RetrogeneDB ID:

retro_hsap_635

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:10:121397967..121398591(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000227437
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RPS8
Ensembl ID:ENSG00000142937
Aliases:RPS8, S8
Description:ribosomal protein S8 [Source:HGNC Symbol;Acc:10441]


Retrocopy-Parental alignment summary:






>retro_hsap_635
ATGGGCATCTCTCAGGACAACTGGCACAAGCGCCGCAAGACTGGCAGCAAGAGAAAGCCCTACGACAAGAAGCGGAAGTA
TGAGTTGGGGCACCTGGCTGCCAACACCAAGATTGGCCCCCACCACATCCACACAGTCCGTGTGCGGGGAGGTAACAATA
AATACGGTGCCCTGAGGCGGGACATGGGGAATTTCTCCTGGGGTTCAGAGTGTTGTACTCGCAAAACAAGGATCACTGAT
GTTGTCTACGATGCGCCCAATAGCAAGCTGGTCCGTACCAAGACCCTGGTGGAGAACTGCTTCGTGCTCACTGACAGCAC
ACCGTACCACCAGTGGTATGAGTCCCACTATGCGCTGCCCCTGGGCTGCAAGAAGGGAGCCAAACTGACTCCTGAGGAAG
AAAAGACTTTAAACAAAAAACGATCTAAAAAAATTCAGAAGAAATACGATGAAAGGGAAAAGAATGCCAAAATCAGCCGT
CTCCTGGGGGAGCAGTTCCAGCAGGGCAAGCTTCTTGCATGCGTCGCTTCAAGGCTGGGACAGTGTGGCCAAGCCCATGT
CTATGTGCCAGGGGGCAAGGAGATGGAGTTCTATCTTAGGAAAATCAAGGCCCGGAAAGGCAAA

ORF - retro_hsap_635 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 78.85 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMGISRDNWHKRRKTGGKRKPYHKKRKYELGRPAANTKIGPRRIHTVRVRGGNKKYRALRLDVGNFSWGSE
MGIS.DNWHKRRKTG.KRKPY.KKRKYELG..AANTKIGP..IHTVRVRGGN.KY.ALR.D.GNFSWGSE
RetrocopyMGISQDNWHKRRKTGSKRKPYDKKRKYELGHLAANTKIGPHHIHTVRVRGGNNKYGALRRDMGNFSWGSE
ParentalCCTRKTRIIDVVYNASNNELVRTKTLVKNCIVLIDSTPYRQWYESHYALPLGRKKGAKLTPEEEEILNKK
CCTRKTRI.DVVY.A.N..LVRTKTLV.NC.VL.DSTPY.QWYESHYALPLG.KKGAKLTPEE.......
RetrocopyCCTRKTRITDVVYDAPNSKLVRTKTLVENCFVLTDSTPYHQWYESHYALPLGCKKGAKLTPEEXXXXXXX
ParentalRSKKIQKKYDERKKNAKISSLLEEQFQQGKLLACIASRPGQCGRADGYVLEGKELEFYLRKIKARKGK
.....QKKYDER.KNAKIS.LL.EQFQQGKLLAC.ASR.GQCG.A..YV..GKE.EFYLRKIKARKGK
RetrocopyXXXXXQKKYDEREKNAKISRLLGEQFQQGKLLACVASRLGQCGQAHVYVPGGKEMEFYLRKIKARKGK

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 539 .85 RPM
bodymap2_adrenal 0 .00 RPM 743 .31 RPM
bodymap2_brain 0 .09 RPM 176 .67 RPM
bodymap2_breast 0 .00 RPM 378 .82 RPM
bodymap2_colon 0 .00 RPM 728 .15 RPM
bodymap2_heart 0 .00 RPM 195 .24 RPM
bodymap2_kidney 0 .00 RPM 362 .07 RPM
bodymap2_liver 0 .00 RPM 310 .90 RPM
bodymap2_lung 0 .00 RPM 931 .68 RPM
bodymap2_lymph_node 0 .00 RPM 1170 .01 RPM
bodymap2_ovary 0 .00 RPM 1161 .80 RPM
bodymap2_prostate 0 .00 RPM 1422 .79 RPM
bodymap2_skeletal_muscle 0 .00 RPM 536 .16 RPM
bodymap2_testis 0 .02 RPM 415 .20 RPM
bodymap2_thyroid 0 .00 RPM 416 .32 RPM
bodymap2_white_blood_cells 0 .00 RPM 1200 .50 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_635 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_635 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_1747449 libraries647 libraries667 libraries62 libraries4 libraries

