RetrogeneDB ID:

retro_hsap_3552

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:6:7339089..7339801(-)
Located in intron of:ENSG00000164304
Retrocopy
information
Ensembl ID:ENSG00000220472
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RPS3
Ensembl ID:ENSG00000149273
Aliases:RPS3, S3
Description:ribosomal protein S3 [Source:HGNC Symbol;Acc:10420]


Retrocopy-Parental alignment summary:






>retro_hsap_3552
ATCGCCTTACAAATTTCCAAGAAGAGGAAGTTTGTCACTGATGGCATCTTCTAAGCTGAAATGAATGAGTTTCTTACTCA
GGAGCTGGCTGAAGATGGCTACTCTGGAGTTGAGATGCGAGTTACACCAACCAGGACAGAAATCATTGTCTTAGCCACCA
GAACACAGAATGTTCTTGGTGAGAAGGGCCGGCGGATTCGGGAACTGACTGCTGTAGTTCAGAAGAGGTTTGGCTCTCCA
GAGGGCAGTGTAGAGCTTTATGCTGAAGAGGTGGCCACTAGGGGTCTGTGTGCCATTGCCCAGGCAGAGTCTCTGCCTTA
CAAACTCCTAGGAGGGCTTGCTGTGCGGAGGGCCTGCTATGGTGTGTCGCGGTTCATCATGGAAACTGGGGCCAAAGGCT
GTGAGGTCGTGGTGTCTGGGAAACTCTGAGGACAGAGAGCTAAATCCATGAAGTTTGTGGACGGCCTGATGATCCACAGC
AGAGACCCTGTTAACTACTACGTTGACACTGCTGTGCGCCATGTGTTGCTCAGACAGAGTGTGCTGGGCATCAAGGTGAA
GATCATGCTGCCCTGGGACCCAACTGGTAAGATTGGCCCTAAGAAGCCCCTGCCTGACCACGTGAGCATCGTGGAACCCA
AAGATGAGATAACTGCCCACCACCCCCATCTCAGAACAGAAGGGTGGGAAGCCAGAGCCTCCTGCCGTGCCC

ORF - retro_hsap_3552 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 92.44 %
Parental protein coverage: 97.53 %
Number of stop codons detected: 2
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMAVQISKKRKFVADGIFKAELNEFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLGEKGRRIRELT
.A.QISKKRKFV.DGIF.AE.NEFLT.ELAEDGYSGVE.RVTPTRTEII.LATRTQNVLGEKGRRIRELT
RetrocopyIALQISKKRKFVTDGIF*AEMNEFLTQELAEDGYSGVEMRVTPTRTEIIVLATRTQNVLGEKGRRIRELT
ParentalAVVQKRFGFPEGSVELYAEKVATRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFIMESGAKGCEVVVSG
AVVQKRFG.PEGSVELYAE.VATRGLCAIAQAESL.YKLLGGLAVRRACYGV.RFIME.GAKGCEVVVSG
RetrocopyAVVQKRFGSPEGSVELYAEEVATRGLCAIAQAESLPYKLLGGLAVRRACYGVSRFIMETGAKGCEVVVSG
ParentalKLRGQRAKSMKFVDGLMIHSGDPVNYYVDTAVRHVLLRQGVLGIKVKIMLPWDPTGKIGPKKPLPDHVSI
KL.GQRAKSMKFVDGLMIHS.DPVNYYVDTAVRHVLLRQ.VLGIKVKIMLPWDPTGKIGPKKPLPDHVSI
RetrocopyKL*GQRAKSMKFVDGLMIHSRDPVNYYVDTAVRHVLLRQSVLGIKVKIMLPWDPTGKIGPKKPLPDHVSI
ParentalVEPKDEI-LPTTPISEQKGGKPEPPAMP
VEPKDEI.LPTTPISEQKGGKPEPPA.P
RetrocopyVEPKDEI>LPTTPISEQKGGKPEPPAVP

