RetrogeneDB ID: retro_hsap_4033

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 8:29974902..29975222(-)
• Located in intron of: ENSG00000104660

Retrocopy information

• Ensembl ID: ENSG00000241511
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPS15A
• Ensembl ID: ENSG00000134419
• Aliases: RPS15A, S15a
• Description: ribosomal protein S15a [Source:HGNC Symbol;Acc:10389]

Sequence

>retro_hsap_4033
CAGGTGCTTATTAGGCCGTGCTCCAAAGTCATCGTCTGGTTTCTCACTGTGATGATGAAGCATGGTTACATTGGCGAATT
TGAAATCATTGATGATCACAGAGCTGGGAAAATTGTTGTGAACCTCACAGACAGGCTAAACAAGTGTGGAGTGATCAGCC
CCAGATTTGATGTGCAACTCAAAGATCTGGAAAAATGGCAGAAAATCTGTTTCCATCCCTTCAGTTTGGTTTCATTGTAC
TGACAACCTCAGCTGGCATCATGGACCATGAAGAAGCAAGATGAAAACACACAGGAGGGAAAATCCTGGGATTCTTTTTC

Alignment

ORF - retro_hsap_4033 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.52 %
• Parental protein coverage: 82.31 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QVLIRPCSKVIVRFLTVMMKHGYIGEFEIIDDHRAGKIVVNLTGRLNKCGVISPRFDVQLKDLEKWQ-NN
          QVLIRPCSKVIV.FLTVMMKHGYIGEFEIIDDHRAGKIVVNLT.RLNKCGVISPRFDVQLKDLEKWQ..N
Retrocopy QVLIRPCSKVIVWFLTVMMKHGYIGEFEIIDDHRAGKIVVNLTDRLNKCGVISPRFDVQLKDLEKWQ<EN

Parental  LLPSRQFGFIVLTTSAGIMDHEEARRKHTGGKILGFFF
          L.PS.QFGFIVLTTSAGIMDHEEAR.KHTGGKILGFFF
Retrocopy LFPSLQFGFIVLTTSAGIMDHEEAR*KHTGGKILGFFF

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	0.06 RPM	200.61 RPM
bodymap2_adrenal	0.35 RPM	353.30 RPM
bodymap2_brain	0.00 RPM	50.30 RPM
bodymap2_breast	0.14 RPM	192.84 RPM
bodymap2_colon	0.04 RPM	301.02 RPM
bodymap2_heart	0.02 RPM	80.56 RPM
bodymap2_kidney	0.00 RPM	127.62 RPM
bodymap2_liver	0.04 RPM	134.30 RPM
bodymap2_lung	0.07 RPM	361.23 RPM
bodymap2_lymph_node	0.53 RPM	417.96 RPM
bodymap2_ovary	0.13 RPM	398.88 RPM
bodymap2_prostate	0.05 RPM	417.43 RPM
bodymap2_skeletal_muscle	0.02 RPM	229.60 RPM
bodymap2_testis	0.00 RPM	192.89 RPM
bodymap2_thyroid	0.09 RPM	171.65 RPM
bodymap2_white_blood_cells	0.02 RPM	528.11 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_4033 was not detected

EST

No EST(s) were mapped for retro_hsap_4033 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_184147	35 libraries	2 libraries	84 libraries	157 libraries	1551 libraries

The graphical summary, for retro_hsap_4033 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_4033 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_4033 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_2706

