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


Retrocopy-Parental alignment summary:






>retro_hsap_209
ATGGAGGGCCATGATCCAAAGGAACCAGAGAAGTTGAGAAAACTGTTTATTGGTGGTCTGAGCTTTGAAACTACAGATGA
TAGTTTAAGAGAACATTTTGAGAAATGGGGCACACTCACAGATTGTGTGGTAATGAGAGACCCCCAAACAAAACGTTCCA
GGGGCTTTGGTTTTGTGACTTATTCTTGTGTTGAAGAGGTGGATGCAGCAATGTGTGCTTGACCACACAAGGTTGATGGG
CGTGTAGTGGAACCAAAGACAGCTGTTTCTAGAGAGGATTCTGTAAAGCCTGGTGCCCATCTAACAGTGAAGAAAATTTT
TGTTGGTGGTATTAAAGAAGATACAGAAGAATATAATTTGAGAGACTTCTTTGAAAAGTATGGCAAAATTGAAACCATAG
AAGTTACGGAAGACAGGCAGAGTGGGAAAAAGAGGATTTGCTTTTGTAACTTTTGATGAGCATGATACAGTTGATAAAAT
TGTTGTTCAGAAATACCACACTATTAATGGGCATAATTGTGAAGTGAAAAAGGCCCTTTCTAAACAAGAGATGCAGTCTG
CTGGATCACAGAGAGGTCGTGGAGGTGGATCTGGCAATTTTATGGGTCGCGGAGGAAACTTTGGAGGTGGTGGAGGAGCT
ATGGTGGTGGAGGTGGTGGCAGCAGAGGTAGTTATGGAGGAGGTGATGGTGGATATAATGGATTTGGAGGTGATGGTGGC
AACTATGGT

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:

ParentalMEGHDPKEPEQLRKLFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAA
MEGHDPKEPE.LRKLFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAA
RetrocopyMEGHDPKEPEKLRKLFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAA
ParentalMCARPHKVDGRVVEPKRAVSREDSVKPGAHLTVKKIFVGGIKEDTEEYNLRDYFEKYGKIETIEVMEDRQ
MCA.PHKVDGRVVEPK.AVSREDSVKPGAHLTVKKIFVGGIKEDTEEYNLRD.FEKYGKIETIEV.EDRQ
RetrocopyMCA*PHKVDGRVVEPKTAVSREDSVKPGAHLTVKKIFVGGIKEDTEEYNLRDFFEKYGKIETIEVTEDRQ
ParentalSGKKRGFAFVTF-DDHDTVDKIVVQKYHTINGHNCEVKKALSKQEMQSAGSQRGRGGGSGNFMGRGGNFG
SGKKR...F..F.D.HDTVDKIVVQKYHTINGHNCEVKKALSKQEMQSAGSQRGRGGGSGNFMGRGGNFG
RetrocopySGKKR-ICFCNF>DEHDTVDKIVVQKYHTINGHNCEVKKALSKQEMQSAGSQRGRGGGSGNFMGRGGNFG
ParentalGGGG-NFGRGGNFGGRGGYGGGGGGSRGSYGGGDGGYNG
GGGG...G.GG..G.RG.YGGG.GG..G...GGDGG..G
RetrocopyGGGG<SYGGGGG-GSRGSYGGGDGGYNGF--GGDGGNYG

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






RNA-Seq - click to see more details

(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

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 - click to see more details

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

EST - click to see more details

No EST(s) were mapped for retro_hsap_209 retrocopy.

TSS - click to see more details



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_80770440 libraries657 libraries715 libraries14 libraries3 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)

Display detail expression values in each library
... or ...
Directly download all expression values

Lab - click to see more details

retro_hsap_209 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_209 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 18 parental genes, and 119 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000215808 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 ENSDNOG000000190223 retrocopies
retro_dnov_540, retro_dnov_711, retro_dnov_959,
Ficedula albicollis ENSFALG000000032151 retrocopy
retro_falb_15,
Felis catus ENSFCAG000000121465 retrocopies
retro_fcat_1231, retro_fcat_572, retro_fcat_662, retro_fcat_677, retro_fcat_842,
Homo sapiens ENSG0000013548657 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 ENSG000001386681 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 ENSG000001974511 retrocopy
retro_hsap_962,
Gallus gallus ENSGALG000000092501 retrocopy
retro_ggal_10,
Gorilla gorilla ENSGGOG000000061306 retrocopies
retro_ggor_1001, retro_ggor_1197, retro_ggor_14, retro_ggor_1736, retro_ggor_576, retro_ggor_702,
Macropus eugenii ENSMEUG000000136226 retrocopies
retro_meug_1264, retro_meug_1760, retro_meug_1913, retro_meug_238, retro_meug_470, retro_meug_56,
Macaca mulatta ENSMMUG000000018584 retrocopies
retro_mmul_1945, retro_mmul_2442, retro_mmul_386, retro_mmul_801,
Mus musculus ENSMUSG000000590056 retrocopies
retro_mmus_133, retro_mmus_1359, retro_mmus_1409, retro_mmus_210, retro_mmus_3635, retro_mmus_60,
Oryctolagus cuniculus ENSOCUG000000027432 retrocopies
retro_ocun_994, retro_ocun_995,
Pelodiscus sinensis ENSPSIG000000030111 retrocopy
retro_psin_16,
Ictidomys tridecemlineatus ENSSTOG000000251254 retrocopies
retro_itri_1444, retro_itri_1878, retro_itri_952, retro_itri_98,
Xenopus tropicalis ENSXETG000000018061 retrocopy
retro_xtro_11,
Xiphophorus maculatus ENSXMAG000000004391 retrocopy
retro_xmac_2,

