RetrogeneDB ID:

retro_hsap_58

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:X:56590306..56592181(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000188021
Aliases:UBQLN2, ALS15, CHAP1, DSK2, N4BP4, PLIC2
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:UBQLN1
Ensembl ID:ENSG00000135018
Aliases:UBQLN1, DA41, DSK2, PLIC-1, UBQN, XDRP1
Description:ubiquilin 1 [Source:HGNC Symbol;Acc:12508]


Retrocopy-Parental alignment summary:






>retro_hsap_58
ATGGCTGAGAATGGCGAGAGCAGCGGCCCCCCGCGCCCCTCCCGCGGCCCTGCTGCGGCCCAAGGCTCGGCTGCTGCCCC
GGCTGAGCCTAAAATCATCAAAGTCACGGTGAAGACTCCCAAAGAGAAAGAGGAGTTCGCGGTGCCCGAGAACAGCTCGG
TTCAGCAGTTTAAGGAAGCGATTTCGAAACGCTTCAAATCCCAAACCGATCAGCTAGTGCTGATTTTTGCCGGAAAAATC
TTAAAAGATCAAGATACCTTGATCCAGCATGGCATCCATGATGGGCTGACTGTTCACCTTGTCATCAAAAGCCAGAACCG
ACCTCAGGGCCAGTCCACGCAGCCTAGCAATGCCGCGGGAACTAACACTACCTCGGCGTCGACTCCCAGGAGTAACTCCA
CACCTATTTCCACAAATAGCAACCCGTTTGGGTTGGGGAGCCTGGGAGGACTTGCAGGCCTTAGCAGCCTGGGCTTGAGC
TCGACCAACTTCTCTGAGCTCCAGAGCCAGATGCAGCAGCAGCTTATGGCCAGCCCTGAGATGATGATCCAAATAATGGA
AAATCCCTTTGTTCAGAGCATGCTTTCGAATCCCGATCTGATGAGGCAGCTCATTATGGCTAATCCACAGATGCAGCAAT
TGATTCAGAGAAACCCAGAAATCAGTCACCTGCTCAACAACCCAGACATAATGAGGCAGACACTCGAAATTGCCAGGAAT
CCAGCCATGATGCAAGAGATGATGAGAAATCAAGACCTGGCTCTTAGCAATCTAGAAAGCATCCCAGGTGGCTATAATGC
TTTACGGCGCATGTACACTGACATTCAAGAGCCGATGCTGAATGCCGCACAAGAGCAGTTTGGGGGTAATCCATTTGCCT
CCGTGGGGAGTAGTTCCTCCTCTGGGGAAGGTACGCAGCCTTCCCGCACAGAAAATCGCGATCCACTACCCAATCCATGG
GCACCACCGCCAGCTACCCAGAGTTCTGCAACTACCAGCACGACCACAAGCACTGGTAGTGGGTCTGGCAATAGTTCCAG
CAATGCTACTGGGAACACCGTTGCTGCCGCTAATTATGTCGCCAGCATCTTTAGTACCCCAGGCATGCAGAGCCTGCTGC
AACAGATAACTGAAAACCCCCAGCTGATTCAGAATATGCTGTCGGCGCCCTACATGAGAAGCATGATGCAGTCGCTGAGC
CAGAATCCAGATTTGGCTGCACAGATGATGCTGAATAGCCCGCTGTTTACTGCAAATCCTCAGCTGCAGGAGCAGATGCG
GCCACAGCTCCCAGCCTTCCTGCAGCAGATGCAGAATCCAGACACACTATCAGCCATGTCAAACCCAAGAGCAATGCAGG
CTTTAATGCAGATCCAGCAGGGGCTACAGACATTAGCCACTGAAGCACCTGGCCTGATTCCGAGCTTCACTCCAGGTGTG
GGGGTGGGGGTGCTGGGAACCGCTATAGGCCCTGTAGGCCCAGTCACCCCCATAGGCCCCATAGGCCCTATAGTCCCTTT
TACCCCCATAGGCCCCATTGGGCCCATAGGACCCACTGGCCCTGCAGCCCCCCCTGGCTCCACCGGCTCTGGTGGCCCCA
CGGGGCCTACTGTGTCCAGCGCTGCACCTAGTGAAACCACGAGTCCTACATCAGAATCTGGACCCAACCAGCAGTTCATT
CAGCAAATGGTGCAGGCCCTGGCTGGAGCAAATGCTCCACAGCTGCCGAATCCAGAAGTCAGATTTCAGCAACAACTGGA
ACAGCTCAACGCAATGGGGTTCTTAAACCGTGAAGCAAACTTGCAGGCCCTAATAGCAACAGGAGGCGACATCAATGCAG
CCATTGAAAGGCTGCTGGGCTCCCAGCCATCGTAA

