RetrogeneDB ID:

retro_hsap_2851

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:3:142545940..142546569(-)
Located in intron of:ENSG00000163710
Retrocopy
information
Ensembl ID:ENSG00000240950
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL8
Ensembl ID:ENSG00000161016
Aliases:RPL8, L8
Description:ribosomal protein L8 [Source:HGNC Symbol;Acc:10368]


Retrocopy-Parental alignment summary:






>retro_hsap_2851
ATCATCCACAACTCGGGTCACAGCGCGCCCCTCCCCAAGGTGGTCTTCCGCGACCCGTACTGGTTTAAGAAGCGGACGGA
GCTTTTCATTGCTGCCGAGGGCATTCACACGGGCCAGTTTGTGTATTGCGGCAAGAAGGCCCAGCTCAACATTGGCAGTG
TGCTCCCTGTGGGCACCATGCCTGAGGGTATGATCGTGTGCTGCCTGGAGGAGAAGCCTGGAGGCCGTAGCAAGCTGTCC
TGGGCATCAGGGAACTATGCCACTGCTATCTCCCACAACCCTGAGACCAAGAAGACCCGTGTGAAGCTGCCCTCTGGCTC
CAAGAAGGTTGTCTCCTCAGCCAACAGAGCTGTGGTTGGTGTGGTGGCTGGAGGTGGCCGAACTGACAAACCCATCTTGA
AGGCTTGCCAAGCCTACCACAAATATAAGGCAAAGAGGAACTGGTGGCCACGAGTATGGGATGTGGCCATGAACCCTATG
GAGCATCCTTTTGGAGGTGGCAACCACCAGCACATCGGCATCCCCTCCGCCATCTCAGAGATGACCCTGCTGGCTGCAAA
ATGGGTCTCATTGCTGCCCGCCAGACTGGACGTCTCTGGGGAACCAAGACTGTGCAGGAGAAAGAGAAC

ORF - retro_hsap_2851 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 85.78 %
Parental protein coverage: 81.71 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalIIHDPGRGAPLAKVVFRDPYRFKKRTELFIAAEGIHTGQFVYCGKKAQLNIGNVLPVGTMPEGTIVCCLE
IIH..G..APL.KVVFRDPY.FKKRTELFIAAEGIHTGQFVYCGKKAQLNIG.VLPVGTMPEG.IVCCLE
RetrocopyIIHNSGHSAPLPKVVFRDPYWFKKRTELFIAAEGIHTGQFVYCGKKAQLNIGSVLPVGTMPEGMIVCCLE
ParentalEKPGDRGKLARASGNYATVISHNPETKKTRVKLPSGSKKVISSANRAVVGVVAGGGRIDKPILKAGRAYH
EKPG.R.KL..ASGNYAT.ISHNPETKKTRVKLPSGSKKV.SSANRAVVGVVAGGGR.DKPILKA..AYH
RetrocopyEKPGGRSKLSWASGNYATAISHNPETKKTRVKLPSGSKKVVSSANRAVVGVVAGGGRTDKPILKACQAYH
ParentalKYKAKRNCWPRVRGVAMNPVEHPFGGGNHQHIGKPSTIR-RDAPAGRKVGLIAARRTGRLRGTKTVQEKE
KYKAKRN.WPRV..VAMNP.EHPFGGGNHQHIG.PS.I..RD.PAG.K.GLIAAR.TGRL.GTKTVQEKE
RetrocopyKYKAKRNWWPRVWDVAMNPMEHPFGGGNHQHIGIPSAIS<RDDPAGCKMGLIAARQTGRLWGTKTVQEKE
ParentalN
N
RetrocopyN

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 .60 RPM 899 .68 RPM
bodymap2_adrenal 0 .04 RPM 879 .37 RPM
bodymap2_brain 0 .00 RPM 177 .86 RPM
bodymap2_breast 0 .19 RPM 529 .13 RPM
bodymap2_colon 0 .02 RPM 1131 .61 RPM
bodymap2_heart 0 .00 RPM 195 .08 RPM
bodymap2_kidney 0 .02 RPM 425 .17 RPM
bodymap2_liver 0 .00 RPM 268 .31 RPM
bodymap2_lung 0 .02 RPM 735 .20 RPM
bodymap2_lymph_node 0 .02 RPM 944 .44 RPM
bodymap2_ovary 0 .08 RPM 1301 .88 RPM
bodymap2_prostate 0 .03 RPM 940 .19 RPM
bodymap2_skeletal_muscle 0 .00 RPM 444 .69 RPM
bodymap2_testis 0 .00 RPM 588 .07 RPM
bodymap2_thyroid 0 .06 RPM 619 .40 RPM
bodymap2_white_blood_cells 0 .02 RPM 728 .49 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity may be related with retro_hsap_2851 in 1 libraries
ENCODE library ID Target ChIP-Seq Peak coordinates
ENCFF002CXQ POLR2A 3:142547447..142548097

