RetrogeneDB ID:

retro_hsap_459

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:1:158145639..158147520(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000227295
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:ELL2
Ensembl ID:ENSG00000118985
Aliases:None
Description:elongation factor, RNA polymerase II, 2 [Source:HGNC Symbol;Acc:17064]


Retrocopy-Parental alignment summary:






>retro_hsap_459
CAGCGCTATGGGCTCTCGTGCGGACGGCTGGGGCAGGACAACATCACCGTACTGCATGTGAAGCTCACCGAGTCGGCGAT
CCAGGCGCTCCAGACTTACCAGAGCCACAAGAATTTAATTTCTTTTCGACCTTCAATTCAGTTCCAAAGACTCCAGGAGC
TTGTCAAAATTCCCAAAAATGATCCCCTCAATGAAGTTCATAACTTTAACTTTTATTTGTCAAATGTGGGCAAAGACAAC
CCTCAGGGCAGCTTTGACTGCGTCCAGCAAACATTCTCCAGCTCTGGAGCCTCCCAGCTCAATTGCCTGGGATTTATACA
AGATAAAATTACAGTGTGTGCAACAAACGACTCGGATCAGATGACACGAGAAAGAACGACCCAGGCAGAGGAGGAATCCC
GCAACCGAAGCACAGAAGTTATCAAACCCGGTGGACCATATGTAGGGAAAAGAGTGCAAATTCGGAAAGCACCTCAAGCT
GTTTCAGATACAGTTCCTGAGAGGAAAAGGTCAACCCCCATGAACCCTGCAAATCCAATTCGATAGACACACAGCAGCAG
CAGCGTCTCTCAGAAGCCATACAGGGACAGGGTGGTTCACTTACTGGCCCTGAAGGCCTACAAGAAACCGGAGCTACTTG
CTAGACTCCAGAAAGATGGTGTCAATCAAAAAGACAGGAACTCCCTGGGAGCAATTCTGCAACAGGTAGCCAATCTGAAT
CCTAAGGACCTCTCGTATACTTCAAAGGATTATGTTTTTAAAGAGCTTCAGAGAGACTGGCCTGGATACAGTGAAATAGA
CACTTGGTCATTGGAGTCAATGCTCTCTAGAAAACTAAATCCATCTCAGAATGCTGCAGGCACCAGCCGTTCAGAATCTC
CAGTATGTTCTAGTAGAAACGCTGTATCTTCTCCTCAGACACGGCTTTTGGATTCAGAGTTTATTGATCATTTAATGGAT
AAAAAAGCCCGAATATCTCACCTGACGAGCAGAGTACCACCAACACTAAATGGTCATTTGAATCCCACCAGTGAAAAATC
TGCTGCAGGCCTCCCTCTGCCCCCTGCAGCTGCTGCCATCCCCACCCCTCCACCGCTTGCCTTCAACCCATCTGCCGGTT
TCACATCCTCCTCAGATTGTAAATTCTAACTCCAATTCCCCTAGCACTCCAGAAGGCCGGGGGCTCAAGACCTACCTGTT
GACAGTTTTAGTCAAAACAATAGTATCTATGAGAACCAACAAGACAAGTATACCTCTAGGACTTCTCTGGAAACCTTACC
CCCTGGTTCAGTTCTATTAAAGTGTCCAAAGCCTATGGAAGAAAACCATTCAGTGTCTCACAAAAAGTCCAAAAAGAAGT
CTAAAAAACATAAGGAAAAGGACCAAATAAAAAAGCACGACATTGAGACTATTGAGGAAAAGGAGAAAGATCTTAAGAGA
GAAGAGGAAATTGCCAAGCTAAATAACTCCAGTCCAAATTCCAGTGGAGGAGCTAAAGAGGATTGCACTGCCTCCATGGA
ACCTTCAGCAATTGAACTCCCAGATTATTTGATAAAATATATTGCTATCATCTCCTATGAGCAACGCCGGAATTATAAAG
ATGACGTCAGTGCAGAGTATGATGAGTACAGAGCTTTGCATGCCAGGATGGAGACTGTAGCTAGAAGATTTATCAAACTA
GATGCACAAAGAAAGCGCCTTTCTCCAGGCTCAAAAGAGTATCAGAATGTTCATGAAGAAGTCTTACAAGAATATCGGAA
GATAAAGCAGTCTAGTCCCAATTACCATGAAGAAAAATACAGATGTGAATATCTTCATAACAAGCTGGCTCACATCAAAA
GGCTACTAGGCGAATTTGACCAACAGCAGGCAGAGTCATGG

