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 symbol: PCBP2
• Ensembl ID: ENSG00000197111
• Aliases: PCBP2, HNRNPE2, HNRPE2, hnRNP-E2
• Description: poly(rC) binding protein 2 [Source:HGNC Symbol;Acc:8648]

Sequence

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

Alignment

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:

Parental  MDTGVIEGGLNVTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCPERIITLAGPTNAIFK
          MD.GV.E.GLNVTLTIRLLMHGKEVGSIIGKKGESVK..REESGARINISEGNCPERIITL.GPTNAIFK
Retrocopy MDAGVTESGLNVTLTIRLLMHGKEVGSIIGKKGESVKRIREESGARINISEGNCPERIITLTGPTNAIFK

Parental  AFAMIIDKLEEDISSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPN
          AFAMIIDKLEEDI.SSMTNSTAASRPPVTLRLVVPA.QCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPN
Retrocopy AFAMIIDKLEEDINSSMTNSTAASRPPVTLRLVVPATQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPN

Parental  STERAITIAGIPQSIIECVKQICVVMLETLSQSPP-KGVTIPYRPKPSSSPVIFAGGQDRYSTGSDSASF
          STERAITIAG.PQS..ECVKQIC.VMLETLSQSP.....TIPY.P.P.SSPVI.AGGQDR.S...D.A..
Retrocopy STERAITIAGVPQSVTECVKQICLVMLETLSQSPQGRVMTIPYQPMPASSPVICAGGQDRCS---DAAGY

Parental  PHTT
          PH.T
Retrocopy PHAT

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	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

RNA Polymerase II activity 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

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

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_124819	20 libraries	0 libraries	62 libraries	426 libraries	1321 libraries
TSS #2	TSS_124820	1 library	0 libraries	0 libraries	0 libraries	1828 libraries
TSS #3	TSS_124821	32 libraries	5 libraries	127 libraries	404 libraries	1261 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)

Lab

retro_hsap_83 was not experimentally validated.

Homology

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	ENSBTAG00000020757	1 retrocopy	retro_btau_175,
Canis familiaris	ENSCAFG00000006821	1 retrocopy	retro_cfam_54,
Callithrix jacchus	ENSCJAG00000018590	2 retrocopies	retro_cjac_3253, retro_cjac_754,
Cavia porcellus	ENSCPOG00000000967	2 retrocopies	retro_cpor_193, retro_cpor_97,
Dasypus novemcinctus	ENSDNOG00000008688	6 retrocopies	retro_dnov_1146, retro_dnov_1399, retro_dnov_1672, retro_dnov_1823, retro_dnov_2434, retro_dnov_452,
Equus caballus	ENSECAG00000022389	1 retrocopy	retro_ecab_67,
Erinaceus europaeus	ENSEEUG00000001077	2 retrocopies	retro_eeur_218, retro_eeur_655,
Echinops telfairi	ENSETEG00000014741	3 retrocopies	retro_etel_1170, retro_etel_2108, retro_etel_840,
Homo sapiens	ENSG00000165119	3 retrocopies	retro_hsap_2323, retro_hsap_2674, retro_hsap_3385,
Homo sapiens	ENSG00000197111	2 retrocopies	retro_hsap_4077, retro_hsap_83 ,
Gorilla gorilla	ENSGGOG00000012613	2 retrocopies	retro_ggor_212, retro_ggor_2734,
Macropus eugenii	ENSMEUG00000001887	7 retrocopies	retro_meug_1143, retro_meug_1988, retro_meug_432, retro_meug_526, retro_meug_618, retro_meug_828, retro_meug_964,
Microcebus murinus	ENSMICG00000011651	2 retrocopies	retro_mmur_1226, retro_mmur_1228,
Myotis lucifugus	ENSMLUG00000009971	3 retrocopies	retro_mluc_2199, retro_mluc_314, retro_mluc_571,
Macaca mulatta	ENSMMUG00000006608	2 retrocopies	retro_mmul_1263, retro_mmul_1994,
Mus musculus	ENSMUSG00000056851	1 retrocopy	retro_mmus_274,
Nomascus leucogenys	ENSNLEG00000017693	1 retrocopy	retro_nleu_10,
Oryctolagus cuniculus	ENSOCUG00000022490	3 retrocopies	retro_ocun_10, retro_ocun_1622, retro_ocun_898,
Ochotona princeps	ENSOPRG00000004680	5 retrocopies	retro_opri_1126, retro_opri_284, retro_opri_313, retro_opri_742, retro_opri_789,
Pongo abelii	ENSPPYG00000004581	2 retrocopies	retro_pabe_3346, retro_pabe_92,
Pan troglodytes	ENSPTRG00000005018	1 retrocopy	retro_ptro_113,
Pteropus vampyrus	ENSPVAG00000012284	3 retrocopies	retro_pvam_1168, retro_pvam_1369, retro_pvam_868,
Rattus norvegicus	ENSRNOG00000036852	2 retrocopies	retro_rnor_1238, retro_rnor_2088,
Sus scrofa	ENSSSCG00000000274	1 retrocopy	retro_sscr_61,
Ictidomys tridecemlineatus	ENSSTOG00000003635	2 retrocopies	retro_itri_1522, retro_itri_557,
Vicugna pacos	ENSVPAG00000000406	1 retrocopy	retro_vpac_471,