RetrogeneDB ID:

retro_hsap_3328

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:5:60686497..60687698(-)
Located in intron of:ENSG00000130449
Retrocopy
information
Ensembl ID:ENSG00000213891
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL3
Ensembl ID:ENSG00000100316
Aliases:RPL3, ASC-1, L3, TARBP-B
Description:ribosomal protein L3 [Source:HGNC Symbol;Acc:10332]


Retrocopy-Parental alignment summary:






>retro_hsap_3328
ATGTCTCACAGAAGGTTCTCCGCTCCCAGACATGGGTCCCTCGGCTTCCTGCCTCAGCAGCGCAGCAGGAAGCATCATGG
GAAGGTGAAGAGCTTTCCTAAGGATGACCCTTCCAAGCTGGTCCACCTCACAGCCTTCCTGGGATACAAGGCTGGCATGA
CCAACATCATGCGGGAAGTCGACAGGCCAGGATCCAAGGTGAACAAGAAGGAAGTGATAGAGGCTGTGACCATTGTGGAG
ATACCACCCATGGTGGTTGTGGCCATTGTGGGCTTCGTGGAAACCCCTCGAGGCCTCCAGACCTTCAATACTGTCTTCGC
TGAGCACATCAGCGATGCATGCAAGAGACATTTCTATAAAAACCGGCATAAATCTAAGAAGAAGGCCTTTACCAAGTACT
GCAAGAAATGTCAGGATGAGGATGGCAAGAAGCAGCTGGAGAAGGACTTCAGCAGCATGAAGAAGTACCGCCAAGTCATC
TGCATCATTGCCTACACCCAGATGTGCCTGCTTCCTCTGCACCAGAGGAAGGCCCACCTGATGGAGATCCAGGTAAAGGG
AGGCACCATGGCCAAGAAGCTGGACTGGGCCCACGAGAGGCTTGAGCAGCAGGTACCTGTGAACCAAGTGTTTGAGCAGG
ACAAGATGATCGACGTCATCAGGTTGACCAAGGGCAATGGCTACAAAGGGGTCACCAGTCGTTGGCACACCAAGAAGCTA
CCCCACAAGACCCATCGAGGCCTGTGCAAAGTGGCCTGTACTGGGACACAGCATCCTGCCCCTGTGGCCTTACCTGTGGC
ATGCATTTGGCAGAAAGGTTACTGTCACAGCACTGAGATCAACAAGATCTATAAGATCAGCCAGGGATACTTTGTCAGGG
ACAGCAAACTGATCAAGAACAATGCCTCCACTGACTATGACCTGTCTGACAAGCCACCCTCTGGGGGCCTTTGTCCACTA
TGGTGAAGTGACCAATGACTTTGTCATGCTGAAAGACTGTGTGGTGGACACCAAGAAGCAAGTGCTCACCCTTCACAAGT
CCTTGCCAGTGCCAACCAAACGGCGGCCTCTGGAGAAGATTGACCTTAAGTTCATTGACACCACCTCCAAGTTTGGCCAT
GGCTGCTTCCAGACCATGGAGGAGAAGACAGCATTCATGGCACCACTCAAGAAAGACCGAATTGCAAAGGAAGAAGGAGC
T

