RetrogeneDB ID:

retro_hsap_4690

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:X:63652280..63654026(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000230889
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:SHC1
Ensembl ID:ENSG00000160691
Aliases:SHC1, SHC, SHCA
Description:SHC (Src homology 2 domain containing) transforming protein 1 [Source:HGNC Symbol;Acc:10840]


Retrocopy-Parental alignment summary:






>retro_hsap_4690
ATGAATCTCCTGCCCCCCAAGTCCAAGTGCAATCCACTGTGGAATGAGTCTCTGTCATCGCTGGAGGAGGGGCCTTCAGG
GTCCACCCCACCAGAGGAGCTGCCTTCCCCATCAGCCTCATCCCTGGGGCCCATCCTGCCCCCTCTGCCTGGGAACCATA
GTCCCACTACCCTGTGCTCCTTCTTCCCCTGGATGAGCAACCTGAGGCTGGCCAATTGGGCCGGGGGACACCTGGGGCCT
AATGGGGAGCCAGGAAGGGCAGCCAATGATGGGGAGGGCATTGTAGGGGCAACCATGCCAGACTCATTCCCCTACCCCTC
CTCCAGGACATGAACAAGCTGAGTGGAGGTGGTGGGTGCAGGACTCAGGTGGAAGGGGGCCAGCTGGGGGGTGAGGAGTG
GACCCGCCATGGGAGCTTTGTCAATAAGCCCATGTGGGGCTAGCTGCATCCCAATGACAAAGTCACGAGACCTGGGGTTT
CCTACTTGGTTTGGTACATGGGCTGTGTGGAGGTCCTGCAGTCAATGAGTGCCCTGGACTTCAACACCTGGACTCAGGTC
ACCAGGGAGGCCATCAGTTTTGTGTGTGAGGCTGTGCCAGGTGCCAAGGGGGTGACAAGGAGGAGAAAGCCCTGTAACCA
TCCACTCAGCTCTATCTTGGGAAGGAGTAACCTGAAATTTGCTGCAATGACAATCACTCTCACCATCTCCACCAGCAGCC
TCAACGTCATGGTTGCAGACTGCAAACAGATTATCACTAACCACCATATGCAATCTATCTCACTTGCATCCAGTGGGGAT
CCGGACACAGCCAAGTATGTCGCCAACGTTGCCAAAGACCCTGTGAGTCAGAAAGCATGCCACATTCTGGAGTGTCCTGA
AGGGCTTGCTCAGGATGTCATCAGCACCACTGGCCAGGCCTTCAAGTTGCACTTTAAACAATACCTCAGAAAACCACCCA
AACTGGTCACCCCCCATGACAGGATGACTGGCTTTGATGGCTTAGCTTGGGATGAGGAGGAGGAAGAGCCGCCTGGCCAT
CAGCACTATAATGACTTCCTGGGAAGGAATCCCCTCTTTGGCATGTGGTATACATGAGGCTTCGGGAAGGAGCCACTCCA
GGGGCTGCTCGACCCACTCCACCCAGTGCCCAGACCCCCAGCCACTTGGGATCTACACTGCCTGTAGGACAGTCTGTTGG
GGGAGATCCAGAAGTTTGCAAATAGATGCCACCTCCACCACCCTGTCCAGGCAGAGAGCTCTTTGATGATCCCTCCAATG
TCAACGTGCAGAACCTAGACAAGGCCCGGCAAGCAGGGGGTGGTGCTGGGACCCCCAATCCTGCCATCAATGGCAGCACA
CCCTGAGACCTGTTTGACATGAAGCCCTTTGAAGACACTCTTCACATGCCTCCTCTTCCCCAGTTGGTGTCCATGGCTAA
GCAGCTCTGAGGGGACCCTGGTTCCAAGGGAAGCTGAGCTAGCAGGGGGCTGAGGCACTGCTGCAGTTCAATGGGGACTT
CCTGGTGCAGGAGAGCATGACCACACCTGGCCAGTATGTGCTCACTGGCTTGCAGAGTGGGGAGTCCAAGCATCTGCTAC
TGGTGGACCCTGAGGGTGTAGTTCGGACAAAGGATCACCGCTTTGAGAGTGTCAGTCACCTCATCAGCTACCACATGGAC
AATCACTTGCCCATCACCTCTGCTGGCAGTGAATTGTGTCTACAGCAACCTGTGGAGCAGAAACTG

ORF - retro_hsap_4690 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 84.98 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 5
Number of frameshifts detected: 3


Retrocopy - Parental Gene Alignment:

