RetrogeneDB ID:

retro_hsap_289

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:1:201489331..201489675(+)
Located in intron of:ENSG00000224536
Retrocopy
information
Ensembl ID:ENSG00000242150
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RPS10
Ensembl ID:ENSG00000124614
Aliases:RPS10, DBA9, S10
Description:ribosomal protein S10 [Source:HGNC Symbol;Acc:10383]


Retrocopy-Parental alignment summary:






>retro_hsap_289
AGTCTCTCAAGTCCCGAGGCTACGTGAAGGAAGTTTGCCTGGAGACATTTCTACTGGTACCTTACCAATGAGGGTATCCA
GTATCTCTGTGATTACCTTCATCTGCCCTCGGAGATTGTGCCTGCCACCTTACACCGCAGCTGTCCAGAGACTGGCAGGC
CTTGGCCTAAAGTCTGGAGGGTGAGCGACCTGCAAGACTCACAAGAGGGGAAGCCAACAGAGATACCTACAAACGGAGTG
CTGTGCCCCCTGGTGCCAACAAGAAAGCCGAGGCTGGGGCCGGGTCAGCAACCAAATTCCAGTTCAGAGATGGATTTGGT
TGTGGACGTGGTCAGCCACCTCAG

ORF - retro_hsap_289 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 81.9 %
Parental protein coverage: 69.7 %
Number of stop codons detected: 1
Number of frameshifts detected: 1


Retrocopy - Parental Gene Alignment:

ParentalSLKSRGYVKEQFAWRHFYWYLTNEGIQYLRDYLHLPPEIVPATLRRSRPETGRPRPK-GLEGERPARLTR
SL.S.......FAWRHFYWYLTNEGIQYL.DYLHLP.EIVPATL.RS.PETGRP.PK..LEGERPARLTR
RetrocopySLSSPEAT*RKFAWRHFYWYLTNEGIQYLCDYLHLPSEIVPATLHRSCPETGRPWPK<SLEGERPARLTR
ParentalGEADRDTYRRSAVPPGADKKAEAGAGSATEFQFRGGFGRGRGQPPQ
GEA.RDTY.RSAVPPGA.KKAEAGAGSAT.FQFR.GFG.GRGQPPQ
RetrocopyGEANRDTYKRSAVPPGANKKAEAGAGSATKFQFRDGFGCGRGQPPQ

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 .32 RPM 30 .51 RPM
bodymap2_adrenal 0 .68 RPM 65 .30 RPM
bodymap2_brain 0 .68 RPM 3 .61 RPM
bodymap2_breast 0 .39 RPM 33 .87 RPM
bodymap2_colon 0 .66 RPM 20 .48 RPM
bodymap2_heart 0 .22 RPM 1 .90 RPM
bodymap2_kidney 0 .46 RPM 6 .35 RPM
bodymap2_liver 0 .28 RPM 2 .53 RPM
bodymap2_lung 0 .18 RPM 7 .21 RPM
bodymap2_lymph_node 0 .11 RPM 9 .17 RPM
bodymap2_ovary 0 .50 RPM 57 .73 RPM
bodymap2_prostate 0 .80 RPM 8 .95 RPM
bodymap2_skeletal_muscle 0 .13 RPM 3 .66 RPM
bodymap2_testis 0 .23 RPM 14 .37 RPM
bodymap2_thyroid 0 .79 RPM 25 .57 RPM
bodymap2_white_blood_cells 0 .81 RPM 9 .71 RPM

ChIP-Seq - click to see more details

RNA Polymerase II activity near the 5' end of retro_hsap_289 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_289 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_289 retrocopy 5' end.