ORF - retro_hsap_58 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 79.28 %
Parental protein coverage: 85.23 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMAESGESGGPPGSQDSAAGAEGAGAPAAAASAEPKIMKVTVKTPKEKEEFAVPENSSVQQFKEEISKRFK
MAE.GES.GPP......A.A.G.....AAA.AEPKI.KVTVKTPKEKEEFAVPENSSVQQFKE.ISKRFK
RetrocopyMAENGESSGPPRPSRGPAAAQGS----AAAPAEPKIIKVTVKTPKEKEEFAVPENSSVQQFKEAISKRFK
ParentalSHTDQLVLIFAGKILKDQDTLSQHGIHDGLTVHLVIKTQNRPQDHSAQQTNTAGSNVTTSSTPNSNSTSG
S.TDQLVLIFAGKILKDQDTL.QHGIHDGLTVHLVIK.QNRPQ..S.Q..N.AG.N.T..STP.SNST..
RetrocopySQTDQLVLIFAGKILKDQDTLIQHGIHDGLTVHLVIKSQNRPQGQSTQPSNAAGTNTTSASTPRSNSTPI
ParentalSATSNPFGLGGLGGLAGLSSLGLNTTNFSELQSQMQRQLLSNPEMMVQIMENPFVQSMLSNPDLMRQLIM
S..SNPFGLG.LGGLAGLSSLGL..TNFSELQSQMQ.QL...PEMM.QIMENPFVQSMLSNPDLMRQLIM
RetrocopySTNSNPFGLGSLGGLAGLSSLGLSSTNFSELQSQMQQQLMASPEMMIQIMENPFVQSMLSNPDLMRQLIM
ParentalANPQMQQLIQRNPEISHMLNNPDIMRQTLELARNPAMMQEMMRNQDRALSNLESIPGGYNALRRMYTDIQ
ANPQMQQLIQRNPEISH.LNNPDIMRQTLE.ARNPAMMQEMMRNQD.ALSNLESIPGGYNALRRMYTDIQ
RetrocopyANPQMQQLIQRNPEISHLLNNPDIMRQTLEIARNPAMMQEMMRNQDLALSNLESIPGGYNALRRMYTDIQ
ParentalEPMLSAAQEQFGGNPFASLVSNTSSGEGSQPSRTENRDPLPNPWAPQTSQSSSASSGTASTVGGTTGSTA
EPML.AAQEQFGGNPFAS..S..SSGEG.QPSRTENRDPLPNPWAP.....SSA...T....G...G...
RetrocopyEPMLNAAQEQFGGNPFASVGSSSSSGEGTQPSRTENRDPLPNPWAPPPATQSSATTSTTTSTGSGSGNSS
ParentalSGTSGQSTTAPNLVPGVGASMFNTPGMQSLLQQITENPQLMQNMLSAPYMRSMMQSLSQNPDLAAQMMLN
S...G....A.N.V....AS.F.TPGMQSLLQQITENPQL.QNMLSAPYMRSMMQSLSQNPDLAAQMMLN
RetrocopySNATGNTVAAANYV----ASIFSTPGMQSLLQQITENPQLIQNMLSAPYMRSMMQSLSQNPDLAAQMMLN
ParentalNPLFAGNPQLQEQMRQQLPTFLQQMQNPDTLSAMSNPRAMQALLQIQQGLQTLATEAPGLIPGFTPGLGA
.PLF..NPQLQEQMR.QLP.FLQQMQNPDTLSAMSNPRAMQAL.QIQQGLQTLATEAPGLIP.FTPG.G.
RetrocopySPLFTANPQLQEQMRPQLPAFLQQMQNPDTLSAMSNPRAMQALMQIQQGLQTLATEAPGLIPSFTPGVG-
ParentalLGSTGGSSGTNG
.G..G...G..G
RetrocopyVGVLGTAIGPVG

