RetrogeneDB ID:

retro_hsap_1095

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:12:25120063..25120438(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000213736
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:BRI3
Ensembl ID:ENSG00000164713
Aliases:BRI3, I3
Description:brain protein I3 [Source:HGNC Symbol;Acc:1109]


Retrocopy-Parental alignment summary:






>retro_hsap_1095
ATGGACCACAAACCTCTGCTGCAGAAGCGGCCTCTGGCCTACAACCTGGAGTCCGTCCAGGTCAACTATGCATGCTGCCT
GCACAGCTATGGCGCCAACCCTGCCAGCCCCCGCCAAGGCCCTACCCCTACCTCGTCACAGGGGTACCCACCCGCCACCC
CAGGGTCTACAACATCCACAGCCAGACCACCACCTGGTACCCTGCCAACTCCATCATGGTCATGGGAAGCTGTCCCGTCT
GCAGGGTCGGGGGTGCTGGAGGACTGCTTCAGCTCCCTGGGCATTTTCTTGGTCATCATCCTGTTCCCCTTTGGGTTCAT
CTGCCGTTTTGCCTTGAGGAAGCGAAGATGCCCCAACTGCGGAGAGACCTTCGCT

ORF - retro_hsap_1095 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 78.74 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMDHKPLLQERPPAYNLEAGQGDYACGPHGYGAIPAAP-PPPPYPYLVTGIPTHHPRVYNIHSRTVTRYPA
MDHKPLLQ.RP.AYNLE..Q..YAC..H.YGA.PA.P.PP.PYPYLVTG.PT.HPRVYNIHS.T.T.YPA
RetrocopyMDHKPLLQKRPLAYNLESVQVNYACCLHSYGANPASP<PPRPYPYLVTGVPTRHPRVYNIHSQTTTWYPA
ParentalNSIVVVGGCPVCRV-GVLEDCFTFLGIFLAIILFPFGFICCFALRKRRCPNCGATFA
NSI.V.G.CPVCRV.GVLEDCF..LGIFL.IILFPFGFIC.FALRKRRCPNCG.TFA
RetrocopyNSIMVMGSCPVCRV>GVLEDCFSSLGIFLVIILFPFGFICRFALRKRRCPNCGETFA

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 49 .79 RPM
bodymap2_adrenal 0 .00 RPM 36 .07 RPM
bodymap2_brain 0 .00 RPM 10 .97 RPM
bodymap2_breast 0 .00 RPM 39 .14 RPM
bodymap2_colon 0 .00 RPM 39 .16 RPM
bodymap2_heart 0 .00 RPM 39 .71 RPM
bodymap2_kidney 0 .00 RPM 30 .90 RPM
bodymap2_liver 0 .00 RPM 58 .75 RPM
bodymap2_lung 0 .00 RPM 78 .13 RPM
bodymap2_lymph_node 0 .00 RPM 54 .42 RPM
bodymap2_ovary 0 .00 RPM 27 .64 RPM
bodymap2_prostate 0 .00 RPM 74 .06 RPM
bodymap2_skeletal_muscle 0 .00 RPM 174 .26 RPM
bodymap2_testis 0 .00 RPM 38 .35 RPM
bodymap2_thyroid 0 .00 RPM 50 .26 RPM
bodymap2_white_blood_cells 0 .00 RPM 101 .22 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_1095 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_1095 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_24148755 libraries702 libraries352 libraries19 libraries1 library

The graphical summary, for retro_hsap_1095 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_1095 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1095 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_698
Pongo abelii retro_pabe_910
Parental genes homology:
Parental genes homology involve 9 parental genes, and 15 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000152271 retrocopy
retro_cjac_2527,
Homo sapiens ENSG00000164713 3 retrocopies
retro_hsap_1095 , retro_hsap_1811, retro_hsap_195,
Gorilla gorilla ENSGGOG000000096461 retrocopy
retro_ggor_205,
Microcebus murinus ENSMICG000000028881 retrocopy
retro_mmur_372,
Macaca mulatta ENSMMUG000000132752 retrocopies
retro_mmul_1248, retro_mmul_849,
Otolemur garnettii ENSOGAG000000006381 retrocopy
retro_ogar_63,
Pongo abelii ENSPPYG000000258153 retrocopies
retro_pabe_1484, retro_pabe_50, retro_pabe_910,
Pan troglodytes ENSPTRG000000194361 retrocopy
retro_ptro_698,
Tursiops truncatus ENSTTRG000000157052 retrocopies
retro_ttru_706, retro_ttru_91,

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 = 0.07 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .07 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .05 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 .00 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 .00 RPM
GBR_HG00119 0 .00 RPM
GBR_HG00131 0 .03 RPM
GBR_HG00133 0 .02 RPM
GBR_HG00134 0 .02 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .03 RPM
GBR_HG00143 0 .03 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .00 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .00 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .00 RPM
TSI_NA20771 0 .00 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .00 RPM
YRI_NA18870 0 .03 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .00 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .03 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .00 RPM
YRI_NA19213 0 .00 RPM
YRI_NA19214 0 .02 RPM
YRI_NA19223 0 .02 RPM

Indel association:

The presence of retro_hsap_1095 across human populations is associated with 1 indel. The percentage values indicate the frequencies of retro_hsap_1095 presence in various populations. Based on Kabza et al. 2015 (PubMed).


# Indel coordinates AFR, African AMR, Ad Mixed American EUR, European EAS, East Asian
ASW YRI LWK MXL PUR CLM CEU IBS GBR FIN TSI JPT CHB CHS
1. 12:25088940..25131900 100 100 100 100 100 100 98.82 100 100 100 100 100 100 100

Indel #1, located at the genomic coordinates 12:25088940..25131900.

image/svg+xml Mexican Ancestryfrom Los Angeles USA MXL 100 % Puerto Ricansfrom Puerto Rico PUR 100 % Colombians fromMedellin, Colombia CLM 100 % Americans of AfricanAncestry in SW USA ASW 100 % Yoruba in Ibadan,Nigeria YRI 100 % Luhya in Webuye,Kenya LWK 100 % Utah Residents (CEPH)with Northern andWestern European Ancestry CEU 98.82 % Iberian Populationin Spain IBS 100 % British in Englandand Scotland GBR 100 % Finnish in Finland FIN 100 % Toscani in Italia TSI 100 % Han Chinese in Bejing,China CHB 100 % Japanese in Tokyo,Japan 100 % Southern Han Chinese CHS 100 % JPT EUROPE AMERICAS AFRICA EAST ASIA




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