RetrogeneDB ID:

retro_hsap_3976

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:8:81213203..81213713(+)
Located in intron of:ENSG00000253238
Retrocopy
information
Ensembl ID:ENSG00000213791
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RPS5
Ensembl ID:ENSG00000083845
Aliases:RPS5, S5
Description:ribosomal protein S5 [Source:HGNC Symbol;Acc:10426]


Retrocopy-Parental alignment summary:






>retro_hsap_3976
TTGCAGGATTACACTGCAGTGAAGGAGAAGTATGCCAAGTACCTGCCTCACAGTGCAGAGCGGTATGCCGCCAAACGCTT
CCGCAAAGCTCAGTGCCCCATCGTGGAGTGCCTCACTTACTCCATGATGACGCACGGCCGCAACAACCGCAAGAAGCTCA
TGATCATGCGCATCGTCAAGCACGCCTTCGAGATCATCCAGCTGCTCACAGGCGACAACCCTCTGCAGGTCCTGGTGAAC
GCCATCATCAACAGTGGTCCCCGGGAGGACTCCACACTCACTGGGCGAGCCAGGATCGTGAGACGACAGGCTGTGGCCGT
GTCCCCATTAAGCCGTGTGAATCAGGCCATCTGGCCGCAGTGCACAGGAGCTCTTGAGGCTGCCTTCCGGAACATCAAGA
CCATTGCTGAGTTCCTGGCAGATGAGCTCATCAGTGCTGTCAAGGGCTCCTCCAACTCCTATGCTAGCAAGAAGAAGGAC
GAGCTTGAGTGTGTGGCCAAGTCCAACCGC

ORF - retro_hsap_3976 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 85.88 %
Parental protein coverage: 83.33 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalLQDYIAVKEKYAKYLPHSAGRYAAKRFRKAQCPIVERLTNSMMMHGRNNGKKLMTVRIVKHAFEIIHLLT
LQDY.AVKEKYAKYLPHSA.RYAAKRFRKAQCPIVE.LT.SMM.HGRNN.KKLM..RIVKHAFEII.LLT
RetrocopyLQDYTAVKEKYAKYLPHSAERYAAKRFRKAQCPIVECLTYSMMTHGRNNRKKLMIMRIVKHAFEIIQLLT
ParentalGENPLQVLVNAIINSGPREDSTRIGRAGTVRRQAVDVSPLRRVNQAIWLLCTGAREAAFRNIKTIAECLA
G.NPLQVLVNAIINSGPREDST..GRA..VRRQAV.VSPL.RVNQAIW..CTGA.EAAFRNIKTIAE.LA
RetrocopyGDNPLQVLVNAIINSGPREDSTLTGRARIVRRQAVAVSPLSRVNQAIWPQCTGALEAAFRNIKTIAEFLA
ParentalDELINAAKGSSNSYAIKKKDELERVAKSNR
DELI.A.KGSSNSYA.KKKDELE.VAKSNR
RetrocopyDELISAVKGSSNSYASKKKDELECVAKSNR

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 249 .17 RPM
bodymap2_adrenal 0 .02 RPM 279 .29 RPM
bodymap2_brain 0 .02 RPM 59 .63 RPM
bodymap2_breast 1 .52 RPM 186 .71 RPM
bodymap2_colon 0 .00 RPM 374 .15 RPM
bodymap2_heart 0 .00 RPM 83 .35 RPM
bodymap2_kidney 0 .00 RPM 138 .43 RPM
bodymap2_liver 0 .00 RPM 138 .78 RPM
bodymap2_lung 0 .00 RPM 323 .07 RPM
bodymap2_lymph_node 0 .00 RPM 384 .86 RPM
bodymap2_ovary 0 .00 RPM 416 .21 RPM
bodymap2_prostate 0 .00 RPM 457 .87 RPM
bodymap2_skeletal_muscle 0 .00 RPM 239 .88 RPM
bodymap2_testis 0 .00 RPM 195 .62 RPM
bodymap2_thyroid 0 .00 RPM 197 .43 RPM
bodymap2_white_blood_cells 0 .00 RPM 395 .35 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3976 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3976 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_1866511279 libraries455 libraries77 libraries11 libraries7 libraries

The graphical summary, for retro_hsap_3976 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_3976 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3976 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pongo abelii retro_pabe_3270
Macaca mulatta retro_mmul_77
Parental genes homology:
Parental genes homology involve 18 parental genes, and 49 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000023661 retrocopy
retro_cfam_1355,
Callithrix jacchus ENSCJAG000000003046 retrocopies
retro_cjac_1463, retro_cjac_2049, retro_cjac_2050, retro_cjac_2508, retro_cjac_4105, retro_cjac_599,
Echinops telfairi ENSETEG000000135431 retrocopy
retro_etel_912,
Homo sapiens ENSG00000083845 5 retrocopies
retro_hsap_2524, retro_hsap_2526, retro_hsap_3649, retro_hsap_3976 , retro_hsap_4224,
Gorilla gorilla ENSGGOG000000042584 retrocopies
retro_ggor_1577, retro_ggor_2465, retro_ggor_2828, retro_ggor_2942,
Macropus eugenii ENSMEUG000000154003 retrocopies
retro_meug_1075, retro_meug_1792, retro_meug_347,
Myotis lucifugus ENSMLUG000000126411 retrocopy
retro_mluc_2266,
Macaca mulatta ENSMMUG000000087293 retrocopies
retro_mmul_1595, retro_mmul_2525, retro_mmul_77,
Mustela putorius furoENSMPUG000000083081 retrocopy
retro_mputfur_1316,
Ornithorhynchus anatinus ENSOANG000000119211 retrocopy
retro_oana_83,
Otolemur garnettii ENSOGAG000000130882 retrocopies
retro_ogar_1711, retro_ogar_3461,
Procavia capensis ENSPCAG000000110342 retrocopies
retro_pcap_168, retro_pcap_58,
Pongo abelii ENSPPYG000000105007 retrocopies
retro_pabe_1857, retro_pabe_1858, retro_pabe_2996, retro_pabe_3270, retro_pabe_3413, retro_pabe_3683, retro_pabe_375,
Pan troglodytes ENSPTRG000000115916 retrocopies
retro_ptro_1469, retro_ptro_1471, retro_ptro_2474, retro_ptro_2700, retro_ptro_2868, retro_ptro_3152,
Ictidomys tridecemlineatus ENSSTOG000000059351 retrocopy
retro_itri_1742,
Tupaia belangeri ENSTBEG000000169552 retrocopies
retro_tbel_1127, retro_tbel_1169,
Tarsius syrichta ENSTSYG000000000762 retrocopies
retro_tsyr_1258, retro_tsyr_1981,
Tursiops truncatus ENSTTRG000000019911 retrocopy
retro_ttru_106,

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 = 0.06 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .02 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .03 RPM
CEU_NA12004 0 .04 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .00 RPM
CEU_NA12760 0 .04 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 .00 RPM
GBR_HG00133 0 .00 RPM
GBR_HG00134 0 .00 RPM
GBR_HG00137 0 .03 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .00 RPM
TSI_NA20518 0 .06 RPM
TSI_NA20532 0 .00 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .02 RPM
TSI_NA20771 0 .00 RPM
TSI_NA20786 0 .03 RPM
TSI_NA20798 0 .00 RPM
YRI_NA18870 0 .00 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .00 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .05 RPM
YRI_NA19118 0 .02 RPM
YRI_NA19213 0 .05 RPM
YRI_NA19214 0 .00 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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