RetrogeneDB ID:

retro_hsap_596

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:10:76414713..76415887(+)
Located in intron of:ENSG00000156110
Retrocopy
information
Ensembl ID:ENSG00000214626
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:POLR3D
Ensembl ID:ENSG00000168495
Aliases:POLR3D, BN51T, RPC4, RPC53, TSBN51
Description:polymerase (RNA) III (DNA directed) polypeptide D, 44kDa [Source:HGNC Symbol;Acc:1080]


Retrocopy-Parental alignment summary:






>retro_hsap_596
ATGTCGGAAGGAAATGCAGTGAGCGAACCCAGCACTCTGCAAGGGCCCCGACCCCTCCTGACTGGGGCCCAGGAGCTCAG
CAGGCAGCGACTGGCACCCCTTCACCCCGGGCCGCCTTCCCTTCATCCGCTCTGGGAACCTTACCCTGGGGGTTGAGGTT
GGGGGTCAAGAAGAAAACCTTCACCCCAAATATCATCAGTCAGAAGAACCCAAGGAAGAAGTAACCGTCAAGAAGGAGAA
ACATGAAAGGGACAGAGATGGACAGAGACAGGTGCATGGACAGGGATGAGGCCACCCAGAAGTGATCCAGTCTCACTCCA
TCTTTGAGAAGGGCCCAGCTGAAATGATGAAGAAAAAAGGAACTGGAATAAGAAAGTGAATGTGTCAGACATGGGACCTT
CTCATATCGTCCACATCAAAAAAGAGAAGAAAGAGTTGGACGAAGACACGAAACATCTCACCATGCTGTAGAAGGACGAT
TTCATTGATGACCCTGGGCTGAGGAATGACACTCGCAACATGCCTGTGCAGCTGCCACTGGCTCACTCAGGGTGGCTTTT
TAAGGAAGAAAACAATGAACCAGATGTTAAACCTTGGCTGGCTGGCCCCAAGAAAGAGGTGGGGGTACCTACTGTGAAAC
TGAAAGAGGAGCTACAAGATGAGGAGGAGGCCAAGATAAAGGCTCCTTCCAGAGCAGCCAGGAAGACCCCCGGGCCTCCC
GAAGGACATATCCGTGGCAGAGCTGCCCAGGGAGCTGAGCCTCACCAAGGAGGAGGAATTGCTGTTCCTCCAGTTGCCAG
ACACCCTCCCTGGCCACCCACCTATCCAGGACATCAAGCCCATCAAGGCAGAGGTACAGGGCAAGGACAGAGAGGTGGTA
CTCATCAAGCAGGAGAACGACCAGGAAGCCAGGCTGGCAAAGAATGCTTCTACCCTAGCTGACCTGACAGAGGGTCAGGT
TGGCAAGCTGCCCATCTGCAAGTCCGAAAGGGTGCAACTCCTCCTGGGCAAGGTGACTCTGGACGTGACCATGGGAACCG
CCTGCTCTTTCCTGCAGGAGCTGGTGTCTGTGGGCCTTGGAGAGAGTAGGACTGGGGAGATGATAGACCTGGGACATGTG
AAGCACAAACTTCTGTGTTCCCCCGATTTTGAATCCCTCTTGGATCACAAACAC

ORF - retro_hsap_596 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 75.56 %
Parental protein coverage: 99.75 %
Number of stop codons detected: 2
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalMSEGNAAGEPSTPGGPRPLLTGARGLIGRRPAPPLTP-GRLPSIRSRDLTLGGVKKKTFTPNIISRKIKE
MSEGNA..EPST..GPRPLLTGA..L...R.A.PL.P.GRLP.IRS..LTL.GV.......N........
RetrocopyMSEGNAVSEPSTLQGPRPLLTGAQELSRQRLA-PLHP>GRLPFIRSGNLTL-GVEVGGQEENLHPKYHQS
ParentalEPKEEVTVKK-EKRERDRDRQREGHGRGRGRPEVIQSHSIFEQGPAEMMKKKG-NWDKTVDVSDMGPSHI
E...E....K.EK.ERDRD.QR..HG.G.G.PEVIQSHSIFE.GPAEMMKKKG.NW.K.V.VSDMGPSHI
RetrocopyEEPKEEVTVKKEKHERDRDGQRQVHGQG*GHPEVIQSHSIFEKGPAEMMKKKG<NWNKKVNVSDMGPSHI
ParentalINIKKEKRETDEETKQILRMLEKDDFLDDPGLRNDTRNMPVQLPLAHSGWLFKEENDEPDVKPWLAGPKE
..IKKEK.E.DE.TK..L.ML.KDDF.DDPGLRNDTRNMPVQLPLAHSGWLFKEEN.EPDVKPWLAGPK.
RetrocopyVHIKKEKKELDEDTKH-LTML*KDDFIDDPGLRNDTRNMPVQLPLAHSGWLFKEENNEPDVKPWLAGPKK
ParentalEDMEVDIPAVKVKEEPRDEEEEAKMKAPPKAARKT-PGLPKDVSVAELLRELSLTKEEELLFLQLPDTLP
E...V..P.VK.KEE..D.EEEAK.KAP..AARKT.PGLPKD.SVAEL.RELSLTKEEELLFLQLPDTLP
RetrocopyE---VGVPTVKLKEELQD-EEEAKIKAPSRAARKT>PGLPKDISVAELPRELSLTKEEELLFLQLPDTLP
ParentalGQPPTQDIKPIKTEVQGEDGQVVLIKQEKDREAKLAENACTLADLTEGQVGKLLIRKSGRVQLLLGKVTL
G.PP.QDIKPIK.EVQG.D..VVLIKQE.D.EA.LA.NA.TLADLTEGQVGKL.I.KS.RVQLLLGKVTL
RetrocopyGHPPIQDIKPIKAEVQGKDREVVLIKQENDQEARLAKNASTLADLTEGQVGKLPICKSERVQLLLGKVTL
ParentalDVTMGTACSFLQELVSVGLGDSRTGEMTVLGHVKHKLVCSPDFESLLDHKH
DVTMGTACSFLQELVSVGLG.SRTGEM..LGHVKHKL.CSPDFESLLDHKH
RetrocopyDVTMGTACSFLQELVSVGLGESRTGEMIDLGHVKHKLLCSPDFESLLDHKH

