RetrogeneDB ID:

retro_hsap_1704

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:16:75226372..75227145(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000213318
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RPS4Y1
Ensembl ID:ENSG00000129824
Aliases:RPS4Y1, RPS4Y, S4
Description:ribosomal protein S4, Y-linked 1 [Source:HGNC Symbol;Acc:10425]


Retrocopy-Parental alignment summary:






>retro_hsap_1704
ATGGCCTGGGGCCCTAAGGAGCACTTGAAGCGTGCTGCAGTGCCGAAGCATTGGATGCTCGACAAACTAAAGGGTATATT
TGCACCTCGTCCATCGACAGGTCCCCACAAGCTGAGGGAATGTCTTCCGCTGATCGTCTTCCTCAGGAATAGACTCAAGT
ATGCATTGACCGGAGATGACGTAAAGGAGATATGTATGCAATGCTTCATTAAAATTGATGGCAAGGTTCGAGTGGCTATC
ACATACCCTGCTGGATTCACGGATGTCATCGGCATCAAGACAGGTGAGCATTTCTGCCTGGTCTGTGACCCAAGGGCTGT
GTTGCTGTTGATCGCGTTACAGTCGAAGAGGCAAAGTACAACCTGTGCAAAGTGAGGAAGGTGACTATGGGGATGAAGGG
AATCCAACGCCTGGTGACTCATGATACTGGAACTATCCACTACCCAGATCCTGTCATCAAGGTGAACAATACTGTGCAGA
TTGATTTAGGGACTGGCAAGATAATCAACTTTATCAAATTCCACACAGGCAATGCGTGTATGGTGATTGGCGGAGCCAGC
CTCCGTCATGTTGGTGTGACCAACAGGGAAGGACATCCTGGTTCTTTAAATGTGGGGCATGTGAGGGATGCCAATGGCAA
CAGCTTTGCCCTGAGGCTTTCCAACATTTTTGTCACTGGCAATGGCAGTAAACCTTGGATTTCCCTGCCCAGGGAAAAGG
GCACCCGACTTACTATTGCTGAAAAGAGAGAGAAGAGGCTGGCCACCAAACAG

ORF - retro_hsap_1704 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 80.46 %
Parental protein coverage: 98.86 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMARGPKKHLKRVAAPKHWMLDKLTGVFAPRPSTGPHKLRECLPLIVFLRNRLKYALTGDEVKKICMQRFI
MA.GPK.HLKR.A.PKHWMLDKL.G.FAPRPSTGPHKLRECLPLIVFLRNRLKYALTGD.VK.ICMQ.FI
RetrocopyMAWGPKEHLKRAAVPKHWMLDKLKGIFAPRPSTGPHKLRECLPLIVFLRNRLKYALTGDDVKEICMQCFI
ParentalKIDGKVRVDVTYPAGFMDVISIEKTGEHFRLVYD-TKGRFAVHRITVEEAKYKLCKVRKITVGVKGIPHL
KIDGKVRV..TYPAGF.DVI.I.KTGEHF.LV.D..KG..AV.R.TVEEAKY.LCKVRK.T.G.KGI..L
RetrocopyKIDGKVRVAITYPAGFTDVIGI-KTGEHFCLVCD<PKGCVAVDRVTVEEAKYNLCKVRKVTMGMKGIQRL
ParentalVTHDARTIRYPDPVIKVNDTVQIDLGTGKIINFIKFDTGNLCMVIGGANLGRVGVITNRERHPGSFDVVH
VTHD..TI.YPDPVIKVN.TVQIDLGTGKIINFIKF.TGN.CMVIGGA.L..VGV.TNRE.HPGS..V.H
RetrocopyVTHDTGTIHYPDPVIKVNNTVQIDLGTGKIINFIKFHTGNACMVIGGASLRHVGV-TNREGHPGSLNVGH
ParentalVKDANGNSFATRLSNIFVIGNGNKPWISLPRGKGIRLTVAEERDKRLATKQ
V.DANGNSFA.RLSNIFV.GNG.KPWISLPR.KG.RLT.AE.R.KRLATKQ
RetrocopyVRDANGNSFALRLSNIFVTGNGSKPWISLPREKGTRLTIAEKREKRLATKQ