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 20 .49 RPM 138 .43 RPM
bodymap2_adrenal 11 .69 RPM 109 .25 RPM
bodymap2_brain 36 .05 RPM 240 .50 RPM
bodymap2_breast 11 .48 RPM 138 .97 RPM
bodymap2_colon 18 .12 RPM 156 .52 RPM
bodymap2_heart 23 .37 RPM 108 .55 RPM
bodymap2_kidney 19 .13 RPM 167 .24 RPM
bodymap2_liver 7 .52 RPM 136 .21 RPM
bodymap2_lung 26 .39 RPM 166 .93 RPM
bodymap2_lymph_node 32 .23 RPM 149 .24 RPM
bodymap2_ovary 24 .83 RPM 158 .96 RPM
bodymap2_prostate 29 .96 RPM 174 .95 RPM
bodymap2_skeletal_muscle 42 .25 RPM 219 .45 RPM
bodymap2_testis 12 .58 RPM 151 .20 RPM
bodymap2_thyroid 19 .30 RPM 166 .41 RPM
bodymap2_white_blood_cells 55 .09 RPM 208 .69 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity may be related with retro_hsap_58 in 49 libraries
ENCODE library ID Target ChIP-Seq Peak coordinates
ENCFF002CGN POLR2A X:56589982..56590197
ENCFF002CIH POLR2A X:56589976..56590263
ENCFF002CIO POLR2A X:56589960..56590303
ENCFF002CJZ POLR2A X:56589910..56590307
ENCFF002CKX POLR2A X:56589940..56590275
ENCFF002CMI POLR2A X:56589896..56590305
ENCFF002COJ POLR2A X:56589877..56590313
ENCFF002CPG POLR2A X:56589834..56590324
ENCFF002CPH POLR2A X:56589870..56590260
ENCFF002CQC POLR2A X:56589960..56590243
ENCFF002CQE POLR2A X:56589943..56590239
ENCFF002CQG POLR2A X:56589980..56590200
ENCFF002CQI POLR2A X:56589966..56590208
ENCFF002CQK POLR2A X:56589952..56590276
ENCFF002CQM POLR2A X:56589944..56590248
ENCFF002CQO POLR2A X:56589982..56590290
ENCFF002CRO POLR2A X:56589870..56590290
ENCFF002CUP POLR2A X:56590091..56590178
ENCFF002CVF POLR2A X:56589901..56590317
ENCFF002CVJ POLR2A X:56589963..56590263
ENCFF002CXO POLR2A X:56589886..56590310
ENCFF002CXP POLR2A X:56590053..56590174
ENCFF002CXR POLR2A X:56589966..56590249
ENCFF002CZC POLR2A X:56589942..56590292
ENCFF002CZD POLR2A X:56589945..56590287
ENCFF002CZQ POLR2A X:56589858..56590308
ENCFF002CZY POLR2A X:56589954..56590279
ENCFF002DAE POLR2A X:56589955..56590265
ENCFF002DAH POLR2A X:56589946..56590230
ENCFF002DBB POLR2A X:56589993..56590193
ENCFF002DBE POLR2A X:56589981..56590199
ENCFF002DBO POLR2A X:56589970..56590229
ENCFF002DBP POLR2A X:56590005..56590206
ENCFF002DBQ POLR2A X:56589909..56590279
ENCFF002DBT POLR2A X:56589892..56590262
ENCFF002CJZ POLR2A X:56590683..56590928
ENCFF002CZD POLR2A X:56590766..56591276
ENCFF002CFW POLR2A X:56589895..56590401
ENCFF002CFX POLR2A X:56589905..56590427
ENCFF002CHO POLR2A X:56589862..56590506
ENCFF002CJE POLR2A X:56589893..56590370
ENCFF002CQA POLR2A X:56589836..56590406
ENCFF002CSY POLR2A X:56589862..56590524
ENCFF002CUQ POLR2A X:56589874..56590378
ENCFF002CXM POLR2A X:56589862..56590352
ENCFF002CXN POLR2A X:56589874..56590370
ENCFF002CZW POLR2A X:56589854..56590604
ENCFF002DAK POLR2A X:56589860..56590360
ENCFF002DAS POLR2A X:56589871..56590347
ENCFF002DAV POLR2A X:56589852..56590396
ENCFF002DAY POLR2A X:56589781..56590417

