RetrogeneDB ID: retro_hsap_209

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 1:113992321..113993050(+)
• Located in intron of: ENSG00000081026

Retrocopy information

• Ensembl ID: ENSG00000232499
• 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_209
ATGGAGGGCCATGATCCAAAGGAACCAGAGAAGTTGAGAAAACTGTTTATTGGTGGTCTGAGCTTTGAAACTACAGATGA
TAGTTTAAGAGAACATTTTGAGAAATGGGGCACACTCACAGATTGTGTGGTAATGAGAGACCCCCAAACAAAACGTTCCA
GGGGCTTTGGTTTTGTGACTTATTCTTGTGTTGAAGAGGTGGATGCAGCAATGTGTGCTTGACCACACAAGGTTGATGGG
CGTGTAGTGGAACCAAAGACAGCTGTTTCTAGAGAGGATTCTGTAAAGCCTGGTGCCCATCTAACAGTGAAGAAAATTTT
TGTTGGTGGTATTAAAGAAGATACAGAAGAATATAATTTGAGAGACTTCTTTGAAAAGTATGGCAAAATTGAAACCATAG
AAGTTACGGAAGACAGGCAGAGTGGGAAAAAGAGGATTTGCTTTTGTAACTTTTGATGAGCATGATACAGTTGATAAAAT
TGTTGTTCAGAAATACCACACTATTAATGGGCATAATTGTGAAGTGAAAAAGGCCCTTTCTAAACAAGAGATGCAGTCTG
CTGGATCACAGAGAGGTCGTGGAGGTGGATCTGGCAATTTTATGGGTCGCGGAGGAAACTTTGGAGGTGGTGGAGGAGCT
ATGGTGGTGGAGGTGGTGGCAGCAGAGGTAGTTATGGAGGAGGTGATGGTGGATATAATGGATTTGGAGGTGATGGTGGC
AACTATGGT

Alignment

ORF - retro_hsap_209 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.76 %
• Parental protein coverage: 69.38 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MEGHDPKEPEQLRKLFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAA
          MEGHDPKEPE.LRKLFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAA
Retrocopy MEGHDPKEPEKLRKLFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAA

Parental  MCARPHKVDGRVVEPKRAVSREDSVKPGAHLTVKKIFVGGIKEDTEEYNLRDYFEKYGKIETIEVMEDRQ
          MCA.PHKVDGRVVEPK.AVSREDSVKPGAHLTVKKIFVGGIKEDTEEYNLRD.FEKYGKIETIEV.EDRQ
Retrocopy MCA*PHKVDGRVVEPKTAVSREDSVKPGAHLTVKKIFVGGIKEDTEEYNLRDFFEKYGKIETIEVTEDRQ

Parental  SGKKRGFAFVTF-DDHDTVDKIVVQKYHTINGHNCEVKKALSKQEMQSAGSQRGRGGGSGNFMGRGGNFG
          SGKKR...F..F.D.HDTVDKIVVQKYHTINGHNCEVKKALSKQEMQSAGSQRGRGGGSGNFMGRGGNFG
Retrocopy SGKKR-ICFCNF>DEHDTVDKIVVQKYHTINGHNCEVKKALSKQEMQSAGSQRGRGGGSGNFMGRGGNFG

Parental  GGGG-NFGRGGNFGGRGGYGGGGGGSRGSYGGGDGGYNG
          GGGG...G.GG..G.RG.YGGG.GG..G...GGDGG..G
Retrocopy GGGG<SYGGGGG-GSRGSYGGGDGGYNGF--GGDGGNYG

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	0.14 RPM	347.23 RPM
bodymap2_adrenal	0.41 RPM	535.07 RPM
bodymap2_brain	0.28 RPM	339.37 RPM
bodymap2_breast	0.19 RPM	267.51 RPM
bodymap2_colon	0.25 RPM	432.85 RPM
bodymap2_heart	0.17 RPM	101.85 RPM
bodymap2_kidney	0.62 RPM	331.49 RPM
bodymap2_liver	0.00 RPM	119.24 RPM
bodymap2_lung	0.14 RPM	430.05 RPM
bodymap2_lymph_node	0.07 RPM	274.00 RPM
bodymap2_ovary	0.27 RPM	698.84 RPM
bodymap2_prostate	0.05 RPM	327.14 RPM
bodymap2_skeletal_muscle	0.07 RPM	119.93 RPM
bodymap2_testis	0.06 RPM	412.92 RPM
bodymap2_thyroid	0.64 RPM	465.04 RPM
bodymap2_white_blood_cells	0.10 RPM	279.96 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_209 was not detected

EST

No EST(s) were mapped for retro_hsap_209 retrocopy.

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_80770	440 libraries	657 libraries	715 libraries	14 libraries	3 libraries

The graphical summary, for retro_hsap_209 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_209 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_209 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,