EST - click to see more details

No EST(s) were mapped for retro_hsap_2851 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_129831258 libraries520 libraries944 libraries101 libraries6 libraries

The graphical summary, for retro_hsap_2851 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_2851 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2851 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1931
Gorilla gorilla retro_ggor_1974
Macaca mulatta retro_mmul_1470
Parental genes homology:
Parental genes homology involve 13 parental genes, and 22 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000179331 retrocopy
retro_acar_31,
Ailuropoda melanoleuca ENSAMEG000000053951 retrocopy
retro_amel_241,
Bos taurus ENSBTAG000000263271 retrocopy
retro_btau_96,
Callithrix jacchus ENSCJAG000000213884 retrocopies
retro_cjac_1109, retro_cjac_1169, retro_cjac_1579, retro_cjac_2047,
Dasypus novemcinctus ENSDNOG000000093002 retrocopies
retro_dnov_2505, retro_dnov_503,
Echinops telfairi ENSETEG000000071044 retrocopies
retro_etel_1100, retro_etel_264, retro_etel_296, retro_etel_916,
Felis catus ENSFCAG000000262881 retrocopy
retro_fcat_570,
Homo sapiens ENSG00000161016 1 retrocopy
retro_hsap_2851 ,
Macaca mulatta ENSMMUG000000133792 retrocopies
retro_mmul_1470, retro_mmul_1531,
Mustela putorius furoENSMPUG000000060221 retrocopy
retro_mputfur_1517,
Oryctolagus cuniculus ENSOCUG000000247161 retrocopy
retro_ocun_146,
Rattus norvegicus ENSRNOG000000485232 retrocopies
retro_rnor_122, retro_rnor_239,
Tursiops truncatus ENSTTRG000000138581 retrocopy
retro_ttru_1147,

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 = 0.22 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .02 RPM
CEU_NA11843 0 .09 RPM
CEU_NA11930 0 .00 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .11 RPM
CEU_NA12751 0 .15 RPM
CEU_NA12760 0 .04 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .03 RPM
CEU_NA12873 0 .10 RPM
FIN_HG00183 0 .05 RPM
FIN_HG00277 0 .22 RPM
FIN_HG00315 0 .11 RPM
FIN_HG00321 0 .03 RPM
FIN_HG00328 0 .09 RPM
FIN_HG00338 0 .04 RPM
FIN_HG00349 0 .03 RPM
FIN_HG00375 0 .05 RPM
FIN_HG00377 0 .03 RPM
FIN_HG00378 0 .08 RPM
GBR_HG00099 0 .06 RPM
GBR_HG00111 0 .04 RPM
GBR_HG00114 0 .18 RPM
GBR_HG00119 0 .02 RPM
GBR_HG00131 0 .03 RPM
GBR_HG00133 0 .05 RPM
GBR_HG00134 0 .00 RPM
GBR_HG00137 0 .16 RPM
GBR_HG00142 0 .06 RPM
GBR_HG00143 0 .10 RPM
TSI_NA20512 0 .06 RPM
TSI_NA20513 0 .02 RPM
TSI_NA20518 0 .03 RPM
TSI_NA20532 0 .07 RPM
TSI_NA20538 0 .05 RPM
TSI_NA20756 0 .03 RPM
TSI_NA20765 0 .06 RPM
TSI_NA20771 0 .17 RPM
TSI_NA20786 0 .08 RPM
TSI_NA20798 0 .12 RPM
YRI_NA18870 0 .07 RPM
YRI_NA18907 0 .03 RPM
YRI_NA18916 0 .04 RPM
YRI_NA19093 0 .03 RPM
YRI_NA19099 0 .13 RPM
YRI_NA19114 0 .21 RPM
YRI_NA19118 0 .06 RPM
YRI_NA19213 0 .05 RPM
YRI_NA19214 0 .10 RPM
YRI_NA19223 0 .04 RPM

Indel association:

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





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