ORF - retro_hsap_459 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 90.14 %
Parental protein coverage: 97.97 %
Number of stop codons detected: 1
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalQRYGLSCGRLGQDNITVLHVKLTETAIRALETYQSHKNLIPFRPSIQFQGLHGLVKIPKNDPLNEVHNFN
QRYGLSCGRLGQDNITVLHVKLTE.AI.AL.TYQSHKNLI.FRPSIQFQ.L..LVKIPKNDPLNEVHNFN
RetrocopyQRYGLSCGRLGQDNITVLHVKLTESAIQALQTYQSHKNLISFRPSIQFQRLQELVKIPKNDPLNEVHNFN
ParentalFYLSNVGKDNPQGSFDCIQQTFSSSGASQLNCLGFIQDKITVCATNDSYQMTRERMTQAEEESRNRSTKV
FYLSNVGKDNPQGSFDC.QQTFSSSGASQLNCLGFIQDKITVCATNDS.QMTRER.TQAEEESRNRST.V
RetrocopyFYLSNVGKDNPQGSFDCVQQTFSSSGASQLNCLGFIQDKITVCATNDSDQMTRERTTQAEEESRNRSTEV
ParentalIKPGGPYVGKRVQIRKAPQAVSDTVPERKRSTPMNPANTIRKTHSSSTISQRPYRDRVIHLLALKAYKKP
IKPGGPYVGKRVQIRKAPQAVSDTVPERKRSTPMNPAN.IR.THSSS..SQ.PYRDRV.HLLALKAYKKP
RetrocopyIKPGGPYVGKRVQIRKAPQAVSDTVPERKRSTPMNPANPIR*THSSSSVSQKPYRDRVVHLLALKAYKKP
ParentalELLARLQKDGVNQKDKNSLGAILQQVANLNSKDLSYTLKDYVFKELQRDWPGYSEIDRRSLESVLSRKLN
ELLARLQKDGVNQKD.NSLGAILQQVANLN.KDLSYT.KDYVFKELQRDWPGYSEID..SLES.LSRKLN
RetrocopyELLARLQKDGVNQKDRNSLGAILQQVANLNPKDLSYTSKDYVFKELQRDWPGYSEIDTWSLESMLSRKLN
ParentalPSQNAAGTSRSESPVCSSRDAVSSPQKRLLDSEFIDPLMNKKARISHLTNRVPPTLNGHLNPTSEKSAAG
PSQNAAGTSRSESPVCSSR.AVSSPQ.RLLDSEFID.LM.KKARISHLT.RVPPTLNGHLNPTSEKSAAG
RetrocopyPSQNAAGTSRSESPVCSSRNAVSSPQTRLLDSEFIDHLMDKKARISHLTSRVPPTLNGHLNPTSEKSAAG
ParentalLPLPPAAAAIPTPPP-LPSTYLPISHPPQIVNSNSNSPSTPEGR-GTQDLPVDSFSQNDSIYEDQQDKYT
LPLPPAAAAIPTPPP.LPST.LP.SHPPQIVNSNSNSPSTPEGR.G.QDLPVDSFSQN.SIYE.QQDKYT
RetrocopyLPLPPAAAAIPTPPP>LPSTHLPVSHPPQIVNSNSNSPSTPEGR<GAQDLPVDSFSQNNSIYENQQDKYT
ParentalSRTSLETLPPGSVLLKCPKPMEENHSMSHKKSKKKSKKHKEKDQIKKHDIETIEEKEEDLKREEEIAKLN
SRTSLETLPPGSVLLKCPKPMEENHS.SH..................HDIETIEEKE.DLKREEEIAKLN
RetrocopySRTSLETLPPGSVLLKCPKPMEENHSVSHXXXXXXXXXXXXXXXXXXHDIETIEEKEKDLKREEEIAKLN
ParentalNSSPNSSGGVKEDCTASMEPSAIELPDYLIKYIAIVSYEQRQNYKDDFNAEYDEYRALHARMETVARRFI
NSSPNSSGG.KEDCTASMEPSAIELPDYLIKYIAI.SYEQR.NYKDD..AEYDEYRALHARMETVARRFI
RetrocopyNSSPNSSGGAKEDCTASMEPSAIELPDYLIKYIAIISYEQRRNYKDDVSAEYDEYRALHARMETVARRFI
ParentalKLDAQRKRLSPGSKEYQNVHEEVLQEYQKIKQSSPNYHEEKYRCEYLHNKLAHIKRLIGEFDQQQAESW
KLDAQRKRLSPGSKEYQNVHEEVLQEY.KIKQSSPNYHEEKYRCEYLHNKLAHIKRL.GEFDQQQAESW
RetrocopyKLDAQRKRLSPGSKEYQNVHEEVLQEYRKIKQSSPNYHEEKYRCEYLHNKLAHIKRLLGEFDQQQAESW