ParentalMDLLPPKPKYNPLRNESLSSLEEGASGSTPPEELPSPSASSLGPILPPLPGDDSPTTLCSFFPRMSNLRL
M.LLPPK.K.NPL.NESLSSLEEG.SGSTPPEELPSPSASSLGPILPPLPG..SPTTLCSFFP.MSNLRL
RetrocopyMNLLPPKSKCNPLWNESLSSLEEGPSGSTPPEELPSPSASSLGPILPPLPGNHSPTTLCSFFPWMSNLRL
ParentalANPAGGRPGSKGEPGRAADDGEGIVGAAMPDSGP-LPLLQDMNKLSGGGGRRTRVEGGQLGGEEWTRHGS
AN.AGG..G..GEPGRAA.DGEGIVGA.MPDS.P.LPLLQDMNKLSGGGG.RT.VEGGQLGGEEWTRHGS
RetrocopyANWAGGHLGPNGEPGRAANDGEGIVGATMPDSFP<LPLLQDMNKLSGGGGCRTQVEGGQLGGEEWTRHGS
ParentalFVNKPTRGWLHPNDKVMGPGVSYLVRYMGCVEVLQSMRALDFNTRTQVTREAISLVCEAVPGAKGATRRR
FVNKP..G.LHPNDKV..PGVSYLV.YMGCVEVLQSM.ALDFNT.TQVTREAIS.VCEAVPGAKG.TRRR
RetrocopyFVNKPMWG*LHPNDKVTRPGVSYLVWYMGCVEVLQSMSALDFNTWTQVTREAISFVCEAVPGAKGVTRRR
ParentalKPCSRPLSSILGRSNLKFAGMPITLTVSTSSLNLMAADCKQIIANHHMQSISFASGGDPDTAEYVAYVAK
KPC..PLSSILGRSNLKFA.M.ITLT.STSSLN.M.ADCKQII.NHHMQSIS.AS.GDPDTA.YVA.VAK
RetrocopyKPCNHPLSSILGRSNLKFAAMTITLTISTSSLNVMVADCKQIITNHHMQSISLASSGDPDTAKYVANVAK
ParentalDPVNQRACHILECPEGLAQDVISTIGQAFELRFKQYLRNPPKLVTPHDRMAGFDGSAWDEEEEEPPDHQY
DPV.Q.ACHILECPEGLAQDVIST.GQAF.L.FKQYLR.PPKLVTPHDRM.GFDG.AWDEEEEEPP.HQ.
RetrocopyDPVSQKACHILECPEGLAQDVISTTGQAFKLHFKQYLRKPPKLVTPHDRMTGFDGLAWDEEEEEPPGHQH
ParentalYNDF-PGKEPPLGGVVDMRLREGAAPGAARPTAPNAQTPSHLGATLPVGQPVGGDPEVRKQMPPPPPCPG
YNDF.PGKE.PL..VV.MRLREGA.PGAARPT.P.AQTPSHLG.TLPVGQ.VGGDPEV.K.MPPPPPCPG
RetrocopyYNDF<PGKESPLWHVVYMRLREGATPGAARPTPPSAQTPSHLGSTLPVGQSVGGDPEVCK*MPPPPPCPG
ParentalRELFDDPSYVNVQNLDKARQAVGGAGPPNPAINGSAPRDLFDMKPFEDALRVPPPPQSVSMAEQLRGE-P
RELFDDPS.VNVQNLDKARQA.GGAG.PNPAINGS.P.DLFDMKPFED.L..PP.PQ.VSMA.QL.G..P
RetrocopyRELFDDPSNVNVQNLDKARQAGGGAGTPNPAINGSTP*DLFDMKPFEDTLHMPPLPQLVSMAKQL*GD<P
ParentalWFHGKLSRREAEALLQLNGDFLVRESTTTPGQYVLTGLQSGQPKHLLLVDPEGVVRTKDHRFESVSHLIS
WF.GKLS...AEALLQ.NGDFLV.ES.TTPGQYVLTGLQSG..KHLLLVDPEGVVRTKDHRFESVSHLIS
RetrocopyWFQGKLS*QGAEALLQFNGDFLVQESMTTPGQYVLTGLQSGESKHLLLVDPEGVVRTKDHRFESVSHLIS
ParentalYHMDNHLPIISAGSELCLQQPVERKL
YHMDNHLPI.SAGSELCLQQPVE.KL
RetrocopyYHMDNHLPITSAGSELCLQQPVEQKL

