_3060, retro_nleu_307, retro_nleu_309, retro_nleu_3098, retro_nleu_310, retro_nleu_336, retro_nleu_339, retro_nleu_508, retro_nleu_591, retro_nleu_598, retro_nleu_705, retro_nleu_718, retro_nleu_740, retro_nleu_877, retro_nleu_883, retro_nleu_925, retro_nleu_950,
Ochotona princeps	ENSOPRG00000004505	16 retrocopies	retro_opri_1083, retro_opri_1167, retro_opri_207, retro_opri_223, retro_opri_281, retro_opri_32, retro_opri_362, retro_opri_423, retro_opri_475, retro_opri_483, retro_opri_491, retro_opri_510, retro_opri_518, retro_opri_635, retro_opri_772, retro_opri_874,
Pan troglodytes	ENSPTRG00000022841	1 retrocopy	retro_ptro_14,
Pteropus vampyrus	ENSPVAG00000007794	19 retrocopies	retro_pvam_1189, retro_pvam_1249, retro_pvam_1335, retro_pvam_1403, retro_pvam_1406, retro_pvam_1443, retro_pvam_1446, retro_pvam_396, retro_pvam_499, retro_pvam_532, retro_pvam_548, retro_pvam_60, retro_pvam_635, retro_pvam_650, retro_pvam_789, retro_pvam_889, retro_pvam_896, retro_pvam_898, retro_pvam_98,
Rattus norvegicus	ENSRNOG00000018645	27 retrocopies	retro_rnor_1004, retro_rnor_1114, retro_rnor_1119, retro_rnor_1213, retro_rnor_1301, retro_rnor_1396, retro_rnor_1481, retro_rnor_1634, retro_rnor_1778, retro_rnor_1840, retro_rnor_1886, retro_rnor_2068, retro_rnor_2153, retro_rnor_2329, retro_rnor_2384, retro_rnor_2444, retro_rnor_2553, retro_rnor_2554, retro_rnor_2589, retro_rnor_2637, retro_rnor_2649, retro_rnor_2701, retro_rnor_2810, retro_rnor_2912, retro_rnor_2958, retro_rnor_645, retro_rnor_702,
Sarcophilus harrisii	ENSSHAG00000006896	2 retrocopies	retro_shar_231, retro_shar_484,
Tupaia belangeri	ENSTBEG00000015946	54 retrocopies	retro_tbel_1001, retro_tbel_1007, retro_tbel_1069, retro_tbel_1257, retro_tbel_1303, retro_tbel_1319, retro_tbel_1324, retro_tbel_1354, retro_tbel_1355, retro_tbel_1382, retro_tbel_1395, retro_tbel_1531, retro_tbel_1563, retro_tbel_1616, retro_tbel_1682, retro_tbel_1712, retro_tbel_1723, retro_tbel_1935, retro_tbel_2006, retro_tbel_245, retro_tbel_2511, retro_tbel_2518, retro_tbel_2544, retro_tbel_2735, retro_tbel_2827, retro_tbel_2906, retro_tbel_3198, retro_tbel_3218, retro_tbel_3241, retro_tbel_3272, retro_tbel_3325, retro_tbel_3351, retro_tbel_341, retro_tbel_3431, retro_tbel_3444, retro_tbel_3555, retro_tbel_3640, retro_tbel_3695, retro_tbel_3915, retro_tbel_3975, retro_tbel_4026, retro_tbel_4219, retro_tbel_4252, retro_tbel_4259, retro_tbel_4355, retro_tbel_4423, retro_tbel_4479, retro_tbel_496, retro_tbel_565, retro_tbel_645, retro_tbel_666, retro_tbel_782, retro_tbel_802, retro_tbel_916,
Tursiops truncatus	ENSTTRG00000014496	24 retrocopies	retro_ttru_1160, retro_ttru_1216, retro_ttru_1222, retro_ttru_1287, retro_ttru_1326, retro_ttru_1432, retro_ttru_1463, retro_ttru_148, retro_ttru_1572, retro_ttru_1693, retro_ttru_1705, retro_ttru_176, retro_ttru_1835, retro_ttru_190, retro_ttru_194, retro_ttru_303, retro_ttru_331, retro_ttru_404, retro_ttru_427, retro_ttru_477, retro_ttru_576, retro_ttru_693, retro_ttru_879, retro_ttru_967,
Vicugna pacos	ENSVPAG00000012307	4 retrocopies	retro_vpac_22, retro_vpac_293, retro_vpac_440, retro_vpac_553,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	60.69 RPM
CEU_NA11843	71.34 RPM
CEU_NA11930	54.14 RPM
CEU_NA12004	69.25 RPM
CEU_NA12400	4.31 RPM
CEU_NA12751	2.40 RPM
CEU_NA12760	11.41 RPM
CEU_NA12827	31.04 RPM
CEU_NA12872	35.90 RPM
CEU_NA12873	11.13 RPM
FIN_HG00183	5.88 RPM
FIN_HG00277	6.29 RPM
FIN_HG00315	35.71 RPM
FIN_HG00321	3.29 RPM
FIN_HG00328	34.75 RPM
FIN_HG00338	39.21 RPM
FIN_HG00349	33.18 RPM
FIN_HG00375	8.24 RPM
FIN_HG00377	2.67 RPM
FIN_HG00378	30.17 RPM
GBR_HG00099	36.99 RPM
GBR_HG00111	6.13 RPM
GBR_HG00114	32.77 RPM
GBR_HG00119	2.44 RPM
GBR_HG00131	33.69 RPM
GBR_HG00133	30.82 RPM
GBR_HG00134	29.26 RPM
GBR_HG00137	35.19 RPM
GBR_HG00142	28.23 RPM
GBR_HG00143	3.35 RPM
TSI_NA20512	7.04 RPM
TSI_NA20513	22.01 RPM
TSI_NA20518	24.04 RPM
TSI_NA20532	29.69 RPM
TSI_NA20538	4.15 RPM
TSI_NA20756	5.35 RPM
TSI_NA20765	25.38 RPM
TSI_NA20771	4.48 RPM
TSI_NA20786	33.87 RPM
TSI_NA20798	10.60 RPM
YRI_NA18870	7.31 RPM
YRI_NA18907	7.18 RPM
YRI_NA18916	8.04 RPM
YRI_NA19093	31.00 RPM
YRI_NA19099	13.63 RPM
YRI_NA19114	89.24 RPM
YRI_NA19118	31.41 RPM
YRI_NA19213	4.59 RPM
YRI_NA19214	24.79 RPM
YRI_NA19223	3.68 RPM

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Indel association:

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