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 symbol: UBQLN1
• Ensembl ID: ENSG00000135018
• Aliases: UBQLN1, DA41, DSK2, PLIC-1, UBQN, XDRP1
• Description: ubiquilin 1 [Source:HGNC Symbol;Acc:12508]

Sequence

>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

Alignment

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:

Parental  MAESGESGGPPGSQDSAAGAEGAGAPAAAASAEPKIMKVTVKTPKEKEEFAVPENSSVQQFKEEISKRFK
          MAE.GES.GPP......A.A.G.....AAA.AEPKI.KVTVKTPKEKEEFAVPENSSVQQFKE.ISKRFK
Retrocopy MAENGESSGPPRPSRGPAAAQGS----AAAPAEPKIIKVTVKTPKEKEEFAVPENSSVQQFKEAISKRFK

Parental  SHTDQLVLIFAGKILKDQDTLSQHGIHDGLTVHLVIKTQNRPQDHSAQQTNTAGSNVTTSSTPNSNSTSG
          S.TDQLVLIFAGKILKDQDTL.QHGIHDGLTVHLVIK.QNRPQ..S.Q..N.AG.N.T..STP.SNST..
Retrocopy SQTDQLVLIFAGKILKDQDTLIQHGIHDGLTVHLVIKSQNRPQGQSTQPSNAAGTNTTSASTPRSNSTPI

Parental  SATSNPFGLGGLGGLAGLSSLGLNTTNFSELQSQMQRQLLSNPEMMVQIMENPFVQSMLSNPDLMRQLIM
          S..SNPFGLG.LGGLAGLSSLGL..TNFSELQSQMQ.QL...PEMM.QIMENPFVQSMLSNPDLMRQLIM
Retrocopy STNSNPFGLGSLGGLAGLSSLGLSSTNFSELQSQMQQQLMASPEMMIQIMENPFVQSMLSNPDLMRQLIM

Parental  ANPQMQQLIQRNPEISHMLNNPDIMRQTLELARNPAMMQEMMRNQDRALSNLESIPGGYNALRRMYTDIQ
          ANPQMQQLIQRNPEISH.LNNPDIMRQTLE.ARNPAMMQEMMRNQD.ALSNLESIPGGYNALRRMYTDIQ
Retrocopy ANPQMQQLIQRNPEISHLLNNPDIMRQTLEIARNPAMMQEMMRNQDLALSNLESIPGGYNALRRMYTDIQ

Parental  EPMLSAAQEQFGGNPFASLVSNTSSGEGSQPSRTENRDPLPNPWAPQTSQSSSASSGTASTVGGTTGSTA
          EPML.AAQEQFGGNPFAS..S..SSGEG.QPSRTENRDPLPNPWAP.....SSA...T....G...G...
Retrocopy EPMLNAAQEQFGGNPFASVGSSSSSGEGTQPSRTENRDPLPNPWAPPPATQSSATTSTTTSTGSGSGNSS

Parental  SGTSGQSTTAPNLVPGVGASMFNTPGMQSLLQQITENPQLMQNMLSAPYMRSMMQSLSQNPDLAAQMMLN
          S...G....A.N.V....AS.F.TPGMQSLLQQITENPQL.QNMLSAPYMRSMMQSLSQNPDLAAQMMLN
Retrocopy SNATGNTVAAANYV----ASIFSTPGMQSLLQQITENPQLIQNMLSAPYMRSMMQSLSQNPDLAAQMMLN

Parental  NPLFAGNPQLQEQMRQQLPTFLQQMQNPDTLSAMSNPRAMQALLQIQQGLQTLATEAPGLIPGFTPGLGA
          .PLF..NPQLQEQMR.QLP.FLQQMQNPDTLSAMSNPRAMQAL.QIQQGLQTLATEAPGLIP.FTPG.G.
Retrocopy SPLFTANPQLQEQMRPQLPAFLQQMQNPDTLSAMSNPRAMQALMQIQQGLQTLATEAPGLIPSFTPGVG-

Parental  LGSTGGSSGTNG
          .G..G...G..G
Retrocopy VGVLGTAIGPVG

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

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

RNA Polymerase II activity 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

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

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_200548	25 libraries	0 libraries	7 libraries	46 libraries	1751 libraries
TSS #2	TSS_200549	246 libraries	315 libraries	1126 libraries	123 libraries	19 libraries
TSS #3	TSS_200550	1107 libraries	665 libraries	52 libraries	5 libraries	0 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)

Lab

retro_hsap_58 was not experimentally validated.

Homology

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

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014827	2 retrocopies	retro_btau_1087, retro_btau_188,
Canis familiaris	ENSCAFG00000001435	1 retrocopy	retro_cfam_236,
Callithrix jacchus	ENSCJAG00000003609	2 retrocopies	retro_cjac_3977, retro_cjac_4067,
Cavia porcellus	ENSCPOG00000004849	1 retrocopy	retro_cpor_113,
Dasypus novemcinctus	ENSDNOG00000012687	1 retrocopy	retro_dnov_14,
Dipodomys ordii	ENSDORG00000015266	1 retrocopy	retro_dord_680,
Equus caballus	ENSECAG00000019110	1 retrocopy	retro_ecab_1063,
Echinops telfairi	ENSETEG00000002822	1 retrocopy	retro_etel_39,
Felis catus	ENSFCAG00000015049	1 retrocopy	retro_fcat_83,
Homo sapiens	ENSG00000135018	1 retrocopy	retro_hsap_58 ,
Homo sapiens	ENSG00000160803	1 retrocopy	retro_hsap_2859,
Myotis lucifugus	ENSMLUG00000002036	2 retrocopies	retro_mluc_1774, retro_mluc_33,
Mustela putorius furo	ENSMPUG00000002028	1 retrocopy	retro_mputfur_55,
Mus musculus	ENSMUSG00000005312	1 retrocopy	retro_mmus_83,
Nomascus leucogenys	ENSNLEG00000003306	1 retrocopy	retro_nleu_31,
Otolemur garnettii	ENSOGAG00000012947	1 retrocopy	retro_ogar_276,
Pongo abelii	ENSPPYG00000019323	1 retrocopy	retro_pabe_87,
Pan troglodytes	ENSPTRG00000021055	1 retrocopy	retro_ptro_93,
Rattus norvegicus	ENSRNOG00000019282	1 retrocopy	retro_rnor_339,
Ictidomys tridecemlineatus	ENSSTOG00000013462	1 retrocopy	retro_itri_157,
Tursiops truncatus	ENSTTRG00000004696	1 retrocopy	retro_ttru_1475,