Expression level across human populations :
image/svg+xml GBR_HG00142 GBR_HG00099 GBR_HG00114 GBR_HG00143 GBR_HG00131 GBR_HG00137 GBR_HG00133 GBR_HG00119 GBR_HG00111 GBR_HG00134 FIN_HG00378 FIN_HG00338 FIN_HG00349 FIN_HG00375 FIN_HG00315 FIN_HG00277 FIN_HG00328 FIN_HG00321 FIN_HG00377 FIN_HG00183 TSI_NA20756 TSI_NA20538 TSI_NA20798 TSI_NA20532 TSI_NA20765 TSI_NA20518 TSI_NA20513 TSI_NA20512 TSI_NA20771 TSI_NA20786 YRI_NA19114 YRI_NA19099 YRI_NA18870 YRI_NA18907 YRI_NA19223 YRI_NA19214 YRI_NA18916 YRI_NA19093 YRI_NA19118 YRI_NA19213 Toscaniin Italia: Finnish inFinland: British in England and Scotland: Utah Residents (CEPH) with Northernand Western European Ancestry: Yoruba in Ibadan, Nigeria: CEU_NA12760 CEU_NA12827 CEU_NA12872 CEU_NA12751 CEU_NA12873 CEU_NA12400 CEU_NA11930 CEU_NA12004 CEU_NA11831 CEU_NA11843 No expression ( = 0 RPM ) > 0 RPM = 0.35 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .17 RPM
CEU_NA11843 0 .23 RPM
CEU_NA11930 0 .20 RPM
CEU_NA12004 0 .04 RPM
CEU_NA12400 0 .07 RPM
CEU_NA12751 0 .07 RPM
CEU_NA12760 0 .09 RPM
CEU_NA12827 0 .09 RPM
CEU_NA12872 0 .11 RPM
CEU_NA12873 0 .16 RPM
FIN_HG00183 0 .11 RPM
FIN_HG00277 0 .22 RPM
FIN_HG00315 0 .03 RPM
FIN_HG00321 0 .06 RPM
FIN_HG00328 0 .17 RPM
FIN_HG00338 0 .19 RPM
FIN_HG00349 0 .34 RPM
FIN_HG00375 0 .07 RPM
FIN_HG00377 0 .18 RPM
FIN_HG00378 0 .15 RPM
GBR_HG00099 0 .15 RPM
GBR_HG00111 0 .11 RPM
GBR_HG00114 0 .08 RPM
GBR_HG00119 0 .10 RPM
GBR_HG00131 0 .06 RPM
GBR_HG00133 0 .02 RPM
GBR_HG00134 0 .13 RPM
GBR_HG00137 0 .08 RPM
GBR_HG00142 0 .11 RPM
GBR_HG00143 0 .35 RPM
TSI_NA20512 0 .08 RPM
TSI_NA20513 0 .05 RPM
TSI_NA20518 0 .08 RPM
TSI_NA20532 0 .10 RPM
TSI_NA20538 0 .23 RPM
TSI_NA20756 0 .15 RPM
TSI_NA20765 0 .08 RPM
TSI_NA20771 0 .14 RPM
TSI_NA20786 0 .03 RPM
TSI_NA20798 0 .06 RPM
YRI_NA18870 0 .20 RPM
YRI_NA18907 0 .21 RPM
YRI_NA18916 0 .08 RPM
YRI_NA19093 0 .10 RPM
YRI_NA19099 0 .13 RPM
YRI_NA19114 0 .10 RPM
YRI_NA19118 0 .17 RPM
YRI_NA19213 0 .10 RPM
YRI_NA19214 0 .05 RPM
YRI_NA19223 0 .24 RPM

Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).



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