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 .02 RPM 735 .72 RPM
bodymap2_adrenal 0 .18 RPM 1220 .25 RPM
bodymap2_brain 0 .00 RPM 171 .82 RPM
bodymap2_breast 0 .00 RPM 579 .52 RPM
bodymap2_colon 0 .02 RPM 1160 .07 RPM
bodymap2_heart 0 .04 RPM 160 .98 RPM
bodymap2_kidney 0 .14 RPM 341 .77 RPM
bodymap2_liver 0 .02 RPM 202 .32 RPM
bodymap2_lung 0 .00 RPM 759 .81 RPM
bodymap2_lymph_node 0 .04 RPM 1084 .08 RPM
bodymap2_ovary 0 .15 RPM 1743 .44 RPM
bodymap2_prostate 0 .05 RPM 1149 .88 RPM
bodymap2_skeletal_muscle 0 .05 RPM 321 .94 RPM
bodymap2_testis 0 .02 RPM 630 .52 RPM
bodymap2_thyroid 0 .08 RPM 649 .30 RPM
bodymap2_white_blood_cells 0 .04 RPM 1368 .87 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3552 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3552 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_167572405 libraries724 libraries689 libraries9 libraries2 libraries

The graphical summary, for retro_hsap_3552 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_3552 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3552 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Macaca mulatta retro_mmul_1816
Parental genes homology:
Parental genes homology involve 30 parental genes, and 97 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000170512 retrocopies
retro_amel_1483, retro_amel_465,
Bos taurus ENSBTAG000000056204 retrocopies
retro_btau_1626, retro_btau_425, retro_btau_909, retro_btau_924,
Canis familiaris ENSCAFG000000054022 retrocopies
retro_cfam_1411, retro_cfam_1569,
Choloepus hoffmanni ENSCHOG000000053288 retrocopies
retro_chof_1301, retro_chof_1369, retro_chof_1492, retro_chof_199, retro_chof_2477, retro_chof_2506, retro_chof_452, retro_chof_571,
Callithrix jacchus ENSCJAG000000154244 retrocopies
retro_cjac_2355, retro_cjac_2593, retro_cjac_388, retro_cjac_3963,
Cavia porcellus ENSCPOG000000046651 retrocopy
retro_cpor_995,
Dipodomys ordii ENSDORG000000029742 retrocopies
retro_dord_608, retro_dord_758,
Equus caballus ENSECAG000000139152 retrocopies
retro_ecab_588, retro_ecab_96,
Echinops telfairi ENSETEG000000155003 retrocopies
retro_etel_1225, retro_etel_1757, retro_etel_857,
Felis catus ENSFCAG000000119423 retrocopies
retro_fcat_1462, retro_fcat_1490, retro_fcat_981,
Homo sapiens ENSG00000149273 4 retrocopies
retro_hsap_1124, retro_hsap_1655, retro_hsap_2736, retro_hsap_3552 ,
Gorilla gorilla ENSGGOG000000065194 retrocopies
retro_ggor_1248, retro_ggor_1509, retro_ggor_216, retro_ggor_878,
Loxodonta africana ENSLAFG000000042973 retrocopies
retro_lafr_278, retro_lafr_600, retro_lafr_861,
Macropus eugenii ENSMEUG000000115814 retrocopies
retro_meug_1724, retro_meug_399, retro_meug_431, retro_meug_774,
Myotis lucifugus ENSMLUG000000040793 retrocopies
retro_mluc_1092, retro_mluc_680, retro_mluc_934,
Macaca mulatta ENSMMUG000000090196 retrocopies
retro_mmul_1166, retro_mmul_1634, retro_mmul_1779, retro_mmul_1816, retro_mmul_665, retro_mmul_871,
Monodelphis domestica ENSMODG000000069451 retrocopy
retro_mdom_304,
Mustela putorius furoENSMPUG000000091973 retrocopies
retro_mputfur_412, retro_mputfur_443, retro_mputfur_936,
Mus musculus ENSMUSG000000307442 retrocopies
retro_mmus_1453, retro_mmus_1776,
Nomascus leucogenys ENSNLEG000000269152 retrocopies
retro_nleu_103, retro_nleu_236,
Oryctolagus cuniculus ENSOCUG000000224123 retrocopies
retro_ocun_11, retro_ocun_1934, retro_ocun_787,
Otolemur garnettii ENSOGAG000000053187 retrocopies
retro_ogar_1180, retro_ogar_1354, retro_ogar_1559, retro_ogar_1574, retro_ogar_2577, retro_ogar_2786, retro_ogar_999,
Pongo abelii ENSPPYG000000036884 retrocopies
retro_pabe_1367, retro_pabe_2274, retro_pabe_2933, retro_pabe_929,
Pteropus vampyrus ENSPVAG000000112711 retrocopy
retro_pvam_1388,
Rattus norvegicus ENSRNOG000000174183 retrocopies
retro_rnor_2328, retro_rnor_283, retro_rnor_930,
Sarcophilus harrisii ENSSHAG000000111981 retrocopy
retro_shar_705,
Sus scrofa ENSSSCG000000148554 retrocopies
retro_sscr_283, retro_sscr_556, retro_sscr_568, retro_sscr_900,
Tupaia belangeri ENSTBEG000000070534 retrocopies
retro_tbel_1194, retro_tbel_2090, retro_tbel_265, retro_tbel_4262,
Tursiops truncatus ENSTTRG000000058585 retrocopies
retro_ttru_1108, retro_ttru_1413, retro_ttru_1927, retro_ttru_50, retro_ttru_544,
Vicugna pacos ENSVPAG000000116152 retrocopies
retro_vpac_131, retro_vpac_145,

