RetrogeneDB ID:

retro_hsap_3122

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:4:170712373..170712853(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000229204
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:PTGES3
Ensembl ID:ENSG00000110958
Aliases:PTGES3, P23, TEBP, cPGES
Description:prostaglandin E synthase 3 (cytosolic) [Source:HGNC Symbol;Acc:16049]


Retrocopy-Parental alignment summary:






>retro_hsap_3122
ATGCAGCCTGCTTTTGCAAAGTGGTACGATCGAAGGGACTGTGTCTTCACTGAATCTTGTGTTGAAGACAATAAGGATGT
TAATGTAAATTTTGAAAAATCCAAACTTACATTCAGTTGTCTTGGAGGAAGTGATAATTTTAAGCATTTAAATGAAATTG
GTCTTTTTTACTCTATTGATCCAAATGATTCCAAGCATAAAAGAACGGACAGATCAATTTTATGTTGTTTACGAAAAGGA
GAATCTGGCCAGTCATGGCCAAGGTTAACAAAAGAAAGGGCAAAGCTTAACTGGCTTAGTATGGACTTCAATCATTGGAA
AGACTGGGAAGATGGTTCAGATGAAGACAGGTCTAATTTTGATCGTTTCTCCGAGATGATGAACAACATGGGTGGGGATG
AGGATGTAGATTTACCAGAAGTAGATGAAGCAGGTGATGATTCACAAGACAGTGATGATGAAAAAATGCCAGATCTGGAG

ORF - retro_hsap_3122 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 91.25 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMQPASAKWYDRRDYVFIEFCVEDSKDVNVNFEKSKLTFSCLGGSDNFKHLNEIDLFHCIDPNDSKHKRTD
MQPA.AKWYDRRD.VF.E.CVED.KDVNVNFEKSKLTFSCLGGSDNFKHLNEI.LF..IDPNDSKHKRTD
RetrocopyMQPAFAKWYDRRDCVFTESCVEDNKDVNVNFEKSKLTFSCLGGSDNFKHLNEIGLFYSIDPNDSKHKRTD
ParentalRSILCCLRKGESGQSWPRLTKERAKLNWLSVDFNNWKDWEDDSDEDMSNFDRFSEMMNNMGGDEDVDLPE
RSILCCLRKGESGQSWPRLTKERAKLNWLS.DFN.WKDWED.SDED.SNFDRFSEMMNNMGGDEDVDLPE
RetrocopyRSILCCLRKGESGQSWPRLTKERAKLNWLSMDFNHWKDWEDGSDEDRSNFDRFSEMMNNMGGDEDVDLPE
ParentalVDGADDDSQDSDDEKMPDLE
VD.A.DDSQDSDDEKMPDLE
RetrocopyVDEAGDDSQDSDDEKMPDLE

