RetrogeneDB ID: retro_hsap_2664

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 3:75263700..75264759(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000213300
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_2664
ATGGAGGTAAAACCGCCGCCCAGTCGCCCCCAGCCCGACTCCGGCCGTCGCCGTCGCCGCCGGGGGGAGGAGGGCCATGA
TCCAAAGGAACCAGAGCAGTTGAGAAAACTGTTTATTGGTGGTCTGAGCTTTGAAACTACAGATGATAGTTTACGAGAAC
ATTTTGAGAAATGGGGCACACTCACAGATTGTGTGGTAATGAGAGACCCCCAAACAAAACGTTCCAGGGGCTTTGGTTTT
GTGACTTATTCTTGTGTTGAAGAGGTGGATGCAGCAATGTGTGCTCGACCACACAAGGTTGATGGGCGTGTAGTGGAACC
AAAGAGAGCTGTTTCTAGAGAGGATTCTGTAAAGCCTGGTGCCCATCTAACAGTGAAGAAAATTTTTGTTGGTGGTATTA
AAGAAGATACAGAAGAATATAATTTGAGAGACTACTTTGAAAAGTATGGCAAGATTGAAACCATAGAAGTTATGGAAGAC
AGGCAGAGTGGAAAAAAGAGAGGATTTGCTTTTGTAACTTTTGATGATCATGATACAGTTGATAAAATTGTTGTTCAGAA
ATACCACACTATTAATGGGCATAATTGTGAAGTGAAAAAGACCCTTTCTAAACAAGAGATGCAGTCTGCTGGATCACGGA
GAGGTCGTGGAGGTGGATCTGGCAATTTTATGGGTCGCGGAGGGAACTTTGGAGGTGGTGGAGGTGGTGGCAGCAGAGGT
AGTTATGGAGGAGGTGATGGTGGATATAATGGATTTGGAGGTGATGGTGGCAACTATGGCGGTGGTCCTGGTTATAGTAG
TAGAGGGGGCTATGGTGATGGTGGACCAGGATATGGAAACCAAGGTGGTGGATATGGTGGAGGTGGAGGATATGATGGTT
ACAATGAAGGAGGAAATTTTGGCGGTGGTAACTATGGTGGTGGTGGGAACTATAATGATTTTGGAAATTATAGTGGACAA
CAGCAATCAAATTATGGACCCATGAAAGGGGGCAGTTTTGGTGGAAGAAGCTCGGGCGGTCCCTATGGTGGTGGTTATGG
ATCTGGTGGTGGAAGTGGT

Alignment

ORF - retro_hsap_2664 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.11 %
• Parental protein coverage: 94.44 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEVKPPPGRPQPDSGRRRRRRGEEGHDPKEPEQLRKLFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDP
          MEVKPPP.RPQPDSGRRRRRRGEEGHDPKEPEQLRKLFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDP
Retrocopy MEVKPPPSRPQPDSGRRRRRRGEEGHDPKEPEQLRKLFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDP

Parental  QTKRSRGFGFVTYSCVEEVDAAMCARPHKVDGRVVEPKRAVSREDSVKPGAHLTVKKIFVGGIKEDTEEY
          QTKRSRGFGFVTYSCVEEVDAAMCARPHKVDGRVVEPKRAVSREDSVKPGAHLTVKKIFVGGIKEDTEEY
Retrocopy QTKRSRGFGFVTYSCVEEVDAAMCARPHKVDGRVVEPKRAVSREDSVKPGAHLTVKKIFVGGIKEDTEEY

Parental  NLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVTFDDHDTVDKIVVQKYHTINGHNCEVKKALSKQEMQSA
          NLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVTFDDHDTVDKIVVQKYHTINGHNCEVKK.LSKQEMQSA
Retrocopy NLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVTFDDHDTVDKIVVQKYHTINGHNCEVKKTLSKQEMQSA

Parental  GSQRGRGGGSGNFMGRGGNFGGGGGNFGRGGNFGGRGGYGGGGGGSRGSYGGGDGGYNGFGGDGGNYGGG
          GS.RGRGGGSGNFMGRGGN.........RG...GG.GGY.G.GG...G.YGGG..GY...GG.G....GG
Retrocopy GSRRGRGGGSGNFMGRGGNXXXXXXXXSRGSYGGGDGGYNGFGGDG-GNYGGGP-GYSSRGGYG---DGG

Parental  PGYSSRGGYGGGGPGYGNQGGGYGGGGGYDGYNEGGNFGG-GNYGG--GGNYNDFGNYSGQQQSNYGPMK
          PGY..................G...GGG...Y..GGN....GNY.G....NY......S....S..GP..
Retrocopy PGYGNXXXXXXXXXXXXXYNEGGNFGGG--NYGGGGNYNDFGNYSGQQQSNYGPMKGGSFGGRSSGGPYG

Parental  GGSFGGRSSG
          GG...G..SG
Retrocopy GGYGSGGGSG

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	0.54 RPM	347.23 RPM
bodymap2_adrenal	1.37 RPM	535.07 RPM
bodymap2_brain	0.89 RPM	339.37 RPM
bodymap2_breast	0.29 RPM	267.51 RPM
bodymap2_colon	1.01 RPM	432.85 RPM
bodymap2_heart	0.17 RPM	101.85 RPM
bodymap2_kidney	0.52 RPM	331.49 RPM
bodymap2_liver	0.30 RPM	119.24 RPM
bodymap2_lung	0.79 RPM	430.05 RPM
bodymap2_lymph_node	0.57 RPM	274.00 RPM
bodymap2_ovary	1.39 RPM	698.84 RPM
bodymap2_prostate	0.74 RPM	327.14 RPM
bodymap2_skeletal_muscle	0.44 RPM	119.93 RPM
bodymap2_testis	0.57 RPM	412.92 RPM
bodymap2_thyroid	1.75 RPM	465.04 RPM
bodymap2_white_blood_cells	0.53 RPM	279.96 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_2664 was not detected

EST

20 EST(s) were mapped to retro_hsap_2664 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
AU126742	75263660	75264229	99.9	502	1	500
BE083973	75264019	75264158	99.3	138	1	137
BI025993	75263783	75264079	99	292	3	288
BU535210	75263841	75264151	100	310	0	310
BU958112	75263671	75264197	99.8	459	1	457
CN395281	75263653	75264209	99.8	489	1	487
CN395282	75263817	75264148	100	331	0	331
DA873825	75263671	75264111	100	374	0	373
DC297576	75263661	75264228	99.7	501	0	498
DC344938	75263661	75264182	99.6	453	0	449
DC360406	75263662	75264239	99.9	511	0	509
DC386496	75263660	75264239	99.9	513	0	511
DC404646	75263660	75264228	99.9	501	1	499
DC404676	75263660	75264057	100	330	0	329
DC407553	75263662	75264185	99.4	455	1	451
DC407560	75263660	75264050	100	324	0	323
DC414176	75263660	75264219	99.8	492	1	490
DC419839	75263665	75264201	100	470	0	469
DW447899	75264048	75264197	99.4	148	1	147
DW447900	75264048	75264197	99.4	148	1	147

TSS

No TSS is located nearby retro_hsap_2664 retrocopy 5' end.

Lab

retro_hsap_2664 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_2664 has 0 orthologous retrocopies within eutheria group .

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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,