RetrogeneDB ID:

retro_hsap_2820

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:3:101295335..101295791(-)
Located in intron of:ENSG00000081154
Retrocopy
information
Ensembl ID:ENSG00000242299
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RPS18
Ensembl ID:ENSG00000096150
Aliases:None
Description:ribosomal protein S18 [Source:HGNC Symbol;Acc:10401]


Retrocopy-Parental alignment summary:






>retro_hsap_2820
ATGTCGCTAGTGATCCCTGAAAAGTTCCAGCATATTTTGCGAGTACTCAACACCAACATCGATGGGCAGCGGAAAATAGC
CTTTGCCATCACTGCCATTAAGGGTGTGGGCCGAAGATATGCTCATGTGGTGTTGAGGAAAGCAGACACTGACCTCACCA
AGAGGGCGGGAGAACTCACTGATGATGAGGTGGAACGTGTGATCACCGTTATGCAGAATCCACGCCAGTACAAGATCCCA
GACTGGTTCTTGAACAGACAGAAGGATGTAAAGGATGGAAAATATAGCCAGGTCCTAGCCAATGGTCTGGACAACAAGCT
CCGTGAAGACCTGGAGCGACTGAAGAAGATTCGGGCCCATAGAGGGCTGCGTCACTTCTGGGGCCTTCGTGTCCGAGGCC
AGCACACCAAGACCACTGGCCGCCGTGGCCGCACCGTGGGTGTGTCCAAGAAGAAA

ORF - retro_hsap_2820 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 97.37 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMSLVIPEKFQHILRVLNTNIDGRRKIAFAITAIKGVGRRYAHVVLRKADIDLTKRAGELTEDEVERVITI
MSLVIPEKFQHILRVLNTNIDG.RKIAFAITAIKGVGRRYAHVVLRKAD.DLTKRAGELT.DEVERVIT.
RetrocopyMSLVIPEKFQHILRVLNTNIDGQRKIAFAITAIKGVGRRYAHVVLRKADTDLTKRAGELTDDEVERVITV
ParentalMQNPRQYKIPDWFLNRQKDVKDGKYSQVLANGLDNKLREDLERLKKIRAHRGLRHFWGLRVRGQHTKTTG
MQNPRQYKIPDWFLNRQKDVKDGKYSQVLANGLDNKLREDLERLKKIRAHRGLRHFWGLRVRGQHTKTTG
RetrocopyMQNPRQYKIPDWFLNRQKDVKDGKYSQVLANGLDNKLREDLERLKKIRAHRGLRHFWGLRVRGQHTKTTG
ParentalRRGRTVGVSKKK
RRGRTVGVSKKK
RetrocopyRRGRTVGVSKKK

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 1 .23 RPM 0 .00 RPM
bodymap2_adrenal 2 .05 RPM 0 .00 RPM
bodymap2_brain 0 .47 RPM 0 .00 RPM
bodymap2_breast 1 .17 RPM 0 .00 RPM
bodymap2_colon 1 .28 RPM 0 .00 RPM
bodymap2_heart 0 .54 RPM 0 .00 RPM
bodymap2_kidney 0 .46 RPM 0 .00 RPM
bodymap2_liver 0 .40 RPM 0 .00 RPM
bodymap2_lung 1 .44 RPM 0 .00 RPM
bodymap2_lymph_node 2 .03 RPM 0 .00 RPM
bodymap2_ovary 2 .14 RPM 0 .00 RPM
bodymap2_prostate 2 .94 RPM 0 .00 RPM
bodymap2_skeletal_muscle 2 .04 RPM 0 .00 RPM
bodymap2_testis 0 .58 RPM 0 .00 RPM
bodymap2_thyroid 0 .89 RPM 0 .00 RPM
bodymap2_white_blood_cells 1 .58 RPM 0 .00 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2820 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2820 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_126823424 libraries571 libraries729 libraries86 libraries19 libraries

The graphical summary, for retro_hsap_2820 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_2820 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2820 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_93
Parental genes homology:
Parental genes homology involve 1 parental gene, and 2 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG00000096150 2 retrocopies
retro_hsap_2558, retro_hsap_2820 ,

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 = 9.03 RPM Legend:


Library Retrogene expression
CEU_NA11831 5 .03 RPM
CEU_NA11843 5 .40 RPM
CEU_NA11930 6 .94 RPM
CEU_NA12004 2 .54 RPM
CEU_NA12400 4 .56 RPM
CEU_NA12751 4 .47 RPM
CEU_NA12760 9 .03 RPM
CEU_NA12827 5 .61 RPM
CEU_NA12872 4 .11 RPM
CEU_NA12873 4 .95 RPM
FIN_HG00183 6 .42 RPM
FIN_HG00277 4 .66 RPM
FIN_HG00315 3 .01 RPM
FIN_HG00321 4 .20 RPM
FIN_HG00328 3 .01 RPM
FIN_HG00338 3 .47 RPM
FIN_HG00349 5 .92 RPM
FIN_HG00375 6 .33 RPM
FIN_HG00377 3 .45 RPM
FIN_HG00378 3 .68 RPM
GBR_HG00099 4 .80 RPM
GBR_HG00111 3 .25 RPM
GBR_HG00114 3 .58 RPM
GBR_HG00119 3 .76 RPM
GBR_HG00131 3 .45 RPM
GBR_HG00133 4 .20 RPM
GBR_HG00134 3 .39 RPM
GBR_HG00137 3 .90 RPM
GBR_HG00142 4 .39 RPM
GBR_HG00143 3 .10 RPM
TSI_NA20512 3 .05 RPM
TSI_NA20513 3 .89 RPM
TSI_NA20518 6 .80 RPM
TSI_NA20532 4 .73 RPM
TSI_NA20538 4 .10 RPM
TSI_NA20756 4 .45 RPM
TSI_NA20765 3 .00 RPM
TSI_NA20771 5 .39 RPM
TSI_NA20786 3 .30 RPM
TSI_NA20798 3 .27 RPM
YRI_NA18870 6 .26 RPM
YRI_NA18907 2 .67 RPM
YRI_NA18916 2 .86 RPM
YRI_NA19093 3 .18 RPM
YRI_NA19099 3 .52 RPM
YRI_NA19114 3 .30 RPM
YRI_NA19118 5 .76 RPM
YRI_NA19213 2 .92 RPM
YRI_NA19214 2 .07 RPM
YRI_NA19223 4 .22 RPM

Indel association:

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



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