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 = 0.98 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .34 RPM
CEU_NA11843 0 .63 RPM
CEU_NA11930 0 .98 RPM
CEU_NA12004 0 .49 RPM
CEU_NA12400 0 .74 RPM
CEU_NA12751 0 .51 RPM
CEU_NA12760 0 .40 RPM
CEU_NA12827 0 .61 RPM
CEU_NA12872 0 .38 RPM
CEU_NA12873 0 .32 RPM
FIN_HG00183 0 .38 RPM
FIN_HG00277 0 .22 RPM
FIN_HG00315 0 .44 RPM
FIN_HG00321 0 .18 RPM
FIN_HG00328 0 .43 RPM
FIN_HG00338 0 .51 RPM
FIN_HG00349 0 .46 RPM
FIN_HG00375 0 .22 RPM
FIN_HG00377 0 .40 RPM
FIN_HG00378 0 .42 RPM
GBR_HG00099 0 .29 RPM
GBR_HG00111 0 .26 RPM
GBR_HG00114 0 .16 RPM
GBR_HG00119 0 .17 RPM
GBR_HG00131 0 .43 RPM
GBR_HG00133 0 .31 RPM
GBR_HG00134 0 .33 RPM
GBR_HG00137 0 .22 RPM
GBR_HG00142 0 .14 RPM
GBR_HG00143 0 .32 RPM
TSI_NA20512 0 .42 RPM
TSI_NA20513 0 .29 RPM
TSI_NA20518 0 .28 RPM
TSI_NA20532 0 .24 RPM
TSI_NA20538 0 .37 RPM
TSI_NA20756 0 .52 RPM
TSI_NA20765 0 .46 RPM
TSI_NA20771 0 .23 RPM
TSI_NA20786 0 .34 RPM
TSI_NA20798 0 .16 RPM
YRI_NA18870 0 .41 RPM
YRI_NA18907 0 .35 RPM
YRI_NA18916 0 .21 RPM
YRI_NA19093 0 .18 RPM
YRI_NA19099 0 .24 RPM
YRI_NA19114 0 .34 RPM
YRI_NA19118 0 .17 RPM
YRI_NA19213 0 .36 RPM
YRI_NA19214 0 .25 RPM
YRI_NA19223 0 .22 RPM

Indel association:

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



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