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 288 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011083	18 retrocopies	retro_amel_106, retro_amel_123, retro_amel_1489, retro_amel_1572, retro_amel_1575, retro_amel_1708, retro_amel_1770, retro_amel_1894, retro_amel_245, retro_amel_271, retro_amel_319, retro_amel_438, retro_amel_442, retro_amel_603, retro_amel_648, retro_amel_66, retro_amel_766, retro_amel_96,
Bos taurus	ENSBTAG00000020733	5 retrocopies	retro_btau_14, retro_btau_171, retro_btau_3, retro_btau_57, retro_btau_98,
Callithrix jacchus	ENSCJAG00000020071	6 retrocopies	retro_cjac_120, retro_cjac_128, retro_cjac_170, retro_cjac_231, retro_cjac_359, retro_cjac_80,
Cavia porcellus	ENSCPOG00000021695	12 retrocopies	retro_cpor_1031, retro_cpor_1087, retro_cpor_1103, retro_cpor_1334, retro_cpor_146, retro_cpor_403, retro_cpor_515, retro_cpor_557, retro_cpor_636, retro_cpor_730, retro_cpor_90, retro_cpor_926,
Dasypus novemcinctus	ENSDNOG00000008341	45 retrocopies	retro_dnov_1029, retro_dnov_1031, retro_dnov_1053, retro_dnov_1060, retro_dnov_1079, retro_dnov_1197, retro_dnov_1246, retro_dnov_147, retro_dnov_1598, retro_dnov_1738, retro_dnov_1766, retro_dnov_1794, retro_dnov_1954, retro_dnov_1963, retro_dnov_2002, retro_dnov_2012, retro_dnov_2047, retro_dnov_2119, retro_dnov_2155, retro_dnov_2182, retro_dnov_2206, retro_dnov_2326, retro_dnov_2338, retro_dnov_2355, retro_dnov_2401, retro_dnov_2437, retro_dnov_2458, retro_dnov_2478, retro_dnov_2479, retro_dnov_2492, retro_dnov_2516, retro_dnov_2519, retro_dnov_2655, retro_dnov_2669, retro_dnov_2689, retro_dnov_462, retro_dnov_494, retro_dnov_505, retro_dnov_629, retro_dnov_653, retro_dnov_667, retro_dnov_686, retro_dnov_774, retro_dnov_785, retro_dnov_87,
Dipodomys ordii	ENSDORG00000001557	5 retrocopies	retro_dord_165, retro_dord_455, retro_dord_496, retro_dord_51, retro_dord_582,
Equus caballus	ENSECAG00000019293	2 retrocopies	retro_ecab_114, retro_ecab_485,
Homo sapiens	ENSG00000134419	37 retrocopies	retro_hsap_1057, retro_hsap_1335, retro_hsap_1411, retro_hsap_1425, retro_hsap_164, retro_hsap_1695, retro_hsap_1769, retro_hsap_1932, retro_hsap_2020, retro_hsap_2087, retro_hsap_2117, retro_hsap_212, retro_hsap_2181, retro_hsap_2459, retro_hsap_2556, retro_hsap_2586, retro_hsap_3044, retro_hsap_3409, retro_hsap_3456, retro_hsap_351, retro_hsap_3514, retro_hsap_3539, retro_hsap_3590, retro_hsap_370, retro_hsap_374, retro_hsap_3904, retro_hsap_3987, retro_hsap_4033 , retro_hsap_4071, retro_hsap_4300, retro_hsap_4802, retro_hsap_509, retro_hsap_629, retro_hsap_636, retro_hsap_685, retro_hsap_727, retro_hsap_861,
Gorilla gorilla	ENSGGOG00000026299	32 retrocopies	retro_ggor_109, retro_ggor_1270, retro_ggor_1406, retro_ggor_1532, retro_ggor_1599, retro_ggor_1619, retro_ggor_1631, retro_ggor_1642, retro_ggor_1728, retro_ggor_2242, retro_ggor_2332, retro_ggor_2376, retro_ggor_2390, retro_ggor_248, retro_ggor_2631, retro_ggor_2706, retro_ggor_283, retro_ggor_2874, retro_ggor_2989, retro_ggor_3075, retro_ggor_340, retro_ggor_365, retro_ggor_384, retro_ggor_466, retro_ggor_469, retro_ggor_551, retro_ggor_557, retro_ggor_558, retro_ggor_588, retro_ggor_614, retro_ggor_835, retro_ggor_85,
Gadus morhua	ENSGMOG00000005862	1 retrocopy	retro_gmor_16,
Latimeria chalumnae	ENSLACG00000011476	1 retrocopy	retro_lcha_55,
Loxodonta africana	ENSLAFG00000026996	13 retrocopies	retro_lafr_1161, retro_lafr_1201, retro_lafr_210, retro_lafr_236, retro_lafr_247, retro_lafr_309, retro_lafr_323, retro_lafr_356, retro_lafr_571, retro_lafr_613, retro_lafr_629, retro_lafr_759, retro_lafr_956,
