RetrogeneDB ID:

retro_hsap_3532

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:6:149915219..149915676(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000220848
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RPS18
Ensembl ID:ENSG00000235650
Aliases:None
Description:ribosomal protein S18 [Source:HGNC Symbol;Acc:10401]


Retrocopy-Parental alignment summary:






>retro_hsap_3532
ATGTCTCTAGTGATCCCTGAAAAGTCCCAGCATATTTTGCCGAGTAGTCAACACCAACATTGATGGGTGGCGGAAAATGG
CCTTTGCCATCACTGCCGTTAAGGGTGTGGGCCGAAGATATGCTCATGTGGTGTTGAGGAAAGCAGACACTGACCTCACC
AAGAGGGCGGGAGAACTCACTGAGGATGAGGTGGAACATGTGATCACCATTATGCAGAATCCACACTAGTACAAGATGCC
AGCCTGGTTCTTGAACAGACAGAAGGATGTAAAGGATGGAAAATATAGCCAGGTCCTAGCCAATGGTCTGGACAACAAGC
TCTGTGAAGACCTGGAGCGACTGAAAAAGATTCGGGCCCGTAGAGGGCTGCGTCACTTCTGGGGCCTTCGTGTCCGAGGC
CAGCACACCAAGACCACAGGCTGCCGTGGCCGCATCGTGGGTGTGTCTAAGAAGAAG

ORF - retro_hsap_3532 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 89.54 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMSLVIPEKFQHIL-RVLNTNIDGRRKIAFAITAIKGVGRRYAHVVLRKADIDLTKRAGELTEDEVERVIT
MSLVIPEK.QHIL.RV.NTNIDG.RK.AFAITA.KGVGRRYAHVVLRKAD.DLTKRAGELTEDEVE.VIT
RetrocopyMSLVIPEKSQHIL>RVVNTNIDGWRKMAFAITAVKGVGRRYAHVVLRKADTDLTKRAGELTEDEVEHVIT
ParentalIMQNPRQYKIPDWFLNRQKDVKDGKYSQVLANGLDNKLREDLERLKKIRAHRGLRHFWGLRVRGQHTKTT
IMQNP..YK.P.WFLNRQKDVKDGKYSQVLANGLDNKL.EDLERLKKIRA.RGLRHFWGLRVRGQHTKTT
RetrocopyIMQNPH*YKMPAWFLNRQKDVKDGKYSQVLANGLDNKLCEDLERLKKIRARRGLRHFWGLRVRGQHTKTT
ParentalGRRGRTVGVSKKK
G.RGR.VGVSKKK
RetrocopyGCRGRIVGVSKKK

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 2 .64 RPM 0 .00 RPM
bodymap2_adrenal 1 .70 RPM 0 .00 RPM
bodymap2_brain 0 .84 RPM 0 .00 RPM
bodymap2_breast 1 .95 RPM 0 .00 RPM
bodymap2_colon 2 .51 RPM 0 .00 RPM
bodymap2_heart 0 .79 RPM 0 .00 RPM
bodymap2_kidney 1 .28 RPM 0 .00 RPM
bodymap2_liver 0 .63 RPM 0 .00 RPM
bodymap2_lung 2 .09 RPM 0 .00 RPM
bodymap2_lymph_node 1 .50 RPM 0 .00 RPM
bodymap2_ovary 2 .91 RPM 0 .00 RPM
bodymap2_prostate 1 .07 RPM 0 .00 RPM
bodymap2_skeletal_muscle 0 .69 RPM 0 .00 RPM
bodymap2_testis 1 .68 RPM 0 .00 RPM
bodymap2_thyroid 2 .41 RPM 0 .00 RPM
bodymap2_white_blood_cells 0 .53 RPM 0 .00 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3532 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3532 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_160536290 libraries439 libraries1004 libraries87 libraries9 libraries

The graphical summary, for retro_hsap_3532 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_3532 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3532 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 1 parental gene, and 3 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG00000235650 3 retrocopies
retro_hsap_1371, retro_hsap_2408, retro_hsap_3532 ,

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 = 2.75 RPM Legend:


Library Retrogene expression
CEU_NA11831 1 .35 RPM
CEU_NA11843 1 .99 RPM
CEU_NA11930 2 .12 RPM
CEU_NA12004 1 .33 RPM
CEU_NA12400 2 .07 RPM
CEU_NA12751 2 .09 RPM
CEU_NA12760 1 .57 RPM
CEU_NA12827 1 .56 RPM
CEU_NA12872 1 .14 RPM
CEU_NA12873 2 .04 RPM
FIN_HG00183 2 .75 RPM
FIN_HG00277 1 .33 RPM
FIN_HG00315 2 .13 RPM
FIN_HG00321 1 .69 RPM
FIN_HG00328 1 .80 RPM
FIN_HG00338 1 .70 RPM
FIN_HG00349 1 .76 RPM
FIN_HG00375 1 .34 RPM
FIN_HG00377 1 .49 RPM
FIN_HG00378 1 .51 RPM
GBR_HG00099 1 .31 RPM
GBR_HG00111 1 .25 RPM
GBR_HG00114 1 .29 RPM
GBR_HG00119 2 .16 RPM
GBR_HG00131 2 .21 RPM
GBR_HG00133 1 .45 RPM
GBR_HG00134 1 .40 RPM
GBR_HG00137 2 .03 RPM
GBR_HG00142 2 .06 RPM
GBR_HG00143 1 .37 RPM
TSI_NA20512 0 .88 RPM
TSI_NA20513 1 .77 RPM
TSI_NA20518 1 .33 RPM
TSI_NA20532 1 .26 RPM
TSI_NA20538 1 .15 RPM
TSI_NA20756 1 .57 RPM
TSI_NA20765 1 .60 RPM
TSI_NA20771 1 .65 RPM
TSI_NA20786 0 .97 RPM
TSI_NA20798 1 .31 RPM
YRI_NA18870 0 .61 RPM
YRI_NA18907 0 .69 RPM
YRI_NA18916 1 .62 RPM
YRI_NA19093 0 .81 RPM
YRI_NA19099 0 .85 RPM
YRI_NA19114 1 .31 RPM
YRI_NA19118 1 .18 RPM
YRI_NA19213 1 .39 RPM
YRI_NA19214 0 .89 RPM
YRI_NA19223 0 .90 RPM

Indel association:

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



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