ORF - retro_hsap_3328 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 82.92 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMSHRKFSAPRHGSLGFLPRKRSSRHRGKVKSFPKDDPSKPVHLTAFLGYKAGMTHIVREVDRPGSKVNKK
MSHR.FSAPRHGSLGFLP..RS..H.GKVKSFPKDDPSK.VHLTAFLGYKAGMT.I.REVDRPGSKVNKK
RetrocopyMSHRRFSAPRHGSLGFLPQQRSRKHHGKVKSFPKDDPSKLVHLTAFLGYKAGMTNIMREVDRPGSKVNKK
ParentalEVVEAVTIVETPPMVVVGIVGYVETPRGLRTFKTVFAEHISDECKRRFYKNWHKSKKKAFTKYCKKWQDE
EV.EAVTIVE.PPMVVV.IVG.VETPRGL.TF.TVFAEHISD.CKR.FYKN.HKSKKKAFTKYCKK.QDE
RetrocopyEVIEAVTIVEIPPMVVVAIVGFVETPRGLQTFNTVFAEHISDACKRHFYKNRHKSKKKAFTKYCKKCQDE
ParentalDGKKQLEKDFSSMKKYCQVIRVIAHTQMRLLPLRQKKAHLMEIQVNGGTVAEKLDWARERLEQQVPVNQV
DGKKQLEKDFSSMKKY.QVI..IA.TQM.LLPL.Q.KAHLMEIQV.GGT.A.KLDWA.ERLEQQVPVNQV
RetrocopyDGKKQLEKDFSSMKKYRQVICIIAYTQMCLLPLHQRKAHLMEIQVKGGTMAKKLDWAHERLEQQVPVNQV
ParentalFGQDEMIDVIGVTKGKGYKGVTSRWHTKKLPRKTHRGLRKVACIGAWHPARVAFSVARAGQKGYHHRTEI
F.QD.MIDVI..TKG.GYKGVTSRWHTKKLP.KTHRGL.KVAC.G..HPA.VA..VA...QKGY.H.TEI
RetrocopyFEQDKMIDVIRLTKGNGYKGVTSRWHTKKLPHKTHRGLCKVACTGTQHPAPVALPVACIWQKGYCHSTEI
ParentalNKKIYKIGQGYLIKDGKLIKNNASTDYDLSDKSINPLGG-FVHYGEVTNDFVMLKGCVVGTKKRVLTLRK
N.KIYKI.QGY...D.KLIKNNASTDYDLSDK...P.GG.FVHYGEVTNDFVMLK.CVV.TKK.VLTL.K
RetrocopyN-KIYKISQGYFVRDSKLIKNNASTDYDLSDKP--PSGG>FVHYGEVTNDFVMLKDCVVDTKKQVLTLHK
ParentalSLLVQTKRRALEKIDLKFIDTTSKFGHGRFQTMEEKKAFMGPLKKDRIAKEEGA
SL.V.TKRR.LEKIDLKFIDTTSKFGHG.FQTMEEK.AFM.PLKKDRIAKEEGA
RetrocopySLPVPTKRRPLEKIDLKFIDTTSKFGHGCFQTMEEKTAFMAPLKKDRIAKEEGA

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 .02 RPM 1680 .36 RPM
bodymap2_adrenal 0 .06 RPM 1617 .45 RPM
bodymap2_brain 0 .00 RPM 431 .16 RPM
bodymap2_breast 0 .35 RPM 1202 .87 RPM
bodymap2_colon 0 .04 RPM 1954 .47 RPM
bodymap2_heart 0 .26 RPM 136 .94 RPM
bodymap2_kidney 0 .06 RPM 828 .19 RPM
bodymap2_liver 0 .00 RPM 515 .37 RPM
bodymap2_lung 0 .37 RPM 1395 .71 RPM
bodymap2_lymph_node 0 .11 RPM 1623 .01 RPM
bodymap2_ovary 0 .13 RPM 2926 .00 RPM
bodymap2_prostate 0 .00 RPM 1872 .53 RPM
bodymap2_skeletal_muscle 0 .00 RPM 319 .11 RPM
bodymap2_testis 0 .00 RPM 1379 .42 RPM
bodymap2_thyroid 0 .00 RPM 1149 .27 RPM
bodymap2_white_blood_cells 0 .00 RPM 1856 .01 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3328 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3328 retrocopy.

TSS - click to see more details



TSS No. TSS Name TSS expression level (Expr) in TPM range:
no expression 0 < Expr ≤ 1 1 < Expr ≤ 5 5 < Expr ≤ 10 Expr > 10
TSS #1 TSS_15499082 libraries37 libraries780 libraries587 libraries343 libraries

The graphical summary, for retro_hsap_3328 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1829 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Display detail expression values in each library
... or ...
Directly download all expression values

