RetrogeneDB ID:

retro_hsap_231

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:1:152372051..152372346(+)
Located in intron of:ENSG00000227415
Retrocopy
information
Ensembl ID:ENSG00000183586
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:HMGN3
Ensembl ID:ENSG00000118418
Aliases:HMGN3, PNAS-25, TRIP7
Description:high mobility group nucleosomal binding domain 3 [Source:HGNC Symbol;Acc:12312]


Retrocopy-Parental alignment summary:






>retro_hsap_231
ATGCAGAAGAGAAAGTCTCCAGAGAATACAGAGGGCAAAGATGGCTCCAAAGTAACTAAACAGGAGCCCACAAGATGGTC
TCCCAGATTGTCAGCAAAACCTCCTCCACCAAAACCTGGACCCAAACCAAGAAAAACATCTGCTAAGAAAGAACCTGGAG
CAAAGGTTAGCAGAGGTGCTAAAGAGAAGAAAGGAAAAGTAGGAAGCTGGAAAGGAAGGTACTGCACCAGCTGAAAATGA
TGAAACTAAAGCTGAAGAGGCACAGAAAACTGAATCTGGAGATAACCAGGGAGAA

ORF - retro_hsap_231 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 69. %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMPKRKSPENTEGKDGSKVTKQEPTRRSARLSAKPAPPKP-EPKPRKTSAKKEPGAKISRGAKGKKEEKQE
M.KRKSPENTEGKDGSKVTKQEPTR.S.RLSAKP.PPKP..P...K....K..........K..KE.K.E
RetrocopyMQKRKSPENTEGKDGSKVTKQEPTRWSPRLSAKPPPPKP>DPNQEKHLLRKNLEQRLAEVLKRRKE-K*E
ParentalAGKEGTAPSENGETKAEEAQKTESVDNEGE
AGKEGTAP.EN.ETKAEEAQKTES.DN.GE
RetrocopyAGKEGTAPAENDETKAEEAQKTESGDNQGE

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 .00 RPM 17 .69 RPM
bodymap2_adrenal 0 .02 RPM 43 .64 RPM
bodymap2_brain 0 .00 RPM 44 .44 RPM
bodymap2_breast 0 .00 RPM 51 .28 RPM
bodymap2_colon 0 .00 RPM 41 .61 RPM
bodymap2_heart 0 .00 RPM 76 .26 RPM
bodymap2_kidney 0 .00 RPM 83 .36 RPM
bodymap2_liver 0 .00 RPM 21 .44 RPM
bodymap2_lung 0 .00 RPM 41 .95 RPM
bodymap2_lymph_node 0 .00 RPM 45 .48 RPM
bodymap2_ovary 0 .00 RPM 66 .97 RPM
bodymap2_prostate 0 .00 RPM 53 .28 RPM
bodymap2_skeletal_muscle 0 .00 RPM 14 .15 RPM
bodymap2_testis 0 .00 RPM 67 .59 RPM
bodymap2_thyroid 0 .02 RPM 57 .38 RPM
bodymap2_white_blood_cells 0 .00 RPM 29 .67 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_231 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_231 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_82571133 libraries97 libraries768 libraries406 libraries425 libraries

The graphical summary, for retro_hsap_231 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_231 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_231 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_200
Pongo abelii retro_pabe_421
Macaca mulatta retro_mmul_414
Parental genes homology:
Parental genes homology involve 13 parental genes, and 20 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG000000070151 retrocopy
retro_chof_2241,
Cavia porcellus ENSCPOG000000124072 retrocopies
retro_cpor_1399, retro_cpor_147,
Felis catus ENSFCAG000000287931 retrocopy
retro_fcat_1400,
Homo sapiens ENSG00000118418 1 retrocopy
retro_hsap_231 ,
Gorilla gorilla ENSGGOG000000069101 retrocopy
retro_ggor_293,
Macaca mulatta ENSMMUG000000043511 retrocopy
retro_mmul_414,
Nomascus leucogenys ENSNLEG000000123772 retrocopies
retro_nleu_68, retro_nleu_851,
Otolemur garnettii ENSOGAG000000164871 retrocopy
retro_ogar_190,
Ochotona princeps ENSOPRG000000096111 retrocopy
retro_opri_799,
Pan troglodytes ENSPTRG000000183662 retrocopies
retro_ptro_1427, retro_ptro_200,
Ictidomys tridecemlineatus ENSSTOG000000143531 retrocopy
retro_itri_251,
Tupaia belangeri ENSTBEG000000154683 retrocopies
retro_tbel_1912, retro_tbel_4714, retro_tbel_615,
Tarsius syrichta ENSTSYG000000052383 retrocopies
retro_tsyr_1569, retro_tsyr_268, retro_tsyr_976,

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 = 0.05 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .03 RPM
CEU_NA11930 0 .00 RPM
CEU_NA12004 0 .04 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .00 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .00 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .00 RPM
FIN_HG00277 0 .00 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .04 RPM
FIN_HG00349 0 .00 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .00 RPM
GBR_HG00099 0 .00 RPM
GBR_HG00111 0 .00 RPM
GBR_HG00114 0 .03 RPM
GBR_HG00119 0 .00 RPM
GBR_HG00131 0 .00 RPM
GBR_HG00133 0 .00 RPM
GBR_HG00134 0 .00 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .00 RPM
TSI_NA20518 0 .03 RPM
TSI_NA20532 0 .00 RPM
TSI_NA20538 0 .05 RPM
TSI_NA20756 0 .03 RPM
TSI_NA20765 0 .02 RPM
TSI_NA20771 0 .00 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .00 RPM
YRI_NA18870 0 .00 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .00 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .00 RPM
YRI_NA19213 0 .00 RPM
YRI_NA19214 0 .00 RPM
YRI_NA19223 0 .00 RPM

Indel association:

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



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