RetrogeneDB ID:

retro_hsap_34

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:5:137088837..137089755(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000177733
Aliases:HNRNPA0, HNRPA0
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:HNRNPA3
Ensembl ID:ENSG00000170144
Aliases:HNRNPA3, 2610510D13Rik, D10S102, FBRNP, HNRPA3
Description:heterogeneous nuclear ribonucleoprotein A3 [Source:HGNC Symbol;Acc:24941]


Retrocopy-Parental alignment summary:






>retro_hsap_34
ATGGAGAATTCTCAGTTGTGTAAGCTGTTCATCGGCGGCCTCAATGTGCAGACGAGTGAGTCGGGCCTGCGCGGCCACTT
TGAGGCCTTTGGGACTCTGACGGACTGCGTGGTGGTGGTGAATCCCCAGACCAAGCGCTCCCGTTGCTTTGGCTTCGTGA
CCTACTCCAATGTGGAGGAGGCGGACGCCGCCATGGCCGCCTCGCCCCATGCCGTGGACGGCAACACTGTGGAGCTGAAG
CGGGCGGTGTCCCGGGAGGATTCGGCGCGGCCCGGTGCCCACGCCAAGGTTAAGAAGCTCTTTGTCGGAGGCCTTAAAGG
AGACGTGGCTGAGGGCGACCTGATCGAGCACTTCTCGCAGTTTGGCACCGTGGAAAAGGCCGAGATTATTGCCGACAAGC
AGTCCGGCAAGAAGCGTGGATTCGGCTTCGTGTATTTCCAGAATCACGACGCGGCAGACAAGGCCGCGGTGGTCAAGTTC
CATCCGATTCAGGGCCATCGCGTGGAGGTGAAGAAAGCAGTCCCCAAGGAGGATATCTACTCCGGTGGGGGTGGAGGCGG
CTCCCGATCCTCCCGGGGCGGCCGAGGCGGCCGGGGGCGCGGCGGTGGTCGAGACCAGAACGGCCTTTCCAAGGGCGGCG
GCGGCGGTTACAACAGCTACGGTGGTTACGGCGGCGGCGGAGGCGGCGGCTACAATGCCTACGGAGGCGGCGGCGGCGGT
TCGTCCTACGGTGGGAGCGACTACGGTAACGGCTTCGGCGGCTTCGGCAGCTACAGCCAGCATCAGTCCTCCTATGGGCC
CATGAAGAGCGGCGGCGGCGGCGGCGGTGGAGGCAGTAGCTGGGGCGGTCGCAGTAATAGTGGACCTTACAGAGGCGGCT
ATGGCGGTGGGGGTGGCTATGGAGGCAGCTCCTTCTAA

ORF - retro_hsap_34 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 54.28 %
Parental protein coverage: 79.37 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalEPEQLRKLFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAAMCARPHK
E..QL.KLFIGGL...T....LR.HFE..GTLTDCVV...PQTKRSR.FGFVTYS.VEE.DAAM.A.PH.
RetrocopyENSQLCKLFIGGLNVQTSESGLRGHFEAFGTLTDCVVVVNPQTKRSRCFGFVTYSNVEEADAAMAASPHA
ParentalVDGRVVEPKRAVSREDSVKPGAHLTVKKIFVGGIKEDTEEYNLRDYFEKYGKIETIEVMEDRQSGKKRGF
VDG..VE.KRAVSREDS..PGAH..VKK.FVGG.K.D..E..L...F...G..E..E...D.QSGKKRGF
RetrocopyVDGNTVELKRAVSREDSARPGAHAKVKKLFVGGLKGDVAEGDLIEHFSQFGTVEKAEIIADKQSGKKRGF
ParentalAFVTFDDHDTVDKIVVQKYHTINGHNCEVKKALSKQEMQSA----GSQRGRGGGSGNFMGRGGNFGGGGG
.FV.F..HD..DK..V.K.H.I.GH..EVKKA..K....S.....GS...RGG..G...GRGG.....G.
RetrocopyGFVYFQNHDAADKAAVVKFHPIQGHRVEVKKAVPKEDIYSGGGGGGSRSSRGGRGGR--GRGGGRDQNGL
ParentalNFGRGGNFGGRGGYGGGGGGSRGSYGGGDGGYNGFGGDGGNYGGGPGYSSRGGYGGGGPGYGNQGGGYGG
..G.GG.....GGYGGGGGG....YGGG.GG....G.D.GN..GG.G..S......G....G..GGG.GG
RetrocopySKGGGGGYNSYGGYGGGGGGGYNAYGGGGGGSSYGGSDYGNGFGGFGSYSQHQSSYGPMKSG--GGGGGG
ParentalGGGYDGYNEGGNFGGGNYGGGGNY
G....G....G...GG.YGGGG.Y
RetrocopyGSSWGGRSNSGPYRGG-YGGGGGY

