RetrogeneDB ID:

retro_hsap_1483

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:15:36909289..36910960(+)
Located in intron of:ENSG00000186073
Retrocopy
information
Ensembl ID:ENSG00000261315
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:LARP4
Ensembl ID:ENSG00000161813
Aliases:None
Description:La ribonucleoprotein domain family, member 4 [Source:HGNC Symbol;Acc:24320]


Retrocopy-Parental alignment summary:






>retro_hsap_1483
ATGTTGTTTTTCGTGGAGCAGGTAACATCTAAAGGAACTGGTTTAAATCCTAATGCCAAAGTATGGCAAGAAATTGCTCC
TGGGAATACTGATGCCACCCCAGTAACTCATAGAACTGAAAGCTCTTGGCATGAAACAGCAGCCACATCGGGTGCTCATC
CTGAGGTTAATGCAGAGCTCTCAGAAGATATATGTAAAGAATATGAAGTAATGTGTTCTTTGTCTTGTGAAACCACAAGA
AATACTACAGGCATTGAAGAATCAACTGATGGGATGATTTTAGGACCAGAAGATCTGAGTTACCAAATATATGATGTTTC
TGGAGAAAGCAATTCAGCAATTTCTACAGAAGACCTAAAAGAATGTCTAAAGAAACAATTAGAATTCTGGTTTTCACGAG
AAAATTTGTCAAAGAATCTTTACTTGATCTCTCAAATGGATAGTGATCAGTTCATCCCAATTTGGACAGTTGTTAACATG
GAAGAAATAAAAAAGTTGACCACAGACCCTGATGTAATTCTTGAAGTGTTAAGTTCTTCTCCCATGGTACAAATTGATGA
GAAGGGTAAAAAAGTGAGCCAAGTCATAAGCGTTGTATTGTGATTCTTAGAGAGATTCCTGAAACAACACCAATAGAGGA
AGTGAAAGCTTTGTTCAAATTGAAAACTGCCCCAAAGTGATAAGTTGTGAGTTTGCACACAGTAGCAGCTGGTATATCAC
TTTCCAGTCAGACACAGATACACAAAAGGCTTTTAAATCCTTAAGAGAAGAAGTTAAAACATTTCAGGGCAAGCCAATTA
TGGCAAGGATAAAAGCCATCAATACATTTTTTGCTAAGAATTGTTACTAATTAATGGATTCTAGTATCTATAGTCAGCCC
ATTCAGACTCAAGCACAGTATGCCTCCCCAGTCTTTATGCAGCCTGTATATAATCTTCACCAGCAGTTCTCGGTCTATAG
TATTATTCCTCAGTCTTGGTCTCCAAATCCTACACCTTACTTTGAAACACCACTGGCCCGCTTTCCCAATGGTAGTTTTG
TGAATGGCATTAATTCACCAGGATCTTATAAAAGACATGCTACTGCTATGAATATGGGTCGACCATTCCAAAAAAAAACC
TGAAGCCTCATTTTAGGTCATCCAGTGGTTCAGAACACTCAACAGAGGACTCTGTATCATTGGGGGATGGACAATTGAAC
AGATCTAGTTCAAAAAATTTTTCAACTGAAAGCATAATCCTACAGTAACTGGGGATTAGGAGCAAACTTAACTTCAAAAG
GAGACTTCCACTTTGCAGATGGAACAAAATGGGGACTATGGTAGGGGCAGGAGAACTCTTTTCAGAGGTCGAAGATGACG
ACAAGATGTCAATCTCAAGACCTCATCCTTCAACAGCTGAATCAAAGCCTCCAACACCAAAGTTTGACTTACTAGCCTCA
AATTTTCCACCTTTACCTGGAAGTTCATCAAGAATCCCAGATAAACTCATTTTGGAGAATAGGATGTCTGATGTTGTTAA
AGGTGTCTACAAAGAAAAGGATAATGAAGTGTTGAGAGTTAGTTGCCCAGTGCCTGCAGATGAGCAGACAGAATGCACTT
CTGCCCAGCAACTCAGTATGAGTACCAGTTCTCCATGTGCAGCTGAGCCTACTGCATTAAGCACAACTCAG

ORF - retro_hsap_1483 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 87.41 %
Parental protein coverage: 77.21 %
Number of stop codons detected: 4
Number of frameshifts detected 5


Retrocopy - Parental Gene Alignment:

