RetrogeneDB ID:

retro_hsap_83

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:2:70314875..70315946(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000169564
Aliases:PCBP1, HEL-S-85, HNRPE1, HNRPX, hnRNP-E1, hnRNP-X
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:PCBP2
Ensembl ID:ENSG00000197111
Aliases:PCBP2, HNRNPE2, HNRPE2, hnRNP-E2
Description:poly(rC) binding protein 2 [Source:HGNC Symbol;Acc:8648]


Retrocopy-Parental alignment summary:






>retro_hsap_83
ATGGATGCCGGTGTGACTGAAAGTGGACTAAATGTGACTCTCACCATTCGGCTTCTTATGCACGGAAAGGAAGTAGGAAG
CATCATTGGGAAGAAAGGGGAGTCGGTTAAGAGGATCCGCGAGGAGAGTGGCGCGCGGATCAACATCTCGGAGGGGAATT
GTCCGGAGAGAATCATCACTCTGACCGGCCCCACCAATGCCATCTTTAAGGCTTTCGCTATGATCATCGACAAGCTGGAG
GAAGATATCAACAGCTCCATGACCAACAGTACCGCGGCCAGCAGGCCCCCGGTCACCCTGAGGCTGGTGGTGCCGGCCAC
CCAGTGCGGCTCCCTGATTGGGAAAGGCGGGTGTAAGATCAAAGAGATCCGCGAGAGTACGGGGGCGCAGGTCCAGGTGG
CGGGGGATATGCTGCCCAACTCCACCGAGCGGGCCATCACCATCGCTGGCGTGCCGCAGTCTGTCACCGAGTGTGTCAAG
CAGATTTGCCTGGTCATGCTGGAGACGCTCTCCCAGTCTCCGCAAGGGAGAGTCATGACCATTCCGTACCAGCCCATGCC
GGCCAGCTCCCCAGTCATCTGCGCGGGCGGCCAAGATCGGTGCAGCGACGCTGCGGGCTACCCCCATGCCACCCATGACC
TGGAGGGACCACCTCTAGATGCCTACTCGATTCAAGGACAACACACCATTTCTCCGCTCGATCTGGCCAAGCTGAACCAG
GTGGCAAGACAACAGTCTCACTTTGCCATGATGCACGGCGGGACCGGATTCGCCGGAATTGACTCCAGCTCTCCAGAGGT
GAAAGGCTATTGGGCAAGTTTGGATGCATCTACTCAAACCACCCATGAACTCACCATTCCAAATAACTTAATTGGCTGCA
TAATCGGGCGCCAAGGCGCCAACATTAATGAGATCCGCCAGATGTCCGGGGCCCAGATCAAAATTGCCAACCCAGTGGAA
GGCTCCTCTGGTAGGCAGGTTACTATCACTGGCTCTGCTGCCAGTATTAGTCTGGCCCAGTATCTAATCAATGCCAGGCT
TTCCTCTGAGAAGGGCATGGGGTGCAGCTAG

ORF - retro_hsap_83 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 86.45 %
Parental protein coverage: 58.2 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMDTGVIEGGLNVTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCPERIITLAGPTNAIFK
MD.GV.E.GLNVTLTIRLLMHGKEVGSIIGKKGESVK..REESGARINISEGNCPERIITL.GPTNAIFK
RetrocopyMDAGVTESGLNVTLTIRLLMHGKEVGSIIGKKGESVKRIREESGARINISEGNCPERIITLTGPTNAIFK
ParentalAFAMIIDKLEEDISSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPN
AFAMIIDKLEEDI.SSMTNSTAASRPPVTLRLVVPA.QCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPN
RetrocopyAFAMIIDKLEEDINSSMTNSTAASRPPVTLRLVVPATQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPN
ParentalSTERAITIAGIPQSIIECVKQICVVMLETLSQSPP-KGVTIPYRPKPSSSPVIFAGGQDRYSTGSDSASF
STERAITIAG.PQS..ECVKQIC.VMLETLSQSP.....TIPY.P.P.SSPVI.AGGQDR.S...D.A..
RetrocopySTERAITIAGVPQSVTECVKQICLVMLETLSQSPQGRVMTIPYQPMPASSPVICAGGQDRCS---DAAGY
ParentalPHTT
PH.T
RetrocopyPHAT

