RetrogeneDB ID:

retro_hsap_3958

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:8:57500965..57501256(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000241431
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL37
Ensembl ID:ENSG00000145592
Aliases:None
Description:ribosomal protein L37 [Source:HGNC Symbol;Acc:10347]


Retrocopy-Parental alignment summary:






>retro_hsap_3958
ATGATGAAGGGAACGTCATCATTTGGAAAGCATTGCAATAAGACGTACACGTTATGCCACCACTGTGGCTCTAAGGCCTA
CCACCTTCAGAAGTCGACCTATGGCAAATGTGGCTACACTGCCAAGCGCAAGAGAAAGTATAACTGGAGTACCAAGGCTA
AAAGACGAAATACCACCAGAACTGGTCAAATGAGGCACCTAAAAATTGTATACCATAGATTCAGGCATGGATTCCGTGAA
GGAACAACACCTAAACCCAAGAGGGCAGCTGTTGCAGCATCCAGTTCATCT

ORF - retro_hsap_3958 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 87.63 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMTKGTSSFGKRRNKTHTLCRRCGSKAYHLQKSTCGKCGYPAKRKRKYNWSAKAKRRNTTGTGRMRHLKIV
M.KGTSSFGK..NKT.TLC..CGSKAYHLQKST.GKCGY.AKRKRKYNWS.KAKRRNTT.TG.MRHLKIV
RetrocopyMMKGTSSFGKHCNKTYTLCHHCGSKAYHLQKSTYGKCGYTAKRKRKYNWSTKAKRRNTTRTGQMRHLKIV
ParentalYRRFRHGFREGTTPKPKRAAVAASSSS
Y.RFRHGFREGTTPKPKRAAVAASSSS
RetrocopyYHRFRHGFREGTTPKPKRAAVAASSSS

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






(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 .10 RPM 379 .97 RPM
bodymap2_adrenal 0 .00 RPM 602 .62 RPM
bodymap2_brain 0 .02 RPM 199 .19 RPM
bodymap2_breast 0 .16 RPM 316 .95 RPM
bodymap2_colon 0 .08 RPM 431 .48 RPM
bodymap2_heart 0 .00 RPM 114 .35 RPM
bodymap2_kidney 0 .00 RPM 162 .88 RPM
bodymap2_liver 0 .00 RPM 154 .67 RPM
bodymap2_lung 0 .02 RPM 449 .12 RPM
bodymap2_lymph_node 0 .05 RPM 528 .89 RPM
bodymap2_ovary 0 .04 RPM 616 .36 RPM
bodymap2_prostate 0 .00 RPM 551 .37 RPM
bodymap2_skeletal_muscle 0 .04 RPM 417 .43 RPM
bodymap2_testis 0 .26 RPM 270 .37 RPM
bodymap2_thyroid 0 .00 RPM 265 .52 RPM
bodymap2_white_blood_cells 0 .00 RPM 595 .52 RPM
RNA Polymerase II actvity near the 5' end of retro_hsap_3958 was not detected
No EST(s) were mapped for retro_hsap_3958 retrocopy.


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_185447524 libraries443 libraries161 libraries262 libraries439 libraries

The graphical summary, for retro_hsap_3958 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)

retro_hsap_3958 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3958 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2687
Gorilla gorilla retro_ggor_2660
Pongo abelii retro_pabe_3260

Parental genes homology:
Parental genes homology involve 11 parental genes, and 117 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG00000145592 21 retrocopies
Latimeria chalumnae ENSLACG000000027871 retrocopy
Loxodonta africana ENSLAFG0000003005213 retrocopies
Myotis lucifugus ENSMLUG0000000156510 retrocopies
Macaca mulatta ENSMMUG000000238076 retrocopies
Monodelphis domestica ENSMODG000000203013 retrocopies
Nomascus leucogenys ENSNLEG000000165084 retrocopies
Otolemur garnettii ENSOGAG000000343007 retrocopies
Pongo abelii ENSPPYG0000001542226 retrocopies
Pan troglodytes ENSPTRG0000001682220 retrocopies
Rattus norvegicus ENSRNOG000000125386 retrocopies

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 = 0.15 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .04 RPM
CEU_NA11843 0 .03 RPM
CEU_NA11930 0 .07 RPM
CEU_NA12004 0 .08 RPM
CEU_NA12400 0 .07 RPM
CEU_NA12751 0 .02 RPM
CEU_NA12760 0 .13 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .03 RPM
CEU_NA12873 0 .06 RPM
FIN_HG00183 0 .05 RPM
FIN_HG00277 0 .04 RPM
FIN_HG00315 0 .03 RPM
FIN_HG00321 0 .03 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .02 RPM
FIN_HG00349 0 .00 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .10 RPM
FIN_HG00378 0 .02 RPM
GBR_HG00099 0 .00 RPM
GBR_HG00111 0 .04 RPM
GBR_HG00114 0 .03 RPM
GBR_HG00119 0 .00 RPM
GBR_HG00131 0 .00 RPM
GBR_HG00133 0 .05 RPM
GBR_HG00134 0 .15 RPM
GBR_HG00137 0 .03 RPM
GBR_HG00142 0 .06 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .03 RPM
TSI_NA20513 0 .05 RPM
TSI_NA20518 0 .03 RPM
TSI_NA20532 0 .07 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .06 RPM
TSI_NA20765 0 .04 RPM
TSI_NA20771 0 .03 RPM
TSI_NA20786 0 .05 RPM
TSI_NA20798 0 .03 RPM
YRI_NA18870 0 .00 RPM
YRI_NA18907 0 .03 RPM
YRI_NA18916 0 .04 RPM
YRI_NA19093 0 .03 RPM
YRI_NA19099 0 .03 RPM
YRI_NA19114 0 .05 RPM
YRI_NA19118 0 .06 RPM
YRI_NA19213 0 .00 RPM
YRI_NA19214 0 .00 RPM
YRI_NA19223 0 .06 RPM


Indel association:

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




Copyright © RetrogeneDB 2014-2017