RetrogeneDB ID:

retro_hsap_230

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:1:151730574..151730908(+)
Located in intron of:ENSG00000269621
Retrocopy
information
Ensembl ID:ENSG00000236940
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RPS11
Ensembl ID:ENSG00000142534
Aliases:RPS11, S11
Description:ribosomal protein S11 [Source:HGNC Symbol;Acc:10384]


Retrocopy-Parental alignment summary:






>retro_hsap_230
TTGGGCTTCAATATGCCCAAATAGGCTATGAGGGCACCTATATTTACACTGATTGCCCTTTATTGGTAACATCTCCATCT
GAGGGTGGATCCTGTCTGGCATGGTGACCAAGATAAAAGATGCAAAAGATCAACATCATCCACCAAGACTATTTCCACTA
CATGTGTAAGTACAGTTGCTTCAAGAAGCACAAGAACATGTTCATGCACCCATCCCCTTGCATCAGGGATGTCCAGATCA
GCAACATCATCATGGTTGGGTAAGCACCAGCATGAGCAAGATGGTACACTTCAACATGCTCATGGTCCCCAATGCCACCA
AGAAGCAATTCCAG

ORF - retro_hsap_230 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 57.14 %
Parental protein coverage: 72.78 %
Number of stop codons detected: 2
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalLGFKTPKEAI-EGTYIDKKCP-FTGNVSIRGRILSGVVTKMK-MQRTIVIRRDYLHYIRKYNRFEKRHKN
LGF..PK.A..EGTYI...CP.F.GN.SI.G.ILSG.VTK.K.MQ....I..DY.HY..KY..F.K.HKN
RetrocopyLGFNMPK*AM<EGTYIYTDCP<FIGNISI*GWILSGMVTKIK>MQKINIIHQDYFHYMCKYSCF-KKHKN
ParentalMSVHLSPCFRDVQIGDIVTVG-ECRPLSKTVRFNVLKVTKAAGTKKQFQ
M..H.SPC.RDVQI..I..VG......SK.V.FN.L.V..A..TKKQFQ
RetrocopyMFMHPSPCIRDVQISNIIMVG<VSTSMSKMVHFNMLMVPNA--TKKQFQ

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 1144 .45 RPM
bodymap2_adrenal 0 .02 RPM 1334 .24 RPM
bodymap2_brain 0 .14 RPM 335 .85 RPM
bodymap2_breast 0 .00 RPM 851 .29 RPM
bodymap2_colon 0 .00 RPM 1349 .87 RPM
bodymap2_heart 0 .00 RPM 186 .88 RPM
bodymap2_kidney 0 .00 RPM 321 .60 RPM
bodymap2_liver 0 .00 RPM 277 .10 RPM
bodymap2_lung 0 .00 RPM 868 .32 RPM
bodymap2_lymph_node 0 .00 RPM 1078 .86 RPM
bodymap2_ovary 0 .08 RPM 1590 .78 RPM
bodymap2_prostate 0 .00 RPM 914 .74 RPM
bodymap2_skeletal_muscle 0 .00 RPM 555 .91 RPM
bodymap2_testis 0 .02 RPM 985 .58 RPM
bodymap2_thyroid 0 .00 RPM 732 .03 RPM
bodymap2_white_blood_cells 0 .00 RPM 1109 .57 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_230 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_230 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_230 retrocopy 5' end.