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 395 .31 RPM 289 .44 RPM
bodymap2_adrenal 250 .40 RPM 245 .72 RPM
bodymap2_brain 96 .64 RPM 125 .31 RPM
bodymap2_breast 246 .70 RPM 223 .74 RPM
bodymap2_colon 283 .54 RPM 234 .66 RPM
bodymap2_heart 87 .25 RPM 137 .26 RPM
bodymap2_kidney 166 .02 RPM 281 .96 RPM
bodymap2_liver 125 .22 RPM 128 .11 RPM
bodymap2_lung 237 .92 RPM 319 .99 RPM
bodymap2_lymph_node 294 .02 RPM 348 .48 RPM
bodymap2_ovary 268 .26 RPM 291 .60 RPM
bodymap2_prostate 241 .06 RPM 305 .94 RPM
bodymap2_skeletal_muscle 512 .39 RPM 189 .15 RPM
bodymap2_testis 196 .34 RPM 271 .79 RPM
bodymap2_thyroid 323 .01 RPM 224 .98 RPM
bodymap2_white_blood_cells 415 .73 RPM 386 .10 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity may be related with retro_hsap_83 in 53 libraries
ENCODE library ID Target ChIP-Seq Peak coordinates
ENCFF001VKU POLR2A 2:70313362..70314677
ENCFF002CFW POLR2A 2:70313246..70314439
ENCFF002CFW POLR2A 2:70315110..70315689
ENCFF002CFW POLR2A 2:70314472..70315035
ENCFF002CFX POLR2A 2:70315093..70315718
ENCFF002CFX POLR2A 2:70313267..70314428
ENCFF002CFX POLR2A 2:70314479..70315007
ENCFF002CGN POLR2A 2:70313262..70313883
ENCFF002CHO POLR2A 2:70313167..70316023
ENCFF002CIH POLR2A 2:70313274..70314041
ENCFF002CIH POLR2A 2:70314771..70315275
ENCFF002CIH POLR2A 2:70314158..70314448
ENCFF002CIO POLR2A 2:70313245..70314205
ENCFF002CIO POLR2A 2:70315150..70315669
ENCFF002CJE POLR2A 2:70312188..70314719
ENCFF002CJE POLR2A 2:70314676..70316039
ENCFF002CJZ POLR2A 2:70313380..70314717
ENCFF002CJZ POLR2A 2:70315125..70315592
ENCFF002CJZ POLR2A 2:70314777..70315089
ENCFF002CKX POLR2A 2:70313289..70314456
ENCFF002CKX POLR2A 2:70315160..70315510
ENCFF002CLM POLR2A 2:70313747..70314287
ENCFF002CLM POLR2A 2:70313978..70314518
ENCFF002CMI POLR2A 2:70313193..70316026
ENCFF002COJ POLR2A 2:70314025..70314461
ENCFF002CPG POLR2A 2:70313332..70314108
ENCFF002CPG POLR2A 2:70314131..70314482
ENCFF002CPG POLR2A 2:70315082..70315572
ENCFF002CPH POLR2A 2:70313779..70314169
ENCFF002CPH POLR2A 2:70314063..70314453
ENCFF002CQA POLR2A 2:70313660..70314112
ENCFF002CQA POLR2A 2:70314130..70314532
ENCFF002CQC POLR2A 2:70314117..70314432
ENCFF002CQC POLR2A 2:70313827..70314193
ENCFF002CQC POLR2A 2:70313502..70313910
ENCFF002CQC POLR2A 2:70315043..70315523
ENCFF002CQE POLR2A 2:70313564..70314429
ENCFF002CQE POLR2A 2:70315168..70315604
ENCFF002CQG POLR2A 2:70313459..70314125
ENCFF002CQG POLR2A 2:70314138..70314426
