RetrogeneDB ID:

retro_hsap_1974

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:19:18159446..18159907(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000243455
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RPS18
Ensembl ID:ENSG00000231500
Aliases:RPS18, D6S218E, HKE3, KE-3, KE3, S18
Description:ribosomal protein S18 [Source:HGNC Symbol;Acc:10401]


Retrocopy-Parental alignment summary:






>retro_hsap_1974
GTGTCTCTAGTGATCCTTGAAAAGTTCCAGCATATTTTGGGAGTACTCAACACCAACATCGATGGGTGGTGGAAAATAGC
CTTTGCTATCACTGCCATTAAAGGTGTGGATGGAAGATACGCTTATGTGGTGTTGAGGAAAACAGACATTGACCTCACCA
AGAGGGCGGGAGACTCACGGAGGATGAGATGGAATGAGTGATCACCATTGTGCAGAATCCACAGCAGTACAAGATCCCAG
ACTGGCTCTTGAACAGACAGAAGGATGTAAAGGATGGAAAATATAGCCAGGTCCTAGCCAGTGGTCTGGACAACAAGCTC
CGTGAAGACCTGGAGCAACCGAAGAAGATTCCGGCCCATAGAGGGATGCACCACTTCTGGGGCCTTCATGTCTGAGGCCA
GCACACCGAGACCATTGGCCGCCATGGCCGTACCTGTACCGTGGGTGTATCCAAGAAGAAA

ORF - retro_hsap_1974 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 81.29 %
Parental protein coverage: 100. %
Number of stop codons detected: 2
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMSLVIPEKFQHILRVLNTNIDGRRKIAFAITAIKGVGRRYAHVVLRKADIDLTKRAGE-LTEDEVERVIT
.SLVI.EKFQHIL.VLNTNIDG..KIAFAITAIKGV..RYA.VVLRK.DIDLTKRAG..LTEDE.E.VIT
RetrocopyVSLVILEKFQHILGVLNTNIDGWWKIAFAITAIKGVDGRYAYVVLRKTDIDLTKRAGD<LTEDEME*VIT
ParentalIMQNPRQYKIPDWFLNRQKDVKDGKYSQVLANGLDNKLREDLERLKKIRAHRGLRHFWGLRVRGQHTKTT
I.QNP.QYKIPDW.LNRQKDVKDGKYSQVLA.GLDNKLREDLE..KKI.AHRG..HFWGL.V.GQHT.T.
RetrocopyIVQNPQQYKIPDWLLNRQKDVKDGKYSQVLASGLDNKLREDLEQPKKIPAHRGMHHFWGLHV*GQHTETI
ParentalGRRGR--TVGVSKKK
GR.GR..TVGVSKKK
RetrocopyGRHGRTCTVGVSKKK

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 .04 RPM 830 .70 RPM
bodymap2_adrenal 0 .00 RPM 808 .67 RPM
bodymap2_brain 0 .00 RPM 141 .95 RPM
bodymap2_breast 0 .00 RPM 574 .42 RPM
bodymap2_colon 0 .00 RPM 938 .47 RPM
bodymap2_heart 0 .00 RPM 208 .48 RPM
bodymap2_kidney 0 .00 RPM 286 .24 RPM
bodymap2_liver 0 .00 RPM 278 .24 RPM
bodymap2_lung 0 .00 RPM 1000 .42 RPM
bodymap2_lymph_node 0 .00 RPM 1070 .21 RPM
bodymap2_ovary 0 .00 RPM 1148 .46 RPM
bodymap2_prostate 0 .09 RPM 1304 .48 RPM
bodymap2_skeletal_muscle 0 .00 RPM 781 .40 RPM
bodymap2_testis 0 .00 RPM 568 .80 RPM
bodymap2_thyroid 0 .04 RPM 404 .72 RPM
bodymap2_white_blood_cells 0 .00 RPM 1343 .61 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_1974 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_1974 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_1974 retrocopy 5' end.