Lab - click to see more details

retro_hsap_3328 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3328 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2150
Gorilla gorilla retro_ggor_1295
Pongo abelii retro_pabe_2743
Parental genes homology:
Parental genes homology involve 25 parental genes, and 109 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000108531 retrocopy
retro_amel_1115,
Bos taurus ENSBTAG000000032283 retrocopies
retro_btau_1644, retro_btau_281, retro_btau_341,
Canis familiaris ENSCAFG000000013461 retrocopy
retro_cfam_97,
Callithrix jacchus ENSCJAG000000162766 retrocopies
retro_cjac_1198, retro_cjac_1972, retro_cjac_2157, retro_cjac_2264, retro_cjac_3079, retro_cjac_823,
Dasypus novemcinctus ENSDNOG000000011214 retrocopies
retro_dnov_1359, retro_dnov_1641, retro_dnov_652, retro_dnov_788,
Erinaceus europaeus ENSEEUG000000146612 retrocopies
retro_eeur_488, retro_eeur_557,
Echinops telfairi ENSETEG000000113805 retrocopies
retro_etel_1646, retro_etel_2199, retro_etel_2212, retro_etel_657, retro_etel_972,
Felis catus ENSFCAG000000058201 retrocopy
retro_fcat_1809,
Homo sapiens ENSG00000100316 9 retrocopies
retro_hsap_1341, retro_hsap_2403, retro_hsap_2529, retro_hsap_3328 , retro_hsap_3448, retro_hsap_3638, retro_hsap_3889, retro_hsap_4081, retro_hsap_4749,
Gorilla gorilla ENSGGOG0000000232610 retrocopies
retro_ggor_1043, retro_ggor_1295, retro_ggor_1582, retro_ggor_1822, retro_ggor_2329, retro_ggor_2616, retro_ggor_2713, retro_ggor_2736, retro_ggor_2955, retro_ggor_36,
Macropus eugenii ENSMEUG0000000978926 retrocopies
retro_meug_1045, retro_meug_118, retro_meug_1210, retro_meug_1403, retro_meug_1452, retro_meug_1492, retro_meug_1516, retro_meug_1554, retro_meug_1589, retro_meug_1604, retro_meug_1698, retro_meug_1856, retro_meug_2150, retro_meug_2151, retro_meug_221, retro_meug_367, retro_meug_412, retro_meug_461, retro_meug_592, retro_meug_677, retro_meug_683, retro_meug_831, retro_meug_851, retro_meug_886, retro_meug_889, retro_meug_898,
Microcebus murinus ENSMICG000000158321 retrocopy
retro_mmur_1307,
Myotis lucifugus ENSMLUG000000237111 retrocopy
retro_mluc_810,
Monodelphis domestica ENSMODG000000095392 retrocopies
retro_mdom_380, retro_mdom_408,
Mustela putorius furoENSMPUG000000132713 retrocopies
retro_mputfur_1284, retro_mputfur_199, retro_mputfur_774,
Nomascus leucogenys ENSNLEG000000152342 retrocopies
retro_nleu_1038, retro_nleu_1449,
Oryctolagus cuniculus ENSOCUG000000277124 retrocopies
retro_ocun_105, retro_ocun_179, retro_ocun_1893, retro_ocun_558,
Otolemur garnettii ENSOGAG000000000327 retrocopies
retro_ogar_1264, retro_ogar_1679, retro_ogar_2096, retro_ogar_2122, retro_ogar_2448, retro_ogar_3431, retro_ogar_960,
Ochotona princeps ENSOPRG000000130883 retrocopies
retro_opri_1004, retro_opri_1014, retro_opri_432,
Procavia capensis ENSPCAG000000106421 retrocopy
retro_pcap_115,
Pongo abelii ENSPPYG0000001183710 retrocopies
retro_pabe_1113, retro_pabe_1861, retro_pabe_2167, retro_pabe_2743, retro_pabe_2985, retro_pabe_3170, retro_pabe_3318, retro_pabe_3349, retro_pabe_3696, retro_pabe_3761,
Pteropus vampyrus ENSPVAG000000032042 retrocopies
retro_pvam_1220, retro_pvam_1390,
Rattus norvegicus ENSRNOG000000168962 retrocopies
retro_rnor_1333, retro_rnor_731,
Sarcophilus harrisii ENSSHAG000000032122 retrocopies
retro_shar_154, retro_shar_662,
Tupaia belangeri ENSTBEG000000059891 retrocopy
retro_tbel_939,

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 = 0.11 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .04 RPM
CEU_NA11843 0 .06 RPM
CEU_NA11930 0 .03 RPM
CEU_NA12004 0 .04 RPM
CEU_NA12400 0 .11 RPM
CEU_NA12751 0 .02 RPM
CEU_NA12760 0 .04 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .00 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .05 RPM
FIN_HG00277 0 .04 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .06 RPM
FIN_HG00328 0 .02 RPM
FIN_HG00338 0 .04 RPM
FIN_HG00349 0 .03 RPM
FIN_HG00375 0 .05 RPM
FIN_HG00377 0 .03 RPM
FIN_HG00378 0 .00 RPM
GBR_HG00099 0 .00 RPM
GBR_HG00111 0 .00 RPM
GBR_HG00114 0 .03 RPM
GBR_HG00119 0 .05 RPM
GBR_HG00131 0 .03 RPM
GBR_HG00133 0 .02 RPM
GBR_HG00134 0 .04 RPM
GBR_HG00137 0 .03 RPM
GBR_HG00142 0 .08 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .03 RPM
TSI_NA20513 0 .05 RPM
TSI_NA20518 0 .06 RPM
TSI_NA20532 0 .00 RPM
TSI_NA20538 0 .05 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .02 RPM
TSI_NA20771 0 .09 RPM
TSI_NA20786 0 .03 RPM
TSI_NA20798 0 .00 RPM
YRI_NA18870 0 .10 RPM
YRI_NA18907 0 .03 RPM
YRI_NA18916 0 .02 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .00 RPM
YRI_NA19213 0 .02 RPM
YRI_NA19214 0 .02 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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