RetrogeneDB ID:

retro_hsap_2249

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:2:42077345..42077741(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000236533
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RPS12
Ensembl ID:ENSG00000112306
Aliases:None
Description:ribosomal protein S12 [Source:HGNC Symbol;Acc:10385]


Retrocopy-Parental alignment summary:






>retro_hsap_2249
ATGGCCGAGGAACGCATTGCTGTTGGAGGTGTAATGGACGTTAATACTGCTTTACAAGAGGTGCTGAAGACCGCCCTCAT
CCACAATGGCCTAGCATGTGGAATTTGCAAAGCTGCCAAAGCCTTAGACAAGCGCCAAGCCCATCTTTGTGTGCTGGCAT
CCAACTGTGATGAGCCTATGGATGTCAAGTTGGTGGAGGCCCTTTGTGCTGAACACCAAATCGACCTAATTAAGGTTGAT
GACAACAAGAAACTAGGGGAATGGGTAGGTCTCTGTAAAACTGACAGAGAGGGGAAACCCCGTAAAGTGGTTGGTCGCAG
TTGTGTAGTAGTTAAGGACTATGGCACGGAGTCCCAGGCCAAGGATGTCATTGAAGAGTACTTCAAATGCAAGAAA

ORF - retro_hsap_2249 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 91.67 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMAEEGIAAGGVMDVNTALQEVLKTALIHDGLARGIREAAKALDKRQAHLCVLASNCDEPMYVKLVEALCA
MAEE.IA.GGVMDVNTALQEVLKTALIH.GLA.GI..AAKALDKRQAHLCVLASNCDEPM.VKLVEALCA
RetrocopyMAEERIAVGGVMDVNTALQEVLKTALIHNGLACGICKAAKALDKRQAHLCVLASNCDEPMDVKLVEALCA
ParentalEHQINLIKVDDNKKLGEWVGLCKIDREGKPRKVVGCSCVVVKDYGKESQAKDVIEEYFKCKK
EHQI.LIKVDDNKKLGEWVGLCK.DREGKPRKVVG.SCVVVKDYG.ESQAKDVIEEYFKCKK
RetrocopyEHQIDLIKVDDNKKLGEWVGLCKTDREGKPRKVVGRSCVVVKDYGTESQAKDVIEEYFKCKK

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 .12 RPM 474 .15 RPM
bodymap2_adrenal 0 .00 RPM 588 .01 RPM
bodymap2_brain 0 .00 RPM 195 .61 RPM
bodymap2_breast 0 .00 RPM 380 .28 RPM
bodymap2_colon 0 .00 RPM 575 .74 RPM
bodymap2_heart 0 .00 RPM 153 .01 RPM
bodymap2_kidney 0 .00 RPM 295 .86 RPM
bodymap2_liver 0 .00 RPM 264 .93 RPM
bodymap2_lung 0 .00 RPM 735 .85 RPM
bodymap2_lymph_node 0 .02 RPM 1024 .27 RPM
bodymap2_ovary 0 .00 RPM 823 .31 RPM
bodymap2_prostate 0 .03 RPM 838 .38 RPM
bodymap2_skeletal_muscle 0 .00 RPM 323 .85 RPM
bodymap2_testis 0 .00 RPM 481 .66 RPM
bodymap2_thyroid 0 .02 RPM 378 .38 RPM
bodymap2_white_blood_cells 0 .02 RPM 1280 .71 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2249 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2249 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_2249 retrocopy 5' end.