ENCFF002CQG POLR2A 2:70314928..70315452
ENCFF002CQI POLR2A 2:70313292..70314190
ENCFF002CQI POLR2A 2:70314098..70314445
ENCFF002CQK POLR2A 2:70313279..70314487
ENCFF002CQM POLR2A 2:70313326..70314471
ENCFF002CQM POLR2A 2:70315083..70315563
ENCFF002CQO POLR2A 2:70313292..70314170
ENCFF002CQO POLR2A 2:70314112..70314476
ENCFF002CRK POLR2A 2:70313374..70313898
ENCFF002CRO POLR2A 2:70313833..70314253
ENCFF002CSY POLR2A 2:70313263..70315654
ENCFF002CSY POLR2A 2:70313263..70315708
ENCFF002CUP POLR2A 2:70314137..70314385
ENCFF002CUP POLR2A 2:70315161..70315477
ENCFF002CUP POLR2A 2:70313639..70313955
ENCFF002CUP POLR2A 2:70314551..70314867
ENCFF002CUQ POLR2A 2:70313283..70314159
ENCFF002CUQ POLR2A 2:70314127..70314652
ENCFF002CUQ POLR2A 2:70315132..70315471
ENCFF002CVF POLR2A 2:70314233..70314345
ENCFF002CVF POLR2A 2:70314794..70315210
ENCFF002CVJ POLR2A 2:70314066..70314620
ENCFF002CVJ POLR2A 2:70313845..70314210
ENCFF002CXM POLR2A 2:70314208..70314395
ENCFF002CXM POLR2A 2:70313393..70313883
ENCFF002CXN POLR2A 2:70314199..70314399
ENCFF002CXO POLR2A 2:70314174..70314387
ENCFF002CXP POLR2A 2:70313422..70313902
ENCFF002CXP POLR2A 2:70314166..70314411
ENCFF002CXQ POLR2A 2:70315110..70315760
ENCFF002CXQ POLR2A 2:70313640..70314290
ENCFF002CXR POLR2A 2:70315178..70315434
ENCFF002CXR POLR2A 2:70313935..70314171
ENCFF002CZC POLR2A 2:70313382..70314717
ENCFF002CZD POLR2A 2:70313433..70314705
ENCFF002CZQ POLR2A 2:70314188..70314405
ENCFF002CZW POLR2A 2:70313523..70314215
ENCFF002CZW POLR2A 2:70315090..70315555
ENCFF002CZY POLR2A 2:70314094..70314471
ENCFF002CZY POLR2A 2:70313360..70314154
ENCFF002CZY POLR2A 2:70314715..70315231
ENCFF002DAE POLR2A 2:70314100..70314410
ENCFF002DAH POLR2A 2:70313950..70314234
ENCFF002DAK POLR2A 2:70313786..70314286
ENCFF002DAS POLR2A 2:70313795..70314271
ENCFF002DAV POLR2A 2:70314033..70314577
ENCFF002DAV POLR2A 2:70313749..70314293
ENCFF002DAY POLR2A 2:70313738..70314374
ENCFF002DAY POLR2A 2:70315084..70315720
ENCFF002DAY POLR2A 2:70313967..70314603
ENCFF002DBB POLR2A 2:70314004..70314204
ENCFF002DBE POLR2A 2:70314760..70315256
ENCFF002DBO POLR2A 2:70313947..70314400
ENCFF002DBO POLR2A 2:70315172..70315484
ENCFF002DBO POLR2A 2:70314670..70314954
ENCFF002DBP POLR2A 2:70314161..70314379
ENCFF002DBP POLR2A 2:70315164..70315494
ENCFF002DBQ POLR2A 2:70314240..70314355
ENCFF002DBQ POLR2A 2:70315159..70315529
ENCFF002DBQ POLR2A 2:70313873..70314243
ENCFF002DBT POLR2A 2:70314101..70314471
ENCFF002DBT POLR2A 2:70315151..70315521