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 .24 RPM 155 .09 RPM
bodymap2_adrenal 0 .00 RPM 63 .33 RPM
bodymap2_brain 0 .16 RPM 114 .76 RPM
bodymap2_breast 0 .02 RPM 92 .28 RPM
bodymap2_colon 0 .10 RPM 66 .86 RPM
bodymap2_heart 0 .02 RPM 108 .35 RPM
bodymap2_kidney 0 .25 RPM 61 .98 RPM
bodymap2_liver 0 .13 RPM 112 .74 RPM
bodymap2_lung 0 .19 RPM 149 .98 RPM
bodymap2_lymph_node 0 .18 RPM 152 .90 RPM
bodymap2_ovary 0 .00 RPM 33 .37 RPM
bodymap2_prostate 0 .03 RPM 82 .20 RPM
bodymap2_skeletal_muscle 0 .15 RPM 91 .36 RPM
bodymap2_testis 0 .53 RPM 49 .70 RPM
bodymap2_thyroid 0 .30 RPM 87 .89 RPM
bodymap2_white_blood_cells 1 .12 RPM 17 .13 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity may be related with retro_hsap_459 in 4 libraries
ENCODE library ID Target ChIP-Seq Peak coordinates
ENCFF002CRO POLR2A 1:158147424..158147844
ENCFF002DAH POLR2A 1:158147524..158147808
ENCFF002DBO POLR2A 1:158147438..158147822
ENCFF002DBP POLR2A 1:158147454..158147784

EST - click to see more details

1 EST(s) were mapped to retro_hsap_459 retrocopy
EST ID Start End Identity Match Mis-match Score
BG928961 158145614 158145949 100 335 0 335

TSS - click to see more details



TSS No. TSS Name TSS expression level (Expr) in TPM range:
no expression 0 < Expr ≤ 1 1 < Expr ≤ 5 5 < Expr ≤ 10 Expr > 10
TSS #1 TSS_839811216 libraries546 libraries65 libraries2 libraries0 libraries

The graphical summary, for retro_hsap_459 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1829 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Display detail expression values in each library
... or ...
Directly download all expression values

Lab - click to see more details

retro_hsap_459 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_459 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000106071 retrocopy
retro_amel_651,
Dasypus novemcinctus ENSDNOG000000051031 retrocopy
retro_dnov_1413,
Equus caballus ENSECAG000000229331 retrocopy
retro_ecab_1092,
Homo sapiens ENSG00000118985 1 retrocopy
retro_hsap_459 ,
Nomascus leucogenys ENSNLEG000000141921 retrocopy
retro_nleu_881,
Pongo abelii ENSPPYG000000156471 retrocopy
retro_pabe_1757,
Pan troglodytes ENSPTRG000000170901 retrocopy
retro_ptro_346,

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 = 0.14 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .06 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .13 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .07 RPM
CEU_NA12751 0 .05 RPM
CEU_NA12760 0 .09 RPM
CEU_NA12827 0 .05 RPM
CEU_NA12872 0 .08 RPM
CEU_NA12873 0 .06 RPM
FIN_HG00183 0 .08 RPM
FIN_HG00277 0 .04 RPM
FIN_HG00315 0 .06 RPM
FIN_HG00321 0 .06 RPM
FIN_HG00328 0 .02 RPM
FIN_HG00338 0 .02 RPM
FIN_HG00349 0 .06 RPM
FIN_HG00375 0 .07 RPM
FIN_HG00377 0 .10 RPM
FIN_HG00378 0 .04 RPM
GBR_HG00099 0 .12 RPM
GBR_HG00111 0 .04 RPM
GBR_HG00114 0 .05 RPM
GBR_HG00119 0 .05 RPM
GBR_HG00131 0 .09 RPM
GBR_HG00133 0 .05 RPM
GBR_HG00134 0 .04 RPM
GBR_HG00137 0 .05 RPM
GBR_HG00142 0 .03 RPM
GBR_HG00143 0 .03 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .00 RPM
TSI_NA20518 0 .11 RPM
TSI_NA20532 0 .07 RPM
TSI_NA20538 0 .14 RPM
TSI_NA20756 0 .09 RPM
TSI_NA20765 0 .12 RPM
TSI_NA20771 0 .06 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .03 RPM
YRI_NA18870 0 .00 RPM
YRI_NA18907 0 .03 RPM
YRI_NA18916 0 .00 RPM
YRI_NA19093 0 .03 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .03 RPM
YRI_NA19118 0 .04 RPM
YRI_NA19213 0 .10 RPM
YRI_NA19214 0 .02 RPM
YRI_NA19223 0 .02 RPM

Indel association:

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



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