RetrogeneDB ID:

retro_hsap_1073

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:12:4219034..4219384(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000242444
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL18
Ensembl ID:ENSG00000063177
Aliases:RPL18, L18
Description:ribosomal protein L18 [Source:HGNC Symbol;Acc:10310]


Retrocopy-Parental alignment summary:






>retro_hsap_1073
GAGGGAGTTGATGTTTGCCATGACAAGGACCAAAAGGTTCGGCATCAGGAGCCCAAGAGCCAGGACATCCACCAAAGGCT
GTTGGTCAAGCTGTTCAGGTTTCCGGCCAGATGAACCAACTCCACCTTCAACCAGGTTGTGCTGAAGACATTGTTAATGA
GTCACAGAAACTGGCCACCTCTGTCTCTCTCCCATATGATGGGGAAGATGAAGCTTTCTGGCTGGAAGAACAAAACAGCT
GTGGTTGTGGGGATCATAATGGATGTTGTGCCCGTGCTGGAGGTGCCCAAACTCAAGGTGTGTGCATTGCATGTGAGCAG
CAGATCTACAGCCGCATCCTCAAGCCTGGG

ORF - retro_hsap_1073 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 70.34 %
Parental protein coverage: 61.58 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalQGVDIRHNKDRKVRRKEPKSQDIYLRLLVKLYRFLARRTNSTFNQVVLKRLFMSRTNRPPLSLSRMIRKM
.GVD..H.KD.KVR..EPKSQDI..RLLVKL.RF.AR.TNSTFNQVVLK.L.MS..N.PPLSLS.M..KM
RetrocopyEGVDVCHDKDQKVRHQEPKSQDIHQRLLVKLFRFPAR*TNSTFNQVVLKTLLMSHRNWPPLSLSHMMGKM
ParentalKLPGRENKTAVVVGTITDDVRVQEVPKLKVCALRVTSRAR-SRILRAG
KL.G..NKTAVVVG.I.D.V.V.EVPKLKVCAL.V.SR...SRIL..G
RetrocopyKLSGWKNKTAVVVGIIMDVVPVLEVPKLKVCALHVSSRST<SRILKPG

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 316 .91 RPM
bodymap2_adrenal 0 .00 RPM 431 .64 RPM
bodymap2_brain 0 .00 RPM 71 .45 RPM
bodymap2_breast 0 .00 RPM 241 .23 RPM
bodymap2_colon 0 .00 RPM 423 .24 RPM
bodymap2_heart 0 .00 RPM 78 .72 RPM
bodymap2_kidney 0 .00 RPM 148 .40 RPM
bodymap2_liver 0 .00 RPM 112 .25 RPM
bodymap2_lung 0 .00 RPM 363 .01 RPM
bodymap2_lymph_node 0 .00 RPM 394 .22 RPM
bodymap2_ovary 0 .00 RPM 633 .30 RPM
bodymap2_prostate 0 .00 RPM 466 .05 RPM
bodymap2_skeletal_muscle 0 .00 RPM 170 .40 RPM
bodymap2_testis 0 .00 RPM 226 .92 RPM
bodymap2_thyroid 0 .00 RPM 247 .40 RPM
bodymap2_white_blood_cells 0 .00 RPM 482 .53 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_1073 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_1073 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_1073 retrocopy 5' end.