Lab - click to see more details

retro_hsap_1974 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1974 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 21 parental genes, and 134 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000026482 retrocopies
retro_btau_1052, retro_btau_614,
Callithrix jacchus ENSCJAG000000216505 retrocopies
retro_cjac_22, retro_cjac_245, retro_cjac_2529, retro_cjac_2893, retro_cjac_2955,
Dasypus novemcinctus ENSDNOG0000001208413 retrocopies
retro_dnov_1295, retro_dnov_1398, retro_dnov_1448, retro_dnov_1675, retro_dnov_1770, retro_dnov_2008, retro_dnov_2115, retro_dnov_2223, retro_dnov_2288, retro_dnov_327, retro_dnov_363, retro_dnov_384, retro_dnov_399,
Erinaceus europaeus ENSEEUG000000102978 retrocopies
retro_eeur_201, retro_eeur_261, retro_eeur_380, retro_eeur_460, retro_eeur_473, retro_eeur_498, retro_eeur_667, retro_eeur_689,
Homo sapiens ENSG00000231500 2 retrocopies
retro_hsap_1806, retro_hsap_1974 ,
Gorilla gorilla ENSGGOG000000065715 retrocopies
retro_ggor_1496, retro_ggor_2310, retro_ggor_344, retro_ggor_77, retro_ggor_93,
Loxodonta africana ENSLAFG000000321731 retrocopy
retro_lafr_1171,
Macropus eugenii ENSMEUG0000001677011 retrocopies
retro_meug_1296, retro_meug_1737, retro_meug_1807, retro_meug_1946, retro_meug_212, retro_meug_310, retro_meug_344, retro_meug_387, retro_meug_566, retro_meug_625, retro_meug_627,
Myotis lucifugus ENSMLUG000000073602 retrocopies
retro_mluc_181, retro_mluc_932,
Macaca mulatta ENSMMUG000000038671 retrocopy
retro_mmul_2198,
Oryctolagus cuniculus ENSOCUG000000105461 retrocopy
retro_ocun_31,
Otolemur garnettii ENSOGAG000000062257 retrocopies
retro_ogar_1498, retro_ogar_1832, retro_ogar_2372, retro_ogar_472, retro_ogar_608, retro_ogar_709, retro_ogar_905,
Pongo abelii ENSPPYG0000002595314 retrocopies
retro_pabe_1138, retro_pabe_128, retro_pabe_1481, retro_pabe_1482, retro_pabe_1813, retro_pabe_1881, retro_pabe_2303, retro_pabe_2407, retro_pabe_2663, retro_pabe_2833, retro_pabe_2967, retro_pabe_3013, retro_pabe_3070, retro_pabe_368,
Pan troglodytes ENSPTRG000000180391 retrocopy
retro_ptro_121,
Pteropus vampyrus ENSPVAG000000019026 retrocopies
retro_pvam_295, retro_pvam_556, retro_pvam_691, retro_pvam_708, retro_pvam_829, retro_pvam_875,
Rattus norvegicus ENSRNOG000000285054 retrocopies
retro_rnor_102, retro_rnor_234, retro_rnor_29, retro_rnor_70,
Sarcophilus harrisii ENSSHAG000000068572 retrocopies
retro_shar_265, retro_shar_563,
Sarcophilus harrisii ENSSHAG000000086581 retrocopy
retro_shar_618,
Sus scrofa ENSSSCG000000015025 retrocopies
retro_sscr_112, retro_sscr_156, retro_sscr_157, retro_sscr_2, retro_sscr_831,
Tupaia belangeri ENSTBEG0000001270840 retrocopies
retro_tbel_1070, retro_tbel_1739, retro_tbel_1745, retro_tbel_1806, retro_tbel_1818, retro_tbel_1827, retro_tbel_1855, retro_tbel_205, retro_tbel_2087, retro_tbel_211, retro_tbel_2299, retro_tbel_2309, retro_tbel_2312, retro_tbel_234, retro_tbel_2364, retro_tbel_2424, retro_tbel_2473, retro_tbel_250, retro_tbel_2682, retro_tbel_2768, retro_tbel_295, retro_tbel_3189, retro_tbel_3317, retro_tbel_3383, retro_tbel_3625, retro_tbel_363, retro_tbel_3686, retro_tbel_3731, retro_tbel_3870, retro_tbel_4100, retro_tbel_4215, retro_tbel_4365, retro_tbel_45, retro_tbel_4562, retro_tbel_4578, retro_tbel_462, retro_tbel_57, retro_tbel_578, retro_tbel_856, retro_tbel_941,
Tursiops truncatus ENSTTRG000000043023 retrocopies
retro_ttru_1012, retro_ttru_1553, retro_ttru_837,

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 = 0.07 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .03 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 .03 RPM
FIN_HG00378 0 .00 RPM
GBR_HG00099 0 .00 RPM
GBR_HG00111 0 .00 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 .07 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 .03 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .00 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .03 RPM
YRI_NA19118 0 .04 RPM
YRI_NA19213 0 .00 RPM
YRI_NA19214 0 .00 RPM
YRI_NA19223 0 .04 RPM

Indel association:

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



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