RetrogeneDB ID:

retro_hsap_4304

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:9:114935985..114936251(-)
Located in intron of:ENSG00000106868
Retrocopy
information
Ensembl ID:ENSG00000225513
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL29
Ensembl ID:ENSG00000162244
Aliases:RPL29, HIP, HUMRPL29, L29, RPL29P10, RPL29_3_370
Description:ribosomal protein L29 [Source:HGNC Symbol;Acc:10331]


Retrocopy-Parental alignment summary:






>retro_hsap_4304
ATGGCCAAATCCAAGCACCACACCACACACAACCAGTCCCGAAAATGGCACAGAAACGGCATCATGAAACCCGGATCACA
AAGATACGAATCTTTTAAAGGGGTGGACCCCAAGTTCCTGACAAACATGCGGTTTGCCAAGAAGCACAATAAGAGGGGCC
TAAAGAAGATGCAGGGCGACAGTGCCAAGGCCATGAGTGCACGTGCTGAGGCCTTGCCCTCATAAACCCCAAGGAGGTTA
AGCCCAAGATTCCAAAGGGTGTCAGC

ORF - retro_hsap_4304 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 78.02 %
Parental protein coverage: 56.6 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMAKSKNHTTHNQSRKWHRNGIKKPRSQRYESLKGVDPKFLRNMRFAKKHNKKGLKKMQANNAKAMSARAE
MAKSK.HTTHNQSRKWHRNGI.KP.SQRYES.KGVDPKFL.NMRFAKKHNK.GLKKMQ...AKAMSARAE
RetrocopyMAKSKHHTTHNQSRKWHRNGIMKPGSQRYESFKGVDPKFLTNMRFAKKHNKRGLKKMQGDSAKAMSARAE
ParentalAIKALVKPKEVKP-KIPKGVS
A......P....P.KIPKGVS
RetrocopyALPS*T-PRRLSP<KIPKGVS

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 345 .40 RPM
bodymap2_adrenal 0 .02 RPM 368 .49 RPM
bodymap2_brain 0 .02 RPM 44 .84 RPM
bodymap2_breast 0 .00 RPM 226 .07 RPM
bodymap2_colon 0 .06 RPM 351 .62 RPM
bodymap2_heart 0 .04 RPM 82 .58 RPM
bodymap2_kidney 0 .00 RPM 143 .27 RPM
bodymap2_liver 0 .00 RPM 120 .41 RPM
bodymap2_lung 0 .00 RPM 323 .61 RPM
bodymap2_lymph_node 0 .00 RPM 374 .43 RPM
bodymap2_ovary 0 .00 RPM 388 .74 RPM
bodymap2_prostate 0 .00 RPM 379 .29 RPM
bodymap2_skeletal_muscle 0 .00 RPM 419 .30 RPM
bodymap2_testis 0 .04 RPM 194 .98 RPM
bodymap2_thyroid 0 .00 RPM 207 .95 RPM
bodymap2_white_blood_cells 0 .00 RPM 354 .52 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity may be related with retro_hsap_4304 in 15 libraries
ENCODE library ID Target ChIP-Seq Peak coordinates
ENCFF002CFW POLR2A 9:114936960..114937638
ENCFF002CFX POLR2A 9:114936957..114937879
ENCFF002CGN POLR2A 9:114936954..114937418
ENCFF002CGN POLR2A 9:114937181..114937645
ENCFF002CJZ POLR2A 9:114937052..114937253
ENCFF002CMI POLR2A 9:114936811..114938212
ENCFF002COJ POLR2A 9:114936890..114937326
ENCFF002CQE POLR2A 9:114937083..114937269
ENCFF002CQK POLR2A 9:114937039..114937310
ENCFF002CQK POLR2A 9:114937129..114937619
ENCFF002CQM POLR2A 9:114936964..114937444
ENCFF002CQO POLR2A 9:114936933..114937463
ENCFF002CSY POLR2A 9:114936923..114937620
ENCFF002CXO POLR2A 9:114936796..114937220
ENCFF002CZD POLR2A 9:114936939..114937449
ENCFF002DAE POLR2A 9:114937087..114937397
ENCFF002DBP POLR2A 9:114936947..114937277

EST - click to see more details

No EST(s) were mapped for retro_hsap_4304 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_4304 retrocopy 5' end.

