RetrogeneDB ID:

retro_hsap_1885

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:18:46004931..46005386(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000266984
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:POLR3G
Ensembl ID:ENSG00000113356
Aliases:POLR3G, RPC32, RPC7
Description:polymerase (RNA) III (DNA directed) polypeptide G (32kD) [Source:HGNC Symbol;Acc:30075]


Retrocopy-Parental alignment summary:






>retro_hsap_1885
ATGGCTGGGAATAAAGGAAGAGGAGGATGTGCTGCTCATACCTTTAATACTGAGGCTGTTGGATTTAGCAAAGGTGAAAA
GTTACCTTATGTAGTGTTGAAACCACCCCCACTATTTCCTGATGCAGATTATAAATCAGTGCCACTGAAAACAGAAGATG
AAGAATACATGCTGGCTTTGAAACAGGAGTTGAGAGAAACAATGAAAAGAATGCCTTATTTTATTGAAACACCTGAAGAA
AGACAAGATATTGAAAGGTATAGTAAAAGATACATGAAGGTATATAAAGAAGAATGGATACCAGATTGGAGAAGACTTCC
AAGAGAGATAACGCCAAGAAATAAATGTAAAAACACAGGCCCAAAACCCGAAAAGGCAAAAGACGCAGGCAAAGTCACCT
CACTAATACTTCAGATGTGTTGAAAAAAATTGAGGAATTGGGAAAGAAAGGTGAT

ORF - retro_hsap_1885 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 82.58 %
Parental protein coverage: 68.61 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMAGNKGRGR-AAYTFNIEAVGFSKGEKLPDVVLKPPPLFPDTDYKPVPLKTGEGEEYMLALKQELRETMK
MAGNKGRG..AA.TFN.EAVGFSKGEKLP.VVLKPPPLFPD.DYK.VPLKT.E.EEYMLALKQELRETMK
RetrocopyMAGNKGRGGCAAHTFNTEAVGFSKGEKLPYVVLKPPPLFPDADYKSVPLKT-EDEEYMLALKQELRETMK
ParentalRMPYFIETPEERQDIERYSKRYMKVYKEEWIPDWRRLPREMMPRNKCKKAGPKP-KKAKDAGKGTPLTNT
RMPYFIETPEERQDIERYSKRYMKVYKEEWIPDWRRLPRE..PRNKCK..GPKP..K.K.......LTNT
RetrocopyRMPYFIETPEERQDIERYSKRYMKVYKEEWIPDWRRLPREITPRNKCKNTGPKP<RKGKRR-RQSHLTNT
ParentalEDVLKKMEELEKRGD
.DVLKK.EEL.K.GD
RetrocopySDVLKKIEELGKKGD

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 1 .59 RPM
bodymap2_adrenal 0 .00 RPM 3 .79 RPM
bodymap2_brain 0 .00 RPM 8 .60 RPM
bodymap2_breast 0 .00 RPM 3 .40 RPM
bodymap2_colon 0 .00 RPM 2 .92 RPM
bodymap2_heart 0 .00 RPM 2 .84 RPM
bodymap2_kidney 0 .00 RPM 3 .21 RPM
bodymap2_liver 0 .00 RPM 2 .75 RPM
bodymap2_lung 0 .00 RPM 1 .49 RPM
bodymap2_lymph_node 0 .00 RPM 3 .42 RPM
bodymap2_ovary 0 .00 RPM 2 .95 RPM
bodymap2_prostate 0 .00 RPM 1 .97 RPM
bodymap2_skeletal_muscle 0 .00 RPM 2 .80 RPM
bodymap2_testis 0 .00 RPM 10 .26 RPM
bodymap2_thyroid 0 .00 RPM 4 .46 RPM
bodymap2_white_blood_cells 0 .00 RPM 1 .83 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_1885 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_1885 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_1885 retrocopy 5' end.

Lab - click to see more details

retro_hsap_1885 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1885 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_1382
Parental genes homology:
Parental genes homology involve 14 parental genes, and 19 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG000000063061 retrocopy
retro_chof_125,
Callithrix jacchus ENSCJAG000000107471 retrocopy
retro_cjac_2691,
Echinops telfairi ENSETEG000000083791 retrocopy
retro_etel_1040,
Homo sapiens ENSG00000113356 2 retrocopies
retro_hsap_1454, retro_hsap_1885 ,
Gorilla gorilla ENSGGOG000000002662 retrocopies
retro_ggor_1119, retro_ggor_1382,
Myotis lucifugus ENSMLUG000000149541 retrocopy
retro_mluc_2233,
Macaca mulatta ENSMMUG000000189721 retrocopy
retro_mmul_1332,
Nomascus leucogenys ENSNLEG000000137491 retrocopy
retro_nleu_1807,
Otolemur garnettii ENSOGAG000000055601 retrocopy
retro_ogar_3512,
Pongo abelii ENSPPYG000000156241 retrocopy
retro_pabe_1564,
Pan troglodytes ENSPTRG000000170682 retrocopies
retro_ptro_1266, retro_ptro_989,
Rattus norvegicus ENSRNOG000000162602 retrocopies
retro_rnor_458, retro_rnor_503,
Ictidomys tridecemlineatus ENSSTOG000000086641 retrocopy
retro_itri_18,
Tupaia belangeri ENSTBEG000000022782 retrocopies
retro_tbel_2495, retro_tbel_3069,

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 .00 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .00 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 .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 .06 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 .02 RPM
GBR_HG00131 0 .00 RPM
GBR_HG00133 0 .00 RPM
GBR_HG00134 0 .00 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .00 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .00 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .00 RPM
TSI_NA20771 0 .00 RPM
TSI_NA20786 0 .00 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 .00 RPM
YRI_NA19118 0 .00 RPM
YRI_NA19213 0 .00 RPM
YRI_NA19214 0 .00 RPM
YRI_NA19223 0 .00 RPM

Indel association:

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





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