EST - click to see more details

36 EST(s) were mapped to retro_hsap_83 retrocopy
EST ID Start End Identity Match Mis-match Score
BF212322 70314854 70315413 99.7 557 2 555
BM797269 70314963 70315483 99.7 517 2 515
BM845698 70314854 70315363 99.7 506 0 503
BM846475 70314854 70315358 100 504 0 504
BM848226 70314854 70315356 100 502 0 502
BP194496 70314868 70315450 99.9 581 1 580
BP194797 70314854 70315437 100 583 0 583
BP203626 70314930 70315479 98.8 542 6 534
BP208186 70314854 70315438 100 584 0 584
BP208342 70314781 70315364 100 583 0 583
BP214566 70314845 70315429 99.9 581 1 579
BP216102 70314854 70315436 100 582 0 582
BP253286 70314854 70315438 100 584 0 584
BP260688 70314834 70315416 100 580 0 580
BP261343 70314839 70315414 99.9 572 0 570
BP288781 70314854 70315436 98.8 573 7 566
BP295247 70314854 70315435 99.9 580 1 579
BP301028 70314839 70315421 100 582 0 582
BP308737 70314832 70315415 99.9 580 1 579
BP324124 70314828 70315409 100 578 0 578
BP339213 70314799 70315366 100 565 0 564
BP370162 70314878 70315437 98.6 545 8 536
BP370622 70314854 70315427 100 573 0 573
BP372378 70314854 70315436 100 582 0 582
CD622129 70314828 70315403 99.7 572 2 569
CD622132 70314834 70315403 99.9 567 1 565
CF145558 70314910 70315464 100 553 0 552
DA106581 70314854 70315412 99.5 558 0 557
DA136705 70314854 70315437 100 583 0 583
DA361796 70314845 70315394 99.1 549 0 547
DA362320 70314854 70315404 100 550 0 550
DA607687 70314820 70315385 100 565 0 565
DA681048 70314816 70315372 100 556 0 556
DA898676 70314855 70315411 100 556 0 556
DB011455 70314836 70315424 100 588 0 588
HY004147 70314854 70315378 100 524 0 524

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_12481920 libraries0 libraries62 libraries426 libraries1321 libraries
TSS #2 TSS_1248201 library0 libraries0 libraries0 libraries1828 libraries
TSS #3 TSS_12482132 libraries5 libraries127 libraries404 libraries1261 libraries

The graphical summary, for retro_hsap_83 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_83 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_83 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_113
Gorilla gorilla retro_ggor_212
Canis familiaris retro_cfam_54
Parental genes homology:
Parental genes homology involve 26 parental genes, and 61 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000207571 retrocopy
retro_btau_175,
Canis familiaris ENSCAFG000000068211 retrocopy
retro_cfam_54,
Callithrix jacchus ENSCJAG000000185902 retrocopies
retro_cjac_3253, retro_cjac_754,
Cavia porcellus ENSCPOG000000009672 retrocopies
retro_cpor_193, retro_cpor_97,
Dasypus novemcinctus ENSDNOG000000086886 retrocopies
retro_dnov_1146, retro_dnov_1399, retro_dnov_1672, retro_dnov_1823, retro_dnov_2434, retro_dnov_452,
Equus caballus ENSECAG000000223891 retrocopy
retro_ecab_67,
Erinaceus europaeus ENSEEUG000000010772 retrocopies
retro_eeur_218, retro_eeur_655,
Echinops telfairi ENSETEG000000147413 retrocopies
retro_etel_1170, retro_etel_2108, retro_etel_840,
Homo sapiens ENSG000001651193 retrocopies
retro_hsap_2323, retro_hsap_2674, retro_hsap_3385,
Homo sapiens ENSG00000197111 2 retrocopies
retro_hsap_4077, retro_hsap_83 ,
Gorilla gorilla ENSGGOG000000126132 retrocopies
retro_ggor_212, retro_ggor_2734,
Macropus eugenii ENSMEUG000000018877 retrocopies
retro_meug_1143, retro_meug_1988, retro_meug_432, retro_meug_526, retro_meug_618, retro_meug_828, retro_meug_964,
Microcebus murinus ENSMICG000000116512 retrocopies
retro_mmur_1226, retro_mmur_1228,
Myotis lucifugus ENSMLUG000000099713 retrocopies
retro_mluc_2199, retro_mluc_314, retro_mluc_571,
Macaca mulatta ENSMMUG000000066082 retrocopies
retro_mmul_1263, retro_mmul_1994,
Mus musculus ENSMUSG000000568511 retrocopy
retro_mmus_274,
Nomascus leucogenys ENSNLEG000000176931 retrocopy
retro_nleu_10,
Oryctolagus cuniculus ENSOCUG000000224903 retrocopies
retro_ocun_10, retro_ocun_1622, retro_ocun_898,
Ochotona princeps ENSOPRG000000046805 retrocopies
retro_opri_1126, retro_opri_284, retro_opri_313, retro_opri_742, retro_opri_789,
Pongo abelii ENSPPYG000000045812 retrocopies
retro_pabe_3346, retro_pabe_92,
Pan troglodytes ENSPTRG000000050181 retrocopy
retro_ptro_113,
Pteropus vampyrus ENSPVAG000000122843 retrocopies
retro_pvam_1168, retro_pvam_1369, retro_pvam_868,
Rattus norvegicus ENSRNOG000000368522 retrocopies
retro_rnor_1238, retro_rnor_2088,
Sus scrofa ENSSSCG000000002741 retrocopy
retro_sscr_61,
Ictidomys tridecemlineatus ENSSTOG000000036352 retrocopies
retro_itri_1522, retro_itri_557,
Vicugna pacos ENSVPAG000000004061 retrocopy
retro_vpac_471,