Lab - click to see more details

retro_hsap_2249 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2249 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1592
Pongo abelii retro_pabe_1961
Parental genes homology:
Parental genes homology involve 24 parental genes, and 192 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000104791 retrocopy
retro_acar_102,
Ailuropoda melanoleuca ENSAMEG000000080152 retrocopies
retro_amel_79, retro_amel_92,
Bos taurus ENSBTAG000000013607 retrocopies
retro_btau_106, retro_btau_1097, retro_btau_1306, retro_btau_1495, retro_btau_1514, retro_btau_1630, retro_btau_1802,
Callithrix jacchus ENSCJAG0000000286534 retrocopies
retro_cjac_1038, retro_cjac_1044, retro_cjac_1205, retro_cjac_1291, retro_cjac_1528, retro_cjac_1602, retro_cjac_1778, retro_cjac_1994, retro_cjac_2039, retro_cjac_2058, retro_cjac_2065, retro_cjac_2101, retro_cjac_2112, retro_cjac_2155, retro_cjac_2337, retro_cjac_2406, retro_cjac_2421, retro_cjac_2461, retro_cjac_2681, retro_cjac_2694, retro_cjac_2858, retro_cjac_301, retro_cjac_3310, retro_cjac_4149, retro_cjac_427, retro_cjac_466, retro_cjac_494, retro_cjac_592, retro_cjac_773, retro_cjac_805, retro_cjac_806, retro_cjac_807, retro_cjac_836, retro_cjac_977,
Cavia porcellus ENSCPOG000000004294 retrocopies
retro_cpor_1096, retro_cpor_304, retro_cpor_32, retro_cpor_380,
Equus caballus ENSECAG000000015998 retrocopies
retro_ecab_1012, retro_ecab_1131, retro_ecab_133, retro_ecab_744, retro_ecab_80, retro_ecab_828, retro_ecab_875, retro_ecab_959,
Echinops telfairi ENSETEG0000000685414 retrocopies
retro_etel_1129, retro_etel_1512, retro_etel_1580, retro_etel_2016, retro_etel_205, retro_etel_2082, retro_etel_2099, retro_etel_2169, retro_etel_26, retro_etel_280, retro_etel_29, retro_etel_55, retro_etel_578, retro_etel_915,
Felis catus ENSFCAG000000284027 retrocopies
retro_fcat_1084, retro_fcat_1314, retro_fcat_1446, retro_fcat_1880, retro_fcat_537, retro_fcat_664, retro_fcat_796,
Homo sapiens ENSG00000112306 26 retrocopies
retro_hsap_1241, retro_hsap_1522, retro_hsap_1738, retro_hsap_1771, retro_hsap_1797, retro_hsap_1962, retro_hsap_1992, retro_hsap_2249 , retro_hsap_2264, retro_hsap_2667, retro_hsap_2722, retro_hsap_3043, retro_hsap_3079, retro_hsap_3249, retro_hsap_3347, retro_hsap_3428, retro_hsap_3467, retro_hsap_3640, retro_hsap_3680, retro_hsap_3994, retro_hsap_4130, retro_hsap_599, retro_hsap_661, retro_hsap_702, retro_hsap_824, retro_hsap_895,
Gorilla gorilla ENSGGOG0000001223422 retrocopies
retro_ggor_1164, retro_ggor_1287, retro_ggor_1322, retro_ggor_139, retro_ggor_1426, retro_ggor_1441, retro_ggor_1686, retro_ggor_1861, retro_ggor_1894, retro_ggor_2115, retro_ggor_2241, retro_ggor_2261, retro_ggor_2339, retro_ggor_2456, retro_ggor_2489, retro_ggor_2680, retro_ggor_3076, retro_ggor_530, retro_ggor_595, retro_ggor_673, retro_ggor_724, retro_ggor_971,
Gadus morhua ENSGMOG000000194551 retrocopy
retro_gmor_11,
Microcebus murinus ENSMICG000000052525 retrocopies
retro_mmur_1260, retro_mmur_1527, retro_mmur_391, retro_mmur_491, retro_mmur_98,
Myotis lucifugus ENSMLUG000000011375 retrocopies
retro_mluc_1479, retro_mluc_1552, retro_mluc_1987, retro_mluc_1988, retro_mluc_582,
Macaca mulatta ENSMMUG000000132371 retrocopy
retro_mmul_12,
Monodelphis domestica ENSMODG000000175201 retrocopy
retro_mdom_779,
Mustela putorius furoENSMPUG000000147711 retrocopy
retro_mputfur_6,
Mus musculus ENSMUSG000000619831 retrocopy
retro_mmus_36,
Pelodiscus sinensis ENSPSIG000000034571 retrocopy
retro_psin_52,
Rattus norvegicus ENSRNOG000000164115 retrocopies
retro_rnor_177, retro_rnor_186, retro_rnor_241, retro_rnor_295, retro_rnor_300,
Sorex araneus ENSSARG000000031702 retrocopies
retro_sara_356, retro_sara_8,
Sarcophilus harrisii ENSSHAG000000089056 retrocopies
retro_shar_187, retro_shar_226, retro_shar_475, retro_shar_492, retro_shar_621, retro_shar_671,
Tarsius syrichta ENSTSYG0000001009724 retrocopies
retro_tsyr_1010, retro_tsyr_102, retro_tsyr_1123, retro_tsyr_1188, retro_tsyr_129, retro_tsyr_1313, retro_tsyr_1345, retro_tsyr_1398, retro_tsyr_1486, retro_tsyr_1668, retro_tsyr_1955, retro_tsyr_1993, retro_tsyr_205, retro_tsyr_249, retro_tsyr_303, retro_tsyr_419, retro_tsyr_453, retro_tsyr_556, retro_tsyr_645, retro_tsyr_733, retro_tsyr_764, retro_tsyr_801, retro_tsyr_970, retro_tsyr_99,
Tursiops truncatus ENSTTRG0000000060911 retrocopies
retro_ttru_1290, retro_ttru_206, retro_ttru_233, retro_ttru_304, retro_ttru_559, retro_ttru_64, retro_ttru_667, retro_ttru_727, retro_ttru_787, retro_ttru_955, retro_ttru_990,
Vicugna pacos ENSVPAG000000115043 retrocopies
retro_vpac_133, retro_vpac_267, retro_vpac_339,

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 = 0.14 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .02 RPM
CEU_NA11843 0 .06 RPM
CEU_NA11930 0 .00 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .14 RPM
CEU_NA12751 0 .02 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .00 RPM
CEU_NA12873 0 .10 RPM
FIN_HG00183 0 .00 RPM
FIN_HG00277 0 .00 RPM
FIN_HG00315 0 .03 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .02 RPM
FIN_HG00349 0 .00 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .02 RPM
GBR_HG00099 0 .06 RPM
GBR_HG00111 0 .02 RPM
GBR_HG00114 0 .00 RPM
GBR_HG00119 0 .05 RPM
GBR_HG00131 0 .00 RPM
GBR_HG00133 0 .00 RPM
GBR_HG00134 0 .02 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .03 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 .00 RPM
YRI_NA19093 0 .03 RPM
YRI_NA19099 0 .05 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .02 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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