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 .08 RPM 0 .18 RPM
bodymap2_adrenal 0 .00 RPM 199 .97 RPM
bodymap2_brain 0 .00 RPM 0 .00 RPM
bodymap2_breast 0 .00 RPM 0 .02 RPM
bodymap2_colon 0 .00 RPM 0 .04 RPM
bodymap2_heart 0 .00 RPM 68 .97 RPM
bodymap2_kidney 0 .00 RPM 0 .00 RPM
bodymap2_liver 0 .00 RPM 51 .58 RPM
bodymap2_lung 0 .00 RPM 193 .72 RPM
bodymap2_lymph_node 0 .00 RPM 0 .00 RPM
bodymap2_ovary 0 .00 RPM 0 .00 RPM
bodymap2_prostate 0 .00 RPM 287 .96 RPM
bodymap2_skeletal_muscle 0 .00 RPM 100 .00 RPM
bodymap2_testis 0 .02 RPM 182 .35 RPM
bodymap2_thyroid 0 .00 RPM 0 .09 RPM
bodymap2_white_blood_cells 0 .00 RPM 274 .76 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_1704 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_1704 retrocopy.

TSS - click to see more details



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_53952986 libraries54 libraries408 libraries283 libraries98 libraries

The graphical summary, for retro_hsap_1704 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)

Display detail expression values in each library
... or ...
Directly download all expression values