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 .61 RPM 262 .75 RPM
bodymap2_adrenal 0 .96 RPM 188 .01 RPM
bodymap2_brain 1 .45 RPM 311 .71 RPM
bodymap2_breast 2 .00 RPM 243 .62 RPM
bodymap2_colon 2 .18 RPM 623 .37 RPM
bodymap2_heart 0 .07 RPM 122 .16 RPM
bodymap2_kidney 0 .81 RPM 328 .32 RPM
bodymap2_liver 0 .02 RPM 143 .96 RPM
bodymap2_lung 0 .39 RPM 366 .39 RPM
bodymap2_lymph_node 0 .20 RPM 390 .73 RPM
bodymap2_ovary 4 .05 RPM 579 .62 RPM
bodymap2_prostate 0 .26 RPM 499 .81 RPM
bodymap2_skeletal_muscle 0 .13 RPM 258 .56 RPM
bodymap2_testis 1 .56 RPM 381 .27 RPM
bodymap2_thyroid 2 .49 RPM 402 .67 RPM
bodymap2_white_blood_cells 0 .57 RPM 314 .81 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3122 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3122 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3122 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3122 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3122 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2111
Gorilla gorilla retro_ggor_154
Parental genes homology:
Parental genes homology involve 25 parental genes, and 87 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000041721 retrocopy
retro_amel_1835,
Bos taurus ENSBTAG000000179672 retrocopies
retro_btau_1766, retro_btau_275,
Choloepus hoffmanni ENSCHOG000000065141 retrocopy
retro_chof_1336,
Callithrix jacchus ENSCJAG000000107246 retrocopies
retro_cjac_1001, retro_cjac_1304, retro_cjac_2122, retro_cjac_3826, retro_cjac_473, retro_cjac_942,
Cavia porcellus ENSCPOG000000000572 retrocopies
retro_cpor_183, retro_cpor_523,
Dasypus novemcinctus ENSDNOG000000113104 retrocopies
retro_dnov_2088, retro_dnov_2571, retro_dnov_472, retro_dnov_969,
Dipodomys ordii ENSDORG000000009642 retrocopies
retro_dord_600, retro_dord_94,
Echinops telfairi ENSETEG000000000241 retrocopy
retro_etel_1612,
Homo sapiens ENSG00000110958 5 retrocopies
retro_hsap_2084, retro_hsap_3122 , retro_hsap_417, retro_hsap_618, retro_hsap_623,
Homo sapiens ENSG000002669671 retrocopy
retro_hsap_4707,
Gorilla gorilla ENSGGOG000000279575 retrocopies
retro_ggor_111, retro_ggor_135, retro_ggor_154, retro_ggor_542, retro_ggor_546,
Loxodonta africana ENSLAFG000000082681 retrocopy
retro_lafr_490,
Macropus eugenii ENSMEUG000000012881 retrocopy
retro_meug_264,
Myotis lucifugus ENSMLUG000000159273 retrocopies
retro_mluc_1111, retro_mluc_2120, retro_mluc_836,
Macaca mulatta ENSMMUG000000137666 retrocopies
retro_mmul_1054, retro_mmul_1988, retro_mmul_2239, retro_mmul_2421, retro_mmul_679, retro_mmul_978,
Mus musculus ENSMUSG000000710722 retrocopies
retro_mmus_2441, retro_mmus_2757,
Nomascus leucogenys ENSNLEG000000174543 retrocopies
retro_nleu_2133, retro_nleu_2486, retro_nleu_446,
Otolemur garnettii ENSOGAG000000286673 retrocopies
retro_ogar_1035, retro_ogar_1748, retro_ogar_2858,
Procavia capensis ENSPCAG000000077792 retrocopies
retro_pcap_29, retro_pcap_434,
Pongo abelii ENSPPYG000000046694 retrocopies
retro_pabe_2010, retro_pabe_2579, retro_pabe_5, retro_pabe_553,
Pan troglodytes ENSPTRG000000051088 retrocopies
retro_ptro_1533, retro_ptro_1945, retro_ptro_2111, retro_ptro_2926, retro_ptro_319, retro_ptro_452, retro_ptro_454, retro_ptro_609,
Rattus norvegicus ENSRNOG000000026425 retrocopies
retro_rnor_1011, retro_rnor_119, retro_rnor_1836, retro_rnor_1931, retro_rnor_2895,
Sorex araneus ENSSARG000000077512 retrocopies
retro_sara_489, retro_sara_507,
Tupaia belangeri ENSTBEG0000000299415 retrocopies
retro_tbel_1658, retro_tbel_2266, retro_tbel_2370, retro_tbel_2383, retro_tbel_2598, retro_tbel_2622, retro_tbel_2823, retro_tbel_3798, retro_tbel_402, retro_tbel_407, retro_tbel_4279, retro_tbel_4432, retro_tbel_4461, retro_tbel_450, retro_tbel_997,
Tarsius syrichta ENSTSYG000000096222 retrocopies
retro_tsyr_1264, retro_tsyr_177,

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 = 1.33 RPM Legend:


Library Retrogene expression
CEU_NA11831 1 .33 RPM
CEU_NA11843 0 .60 RPM
CEU_NA11930 0 .59 RPM
CEU_NA12004 0 .65 RPM
CEU_NA12400 0 .32 RPM
CEU_NA12751 0 .41 RPM
CEU_NA12760 0 .85 RPM
CEU_NA12827 1 .08 RPM
CEU_NA12872 0 .68 RPM
CEU_NA12873 0 .89 RPM
FIN_HG00183 0 .96 RPM
FIN_HG00277 0 .81 RPM
FIN_HG00315 0 .44 RPM
FIN_HG00321 0 .42 RPM
FIN_HG00328 0 .31 RPM
FIN_HG00338 0 .55 RPM
FIN_HG00349 0 .48 RPM
FIN_HG00375 0 .88 RPM
FIN_HG00377 0 .63 RPM
FIN_HG00378 0 .68 RPM
GBR_HG00099 0 .70 RPM
GBR_HG00111 0 .54 RPM
GBR_HG00114 0 .92 RPM
GBR_HG00119 0 .65 RPM
GBR_HG00131 0 .69 RPM
GBR_HG00133 0 .70 RPM
GBR_HG00134 0 .44 RPM
GBR_HG00137 0 .80 RPM
GBR_HG00142 0 .69 RPM
GBR_HG00143 1 .05 RPM
TSI_NA20512 0 .40 RPM
TSI_NA20513 0 .58 RPM
TSI_NA20518 0 .89 RPM
TSI_NA20532 0 .95 RPM
TSI_NA20538 1 .01 RPM
TSI_NA20756 0 .84 RPM
TSI_NA20765 0 .52 RPM
TSI_NA20771 0 .77 RPM
TSI_NA20786 0 .81 RPM
TSI_NA20798 0 .75 RPM
YRI_NA18870 0 .88 RPM
YRI_NA18907 0 .87 RPM
YRI_NA18916 0 .53 RPM
YRI_NA19093 0 .52 RPM
YRI_NA19099 0 .75 RPM
YRI_NA19114 0 .89 RPM
YRI_NA19118 0 .62 RPM
YRI_NA19213 0 .45 RPM
YRI_NA19214 0 .61 RPM
YRI_NA19223 0 .62 RPM

Indel association:

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





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