ParentalMLLFVEQVASKGTGLNPNAKVWQEIAPGNTDATPVTHGTESSWHEIAATSGAHPEGNAELSEDICKEYEV
ML.FVEQV.SKGTGLNPNAKVWQEIAPGNTDATPVTH.TESSWHE.AATSGAHPE.NAELSEDICKEYEV
RetrocopyMLFFVEQVTSKGTGLNPNAKVWQEIAPGNTDATPVTHRTESSWHETAATSGAHPEVNAELSEDICKEYEV
ParentalMYSSSCETTRNTTGIEESTDGMILGPEDLSYQIYDVSGESNSAVSTEDLKECLKKQLEFCFSRENLSKDL
M.S.SCETTRNTTGIEESTDGMILGPEDLSYQIYDVSGESNSA.STEDLKECLKKQLEF.FSRENLSK.L
RetrocopyMCSLSCETTRNTTGIEESTDGMILGPEDLSYQIYDVSGESNSAISTEDLKECLKKQLEFWFSRENLSKNL
ParentalYLISQMDSDQFIPIWTVANMEEIKKLTTDPDLILEVLRSSPMVQVDEKGEKV-RPSHKRCIVILREIPET
YLISQMDSDQFIPIWTV.NMEEIKKLTTDPD.ILEVL.SSPMVQ.DEKG.KV..PSHKRCIVILREIPET
RetrocopyYLISQMDSDQFIPIWTVVNMEEIKKLTTDPDVILEVLSSSPMVQIDEKGKKV<EPSHKRCIVILREIPET
ParentalTPIEEVKGLFKS-ENCPKVISCEFAHNSNWYITFQSDTDAQQAFKYLREEVKTFQGKPIMARIKAINTFF
TPIEEVK.LFK..ENCPKVISCEFAH.S.WYITFQSDTD.Q.AFK.LREEVKTFQGKPIMARIKAINTFF
RetrocopyTPIEEVKALFKL<ENCPKVISCEFAHSSSWYITFQSDTDTQKAFKSLREEVKTFQGKPIMARIKAINTFF
ParentalAKNGYRLMDSSIYSHPIQTQAQYASPVFMQPVYNPHQQYSVYSIVPQSWSPNPTPYFETPLAPFPNGSFV
AKN.Y.LMDSSIYS.PIQTQAQYASPVFMQPVYN.HQQ.SVYSI.PQSWSPNPTPYFETPLA.FPNGSFV
RetrocopyAKNCY*LMDSSIYSQPIQTQAQYASPVFMQPVYNLHQQFSVYSIIPQSWSPNPTPYFETPLARFPNGSFV
ParentalNGFNSPGSYKTNAAAMNMGRPFQKNR-VKPQFRSSGGSEHSTEGSVSLGDGQLNRYSSRNFPAE-RHNPT
NG.NSPGSYK..A.AMNMGRPF......KP.FRSS.GSEHSTE.SVSLGDGQLNR.SS.NF..E..HNPT
RetrocopyNGINSPGSYKRHATAMNMGRPFXXXX<LKPHFRSSSGSEHSTEDSVSLGDGQLNRSSSKNFSTE<KHNPT
ParentalVTGHQEQTYLQKETSTLQVEQNGDYGRGRRTLFRGRRRREDD-RISRPHPSTAESKAPTPKFDLLASNFP
VTG..EQT.LQKETSTLQ.EQNGDYGRGRRTLFRG.RR...D..ISRPHPSTAESK.PTPKFDLLASNFP
RetrocopyVTGD*EQT*LQKETSTLQMEQNGDYGRGRRTLFRG-RR*RQD>SISRPHPSTAESKPPTPKFDLLASNFP
ParentalPLPGSSSRMPGELVLENRMSDVVKGVYKEKDNEELTISCPVPADEQTECTSAQQLNMSTSSPCAAELTAL
PLPGSSSR.P..L.LENRMSDVVKGVYKEKDNE.L..SCPVPADEQTECTSAQQL.MSTSSPCAAE.TAL
RetrocopyPLPGSSSRIPDKLILENRMSDVVKGVYKEKDNEVLRVSCPVPADEQTECTSAQQLSMSTSSPCAAEPTAL
ParentalSTTQ
STTQ
RetrocopySTTQ

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 61 .14 RPM
bodymap2_adrenal 0 .02 RPM 47 .45 RPM
bodymap2_brain 0 .00 RPM 36 .57 RPM
bodymap2_breast 0 .00 RPM 53 .37 RPM
bodymap2_colon 0 .00 RPM 61 .06 RPM
bodymap2_heart 0 .52 RPM 68 .38 RPM
bodymap2_kidney 0 .00 RPM 137 .03 RPM
bodymap2_liver 0 .00 RPM 98 .84 RPM
bodymap2_lung 0 .00 RPM 77 .81 RPM
bodymap2_lymph_node 0 .00 RPM 66 .17 RPM
bodymap2_ovary 0 .00 RPM 71 .88 RPM
bodymap2_prostate 0 .00 RPM 63 .06 RPM
bodymap2_skeletal_muscle 0 .00 RPM 59 .38 RPM
bodymap2_testis 0 .00 RPM 74 .73 RPM
bodymap2_thyroid 0 .09 RPM 91 .11 RPM
bodymap2_white_blood_cells 0 .00 RPM 48 .73 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_1483 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_1483 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_1483 retrocopy 5' end.

Lab - click to see more details

retro_hsap_1483 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1483 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1003
Parental genes homology:
Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG00000161813 1 retrocopy
retro_hsap_1483 ,
Myotis lucifugus ENSMLUG000000125131 retrocopy
retro_mluc_1180,
Macaca mulatta ENSMMUG000000081721 retrocopy
retro_mmul_2129,
Mus musculus ENSMUSG000000230251 retrocopy
retro_mmus_3568,
Nomascus leucogenys ENSNLEG000000177981 retrocopy
retro_nleu_2388,
Pan troglodytes ENSPTRG000000049351 retrocopy
retro_ptro_1003,
Rattus norvegicus ENSRNOG000000490911 retrocopy
retro_rnor_644,

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 = 0.06 RPM Legend:


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

Indel association:

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





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