RetrogeneDB ID:

retro_hsap_4284

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:9:92843801..92844446(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000234910
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:IL6R
Ensembl ID:ENSG00000160712
Aliases:IL6R, CD126, IL-6R-1, IL-6RA, IL6Q, IL6RA, IL6RQ, gp80
Description:interleukin 6 receptor [Source:HGNC Symbol;Acc:6019]


Retrocopy-Parental alignment summary:






>retro_hsap_4284
AAAGCTGTGCTATTGCTGAGAAAGTTTCAGAACTGTCAGGCAGAACTCTTCCAGGAGCCGTGTCAGTATTCTCAGGAGTC
CCAGAAGTTCTGCCAGTTGGCAGTGCCAGAGGGAGATTACTCTTTCTATACAGTGTCCCTGTGTGTCACCAACAGTATTG
GGAGCAAGTTCAGCAAAACCCAAATATTAGAGGGTTATGGAATCCTGCAGTCCGACCCACCTGTCAACATCACAGTCATT
GCTGTGGCCAGAAAGCCCTGCTGGCTCAACGTCACCTAGCAAGACCCCCACTCCTGGAACTTATATTTCTACAGACTATG
GTTTGAGCTTTGATACCTGGCTAAATAGTCAAAAATGTTCATAACATGGATGGCCAAGGATCTCCAACATCAGTGTGTCA
TTCACAACACCTGGAAAGGCATGAGGCACCAGACACAGCTTCAGGCCCAGGAGGAGCTGGGGCAAGGCTTGTGAAGTAAG
TGGAGCCCAGAGGTCATGGGAATCCTTTGGGCAGACTCCAGGAGTCCTCCAGCTGAGACCACCTCCATGCAAACACCTAC
TACTAATAAAGATGATGATAATATTCTCCCCAGAGATTCTGCAAATGCAACAAGCTTTCTGGGTTAAAGAAGACGTGGAA
GTTGC

ORF - retro_hsap_4284 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 72.6 %
Parental protein coverage: 60.0 %
Number of stop codons detected: 5
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalKAVLLVRKFQNSPAEDFQEPCQYSQESQKFSCQLAVPEGDSSFYIVSMCVASSVGSKFSKTQTFQGCGIL
KAVLL.RKFQN..AE.FQEPCQYSQESQKF.CQLAVPEGD.SFY.VS.CV..S.GSKFSKTQ...G.GIL
RetrocopyKAVLLLRKFQNCQAELFQEPCQYSQESQKF-CQLAVPEGDYSFYTVSLCVTNSIGSKFSKTQILEGYGIL
ParentalQPDPPANITVTAVARNPRWLSVTWQDPHSWNSSFYRLRFELRYRAERSKTFTTWMVKDLQHHCVIHDAWS
Q.DPP.NITV.AVAR.P.WL.VT.QDPHSWN..FYRL.FEL.Y.A..SK.F.TWM.KDLQH.CVIH..W.
RetrocopyQSDPPVNITVIAVARKPCWLNVT*QDPHSWNLYFYRLWFEL*YLAK*SKMFITWMAKDLQHQCVIHNTWK
ParentalGLRHVVQLRAQEEFGQGEWSEWSPEAMGTPWTESRSPPAENEVSTPMQALTTNKDDDNILFRDSANATSL
G.RH..QL.AQEE.GQG..S.WSPE.MG..W..SRSPPAE....T.MQ..TTNKDDDNIL.RDSANATS.
RetrocopyGMRHQTQLQAQEELGQGL*SKWSPEVMGILWADSRSPPAE---TTSMQTPTTNKDDDNILPRDSANATSF
ParentalPGSRRRGSC
.G.RRRGSC
RetrocopyLG*RRRGSC

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 25 .38 RPM
bodymap2_adrenal 0 .00 RPM 27 .84 RPM
bodymap2_brain 0 .00 RPM 16 .74 RPM
bodymap2_breast 0 .00 RPM 21 .17 RPM
bodymap2_colon 0 .00 RPM 35 .60 RPM
bodymap2_heart 0 .00 RPM 7 .29 RPM
bodymap2_kidney 0 .00 RPM 36 .87 RPM
bodymap2_liver 0 .00 RPM 55 .53 RPM
bodymap2_lung 0 .00 RPM 49 .95 RPM
bodymap2_lymph_node 0 .00 RPM 52 .79 RPM
bodymap2_ovary 0 .00 RPM 20 .61 RPM
bodymap2_prostate 0 .00 RPM 24 .65 RPM
bodymap2_skeletal_muscle 0 .00 RPM 211 .07 RPM
bodymap2_testis 0 .00 RPM 15 .16 RPM
bodymap2_thyroid 0 .00 RPM 21 .66 RPM
bodymap2_white_blood_cells 0 .00 RPM 425 .77 RPM

ChIP-Seq - click to see more details

RNA Polymerase II activity near the 5' end of retro_hsap_4284 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_4284 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_4284 retrocopy 5' end.

Lab - click to see more details

retro_hsap_4284 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4284 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG00000160712 1 retrocopy
retro_hsap_4284 ,

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 = 0.02 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 .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 .02 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 .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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