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 19 .58 RPM
bodymap2_adrenal 0 .04 RPM 21 .55 RPM
bodymap2_brain 0 .00 RPM 11 .23 RPM
bodymap2_breast 0 .00 RPM 11 .30 RPM
bodymap2_colon 0 .00 RPM 21 .02 RPM
bodymap2_heart 0 .02 RPM 10 .26 RPM
bodymap2_kidney 0 .00 RPM 14 .58 RPM
bodymap2_liver 0 .02 RPM 6 .04 RPM
bodymap2_lung 0 .00 RPM 23 .77 RPM
bodymap2_lymph_node 0 .00 RPM 22 .20 RPM
bodymap2_ovary 0 .12 RPM 29 .72 RPM
bodymap2_prostate 0 .09 RPM 24 .21 RPM
bodymap2_skeletal_muscle 0 .00 RPM 38 .70 RPM
bodymap2_testis 0 .00 RPM 36 .37 RPM
bodymap2_thyroid 0 .00 RPM 23 .75 RPM
bodymap2_white_blood_cells 0 .00 RPM 15 .65 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_596 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_596 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_596 retrocopy 5' end.

Lab - click to see more details

retro_hsap_596 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_596 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_439
Pongo abelii retro_pabe_594
Macaca mulatta retro_mmul_2449
Parental genes homology:
Parental genes homology involve 12 parental genes, and 13 retrocopies.

Species Parental gene accession Retrocopies number
Dasypus novemcinctus ENSDNOG000000134881 retrocopy
retro_dnov_1681,
Equus caballus ENSECAG000000250901 retrocopy
retro_ecab_43,
Erinaceus europaeus ENSEEUG000000076322 retrocopies
retro_eeur_277, retro_eeur_705,
Homo sapiens ENSG00000168495 1 retrocopy
retro_hsap_596 ,
Macropus eugenii ENSMEUG000000004651 retrocopy
retro_meug_1550,
Myotis lucifugus ENSMLUG000000021091 retrocopy
retro_mluc_2339,
Macaca mulatta ENSMMUG000000232261 retrocopy
retro_mmul_2449,
Monodelphis domestica ENSMODG000000094911 retrocopy
retro_mdom_988,
Nomascus leucogenys ENSNLEG000000155021 retrocopy
retro_nleu_2218,
Pongo abelii ENSPPYG000000184191 retrocopy
retro_pabe_594,
Pan troglodytes ENSPTRG000000200561 retrocopy
retro_ptro_439,
Tursiops truncatus ENSTTRG000000127451 retrocopy
retro_ttru_1189,

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 = 0.17 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .02 RPM
CEU_NA11843 0 .09 RPM
CEU_NA11930 0 .07 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .00 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .05 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .03 RPM
FIN_HG00277 0 .04 RPM
FIN_HG00315 0 .03 RPM
FIN_HG00321 0 .06 RPM
FIN_HG00328 0 .05 RPM
FIN_HG00338 0 .02 RPM
FIN_HG00349 0 .00 RPM
FIN_HG00375 0 .05 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .00 RPM
GBR_HG00099 0 .03 RPM
GBR_HG00111 0 .04 RPM
GBR_HG00114 0 .08 RPM
GBR_HG00119 0 .00 RPM
GBR_HG00131 0 .06 RPM
GBR_HG00133 0 .02 RPM
GBR_HG00134 0 .04 RPM
GBR_HG00137 0 .08 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .05 RPM
TSI_NA20518 0 .06 RPM
TSI_NA20532 0 .14 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .17 RPM
TSI_NA20771 0 .00 RPM
TSI_NA20786 0 .03 RPM
TSI_NA20798 0 .00 RPM
YRI_NA18870 0 .00 RPM
YRI_NA18907 0 .07 RPM
YRI_NA18916 0 .02 RPM
YRI_NA19093 0 .03 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .04 RPM
YRI_NA19213 0 .00 RPM
YRI_NA19214 0 .05 RPM
YRI_NA19223 0 .06 RPM

Indel association:

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





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