EST - click to see more details

38 EST(s) were mapped to retro_hsap_58 retrocopy
EST ID Start End Identity Match Mis-match Score
AA211771 56591408 56591772 97.5 359 1 352
AA235610 56590733 56590848 100 115 0 115
AA721472 56590332 56590577 97.2 240 3 233
AI677838 56590325 56590811 99.2 482 4 478
AI738604 56590326 56590827 100 501 0 501
AI970587 56590297 56590845 99.7 545 2 543
AI140828 56590297 56590749 100 452 0 452
AW009308 56590325 56590886 98.4 549 8 539
AW087180 56590323 56590762 98.7 436 3 432
BE002124 56591157 56591491 99.7 328 1 322
BE170732 56591184 56591613 99.8 428 0 426
BE613953 56590658 56591420 98.7 754 5 744
BF833002 56590610 56590997 99.8 384 1 381
BM452656 56590402 56591322 98.2 912 1 899
BM455419 56591556 56591752 99.5 195 1 194
BM546710 56590723 56591389 97.1 639 9 622
BM922811 56591061 56591620 96.6 521 8 505
BQ224786 56591008 56591587 96.9 566 13 551
BQ307890 56591166 56591705 99.5 535 2 530
BQ320425 56590857 56591164 98.6 278 2 270
BU159505 56590702 56591511 98.4 797 2 788
BU178931 56591469 56591758 99.7 287 0 285
BY795607 56590471 56591073 99.9 601 1 600
CA390135 56591054 56591505 100 451 0 451
CD359581 56591591 56591797 97.1 200 5 193
CN304944 56590423 56590682 100 259 0 259
CR983559 56590597 56591321 99.4 724 0 722
D81089 56591391 56591593 98 199 1 197
DB485896 56590517 56590962 99.8 443 1 441
DB489253 56590517 56590978 99.6 459 2 457
DB491959 56590517 56590918 99.8 400 1 399
DN998061 56590218 56590942 100 724 0 724
HY061829 56590288 56590798 99.1 510 0 508
HY149590 56591190 56591613 99.8 422 1 421
N56258 56591939 56592057 98.3 115 2 112
R49915 56591374 56591689 97.8 315 0 312
T06622 56590363 56590690 98.5 324 2 321
Z39763 56590307 56590593 99.7 283 0 281

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_20054825 libraries0 libraries7 libraries46 libraries1751 libraries
TSS #2 TSS_200549246 libraries315 libraries1126 libraries123 libraries19 libraries
TSS #3 TSS_2005501107 libraries665 libraries52 libraries5 libraries0 libraries

