RetrogeneDB ID:

retro_hsap_2556

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:22:31509085..31509379(+)
Located in intron of:ENSG00000198832
Retrocopy
information
Ensembl ID:ENSG00000235573
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RPS15A
Ensembl ID:ENSG00000134419
Aliases:RPS15A, S15a
Description:ribosomal protein S15a [Source:HGNC Symbol;Acc:10389]


Retrocopy-Parental alignment summary:






>retro_hsap_2556
GTCGTCGTCTGGTTTCTAACTGTGGTGATGAAGCATAGTTACACTGGTGAAGTTGAAGTCATTGATGATCACAGAGCTAG
GAAAACTGCTGTGAACCTCACAGGCAGGTTAAACAAGTGTGGAGTAATCAGCCCCTGATTTGATGTGCAACTCAAAAATC
TAGAAAAATGGCAGAATAATCTGCTCCCATCCTGCCAGTTGGGTTTCATTGTACTCACAACCTCAGCTGGCATCATGGAT
CACAAAGAAGCAAGACGAAAACACACAGGAGGTAAAATCCTGGAATTCTTTTTC

ORF - retro_hsap_2556 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 83.67 %
Parental protein coverage: 75.38 %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalVIVRFLTVMMKHGYIGEFEIIDDHRAGKIVVNLTGRLNKCGVISPRFDVQLKDLEKWQNNLLPSRQFGFI
V.V.FLTV.MKH.Y.GE.E.IDDHRA.K..VNLTGRLNKCGVISP.FDVQLK.LEKWQNNLLPS.Q.GFI
RetrocopyVVVWFLTVVMKHSYTGEVEVIDDHRARKTAVNLTGRLNKCGVISP*FDVQLKNLEKWQNNLLPSCQLGFI
ParentalVLTTSAGIMDHEEARRKHTGGKILGFFF
VLTTSAGIMDH.EARRKHTGGKIL.FFF
RetrocopyVLTTSAGIMDHKEARRKHTGGKILEFFF

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 200 .61 RPM
bodymap2_adrenal 0 .00 RPM 353 .30 RPM
bodymap2_brain 0 .00 RPM 50 .30 RPM
bodymap2_breast 0 .00 RPM 192 .84 RPM
bodymap2_colon 0 .00 RPM 301 .02 RPM
bodymap2_heart 0 .04 RPM 80 .56 RPM
bodymap2_kidney 0 .00 RPM 127 .62 RPM
bodymap2_liver 0 .00 RPM 134 .30 RPM
bodymap2_lung 0 .00 RPM 361 .23 RPM
bodymap2_lymph_node 0 .00 RPM 417 .96 RPM
bodymap2_ovary 0 .00 RPM 398 .88 RPM
bodymap2_prostate 0 .07 RPM 417 .43 RPM
bodymap2_skeletal_muscle 0 .00 RPM 229 .60 RPM
bodymap2_testis 0 .00 RPM 192 .89 RPM
bodymap2_thyroid 0 .04 RPM 171 .65 RPM
bodymap2_white_blood_cells 0 .00 RPM 528 .11 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2556 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2556 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_2556 retrocopy 5' end.

Lab - click to see more details

retro_hsap_2556 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2556 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_1599
Parental genes homology:
Parental genes homology involve 21 parental genes, and 288 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG0000001108318 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 ENSBTAG000000207335 retrocopies
retro_btau_14, retro_btau_171, retro_btau_3, retro_btau_57, retro_btau_98,
Callithrix jacchus ENSCJAG000000200716 retrocopies
retro_cjac_120, retro_cjac_128, retro_cjac_170, retro_cjac_231, retro_cjac_359, retro_cjac_80,
Cavia porcellus ENSCPOG0000002169512 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 ENSDNOG0000000834145 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 ENSDORG000000015575 retrocopies
retro_dord_165, retro_dord_455, retro_dord_496, retro_dord_51, retro_dord_582,
Equus caballus ENSECAG000000192932 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 ENSGGOG0000002629932 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 ENSGMOG000000058621 retrocopy
retro_gmor_16,
Latimeria chalumnae ENSLACG000000114761 retrocopy
retro_lcha_55,
Loxodonta africana ENSLAFG0000002699613 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 ENSMICG0000001224120 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 ENSMMUG000000055933 retrocopies
retro_mmul_112, retro_mmul_293, retro_mmul_486,
Oryctolagus cuniculus ENSOCUG0000000017925 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 ENSOGAG0000001319914 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 ENSPPYG000000071392 retrocopies
retro_pabe_2008, retro_pabe_34,
Pan troglodytes ENSPTRG000000078232 retrocopies
retro_ptro_289, retro_ptro_76,
Pteropus vampyrus ENSPVAG0000000290114 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 ENSRNOG000000183205 retrocopies
retro_rnor_1808, retro_rnor_2080, retro_rnor_2586, retro_rnor_324, retro_rnor_378,
Ictidomys tridecemlineatus ENSSTOG0000002522226 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,

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 ) > 0 RPM = 0.02 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 .02 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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