RetrogeneDB ID:

retro_hsap_475

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:1:174059280..174059610(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000225713
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL30
Ensembl ID:ENSG00000156482
Aliases:RPL30, L30
Description:ribosomal protein L30 [Source:HGNC Symbol;Acc:10333]


Retrocopy-Parental alignment summary:






>retro_hsap_475
ATGGTGCTTGCAAAGAAGATTAAAAAGTCAGTGGAATGGATCAACTCTAGGCTTCTACTTGTTATAAAAAGTGGAAAGTA
CATACTGGCGTACAAGCAGACTCCAAAGATGATCAGGCAAGGCAAAGCAAAATTGGCTATCCACACTGAAAACTGTCCAG
CTTTGAGGAAATCCAAAATAGAGTACTATACCATGTTGACCAAAACTGGTGTCCATCACTACAGTGACAATAATTTTGAA
TTGGGCATAGCATGTGGTAAATACTGCAGAGTATGCATGTTGTCTATCATTGATCCAGACGATTCTGATATCGTTAGAAG
CGTGCCAGAA

ORF - retro_hsap_475 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 77.27 %
Parental protein coverage: 96.49 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalMVAAKKTKKSLESINSRLQLVMKSGKYVLGYKQTLKMIRQGKAKLVILANNCPALRKSEIEYYAMLAKTG
MV.AKK.KKS.E.INSRL.LV.KSGKY.L.YKQT.KMIRQGKAKL.I...NCPALRKS.IEYY.ML.KTG
RetrocopyMVLAKKIKKSVEWINSRLLLVIKSGKYILAYKQTPKMIRQGKAKLAIHTENCPALRKSKIEYYTMLTKTG
ParentalVHHYSGNNIELGTACGKYYRVCTLAIIDPGDSDIIRSMPE
VHHYS.NN.ELG.ACGKY.RVC.L.IIDP.DSDI.RS.PE
RetrocopyVHHYSDNNFELGIACGKYCRVCMLSIIDPDDSDIVRSVPE

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 347 .03 RPM
bodymap2_adrenal 0 .00 RPM 492 .31 RPM
bodymap2_brain 0 .00 RPM 127 .28 RPM
bodymap2_breast 0 .00 RPM 265 .84 RPM
bodymap2_colon 0 .00 RPM 462 .49 RPM
bodymap2_heart 0 .00 RPM 109 .42 RPM
bodymap2_kidney 0 .00 RPM 125 .26 RPM
bodymap2_liver 0 .00 RPM 136 .86 RPM
bodymap2_lung 0 .00 RPM 406 .82 RPM
bodymap2_lymph_node 0 .00 RPM 535 .80 RPM
bodymap2_ovary 0 .00 RPM 727 .53 RPM
bodymap2_prostate 0 .00 RPM 510 .06 RPM
bodymap2_skeletal_muscle 0 .00 RPM 316 .83 RPM
bodymap2_testis 0 .00 RPM 315 .64 RPM
bodymap2_thyroid 0 .00 RPM 306 .82 RPM
bodymap2_white_blood_cells 0 .00 RPM 718 .61 RPM

ChIP-Seq - click to see more details

RNA Polymerase II activity near the 5' end of retro_hsap_475 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_475 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_475 retrocopy 5' end.