Lab - click to see more details

retro_hsap_1704 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1704 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1153
Gorilla gorilla retro_ggor_1278
Pongo abelii retro_pabe_1401
Parental genes homology:
Parental genes homology involve 36 parental genes, and 360 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000146011 retrocopy
retro_acar_82,
Ailuropoda melanoleuca ENSAMEG0000000580514 retrocopies
retro_amel_1003, retro_amel_1128, retro_amel_1296, retro_amel_1381, retro_amel_1695, retro_amel_1869, retro_amel_195, retro_amel_259, retro_amel_327, retro_amel_576, retro_amel_767, retro_amel_869, retro_amel_968, retro_amel_971,
Bos taurus ENSBTAG000000188005 retrocopies
retro_btau_119, retro_btau_125, retro_btau_146, retro_btau_33, retro_btau_76,
Canis familiaris ENSCAFG000000171512 retrocopies
retro_cfam_165, retro_cfam_194,
Callithrix jacchus ENSCJAG000000041922 retrocopies
retro_cjac_19, retro_cjac_361,
Cavia porcellus ENSCPOG000000063373 retrocopies
retro_cpor_1023, retro_cpor_1075, retro_cpor_31,
Dipodomys ordii ENSDORG000000085714 retrocopies
retro_dord_289, retro_dord_650, retro_dord_68, retro_dord_745,
Equus caballus ENSECAG000000108526 retrocopies
retro_ecab_34, retro_ecab_435, retro_ecab_443, retro_ecab_614, retro_ecab_757, retro_ecab_850,
Felis catus ENSFCAG0000001204111 retrocopies
retro_fcat_1155, retro_fcat_1498, retro_fcat_1562, retro_fcat_1751, retro_fcat_1773, retro_fcat_2024, retro_fcat_229, retro_fcat_290, retro_fcat_454, retro_fcat_563, retro_fcat_766,
Homo sapiens ENSG00000129824 1 retrocopy
retro_hsap_1704 ,
Homo sapiens ENSG0000019803419 retrocopies
retro_hsap_1070, retro_hsap_1151, retro_hsap_120, retro_hsap_1204, retro_hsap_1792, retro_hsap_1868, retro_hsap_2026, retro_hsap_2051, retro_hsap_2052, retro_hsap_2270, retro_hsap_2437, retro_hsap_2443, retro_hsap_3162, retro_hsap_3423, retro_hsap_3519, retro_hsap_3986, retro_hsap_4051, retro_hsap_656, retro_hsap_875,
Gorilla gorilla ENSGGOG0000002307918 retrocopies
retro_ggor_1278, retro_ggor_1319, retro_ggor_1354, retro_ggor_1367, retro_ggor_1478, retro_ggor_1479, retro_ggor_1517, retro_ggor_1520, retro_ggor_1689, retro_ggor_223, retro_ggor_2676, retro_ggor_2719, retro_ggor_572, retro_ggor_711, retro_ggor_844, retro_ggor_894, retro_ggor_895, retro_ggor_939,
Loxodonta africana ENSLAFG000000026544 retrocopies
retro_lafr_1007, retro_lafr_1081, retro_lafr_1238, retro_lafr_208,
Macropus eugenii ENSMEUG0000000796916 retrocopies
retro_meug_131, retro_meug_141, retro_meug_1644, retro_meug_1732, retro_meug_1814, retro_meug_194, retro_meug_2098, retro_meug_2121, retro_meug_228, retro_meug_562, retro_meug_628, retro_meug_673, retro_meug_843, retro_meug_872, retro_meug_972, retro_meug_999,
Meleagris gallopavo ENSMGAG000000096711 retrocopy
retro_mgal_3,
Microcebus murinus ENSMICG0000001660658 retrocopies
retro_mmur_1107, retro_mmur_1108, retro_mmur_1123, retro_mmur_1136, retro_mmur_1168, retro_mmur_1208, retro_mmur_1209, retro_mmur_1229, retro_mmur_1231, retro_mmur_1257, retro_mmur_1268, retro_mmur_1334, retro_mmur_1411, retro_mmur_1416, retro_mmur_1430, retro_mmur_1442, retro_mmur_1454, retro_mmur_1467, retro_mmur_1471, retro_mmur_1519, retro_mmur_1578, retro_mmur_1584, retro_mmur_1599, retro_mmur_1600, retro_mmur_1611, retro_mmur_166, retro_mmur_241, retro_mmur_281, retro_mmur_289, retro_mmur_293, retro_mmur_347, retro_mmur_363, retro_mmur_390, retro_mmur_510, retro_mmur_511, retro_mmur_521, retro_mmur_523, retro_mmur_530, retro_mmur_54, retro_mmur_551, retro_mmur_591, retro_mmur_609, retro_mmur_619, retro_mmur_663, retro_mmur_665, retro_mmur_687, retro_mmur_767, retro_mmur_784, retro_mmur_828, retro_mmur_840, retro_mmur_917, retro_mmur_918, retro_mmur_931, retro_mmur_943, retro_mmur_946, retro_mmur_949, retro_mmur_96, retro_mmur_995,
Myotis lucifugus ENSMLUG000000116855 retrocopies
retro_mluc_1638, retro_mluc_2253, retro_mluc_301, retro_mluc_536, retro_mluc_736,
Macaca mulatta ENSMMUG000000032957 retrocopies
retro_mmul_1243, retro_mmul_1589, retro_mmul_1895, retro_mmul_1999, retro_mmul_2338, retro_mmul_43, retro_mmul_97,
Monodelphis domestica ENSMODG000000110701 retrocopy
retro_mdom_238,
Mustela putorius furoENSMPUG0000000529411 retrocopies