Microcebus murinus	ENSMICG00000012241	20 retrocopies	retro_mmur_1007, retro_mmur_1051, retro_mmur_1112, retro_mmur_113, retro_mmur_1256, retro_mmur_1459, retro_mmur_1536, retro_mmur_185, retro_mmur_239, retro_mmur_250, retro_mmur_261, retro_mmur_297, retro_mmur_319, retro_mmur_486, retro_mmur_536, retro_mmur_570, retro_mmur_587, retro_mmur_772, retro_mmur_788, retro_mmur_984,
Macaca mulatta	ENSMMUG00000005593	3 retrocopies	retro_mmul_112, retro_mmul_293, retro_mmul_486,
Oryctolagus cuniculus	ENSOCUG00000000179	25 retrocopies	retro_ocun_1018, retro_ocun_1067, retro_ocun_1078, retro_ocun_1154, retro_ocun_1157, retro_ocun_1168, retro_ocun_1181, retro_ocun_1310, retro_ocun_1343, retro_ocun_1384, retro_ocun_1435, retro_ocun_144, retro_ocun_1600, retro_ocun_239, retro_ocun_253, retro_ocun_540, retro_ocun_559, retro_ocun_581, retro_ocun_587, retro_ocun_594, retro_ocun_634, retro_ocun_748, retro_ocun_780, retro_ocun_806, retro_ocun_92,
Otolemur garnettii	ENSOGAG00000013199	14 retrocopies	retro_ogar_102, retro_ogar_1254, retro_ogar_1302, retro_ogar_1361, retro_ogar_1636, retro_ogar_2241, retro_ogar_2361, retro_ogar_269, retro_ogar_2775, retro_ogar_3283, retro_ogar_3367, retro_ogar_563, retro_ogar_712, retro_ogar_87,
Pongo abelii	ENSPPYG00000007139	2 retrocopies	retro_pabe_2008, retro_pabe_34,
Pan troglodytes	ENSPTRG00000007823	2 retrocopies	retro_ptro_289, retro_ptro_76,
Pteropus vampyrus	ENSPVAG00000002901	14 retrocopies	retro_pvam_102, retro_pvam_1132, retro_pvam_1238, retro_pvam_1341, retro_pvam_344, retro_pvam_362, retro_pvam_364, retro_pvam_381, retro_pvam_383, retro_pvam_494, retro_pvam_50, retro_pvam_573, retro_pvam_834, retro_pvam_943,
Rattus norvegicus	ENSRNOG00000018320	5 retrocopies	retro_rnor_1808, retro_rnor_2080, retro_rnor_2586, retro_rnor_324, retro_rnor_378,
Ictidomys tridecemlineatus	ENSSTOG00000025222	26 retrocopies	retro_itri_1013, retro_itri_1037, retro_itri_1092, retro_itri_1103, retro_itri_1213, retro_itri_1297, retro_itri_1407, retro_itri_1493, retro_itri_1504, retro_itri_1516, retro_itri_1726, retro_itri_205, retro_itri_255, retro_itri_443, retro_itri_452, retro_itri_475, retro_itri_491, retro_itri_498, retro_itri_536, retro_itri_624, retro_itri_692, retro_itri_716, retro_itri_829, retro_itri_839, retro_itri_844, retro_itri_927,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.06 RPM
CEU_NA11843	0.23 RPM
CEU_NA11930	0.23 RPM
CEU_NA12004	0.04 RPM
CEU_NA12400	0.14 RPM
CEU_NA12751	0.07 RPM
CEU_NA12760	0.22 RPM
CEU_NA12827	0.19 RPM
CEU_NA12872	0.11 RPM
CEU_NA12873	0.10 RPM
FIN_HG00183	0.27 RPM
FIN_HG00277	0.11 RPM
FIN_HG00315	0.28 RPM
FIN_HG00321	0.06 RPM
FIN_HG00328	0.12 RPM
FIN_HG00338	0.11 RPM
FIN_HG00349	0.06 RPM
FIN_HG00375	0.12 RPM
FIN_HG00377	0.08 RPM
FIN_HG00378	0.08 RPM
GBR_HG00099	0.12 RPM
GBR_HG00111	0.06 RPM
GBR_HG00114	0.03 RPM
GBR_HG00119	0.05 RPM
GBR_HG00131	0.09 RPM
GBR_HG00133	0.00 RPM
GBR_HG00134	0.07 RPM
GBR_HG00137	0.11 RPM
GBR_HG00142	0.06 RPM
GBR_HG00143	0.13 RPM
TSI_NA20512	0.14 RPM
TSI_NA20513	0.05 RPM
TSI_NA20518	0.36 RPM
TSI_NA20532	0.14 RPM
TSI_NA20538	0.14 RPM
TSI_NA20756	0.03 RPM
TSI_NA20765	0.08 RPM
TSI_NA20771	0.09 RPM
TSI_NA20786	0.10 RPM
TSI_NA20798	0.03 RPM
YRI_NA18870	0.03 RPM
YRI_NA18907	0.03 RPM
YRI_NA18916	0.13 RPM
YRI_NA19093	0.10 RPM
YRI_NA19099	0.13 RPM
YRI_NA19114	0.16 RPM
YRI_NA19118	0.17 RPM
YRI_NA19213	0.05 RPM
YRI_NA19214	0.02 RPM
YRI_NA19223	0.10 RPM

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Indel association:

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