Lab - click to see more details

retro_hsap_475 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_475 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_356
Gorilla gorilla retro_ggor_178
Pongo abelii retro_pabe_8
Macaca mulatta retro_mmul_576
Parental genes homology:
Parental genes homology involve 19 parental genes, and 156 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000160472 retrocopies
retro_acar_170, retro_acar_47,
Ailuropoda melanoleuca ENSAMEG0000000060518 retrocopies
retro_amel_1007, retro_amel_1148, retro_amel_1205, retro_amel_1456, retro_amel_1490, retro_amel_1596, retro_amel_1709, retro_amel_1738, retro_amel_26, retro_amel_384, retro_amel_40, retro_amel_456, retro_amel_50, retro_amel_534, retro_amel_551, retro_amel_642, retro_amel_745, retro_amel_806,
Bos taurus ENSBTAG000000162782 retrocopies
retro_btau_34, retro_btau_992,
Callithrix jacchus ENSCJAG000000155494 retrocopies
retro_cjac_14, retro_cjac_253, retro_cjac_320, retro_cjac_351,
Cavia porcellus ENSCPOG000000260304 retrocopies
retro_cpor_1287, retro_cpor_1325, retro_cpor_505, retro_cpor_764,
Dasypus novemcinctus ENSDNOG0000001382812 retrocopies
retro_dnov_1331, retro_dnov_1754, retro_dnov_1883, retro_dnov_2094, retro_dnov_2208, retro_dnov_2455, retro_dnov_2484, retro_dnov_2513, retro_dnov_2670, retro_dnov_293, retro_dnov_334, retro_dnov_415,
Dipodomys ordii ENSDORG0000001238310 retrocopies
retro_dord_111, retro_dord_204, retro_dord_361, retro_dord_407, retro_dord_49, retro_dord_69, retro_dord_710, retro_dord_736, retro_dord_83, retro_dord_97,
Equus caballus ENSECAG000000217057 retrocopies
retro_ecab_1094, retro_ecab_227, retro_ecab_406, retro_ecab_508, retro_ecab_599, retro_ecab_63, retro_ecab_945,
Erinaceus europaeus ENSEEUG000000009649 retrocopies
retro_eeur_137, retro_eeur_214, retro_eeur_237, retro_eeur_355, retro_eeur_432, retro_eeur_59, retro_eeur_614, retro_eeur_69, retro_eeur_83,
Felis catus ENSFCAG000000021659 retrocopies
retro_fcat_1261, retro_fcat_1391, retro_fcat_1473, retro_fcat_1689, retro_fcat_1872, retro_fcat_323, retro_fcat_45, retro_fcat_49, retro_fcat_754,
Homo sapiens ENSG00000156482 9 retrocopies
retro_hsap_1104, retro_hsap_1947, retro_hsap_2229, retro_hsap_2767, retro_hsap_3509, retro_hsap_3959, retro_hsap_4000, retro_hsap_4652, retro_hsap_475 ,
Loxodonta africana ENSLAFG000000020772 retrocopies
retro_lafr_122, retro_lafr_882,
Microcebus murinus ENSMICG000000046203 retrocopies
retro_mmur_258, retro_mmur_644, retro_mmur_693,
Myotis lucifugus ENSMLUG0000000363711 retrocopies
retro_mluc_1425, retro_mluc_2001, retro_mluc_2274, retro_mluc_2295, retro_mluc_2409, retro_mluc_409, retro_mluc_583, retro_mluc_639, retro_mluc_827, retro_mluc_838, retro_mluc_894,
Macaca mulatta ENSMMUG0000002007312 retrocopies
retro_mmul_1353, retro_mmul_2275, retro_mmul_2291, retro_mmul_2309, retro_mmul_2322, retro_mmul_2473, retro_mmul_29, retro_mmul_319, retro_mmul_416, retro_mmul_576, retro_mmul_663, retro_mmul_857,
Oryctolagus cuniculus ENSOCUG000000173864 retrocopies
retro_ocun_1447, retro_ocun_1580, retro_ocun_178, retro_ocun_279,
Pan troglodytes ENSPTRG0000002045410 retrocopies
retro_ptro_1146, retro_ptro_1302, retro_ptro_1575, retro_ptro_1874, retro_ptro_2334, retro_ptro_2380, retro_ptro_2688, retro_ptro_3091, retro_ptro_356, retro_ptro_693,
Pteropus vampyrus ENSPVAG000000144619 retrocopies
retro_pvam_1079, retro_pvam_1090, retro_pvam_1099, retro_pvam_161, retro_pvam_276, retro_pvam_279, retro_pvam_407, retro_pvam_506, retro_pvam_561,
Rattus norvegicus ENSRNOG0000000597519 retrocopies
retro_rnor_1, retro_rnor_1038, retro_rnor_1631, retro_rnor_1812, retro_rnor_1830, retro_rnor_1876, retro_rnor_1893, retro_rnor_1946, retro_rnor_1975, retro_rnor_2211, retro_rnor_2598, retro_rnor_2636, retro_rnor_2666, retro_rnor_2736, retro_rnor_739, retro_rnor_745, retro_rnor_753, retro_rnor_761, retro_rnor_940,

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 = 0.02 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 .00 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 .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 .00 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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