Lab - click to see more details

retro_hsap_4304 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4304 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 18 parental genes, and 186 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000091636 retrocopies
retro_amel_1373, retro_amel_1740, retro_amel_345, retro_amel_379, retro_amel_686, retro_amel_913,
Callithrix jacchus ENSCJAG000000059519 retrocopies
retro_cjac_135, retro_cjac_160, retro_cjac_241, retro_cjac_29, retro_cjac_331, retro_cjac_348, retro_cjac_358, retro_cjac_73, retro_cjac_96,
Felis catus ENSFCAG000000017629 retrocopies
retro_fcat_1032, retro_fcat_1132, retro_fcat_1753, retro_fcat_1774, retro_fcat_1897, retro_fcat_249, retro_fcat_485, retro_fcat_687, retro_fcat_952,
Homo sapiens ENSG00000162244 23 retrocopies
retro_hsap_1098, retro_hsap_1146, retro_hsap_123, retro_hsap_1283, retro_hsap_1406, retro_hsap_1587, retro_hsap_170, retro_hsap_1759, retro_hsap_2053, retro_hsap_2358, retro_hsap_263, retro_hsap_2772, retro_hsap_2899, retro_hsap_3201, retro_hsap_3289, retro_hsap_3316, retro_hsap_3511, retro_hsap_3562, retro_hsap_3951, retro_hsap_3998, retro_hsap_4304 , retro_hsap_863, retro_hsap_882,
Gorilla gorilla ENSGGOG0000002469116 retrocopies
retro_ggor_1007, retro_ggor_1090, retro_ggor_1205, retro_ggor_1315, retro_ggor_1330, retro_ggor_142, retro_ggor_1480, retro_ggor_1929, retro_ggor_224, retro_ggor_2247, retro_ggor_254, retro_ggor_2684, retro_ggor_312, retro_ggor_715, retro_ggor_863, retro_ggor_892,
Microcebus murinus ENSMICG000000027059 retrocopies
retro_mmur_192, retro_mmur_198, retro_mmur_303, retro_mmur_446, retro_mmur_508, retro_mmur_519, retro_mmur_657, retro_mmur_816, retro_mmur_938,
Myotis lucifugus ENSMLUG0000001508814 retrocopies
retro_mluc_1086, retro_mluc_1160, retro_mluc_134, retro_mluc_1377, retro_mluc_1699, retro_mluc_1955, retro_mluc_2228, retro_mluc_2522, retro_mluc_2523, retro_mluc_2575, retro_mluc_297, retro_mluc_421, retro_mluc_889, retro_mluc_915,
Macaca mulatta ENSMMUG000000192482 retrocopies
retro_mmul_1352, retro_mmul_218,
Monodelphis domestica ENSMODG0000002875017 retrocopies
retro_mdom_1013, retro_mdom_1187, retro_mdom_1201, retro_mdom_1328, retro_mdom_1445, retro_mdom_1452, retro_mdom_1505, retro_mdom_1532, retro_mdom_1604, retro_mdom_1665, retro_mdom_1904, retro_mdom_35, retro_mdom_504, retro_mdom_589, retro_mdom_612, retro_mdom_639, retro_mdom_995,
Mustela putorius furoENSMPUG000000117346 retrocopies
retro_mputfur_137, retro_mputfur_187, retro_mputfur_370, retro_mputfur_467, retro_mputfur_816, retro_mputfur_970,
Mus musculus ENSMUSG000000487583 retrocopies
retro_mmus_203, retro_mmus_231, retro_mmus_86,
Otolemur garnettii ENSOGAG000000137662 retrocopies
retro_ogar_290, retro_ogar_31,
Ochotona princeps ENSOPRG0000000882110 retrocopies
retro_opri_1166, retro_opri_277, retro_opri_373, retro_opri_535, retro_opri_607, retro_opri_69, retro_opri_700, retro_opri_877, retro_opri_983, retro_opri_99,
Pongo abelii ENSPPYG0000001381821 retrocopies
retro_pabe_1062, retro_pabe_1162, retro_pabe_1306, retro_pabe_1503, retro_pabe_1714, retro_pabe_1882, retro_pabe_2125, retro_pabe_2131, retro_pabe_2398, retro_pabe_2718, retro_pabe_2952, retro_pabe_3254, retro_pabe_3284, retro_pabe_3504, retro_pabe_3525, retro_pabe_404, retro_pabe_459, retro_pabe_491, retro_pabe_673, retro_pabe_687, retro_pabe_911,
Rattus norvegicus ENSRNOG0000001113815 retrocopies
retro_rnor_1045, retro_rnor_1158, retro_rnor_1161, retro_rnor_1422, retro_rnor_1702, retro_rnor_184, retro_rnor_1951, retro_rnor_2207, retro_rnor_2222, retro_rnor_2356, retro_rnor_2561, retro_rnor_338, retro_rnor_397, retro_rnor_63, retro_rnor_928,
Sorex araneus ENSSARG000000135728 retrocopies
retro_sara_108, retro_sara_309, retro_sara_329, retro_sara_347, retro_sara_400, retro_sara_53, retro_sara_637, retro_sara_669,
Sarcophilus harrisii ENSSHAG000000068542 retrocopies
retro_shar_355, retro_shar_444,
Ictidomys tridecemlineatus ENSSTOG0000002048814 retrocopies
retro_itri_1345, retro_itri_1433, retro_itri_1482, retro_itri_1586, retro_itri_1664, retro_itri_1667, retro_itri_194, retro_itri_482, retro_itri_520, retro_itri_592, retro_itri_622, retro_itri_874, retro_itri_934, retro_itri_942,

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 = 0.1 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .04 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .07 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .04 RPM
CEU_NA12751 0 .00 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .05 RPM
CEU_NA12872 0 .05 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .05 RPM
FIN_HG00277 0 .04 RPM
FIN_HG00315 0 .03 RPM
FIN_HG00321 0 .09 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .04 RPM
FIN_HG00349 0 .00 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .04 RPM
GBR_HG00099 0 .00 RPM
GBR_HG00111 0 .02 RPM
GBR_HG00114 0 .08 RPM
GBR_HG00119 0 .00 RPM
GBR_HG00131 0 .00 RPM
GBR_HG00133 0 .00 RPM
GBR_HG00134 0 .07 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .10 RPM
TSI_NA20512 0 .03 RPM
TSI_NA20513 0 .02 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .03 RPM
TSI_NA20538 0 .09 RPM
TSI_NA20756 0 .03 RPM
TSI_NA20765 0 .06 RPM
TSI_NA20771 0 .03 RPM
TSI_NA20786 0 .10 RPM
TSI_NA20798 0 .09 RPM
YRI_NA18870 0 .00 RPM
YRI_NA18907 0 .03 RPM
YRI_NA18916 0 .02 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .03 RPM
YRI_NA19118 0 .04 RPM
YRI_NA19213 0 .05 RPM
YRI_NA19214 0 .02 RPM
YRI_NA19223 0 .08 RPM

Indel association:

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





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