retro_mputfur_1044, retro_mputfur_1176, retro_mputfur_1325, retro_mputfur_1326, retro_mputfur_1393, retro_mputfur_160, retro_mputfur_205, retro_mputfur_48, retro_mputfur_725, retro_mputfur_876, retro_mputfur_988,
Mus musculus ENSMUSG0000003132013 retrocopies
retro_mmus_1092, retro_mmus_1686, retro_mmus_2052, retro_mmus_2197, retro_mmus_2487, retro_mmus_2541, retro_mmus_2916, retro_mmus_3025, retro_mmus_3702, retro_mmus_499, retro_mmus_797, retro_mmus_92, retro_mmus_987,
Nomascus leucogenys ENSNLEG0000001812125 retrocopies
retro_nleu_1127, retro_nleu_1226, retro_nleu_1361, retro_nleu_142, retro_nleu_1442, retro_nleu_1907, retro_nleu_1908, retro_nleu_2089, retro_nleu_2256, retro_nleu_244, retro_nleu_2461, retro_nleu_2495, retro_nleu_2587, retro_nleu_2613, retro_nleu_2640, retro_nleu_2646, retro_nleu_2776, retro_nleu_2801, retro_nleu_2932, retro_nleu_2967, retro_nleu_2968, retro_nleu_486, retro_nleu_500, retro_nleu_560, retro_nleu_947,
Otolemur garnettii ENSOGAG000000118082 retrocopies
retro_ogar_121, retro_ogar_229,
Procavia capensis ENSPCAG000000007613 retrocopies
retro_pcap_334, retro_pcap_35, retro_pcap_360,
Pongo abelii ENSPPYG0000002046224 retrocopies
retro_pabe_1005, retro_pabe_1401, retro_pabe_1472, retro_pabe_1524, retro_pabe_1586, retro_pabe_1657, retro_pabe_1673, retro_pabe_1702, retro_pabe_1784, retro_pabe_1948, retro_pabe_2455, retro_pabe_2629, retro_pabe_2836, retro_pabe_2923, retro_pabe_3275, retro_pabe_3325, retro_pabe_340, retro_pabe_493, retro_pabe_579, retro_pabe_580, retro_pabe_679, retro_pabe_891, retro_pabe_921, retro_pabe_954,
Pan troglodytes ENSPTRG000000220259 retrocopies
retro_ptro_1280, retro_ptro_131, retro_ptro_1366, retro_ptro_1367, retro_ptro_1408, retro_ptro_2276, retro_ptro_3032, retro_ptro_728, retro_ptro_784,
Pan troglodytes ENSPTRG000000224701 retrocopy
retro_ptro_1153,
Pteropus vampyrus ENSPVAG0000001288221 retrocopies
retro_pvam_1021, retro_pvam_1082, retro_pvam_1158, retro_pvam_1264, retro_pvam_1298, retro_pvam_1312, retro_pvam_1327, retro_pvam_1364, retro_pvam_1419, retro_pvam_177, retro_pvam_191, retro_pvam_214, retro_pvam_219, retro_pvam_335, retro_pvam_473, retro_pvam_628, retro_pvam_714, retro_pvam_809, retro_pvam_835, retro_pvam_921, retro_pvam_930,
Rattus norvegicus ENSRNOG000000032011 retrocopy
retro_rnor_135,
Sorex araneus ENSSARG000000108066 retrocopies
retro_sara_202, retro_sara_245, retro_sara_297, retro_sara_311, retro_sara_321, retro_sara_612,
Sus scrofa ENSSSCG000000124055 retrocopies
retro_sscr_1070, retro_sscr_563, retro_sscr_580, retro_sscr_665, retro_sscr_973,
Ictidomys tridecemlineatus ENSSTOG000000286928 retrocopies
retro_itri_1179, retro_itri_1607, retro_itri_291, retro_itri_306, retro_itri_368, retro_itri_495, retro_itri_738, retro_itri_985,
Tupaia belangeri ENSTBEG0000000291820 retrocopies
retro_tbel_1108, retro_tbel_1367, retro_tbel_1465, retro_tbel_1798, retro_tbel_2241, retro_tbel_2659, retro_tbel_2711, retro_tbel_2715, retro_tbel_2722, retro_tbel_2743, retro_tbel_2944, retro_tbel_310, retro_tbel_3172, retro_tbel_3232, retro_tbel_4263, retro_tbel_4569, retro_tbel_4572, retro_tbel_4648, retro_tbel_511, retro_tbel_877,
Tarsius syrichta ENSTSYG0000000313716 retrocopies
retro_tsyr_1159, retro_tsyr_1167, retro_tsyr_118, retro_tsyr_1302, retro_tsyr_1333, retro_tsyr_1774, retro_tsyr_1792, retro_tsyr_1931, retro_tsyr_1936, retro_tsyr_2116, retro_tsyr_409, retro_tsyr_440, retro_tsyr_522, retro_tsyr_529, retro_tsyr_750, retro_tsyr_917,
Tursiops truncatus ENSTTRG0000000616413 retrocopies
retro_ttru_104, retro_ttru_1104, retro_ttru_1129, retro_ttru_1748, retro_ttru_260, retro_ttru_465, retro_ttru_470, retro_ttru_512, retro_ttru_565, retro_ttru_618, retro_ttru_631, retro_ttru_728, retro_ttru_734,
Vicugna pacos ENSVPAG000000109524 retrocopies
retro_vpac_244, retro_vpac_460, retro_vpac_604, retro_vpac_653,

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 = 0.06 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .02 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 .03 RPM
FIN_HG00277 0 .00 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .02 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .03 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 .06 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .00 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .03 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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