The graphical summary, for retro_hsap_635 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_635 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_635 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_556
Parental genes homology:
Parental genes homology involve 16 parental genes, and 91 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000156971 retrocopy
retro_acar_124,
Choloepus hoffmanni ENSCHOG0000000878510 retrocopies
retro_chof_1197, retro_chof_1258, retro_chof_1466, retro_chof_1638, retro_chof_2066, retro_chof_2617, retro_chof_2633, retro_chof_274, retro_chof_331, retro_chof_951,
Callithrix jacchus ENSCJAG000000041975 retrocopies
retro_cjac_1068, retro_cjac_181, retro_cjac_3138, retro_cjac_6, retro_cjac_951,
Dipodomys ordii ENSDORG000000092871 retrocopy
retro_dord_429,
Homo sapiens ENSG00000142937 8 retrocopies
retro_hsap_1467, retro_hsap_1536, retro_hsap_1942, retro_hsap_2034, retro_hsap_2791, retro_hsap_3158, retro_hsap_3410, retro_hsap_635 ,
Gorilla gorilla ENSGGOG000000056455 retrocopies
retro_ggor_1127, retro_ggor_1170, retro_ggor_1357, retro_ggor_1465, retro_ggor_556,
Myotis lucifugus ENSMLUG0000000155930 retrocopies
retro_mluc_1114, retro_mluc_1132, retro_mluc_1165, retro_mluc_1277, retro_mluc_1288, retro_mluc_1418, retro_mluc_1467, retro_mluc_1476, retro_mluc_1486, retro_mluc_1634, retro_mluc_1656, retro_mluc_1689, retro_mluc_1808, retro_mluc_1911, retro_mluc_1938, retro_mluc_2043, retro_mluc_2055, retro_mluc_2085, retro_mluc_2111, retro_mluc_2153, retro_mluc_2182, retro_mluc_2209, retro_mluc_2414, retro_mluc_460, retro_mluc_662, retro_mluc_730, retro_mluc_773, retro_mluc_820, retro_mluc_821, retro_mluc_906,
Macaca mulatta ENSMMUG000000152702 retrocopies
retro_mmul_275, retro_mmul_70,
Monodelphis domestica ENSMODG000000283891 retrocopy
retro_mdom_998,
Oryctolagus cuniculus ENSOCUG000000124761 retrocopy
retro_ocun_168,
Otolemur garnettii ENSOGAG0000000692216 retrocopies
retro_ogar_1156, retro_ogar_1746, retro_ogar_1895, retro_ogar_2501, retro_ogar_2529, retro_ogar_2556, retro_ogar_2699, retro_ogar_2723, retro_ogar_2947, retro_ogar_308, retro_ogar_3291, retro_ogar_3436, retro_ogar_394, retro_ogar_521, retro_ogar_730, retro_ogar_805,
Pan troglodytes ENSPTRG000000006591 retrocopy
retro_ptro_30,
Rattus norvegicus ENSRNOG000000187682 retrocopies
retro_rnor_222, retro_rnor_235,
Sorex araneus ENSSARG000000008991 retrocopy
retro_sara_462,
Ictidomys tridecemlineatus ENSSTOG000000063223 retrocopies
retro_itri_1337, retro_itri_1380, retro_itri_750,
Tursiops truncatus ENSTTRG000000033884 retrocopies
retro_ttru_1839, retro_ttru_282, retro_ttru_300, retro_ttru_344,

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 = 0.03 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 .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 .02 RPM
GBR_HG00099 0 .00 RPM
GBR_HG00111 0 .02 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 .03 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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