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 = 549.97 RPM Legend:


Library Retrogene expression
CEU_NA11831 494 .06 RPM
CEU_NA11843 384 .78 RPM
CEU_NA11930 345 .82 RPM
CEU_NA12004 454 .48 RPM
CEU_NA12400 432 .48 RPM
CEU_NA12751 340 .22 RPM
CEU_NA12760 507 .96 RPM
CEU_NA12827 439 .70 RPM
CEU_NA12872 426 .43 RPM
CEU_NA12873 450 .21 RPM
FIN_HG00183 343 .26 RPM
FIN_HG00277 388 .22 RPM
FIN_HG00315 376 .71 RPM
FIN_HG00321 377 .30 RPM
FIN_HG00328 480 .89 RPM
FIN_HG00338 406 .66 RPM
FIN_HG00349 418 .25 RPM
FIN_HG00375 430 .46 RPM
FIN_HG00377 422 .94 RPM
FIN_HG00378 422 .51 RPM
GBR_HG00099 469 .13 RPM
GBR_HG00111 474 .03 RPM
GBR_HG00114 499 .56 RPM
GBR_HG00119 362 .34 RPM
GBR_HG00131 339 .03 RPM
GBR_HG00133 409 .00 RPM
GBR_HG00134 484 .20 RPM
GBR_HG00137 479 .45 RPM
GBR_HG00142 343 .78 RPM
GBR_HG00143 484 .37 RPM
TSI_NA20512 542 .98 RPM
TSI_NA20513 434 .09 RPM
TSI_NA20518 448 .97 RPM
TSI_NA20532 358 .75 RPM
TSI_NA20538 360 .75 RPM
TSI_NA20756 438 .50 RPM
TSI_NA20765 360 .66 RPM
TSI_NA20771 401 .40 RPM
TSI_NA20786 456 .74 RPM
TSI_NA20798 523 .21 RPM
YRI_NA18870 522 .68 RPM
YRI_NA18907 489 .52 RPM
YRI_NA18916 393 .48 RPM
YRI_NA19093 549 .97 RPM
YRI_NA19099 448 .06 RPM
YRI_NA19114 433 .75 RPM
YRI_NA19118 488 .12 RPM
YRI_NA19213 360 .54 RPM
YRI_NA19214 511 .33 RPM
YRI_NA19223 459 .02 RPM

Indel association:

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





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