Lab - click to see more details

retro_hsap_230 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_230 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_292
Macaca mulatta retro_mmul_413
Parental genes homology:
Parental genes homology involve 20 parental genes, and 110 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG0000001402013 retrocopies
retro_amel_1038, retro_amel_1071, retro_amel_1398, retro_amel_1406, retro_amel_1475, retro_amel_246, retro_amel_262, retro_amel_317, retro_amel_64, retro_amel_757, retro_amel_759, retro_amel_764, retro_amel_859,
Bos taurus ENSBTAG000000139245 retrocopies
retro_btau_1282, retro_btau_1369, retro_btau_1499, retro_btau_1529, retro_btau_888,
Canis familiaris ENSCAFG000000036319 retrocopies
retro_cfam_126, retro_cfam_1333, retro_cfam_1572, retro_cfam_1656, retro_cfam_1669, retro_cfam_1900, retro_cfam_1955, retro_cfam_2121, retro_cfam_248,
Callithrix jacchus ENSCJAG000000000691 retrocopy
retro_cjac_340,
Cavia porcellus ENSCPOG000000151451 retrocopy
retro_cpor_534,
Danio rerio ENSDARG000000530581 retrocopy
retro_drer_15,
Equus caballus ENSECAG000000003701 retrocopy
retro_ecab_868,
Erinaceus europaeus ENSEEUG000000033921 retrocopy
retro_eeur_75,
Homo sapiens ENSG00000142534 6 retrocopies
retro_hsap_1017, retro_hsap_1068, retro_hsap_230 , retro_hsap_2449, retro_hsap_4242, retro_hsap_4674,
Loxodonta africana ENSLAFG000000162172 retrocopies
retro_lafr_622, retro_lafr_658,
Monodelphis domestica ENSMODG000000134347 retrocopies
retro_mdom_1185, retro_mdom_1284, retro_mdom_1421, retro_mdom_1950, retro_mdom_636, retro_mdom_922, retro_mdom_978,
Mustela putorius furoENSMPUG0000000259910 retrocopies
retro_mputfur_1402, retro_mputfur_1507, retro_mputfur_200, retro_mputfur_306, retro_mputfur_345, retro_mputfur_485, retro_mputfur_491, retro_mputfur_626, retro_mputfur_781, retro_mputfur_897,
Otolemur garnettii ENSOGAG000000046277 retrocopies
retro_ogar_1290, retro_ogar_1813, retro_ogar_1910, retro_ogar_2037, retro_ogar_2573, retro_ogar_2640, retro_ogar_840,
Procavia capensis ENSPCAG000000041462 retrocopies
retro_pcap_333, retro_pcap_54,
Pongo abelii ENSPPYG000000258605 retrocopies
retro_pabe_1800, retro_pabe_3396, retro_pabe_3631, retro_pabe_855, retro_pabe_889,
Pan troglodytes ENSPTRG000000112991 retrocopy
retro_ptro_88,
Rattus norvegicus ENSRNOG0000002059518 retrocopies
retro_rnor_1132, retro_rnor_1159, retro_rnor_1261, retro_rnor_1299, retro_rnor_1363, retro_rnor_1414, retro_rnor_1435, retro_rnor_1451, retro_rnor_1635, retro_rnor_1790, retro_rnor_2000, retro_rnor_2647, retro_rnor_385, retro_rnor_394, retro_rnor_538, retro_rnor_737, retro_rnor_835, retro_rnor_989,
Sorex araneus ENSSARG000000032362 retrocopies
retro_sara_11, retro_sara_469,
Ictidomys tridecemlineatus ENSSTOG000000234432 retrocopies
retro_itri_1033, retro_itri_805,
Tupaia belangeri ENSTBEG0000001667716 retrocopies
retro_tbel_125, retro_tbel_1361, retro_tbel_1753, retro_tbel_2071, retro_tbel_2207, retro_tbel_2808, retro_tbel_2947, retro_tbel_319, retro_tbel_3401, retro_tbel_3571, retro_tbel_3600, retro_tbel_3742, retro_tbel_449, retro_tbel_604, retro_tbel_801, retro_tbel_836,

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 .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 .03 RPM
GBR_HG00119 0 .02 RPM
GBR_HG00131 0 .00 RPM
GBR_HG00133 0 .00 RPM
GBR_HG00134 0 .00 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .03 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 .02 RPM
TSI_NA20771 0 .00 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .00 RPM
YRI_NA18870 0 .03 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .02 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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