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 symbol: HNRNPA3
• Ensembl ID: ENSG00000170144
• Aliases: HNRNPA3, 2610510D13Rik, D10S102, FBRNP, HNRPA3
• Description: heterogeneous nuclear ribonucleoprotein A3 [Source:HGNC Symbol;Acc:24941]

Sequence

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

Alignment

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:

Parental  EPEQLRKLFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAAMCARPHK
          E..QL.KLFIGGL...T....LR.HFE..GTLTDCVV...PQTKRSR.FGFVTYS.VEE.DAAM.A.PH.
Retrocopy ENSQLCKLFIGGLNVQTSESGLRGHFEAFGTLTDCVVVVNPQTKRSRCFGFVTYSNVEEADAAMAASPHA

Parental  VDGRVVEPKRAVSREDSVKPGAHLTVKKIFVGGIKEDTEEYNLRDYFEKYGKIETIEVMEDRQSGKKRGF
          VDG..VE.KRAVSREDS..PGAH..VKK.FVGG.K.D..E..L...F...G..E..E...D.QSGKKRGF
Retrocopy VDGNTVELKRAVSREDSARPGAHAKVKKLFVGGLKGDVAEGDLIEHFSQFGTVEKAEIIADKQSGKKRGF

Parental  AFVTFDDHDTVDKIVVQKYHTINGHNCEVKKALSKQEMQSA----GSQRGRGGGSGNFMGRGGNFGGGGG
          .FV.F..HD..DK..V.K.H.I.GH..EVKKA..K....S.....GS...RGG..G...GRGG.....G.
Retrocopy GFVYFQNHDAADKAAVVKFHPIQGHRVEVKKAVPKEDIYSGGGGGGSRSSRGGRGGR--GRGGGRDQNGL

Parental  NFGRGGNFGGRGGYGGGGGGSRGSYGGGDGGYNGFGGDGGNYGGGPGYSSRGGYGGGGPGYGNQGGGYGG
          ..G.GG.....GGYGGGGGG....YGGG.GG....G.D.GN..GG.G..S......G....G..GGG.GG
Retrocopy SKGGGGGYNSYGGYGGGGGGGYNAYGGGGGGSSYGGSDYGNGFGGFGSYSQHQSSYGPMKSG--GGGGGG

Parental  GGGYDGYNEGGNFGGGNYGGGGNY
          G....G....G...GG.YGGGG.Y
Retrocopy GSSWGGRSNSGPYRGG-YGGGGGY

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	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

RNA Polymerase II activity 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

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

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_149199	2 libraries	0 libraries	1 library	0 libraries	1826 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)

Lab

retro_hsap_34 was not experimentally validated.

Homology

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	ENSBTAG00000021580	8 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	ENSDNOG00000019022	3 retrocopies	retro_dnov_540, retro_dnov_711, retro_dnov_959,
Ficedula albicollis	ENSFALG00000003215	1 retrocopy	retro_falb_15,
Felis catus	ENSFCAG00000012146	5 retrocopies	retro_fcat_1231, retro_fcat_572, retro_fcat_662, retro_fcat_677, retro_fcat_842,
Homo sapiens	ENSG00000135486	57 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	ENSG00000138668	1 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	ENSG00000197451	1 retrocopy	retro_hsap_962,
Gallus gallus	ENSGALG00000009250	1 retrocopy	retro_ggal_10,
Gorilla gorilla	ENSGGOG00000006130	6 retrocopies	retro_ggor_1001, retro_ggor_1197, retro_ggor_14, retro_ggor_1736, retro_ggor_576, retro_ggor_702,
Macropus eugenii	ENSMEUG00000013622	6 retrocopies	retro_meug_1264, retro_meug_1760, retro_meug_1913, retro_meug_238, retro_meug_470, retro_meug_56,
Macaca mulatta	ENSMMUG00000001858	4 retrocopies	retro_mmul_1945, retro_mmul_2442, retro_mmul_386, retro_mmul_801,
Mus musculus	ENSMUSG00000059005	6 retrocopies	retro_mmus_133, retro_mmus_1359, retro_mmus_1409, retro_mmus_210, retro_mmus_3635, retro_mmus_60,
Oryctolagus cuniculus	ENSOCUG00000002743	2 retrocopies	retro_ocun_994, retro_ocun_995,
Pelodiscus sinensis	ENSPSIG00000003011	1 retrocopy	retro_psin_16,
Ictidomys tridecemlineatus	ENSSTOG00000025125	4 retrocopies	retro_itri_1444, retro_itri_1878, retro_itri_952, retro_itri_98,
Xenopus tropicalis	ENSXETG00000001806	1 retrocopy	retro_xtro_11,
Xiphophorus maculatus	ENSXMAG00000000439	1 retrocopy	retro_xmac_2,