RetrogeneDB ID:

retro_hsap_963

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:12:10922905..10923205(+)
Located in intron of:ENSG00000256888
Retrocopy
information
Ensembl ID:ENSG00000235930
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:HSPE1
Ensembl ID:ENSG00000115541
Aliases:HSPE1, CPN10, EPF, GROES, HSP10
Description:heat shock 10kDa protein 1 (chaperonin 10) [Source:HGNC Symbol;Acc:5269]


Retrocopy-Parental alignment summary:






>retro_hsap_963
ATGGCAGGACAAGTGTTTAGAAAGTTACTTCCACTCTTTGACTAAGTATTGGTTGAAAGGTGTGCCGCCAAAACTGTAAC
CAAAGGAGCCATTATGCTTCTGGAAAAATCTCAAGGAAAAGTATTGGCAGCCACAGTAGTAGCTGTTGGATCAGGCTCTA
AAGGAAAGGGTGGAGAGATTCAACCAGTTCGTGTGAACGTTAGAGATAATGTTCTTCTTCCAGAATATGGAGGCACCAAA
GTAGATGACAAGGATTAGTTCTCATTTAGAGATGGTGACATTCTTGGGAAGTATGTAGAC

ORF - retro_hsap_963 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 84.31 %
Parental protein coverage: 100. %
Number of stop codons detected: 2
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMAGQAFRKFLPLFDRVLVERSAAETVTKGGIMLPEKSQGKVLQATVVAVGSGSKGKGGEIQPVSVKVGDK
MAGQ.FRK.LPLFD.VLVER.AA.TVTKG.IML.EKSQGKVL.ATVVAVGSGSKGKGGEIQPV.V.V.D.
RetrocopyMAGQVFRKLLPLFD*VLVERCAAKTVTKGAIMLLEKSQGKVLAATVVAVGSGSKGKGGEIQPVRVNVRDN
ParentalVLLPEYGGTKVVLDDKDYFLFRDGDILGKYVD
VLLPEYGGTKV..DDKD.F.FRDGDILGKYVD
RetrocopyVLLPEYGGTKV--DDKD*FSFRDGDILGKYVD

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 21 .55 RPM
bodymap2_adrenal 0 .00 RPM 44 .48 RPM
bodymap2_brain 0 .05 RPM 61 .79 RPM
bodymap2_breast 0 .00 RPM 45 .72 RPM
bodymap2_colon 0 .00 RPM 87 .78 RPM
bodymap2_heart 0 .00 RPM 19 .22 RPM
bodymap2_kidney 0 .00 RPM 94 .55 RPM
bodymap2_liver 0 .00 RPM 89 .42 RPM
bodymap2_lung 0 .00 RPM 41 .81 RPM
bodymap2_lymph_node 0 .00 RPM 56 .39 RPM
bodymap2_ovary 0 .00 RPM 72 .73 RPM
bodymap2_prostate 0 .00 RPM 32 .84 RPM
bodymap2_skeletal_muscle 0 .00 RPM 12 .90 RPM
bodymap2_testis 0 .00 RPM 56 .35 RPM
bodymap2_thyroid 0 .00 RPM 105 .98 RPM
bodymap2_white_blood_cells 0 .00 RPM 13 .53 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_963 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_963 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_963 retrocopy 5' end.

Lab - click to see more details

retro_hsap_963 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_963 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_667
Gorilla gorilla retro_ggor_775
Parental genes homology:
Parental genes homology involve 5 parental genes, and 54 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000040081 retrocopy
retro_cjac_254,
Dasypus novemcinctus ENSDNOG0000001324627 retrocopies
retro_dnov_1088, retro_dnov_1117, retro_dnov_1214, retro_dnov_1375, retro_dnov_1391, retro_dnov_1405, retro_dnov_1412, retro_dnov_1428, retro_dnov_1445, retro_dnov_1546, retro_dnov_1647, retro_dnov_1652, retro_dnov_1686, retro_dnov_1821, retro_dnov_2176, retro_dnov_2291, retro_dnov_2413, retro_dnov_2569, retro_dnov_2625, retro_dnov_2652, retro_dnov_418, retro_dnov_481, retro_dnov_483, retro_dnov_490, retro_dnov_524, retro_dnov_554, retro_dnov_966,
Homo sapiens ENSG00000115541 18 retrocopies
retro_hsap_1066, retro_hsap_1152, retro_hsap_1351, retro_hsap_1524, retro_hsap_1646, retro_hsap_1703, retro_hsap_2248, retro_hsap_2402, retro_hsap_2480, retro_hsap_2812, retro_hsap_2813, retro_hsap_3455, retro_hsap_3540, retro_hsap_366, retro_hsap_3664, retro_hsap_4194, retro_hsap_495, retro_hsap_963 ,
Procavia capensis ENSPCAG000000095411 retrocopy
retro_pcap_330,
Sus scrofa ENSSSCG000000160787 retrocopies
retro_sscr_103, retro_sscr_1059, retro_sscr_106, retro_sscr_1088, retro_sscr_294, retro_sscr_298, retro_sscr_401,

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 = 0.04 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 .04 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 .02 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 .02 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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