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 55 .56 RPM 347 .23 RPM
bodymap2_adrenal 59 .46 RPM 535 .07 RPM
bodymap2_brain 19 .55 RPM 339 .37 RPM
bodymap2_breast 28 .64 RPM 267 .51 RPM
bodymap2_colon 30 .28 RPM 432 .85 RPM
bodymap2_heart 10 .65 RPM 101 .85 RPM
bodymap2_kidney 20 .64 RPM 331 .49 RPM
bodymap2_liver 9 .00 RPM 119 .24 RPM
bodymap2_lung 40 .84 RPM 430 .05 RPM
bodymap2_lymph_node 32 .98 RPM 274 .00 RPM
bodymap2_ovary 60 .55 RPM 698 .84 RPM
bodymap2_prostate 24 .54 RPM 327 .14 RPM
bodymap2_skeletal_muscle 12 .39 RPM 119 .93 RPM
bodymap2_testis 29 .30 RPM 412 .92 RPM
bodymap2_thyroid 57 .70 RPM 465 .04 RPM
bodymap2_white_blood_cells 35 .24 RPM 279 .96 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity may be related with retro_hsap_34 in 52 libraries
ENCODE library ID Target ChIP-Seq Peak coordinates
ENCFF001VKU POLR2A 5:137089845..137090446
ENCFF002CFW POLR2A 5:137089772..137090758
ENCFF002CFW POLR2A 5:137089089..137089519
ENCFF002CFX POLR2A 5:137089776..137090745
ENCFF002CFX POLR2A 5:137089137..137089533
ENCFF002CGN POLR2A 5:137089837..137090195
ENCFF002CGN POLR2A 5:137090137..137090374
ENCFF002CHO POLR2A 5:137088772..137091057
ENCFF002CIH POLR2A 5:137089841..137090178
ENCFF002CIH POLR2A 5:137090215..137090363
ENCFF002CIO POLR2A 5:137089800..137090437
ENCFF002CIO POLR2A 5:137088987..137089531
ENCFF002CJE POLR2A 5:137089623..137091123
ENCFF002CJZ POLR2A 5:137089755..137090743
ENCFF002CKX POLR2A 5:137089820..137090409
ENCFF002CLM POLR2A 5:137089775..137090315
ENCFF002CLM POLR2A 5:137089974..137090514
ENCFF002CMI POLR2A 5:137089464..137090840
ENCFF002COJ POLR2A 5:137090032..137090468
ENCFF002COJ POLR2A 5:137089803..137090239
ENCFF002COJ POLR2A 5:137090357..137090793
ENCFF002CPG POLR2A 5:137089854..137090194
ENCFF002CPG POLR2A 5:137089978..137090468
ENCFF002CPH POLR2A 5:137089986..137090143
ENCFF002CPH POLR2A 5:137090051..137090441
ENCFF002CQA POLR2A 5:137089925..137090495
ENCFF002CQA POLR2A 5:137090125..137090695
ENCFF002CQC POLR2A 5:137089840..137090402
ENCFF002CQC POLR2A 5:137090413..137090739
ENCFF002CQE POLR2A 5:137089823..137090412
ENCFF002CQE POLR2A 5:137090360..137090740
ENCFF002CQG POLR2A 5:137089856..137090416
ENCFF002CQG POLR2A 5:137090411..137090640
ENCFF002CQI POLR2A 5:137089848..137090198
ENCFF002CQI POLR2A 5:137090091..137090387
ENCFF002CQI POLR2A 5:137090389..137090711
ENCFF002CQK POLR2A 5:137089820..137090419
ENCFF002CQK POLR2A 5:137090365..137090761
ENCFF002CQM POLR2A 5:137089847..137090310
