RetrogeneDB ID:

retro_hsap_2643

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:3:46064787..46065645(+)
Located in intron of:ENSG00000173578
Retrocopy
information
Ensembl ID:ENSG00000226933
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:NRBF2
Ensembl ID:ENSG00000148572
Aliases:NRBF2, COPR1, COPR2, NRBF-2
Description:nuclear receptor binding factor 2 [Source:HGNC Symbol;Acc:19692]


Retrocopy-Parental alignment summary:






>retro_hsap_2643
ATGGAAGTAATGGAAGGACCCCTCAACCTGGCTCATCAGCAGAGCAGACGAGCCGACCGTTTATTAGCTGCAGGCAAATA
CGAAGAGGCGATTTCTTGTCACAAAAAGGCTGCGGCATATCTTTCTGAAGCCATGAAGCTGACACAATCTGAGCAGGCTC
GTCTTTCACTGGAATTGCAAAGGGATAGCCACATGAAACAGCTCCTCCTCATCCAAGAGAGATGGAAAAGGGCCCAGCGT
GAGGAAAGATTGAAAGCCTAGCAGAACACAGACAAGGATGTAGCTGCCCATCTTCAGGCATCTCACAAACTCTCTGCCGA
GGATGCGGAGGGCCAGAGCCCCCTTTCTCAGAAGTACAGCCCTTCTTCAGAGAAACGCCTGCTTGAGATTCAGGGGATCT
TTGACAGGGATCCAGACACACTACTATATTTACTTCAGCAAAAGAGTGAGACAGCAGAGCCATGTATTGGAAGCAAAGCC
CCAGAAGATGATAAAACAATTATAGAGGAATAGGCAACCAAAATTGCAGATTTGAAGAGACGTGTGGAATTCCTTGTGGC
TGAGAATGAAAGATTAAGGAAAGAAAATAACTAAAGGCTGAAAAGGCCAGACTTCTAAAAAGGTCCAGTAGAAAAGGAGC
TGGATGTAGATGCTGATTTTGTAGAAACGTCAGAATTACGGAGCTTGCCGCCACATTCAGAAACTGCTACAGCCTCCTCA
ACCTGGCAGAAGTTTGCAGCAAATGCCGGGAAAGCCAAGGACATTCCAATCCCCAGTCTTCCTCCCTTGGATTTTACATC
TCCAGAACTTCCCCTTATGGATCTCCCTGAGAATATTCTGAAAGGATTTATGAATAAT

ORF - retro_hsap_2643 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 88.85 %
Parental protein coverage: 100. %
Number of stop codons detected: 4
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMEVMEGPLNLAHQQSRRADRLLAAGKYEEAISCHKKAAAYLSEAMKLTQSEQAHLSLELQRDSHMKQLLL
MEVMEGPLNLAHQQSRRADRLLAAGKYEEAISCHKKAAAYLSEAMKLTQSEQA.LSLELQRDSHMKQLLL
RetrocopyMEVMEGPLNLAHQQSRRADRLLAAGKYEEAISCHKKAAAYLSEAMKLTQSEQARLSLELQRDSHMKQLLL
ParentalIQERWKRAQREERLKAQQNTDKDAAAHLQTSHKPSAEDAEGQSPLSQKYSPSTEKCLPEIQGIFDRDPDT
IQERWKRAQREERLKA.QNTDKD.AAHLQ.SHK.SAEDAEGQSPLSQKYSPS.EK.L.EIQGIFDRDPDT
RetrocopyIQERWKRAQREERLKA*QNTDKDVAAHLQASHKLSAEDAEGQSPLSQKYSPSSEKRLLEIQGIFDRDPDT
ParentalLLYLLQQKSEPAEPCIGSKAPKDDKTIIEEQATKIADLKRHVEFLVAENERLRKENKQLKAEKARLLKGP
LLYLLQQKSE.AEPCIGSKAP.DDKTIIEE.ATKIADLKR.VEFLVAENERLRKEN...........KGP
RetrocopyLLYLLQQKSETAEPCIGSKAPEDDKTIIEE*ATKIADLKRRVEFLVAENERLRKEN-N*RLKRPDF*KGP
ParentalIEKELDVDADFVETSELWSLPPHAETATASSTWQKFAANTGKAKDIPIPNLPPLDFPSPELPLMELSEDI
.EKELDVDADFVETSEL.SLPPH.ETATASSTWQKFAAN.GKAKDIPIP.LPPLDF.SPELPLM.L.E.I
RetrocopyVEKELDVDADFVETSELRSLPPHSETATASSTWQKFAANAGKAKDIPIPSLPPLDFTSPELPLMDLPENI
ParentalLKGFMNN
LKGFMNN
RetrocopyLKGFMNN