Lab - click to see more details

retro_hsap_289 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_289 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_238
Macaca mulatta retro_mmul_555
Parental genes homology:
Parental genes homology involve 21 parental genes, and 139 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000152504 retrocopies
retro_cjac_215, retro_cjac_296, retro_cjac_325, retro_cjac_63,
Dasypus novemcinctus ENSDNOG000000116702 retrocopies
retro_dnov_2303, retro_dnov_2558,
Dipodomys ordii ENSDORG000000120606 retrocopies
retro_dord_225, retro_dord_494, retro_dord_641, retro_dord_73, retro_dord_74, retro_dord_767,
Equus caballus ENSECAG000000064301 retrocopy
retro_ecab_198,
Homo sapiens ENSG00000124614 24 retrocopies
retro_hsap_1509, retro_hsap_1628, retro_hsap_1630, retro_hsap_1657, retro_hsap_1923, retro_hsap_2003, retro_hsap_2113, retro_hsap_229, retro_hsap_2415, retro_hsap_2573, retro_hsap_2574, retro_hsap_2830, retro_hsap_289 , retro_hsap_3007, retro_hsap_3170, retro_hsap_3243, retro_hsap_3436, retro_hsap_3454, retro_hsap_3720, retro_hsap_4114, retro_hsap_4190, retro_hsap_460, retro_hsap_869, retro_hsap_992,
Latimeria chalumnae ENSLACG000000172191 retrocopy
retro_lcha_26,
Loxodonta africana ENSLAFG000000085391 retrocopy
retro_lafr_756,
Macaca mulatta ENSMMUG000000002672 retrocopies
retro_mmul_332, retro_mmul_555,
Monodelphis domestica ENSMODG000000139292 retrocopies
retro_mdom_1889, retro_mdom_437,
Mus musculus ENSMUSG000000521469 retrocopies
retro_mmus_1376, retro_mmus_1500, retro_mmus_1831, retro_mmus_2431, retro_mmus_2551, retro_mmus_2708, retro_mmus_3651, retro_mmus_5, retro_mmus_858,
Nomascus leucogenys ENSNLEG0000000833624 retrocopies
retro_nleu_1064, retro_nleu_1206, retro_nleu_1217, retro_nleu_1366, retro_nleu_1463, retro_nleu_1496, retro_nleu_165, retro_nleu_1694, retro_nleu_1748, retro_nleu_1969, retro_nleu_2120, retro_nleu_2452, retro_nleu_2678, retro_nleu_2791, retro_nleu_2833, retro_nleu_2834, retro_nleu_2950, retro_nleu_2955, retro_nleu_3021, retro_nleu_3047, retro_nleu_3052, retro_nleu_579, retro_nleu_850, retro_nleu_882,
Oryctolagus cuniculus ENSOCUG000000113732 retrocopies
retro_ocun_250, retro_ocun_874,
Ochotona princeps ENSOPRG000000026932 retrocopies
retro_opri_297, retro_opri_800,
Procavia capensis ENSPCAG000000127951 retrocopy
retro_pcap_309,
Pongo abelii ENSPPYG000000165162 retrocopies
retro_pabe_2319, retro_pabe_97,
Pan troglodytes ENSPTRG0000001806326 retrocopies
retro_ptro_1021, retro_ptro_1090, retro_ptro_1092, retro_ptro_1126, retro_ptro_1160, retro_ptro_1287, retro_ptro_1335, retro_ptro_1391, retro_ptro_1497, retro_ptro_1502, retro_ptro_1503, retro_ptro_1788, retro_ptro_1918, retro_ptro_199, retro_ptro_2192, retro_ptro_2330, retro_ptro_2342, retro_ptro_238, retro_ptro_2519, retro_ptro_2793, retro_ptro_2797, retro_ptro_2919, retro_ptro_3051, retro_ptro_3078, retro_ptro_347, retro_ptro_603,
Rattus norvegicus ENSRNOG000000004904 retrocopies
retro_rnor_169, retro_rnor_224, retro_rnor_359, retro_rnor_74,
Sarcophilus harrisii ENSSHAG000000007313 retrocopies
retro_shar_243, retro_shar_334, retro_shar_724,
Ictidomys tridecemlineatus ENSSTOG000000134865 retrocopies
retro_itri_1448, retro_itri_1515, retro_itri_230, retro_itri_787, retro_itri_963,
Tupaia belangeri ENSTBEG0000000149216 retrocopies
retro_tbel_1302, retro_tbel_175, retro_tbel_1775, retro_tbel_2039, retro_tbel_2061, retro_tbel_2062, retro_tbel_2766, retro_tbel_2814, retro_tbel_314, retro_tbel_3359, retro_tbel_483, retro_tbel_522, retro_tbel_667, retro_tbel_980, retro_tbel_981, retro_tbel_986,
Tursiops truncatus ENSTTRG000000150642 retrocopies
retro_ttru_1089, retro_ttru_1211,

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 = 2.89 RPM Legend:


Library Retrogene expression
CEU_NA11831 1 .56 RPM
CEU_NA11843 1 .59 RPM
CEU_NA11930 1 .27 RPM
CEU_NA12004 0 .34 RPM
CEU_NA12400 1 .33 RPM
CEU_NA12751 1 .31 RPM
CEU_NA12760 1 .30 RPM
CEU_NA12827 1 .46 RPM
CEU_NA12872 1 .09 RPM
CEU_NA12873 0 .73 RPM
FIN_HG00183 1 .56 RPM
FIN_HG00277 1 .40 RPM
FIN_HG00315 1 .27 RPM
FIN_HG00321 1 .63 RPM
FIN_HG00328 1 .40 RPM
FIN_HG00338 1 .47 RPM
FIN_HG00349 0 .63 RPM
FIN_HG00375 1 .08 RPM
FIN_HG00377 0 .93 RPM
FIN_HG00378 1 .47 RPM
GBR_HG00099 0 .81 RPM
GBR_HG00111 0 .90 RPM
GBR_HG00114 1 .18 RPM
GBR_HG00119 1 .60 RPM
GBR_HG00131 1 .03 RPM
GBR_HG00133 0 .72 RPM
GBR_HG00134 0 .90 RPM
GBR_HG00137 1 .18 RPM
GBR_HG00142 1 .56 RPM
GBR_HG00143 0 .93 RPM
TSI_NA20512 1 .16 RPM
TSI_NA20513 1 .48 RPM
TSI_NA20518 0 .86 RPM
TSI_NA20532 1 .84 RPM
TSI_NA20538 1 .34 RPM
TSI_NA20756 1 .16 RPM
TSI_NA20765 1 .95 RPM
TSI_NA20771 1 .30 RPM
TSI_NA20786 1 .12 RPM
TSI_NA20798 1 .59 RPM
YRI_NA18870 1 .86 RPM
YRI_NA18907 1 .53 RPM
YRI_NA18916 1 .60 RPM
YRI_NA19093 1 .35 RPM
YRI_NA19099 2 .02 RPM
YRI_NA19114 1 .15 RPM
YRI_NA19118 1 .16 RPM
YRI_NA19213 2 .89 RPM
YRI_NA19214 1 .65 RPM
YRI_NA19223 1 .49 RPM

Indel association:

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



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