ENCFF002CQM POLR2A 5:137089847..137090346
ENCFF002CQM POLR2A 5:137090401..137090711
ENCFF002CQO POLR2A 5:137089812..137090451
ENCFF002CQO POLR2A 5:137090331..137090743
ENCFF002CRK POLR2A 5:137089972..137090496
ENCFF002CRK POLR2A 5:137090177..137090701
ENCFF002CRO POLR2A 5:137090340..137090760
ENCFF002CRO POLR2A 5:137090099..137090519
ENCFF002CRO POLR2A 5:137089987..137090096
ENCFF002CSY POLR2A 5:137089416..137090943
ENCFF002CUP POLR2A 5:137089898..137090160
ENCFF002CUP POLR2A 5:137090138..137090349
ENCFF002CUQ POLR2A 5:137089830..137090324
ENCFF002CUQ POLR2A 5:137089830..137090346
ENCFF002CVF POLR2A 5:137089908..137090118
ENCFF002CVF POLR2A 5:137090019..137090435
ENCFF002CVJ POLR2A 5:137089732..137090408
ENCFF002CXM POLR2A 5:137089873..137090149
ENCFF002CXM POLR2A 5:137089975..137090465
ENCFF002CXN POLR2A 5:137089960..137090087
ENCFF002CXN POLR2A 5:137089993..137090489
ENCFF002CXO POLR2A 5:137089927..137090123
ENCFF002CXO POLR2A 5:137090028..137090452
ENCFF002CXP POLR2A 5:137089836..137090148
ENCFF002CXP POLR2A 5:137090147..137090392
ENCFF002CXP POLR2A 5:137090476..137090685
ENCFF002CXR POLR2A 5:137089828..137090418
ENCFF002CZC POLR2A 5:137089750..137090768
ENCFF002CZD POLR2A 5:137089624..137090750
ENCFF002CZQ POLR2A 5:137089876..137090263
ENCFF002CZQ POLR2A 5:137090419..137090643
ENCFF002CZW POLR2A 5:137089644..137090768
ENCFF002CZY POLR2A 5:137089816..137090685
ENCFF002DAE POLR2A 5:137089896..137090087
ENCFF002DAE POLR2A 5:137090368..137090678
ENCFF002DAH POLR2A 5:137089940..137090115
ENCFF002DAH POLR2A 5:137090352..137090636
ENCFF002DAK POLR2A 5:137089948..137090075
ENCFF002DAK POLR2A 5:137089980..137090480
ENCFF002DAS POLR2A 5:137089955..137090100
ENCFF002DAS POLR2A 5:137089995..137090471
ENCFF002DAV POLR2A 5:137090164..137090381
ENCFF002DAV POLR2A 5:137090196..137090740
ENCFF002DAY POLR2A 5:137089892..137090134
ENCFF002DAY POLR2A 5:137089950..137090586
ENCFF002DAY POLR2A 5:137090150..137090786
ENCFF002DBB POLR2A 5:137089903..137090103
ENCFF002DBB POLR2A 5:137090440..137090640
ENCFF002DBE POLR2A 5:137089853..137090322
ENCFF002DBE POLR2A 5:137090141..137090637
ENCFF002DBO POLR2A 5:137089835..137090163
ENCFF002DBO POLR2A 5:137090119..137090413
ENCFF002DBP POLR2A 5:137089866..137090135
ENCFF002DBP POLR2A 5:137090209..137090363
ENCFF002DBP POLR2A 5:137090312..137090642
ENCFF002DBQ POLR2A 5:137089919..137090092
ENCFF002DBQ POLR2A 5:137090043..137090413
ENCFF002DBT POLR2A 5:137089949..137090114
ENCFF002DBT POLR2A 5:137090364..137090734