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 22 .12 RPM
bodymap2_adrenal 0 .02 RPM 16 .76 RPM
bodymap2_brain 0 .00 RPM 19 .41 RPM
bodymap2_breast 0 .00 RPM 22 .22 RPM
bodymap2_colon 0 .00 RPM 15 .00 RPM
bodymap2_heart 0 .00 RPM 7 .40 RPM
bodymap2_kidney 0 .00 RPM 13 .69 RPM
bodymap2_liver 0 .00 RPM 29 .85 RPM
bodymap2_lung 0 .00 RPM 19 .73 RPM
bodymap2_lymph_node 0 .00 RPM 25 .67 RPM
bodymap2_ovary 0 .00 RPM 17 .10 RPM
bodymap2_prostate 0 .00 RPM 18 .22 RPM
bodymap2_skeletal_muscle 0 .00 RPM 24 .03 RPM
bodymap2_testis 0 .62 RPM 21 .79 RPM
bodymap2_thyroid 0 .06 RPM 17 .04 RPM
bodymap2_white_blood_cells 0 .00 RPM 83 .63 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity may be related with retro_hsap_2643 in 7 libraries
ENCODE library ID Target ChIP-Seq Peak coordinates
ENCFF002CMI POLR2A 3:46064537..46064884
ENCFF002CXM POLR2A 3:46064483..46064973
ENCFF002CXN POLR2A 3:46064484..46064980
ENCFF002CXO POLR2A 3:46064501..46064925
ENCFF002CXP POLR2A 3:46064485..46064965
ENCFF002CXR POLR2A 3:46064580..46064822
ENCFF002DBE POLR2A 3:46064609..46064813

EST - click to see more details

No EST(s) were mapped for retro_hsap_2643 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_2643 retrocopy 5' end.

Lab - click to see more details

retro_hsap_2643 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2643 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1780
Pongo abelii retro_pabe_2327
Macaca mulatta retro_mmul_1523
Parental genes homology:
Parental genes homology involve 13 parental genes, and 26 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG000000046483 retrocopies
retro_chof_1032, retro_chof_2250, retro_chof_2568,
Homo sapiens ENSG00000148572 3 retrocopies
retro_hsap_2643 , retro_hsap_3999, retro_hsap_433,
Gorilla gorilla ENSGGOG000000130162 retrocopies
retro_ggor_1846, retro_ggor_2685,
Macropus eugenii ENSMEUG000000108493 retrocopies
retro_meug_1385, retro_meug_2049, retro_meug_671,
Macaca mulatta ENSMMUG000000177261 retrocopy
retro_mmul_1523,
Monodelphis domestica ENSMODG000000171831 retrocopy
retro_mdom_1995,
Mus musculus ENSMUSG000000750002 retrocopies
retro_mmus_1278, retro_mmus_1279,
Otolemur garnettii ENSOGAG000000058561 retrocopy
retro_ogar_2110,
Pongo abelii ENSPPYG000000024113 retrocopies
retro_pabe_2327, retro_pabe_3285, retro_pabe_3286,
Pan troglodytes ENSPTRG000000025393 retrocopies
retro_ptro_1780, retro_ptro_194, retro_ptro_2715,
Rattus norvegicus ENSRNOG000000006412 retrocopies
retro_rnor_1681, retro_rnor_994,
Sarcophilus harrisii ENSSHAG000000047441 retrocopy
retro_shar_427,
Ictidomys tridecemlineatus ENSSTOG000000113411 retrocopy
retro_itri_183,

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 = 0.03 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 .02 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 .03 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 .03 RPM
GBR_HG00119 0 .00 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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