Lab - click to see more details

retro_hsap_1073 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1073 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_730
Gorilla gorilla retro_ggor_847
Parental genes homology:
Parental genes homology involve 15 parental genes, and 92 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG000000091406 retrocopies
retro_chof_1408, retro_chof_1668, retro_chof_1697, retro_chof_2025, retro_chof_427, retro_chof_436,
Callithrix jacchus ENSCJAG000000003774 retrocopies
retro_cjac_1659, retro_cjac_2114, retro_cjac_2296, retro_cjac_529,
Felis catus ENSFCAG000000086524 retrocopies
retro_fcat_1055, retro_fcat_1268, retro_fcat_1596, retro_fcat_718,
Homo sapiens ENSG00000063177 11 retrocopies
retro_hsap_1073 , retro_hsap_1202, retro_hsap_1331, retro_hsap_1617, retro_hsap_1706, retro_hsap_3235, retro_hsap_3794, retro_hsap_3895, retro_hsap_4001, retro_hsap_4111, retro_hsap_772,
Gorilla gorilla ENSGGOG000000248787 retrocopies
retro_ggor_1038, retro_ggor_1280, retro_ggor_2200, retro_ggor_2550, retro_ggor_2624, retro_ggor_847, retro_ggor_937,
Macropus eugenii ENSMEUG000000006401 retrocopy
retro_meug_1568,
Monodelphis domestica ENSMODG000000140991 retrocopy
retro_mdom_906,
Mustela putorius furoENSMPUG000000038914 retrocopies
retro_mputfur_135, retro_mputfur_1410, retro_mputfur_529, retro_mputfur_974,
Nomascus leucogenys ENSNLEG0000000453711 retrocopies
retro_nleu_1124, retro_nleu_1136, retro_nleu_1410, retro_nleu_1799, retro_nleu_2006, retro_nleu_2380, retro_nleu_2464, retro_nleu_2597, retro_nleu_547, retro_nleu_577, retro_nleu_976,
Otolemur garnettii ENSOGAG0000000356216 retrocopies
retro_ogar_1167, retro_ogar_1474, retro_ogar_1563, retro_ogar_1753, retro_ogar_1978, retro_ogar_2394, retro_ogar_2419, retro_ogar_2527, retro_ogar_2613, retro_ogar_2833, retro_ogar_3319, retro_ogar_3456, retro_ogar_3458, retro_ogar_3459, retro_ogar_492, retro_ogar_996,
Oreochromis niloticus ENSONIG000000065391 retrocopy
retro_onil_43,
Rattus norvegicus ENSRNOG0000002103514 retrocopies
retro_rnor_1068, retro_rnor_1072, retro_rnor_1154, retro_rnor_1186, retro_rnor_1337, retro_rnor_1359, retro_rnor_2174, retro_rnor_2224, retro_rnor_2847, retro_rnor_2890, retro_rnor_516, retro_rnor_685, retro_rnor_856, retro_rnor_857,
Sarcophilus harrisii ENSSHAG000000065642 retrocopies
retro_shar_571, retro_shar_659,
Sus scrofa ENSSSCG000000259285 retrocopies
retro_sscr_1028, retro_sscr_118, retro_sscr_836, retro_sscr_864, retro_sscr_925,
Ictidomys tridecemlineatus ENSSTOG000000122585 retrocopies
retro_itri_261, retro_itri_323, retro_itri_828, retro_itri_853, retro_itri_957,

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 = 4.21 RPM Legend:


Library Retrogene expression
CEU_NA11831 1 .99 RPM
CEU_NA11843 0 .26 RPM
CEU_NA11930 0 .72 RPM
CEU_NA12004 0 .57 RPM
CEU_NA12400 0 .18 RPM
CEU_NA12751 1 .48 RPM
CEU_NA12760 1 .21 RPM
CEU_NA12827 0 .66 RPM
CEU_NA12872 2 .61 RPM
CEU_NA12873 0 .22 RPM
FIN_HG00183 1 .02 RPM
FIN_HG00277 1 .37 RPM
FIN_HG00315 1 .46 RPM
FIN_HG00321 2 .06 RPM
FIN_HG00328 1 .80 RPM
FIN_HG00338 1 .04 RPM
FIN_HG00349 0 .68 RPM
FIN_HG00375 1 .64 RPM
FIN_HG00377 0 .86 RPM
FIN_HG00378 2 .21 RPM
GBR_HG00099 1 .16 RPM
GBR_HG00111 1 .01 RPM
GBR_HG00114 1 .03 RPM
GBR_HG00119 2 .87 RPM
GBR_HG00131 2 .27 RPM
GBR_HG00133 1 .62 RPM
GBR_HG00134 1 .40 RPM
GBR_HG00137 1 .04 RPM
GBR_HG00142 1 .64 RPM
GBR_HG00143 1 .69 RPM
TSI_NA20512 2 .77 RPM
TSI_NA20513 2 .25 RPM
TSI_NA20518 2 .05 RPM
TSI_NA20532 0 .71 RPM
TSI_NA20538 2 .30 RPM
TSI_NA20756 2 .07 RPM
TSI_NA20765 2 .40 RPM
TSI_NA20771 0 .82 RPM
TSI_NA20786 2 .54 RPM
TSI_NA20798 4 .21 RPM
YRI_NA18870 2 .30 RPM
YRI_NA18907 2 .01 RPM
YRI_NA18916 1 .28 RPM
YRI_NA19093 2 .21 RPM
YRI_NA19099 2 .72 RPM
YRI_NA19114 2 .04 RPM
YRI_NA19118 1 .31 RPM
YRI_NA19213 2 .42 RPM
YRI_NA19214 3 .22 RPM
YRI_NA19223 1 .73 RPM

Indel association:

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





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