EST - click to see more details

3 EST(s) were mapped to retro_hsap_34 retrocopy
EST ID Start End Identity Match Mis-match Score
AW614422 137089215 137089515 100 300 0 300
BE394303 137088945 137089338 98.5 392 1 389
BF900701 137089161 137089404 97.9 230 4 221

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_1491992 libraries0 libraries1 library0 libraries1826 libraries

The graphical summary, for retro_hsap_34 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_34 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_34 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_14
Bos taurus retro_btau_212
Canis familiaris retro_cfam_65
Parental genes homology:
Parental genes homology involve 18 parental genes, and 119 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000215808 retrocopies
retro_btau_1029, retro_btau_1310, retro_btau_1587, retro_btau_212, retro_btau_277, retro_btau_370, retro_btau_811, retro_btau_90,
Dasypus novemcinctus ENSDNOG000000190223 retrocopies
retro_dnov_540, retro_dnov_711, retro_dnov_959,
Ficedula albicollis ENSFALG000000032151 retrocopy
retro_falb_15,
Felis catus ENSFCAG000000121465 retrocopies
retro_fcat_1231, retro_fcat_572, retro_fcat_662, retro_fcat_677, retro_fcat_842,
Homo sapiens ENSG0000013548657 retrocopies
retro_hsap_1021, retro_hsap_1042, retro_hsap_1082, retro_hsap_1240, retro_hsap_1276, retro_hsap_1282, retro_hsap_1287, retro_hsap_1481, retro_hsap_158, retro_hsap_1584, retro_hsap_1613, retro_hsap_1638, retro_hsap_1711, retro_hsap_1899, retro_hsap_1933, retro_hsap_2002, retro_hsap_2029, retro_hsap_2091, retro_hsap_2096, retro_hsap_2197, retro_hsap_2347, retro_hsap_2379, retro_hsap_2636, retro_hsap_2640, retro_hsap_2668, retro_hsap_2718, retro_hsap_2857, retro_hsap_291, retro_hsap_2917, retro_hsap_2944, retro_hsap_3049, retro_hsap_3055, retro_hsap_332, retro_hsap_3343, retro_hsap_3393, retro_hsap_3432, retro_hsap_3439, retro_hsap_3449, retro_hsap_3549, retro_hsap_3745, retro_hsap_3756, retro_hsap_3757, retro_hsap_394, retro_hsap_3979, retro_hsap_4011, retro_hsap_4084, retro_hsap_414, retro_hsap_4218, retro_hsap_4282, retro_hsap_437, retro_hsap_4747, retro_hsap_482, retro_hsap_4883, retro_hsap_668, retro_hsap_84, retro_hsap_845, retro_hsap_924,
Homo sapiens ENSG000001386681 retrocopy
retro_hsap_4689,
Homo sapiens ENSG00000170144 11 retrocopies
retro_hsap_1117, retro_hsap_1274, retro_hsap_1572, retro_hsap_209, retro_hsap_2194, retro_hsap_2664, retro_hsap_2951, retro_hsap_34 , retro_hsap_4764, retro_hsap_665, retro_hsap_862,
Homo sapiens ENSG000001974511 retrocopy
retro_hsap_962,
Gallus gallus ENSGALG000000092501 retrocopy
retro_ggal_10,
Gorilla gorilla ENSGGOG000000061306 retrocopies
retro_ggor_1001, retro_ggor_1197, retro_ggor_14, retro_ggor_1736, retro_ggor_576, retro_ggor_702,
Macropus eugenii ENSMEUG000000136226 retrocopies
retro_meug_1264, retro_meug_1760, retro_meug_1913, retro_meug_238, retro_meug_470, retro_meug_56,
Macaca mulatta ENSMMUG000000018584 retrocopies
retro_mmul_1945, retro_mmul_2442, retro_mmul_386, retro_mmul_801,
Mus musculus ENSMUSG000000590056 retrocopies
retro_mmus_133, retro_mmus_1359, retro_mmus_1409, retro_mmus_210, retro_mmus_3635, retro_mmus_60,
Oryctolagus cuniculus ENSOCUG000000027432 retrocopies
retro_ocun_994, retro_ocun_995,
Pelodiscus sinensis ENSPSIG000000030111 retrocopy
retro_psin_16,
Ictidomys tridecemlineatus ENSSTOG000000251254 retrocopies
retro_itri_1444, retro_itri_1878, retro_itri_952, retro_itri_98,
Xenopus tropicalis ENSXETG000000018061 retrocopy
retro_xtro_11,
Xiphophorus maculatus ENSXMAG000000004391 retrocopy
retro_xmac_2,

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 = 129.79 RPM Legend:


Library Retrogene expression
CEU_NA11831 80 .93 RPM
CEU_NA11843 64 .01 RPM
CEU_NA11930 58 .28 RPM
CEU_NA12004 100 .13 RPM
CEU_NA12400 63 .94 RPM
CEU_NA12751 64 .81 RPM
CEU_NA12760 94 .09 RPM
CEU_NA12827 80 .42 RPM
CEU_NA12872 69 .71 RPM
CEU_NA12873 82 .15 RPM
FIN_HG00183 46 .68 RPM
FIN_HG00277 53 .65 RPM
FIN_HG00315 66 .07 RPM
FIN_HG00321 45 .55 RPM
FIN_HG00328 67 .78 RPM
FIN_HG00338 60 .50 RPM
FIN_HG00349 87 .07 RPM
FIN_HG00375 82 .21 RPM
FIN_HG00377 74 .68 RPM
FIN_HG00378 73 .48 RPM
GBR_HG00099 85 .24 RPM
GBR_HG00111 86 .51 RPM
GBR_HG00114 103 .48 RPM
GBR_HG00119 46 .10 RPM
GBR_HG00131 55 .73 RPM
GBR_HG00133 72 .40 RPM
GBR_HG00134 98 .74 RPM
GBR_HG00137 98 .96 RPM
GBR_HG00142 53 .96 RPM
GBR_HG00143 105 .23 RPM
TSI_NA20512 113 .18 RPM
TSI_NA20513 94 .84 RPM
TSI_NA20518 71 .19 RPM
TSI_NA20532 77 .54 RPM
TSI_NA20538 62 .56 RPM
TSI_NA20756 56 .94 RPM
TSI_NA20765 73 .76 RPM
TSI_NA20771 72 .88 RPM
TSI_NA20786 97 .69 RPM
TSI_NA20798 105 .84 RPM
YRI_NA18870 92 .57 RPM
YRI_NA18907 113 .11 RPM
YRI_NA18916 73 .97 RPM
YRI_NA19093 129 .79 RPM
YRI_NA19099 62 .82 RPM
YRI_NA19114 68 .39 RPM
YRI_NA19118 109 .28 RPM
YRI_NA19213 51 .61 RPM
YRI_NA19214 106 .18 RPM
YRI_NA19223 110 .98 RPM

Indel association:

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



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