The graphical summary, for retro_hsap_58 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_58 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_58 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_93
Pongo abelii retro_pabe_87
Parental genes homology:
Parental genes homology involve 21 parental genes, and 24 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000148272 retrocopies
retro_btau_1087, retro_btau_188,
Canis familiaris ENSCAFG000000014351 retrocopy
retro_cfam_236,
Callithrix jacchus ENSCJAG000000036092 retrocopies
retro_cjac_3977, retro_cjac_4067,
Cavia porcellus ENSCPOG000000048491 retrocopy
retro_cpor_113,
Dasypus novemcinctus ENSDNOG000000126871 retrocopy
retro_dnov_14,
Dipodomys ordii ENSDORG000000152661 retrocopy
retro_dord_680,
Equus caballus ENSECAG000000191101 retrocopy
retro_ecab_1063,
Echinops telfairi ENSETEG000000028221 retrocopy
retro_etel_39,
Felis catus ENSFCAG000000150491 retrocopy
retro_fcat_83,
Homo sapiens ENSG00000135018 1 retrocopy
retro_hsap_58 ,
Homo sapiens ENSG000001608031 retrocopy
retro_hsap_2859,
Myotis lucifugus ENSMLUG000000020362 retrocopies
retro_mluc_1774, retro_mluc_33,
Mustela putorius furoENSMPUG000000020281 retrocopy
retro_mputfur_55,
Mus musculus ENSMUSG000000053121 retrocopy
retro_mmus_83,
Nomascus leucogenys ENSNLEG000000033061 retrocopy
retro_nleu_31,
Otolemur garnettii ENSOGAG000000129471 retrocopy
retro_ogar_276,
Pongo abelii ENSPPYG000000193231 retrocopy
retro_pabe_87,
Pan troglodytes ENSPTRG000000210551 retrocopy
retro_ptro_93,
Rattus norvegicus ENSRNOG000000192821 retrocopy
retro_rnor_339,
Ictidomys tridecemlineatus ENSSTOG000000134621 retrocopy
retro_itri_157,
Tursiops truncatus ENSTTRG000000046961 retrocopy
retro_ttru_1475,

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 = 36.27 RPM Legend:


Library Retrogene expression
CEU_NA11831 23 .20 RPM
CEU_NA11843 14 .19 RPM
CEU_NA11930 32 .04 RPM
CEU_NA12004 23 .40 RPM
CEU_NA12400 22 .62 RPM
CEU_NA12751 29 .63 RPM
CEU_NA12760 32 .43 RPM
CEU_NA12827 27 .26 RPM
CEU_NA12872 30 .57 RPM
CEU_NA12873 29 .64 RPM
FIN_HG00183 28 .11 RPM
FIN_HG00277 33 .65 RPM
FIN_HG00315 22 .08 RPM
FIN_HG00321 33 .07 RPM
FIN_HG00328 25 .83 RPM
FIN_HG00338 26 .85 RPM
FIN_HG00349 24 .87 RPM
FIN_HG00375 24 .77 RPM
FIN_HG00377 24 .13 RPM
FIN_HG00378 31 .26 RPM
GBR_HG00099 33 .57 RPM
GBR_HG00111 19 .58 RPM
GBR_HG00114 25 .06 RPM
GBR_HG00119 35 .54 RPM
GBR_HG00131 26 .76 RPM
GBR_HG00133 24 .55 RPM
GBR_HG00134 28 .61 RPM
GBR_HG00137 20 .51 RPM
GBR_HG00142 29 .54 RPM
GBR_HG00143 29 .20 RPM
TSI_NA20512 14 .84 RPM
TSI_NA20513 36 .27 RPM
TSI_NA20518 34 .86 RPM
TSI_NA20532 23 .94 RPM
TSI_NA20538 30 .68 RPM
TSI_NA20756 27 .96 RPM
TSI_NA20765 27 .25 RPM
TSI_NA20771 32 .17 RPM
TSI_NA20786 30 .31 RPM
TSI_NA20798 28 .60 RPM
YRI_NA18870 24 .30 RPM
YRI_NA18907 25 .96 RPM
YRI_NA18916 24 .59 RPM
YRI_NA19093 32 .80 RPM
YRI_NA19099 29 .66 RPM
YRI_NA19114 33 .82 RPM
YRI_NA19118 29 .07 RPM
YRI_NA19213 36 .23 RPM
YRI_NA19214 30 .28 RPM
YRI_NA19223 32 .25 RPM

Indel association:

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





Copyright © RetrogeneDB 2014-2017