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






(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 187 .55 RPM
bodymap2_adrenal 0 .00 RPM 217 .06 RPM
bodymap2_brain 0 .00 RPM 19 .85 RPM
bodymap2_breast 0 .04 RPM 88 .64 RPM
bodymap2_colon 0 .00 RPM 110 .99 RPM
bodymap2_heart 0 .00 RPM 29 .37 RPM
bodymap2_kidney 0 .00 RPM 68 .37 RPM
bodymap2_liver 0 .00 RPM 65 .19 RPM
bodymap2_lung 0 .00 RPM 131 .65 RPM
bodymap2_lymph_node 0 .00 RPM 123 .60 RPM
bodymap2_ovary 0 .00 RPM 91 .97 RPM
bodymap2_prostate 0 .00 RPM 75 .08 RPM
bodymap2_skeletal_muscle 0 .00 RPM 34 .16 RPM
bodymap2_testis 0 .00 RPM 52 .58 RPM
bodymap2_thyroid 0 .02 RPM 90 .67 RPM
bodymap2_white_blood_cells 0 .00 RPM 58 .41 RPM
RNA Polymerase II activity near the 5' end of retro_hsap_4690 was not detected
No EST(s) were mapped for retro_hsap_4690 retrocopy.


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_2006501260 libraries 298 libraries 265 libraries 5 libraries 1 library
TSS #2 TSS_2006511489 libraries 239 libraries 96 libraries 5 libraries 0 libraries

The graphical summary, for retro_hsap_4690 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)

retro_hsap_4690 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4690 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_3117
Pongo abelii retro_pabe_3643

Parental genes homology:
Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000092361 retrocopy
Homo sapiens ENSG00000160691 1 retrocopy
retro_hsap_4690 ,
Nomascus leucogenys ENSNLEG000000115151 retrocopy
Pongo abelii ENSPPYG000000007691 retrocopy
Pan troglodytes ENSPTRG000000013971 retrocopy
Tarsius syrichta ENSTSYG000000113801 retrocopy

Expression level across human populations :

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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



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Deprecated: number_format(): Passing null to parameter #1 ($num) of type float is deprecated in /home/rosikiewicz/RetrogeneDB2/BETA/retrogene_maps.php on line 3375

Warning: Undefined variable $populationsDict in /home/rosikiewicz/RetrogeneDB2/BETA/retrogene_maps.php on line 3372

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Deprecated: number_format(): Passing null to parameter #1 ($num) of type float is deprecated in /home/rosikiewicz/RetrogeneDB2/BETA/retrogene_maps.php on line 3375

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Deprecated: number_format(): Passing null to parameter #1 ($num) of type float is deprecated in /home/rosikiewicz/RetrogeneDB2/BETA/retrogene_maps.php on line 3375

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Warning: Undefined variable $populationsDict in /home/rosikiewicz/RetrogeneDB2/BETA/retrogene_maps.php on line 3375

Warning: Trying to access array offset on value of type null in /home/rosikiewicz/RetrogeneDB2/BETA/retrogene_maps.php on line 3375

Deprecated: number_format(): Passing null to parameter #1 ($num) of type float is deprecated in /home/rosikiewicz/RetrogeneDB2/BETA/retrogene_maps.php on line 3375

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Deprecated: number_format(): Passing null to parameter #1 ($num) of type float is deprecated in /home/rosikiewicz/RetrogeneDB2/BETA/retrogene_maps.php on line 3375

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Warning: Trying to access array offset on value of type null in /home/rosikiewicz/RetrogeneDB2/BETA/retrogene_maps.php on line 3375

Deprecated: number_format(): Passing null to parameter #1 ($num) of type float is deprecated in /home/rosikiewicz/RetrogeneDB2/BETA/retrogene_maps.php on line 3375

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Deprecated: number_format(): Passing null to parameter #1 ($num) of type float is deprecated in /home/rosikiewicz/RetrogeneDB2/BETA/retrogene_maps.php on line 3375

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Deprecated: number_format(): Passing null to parameter #1 ($num) of type float is deprecated in /home/rosikiewicz/RetrogeneDB2/BETA/retrogene_maps.php on line 3375

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Deprecated: number_format(): Passing null to parameter #1 ($num) of type float is deprecated in /home/rosikiewicz/RetrogeneDB2/BETA/retrogene_maps.php on line 3375

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Deprecated: number_format(): Passing null to parameter #1 ($num) of type float is deprecated in /home/rosikiewicz/RetrogeneDB2/BETA/retrogene_maps.php on line 3375
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 .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 .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

Fatal error: Uncaught Error: Call to undefined function mysql_query() in /home/rosikiewicz/RetrogeneDB2/BETA/retrogene_maps.php:3390 Stack trace: #0 /home/rosikiewicz/RetrogeneDB2/BETA/retrogene.php(1158): include() #1 {main} thrown in /home/rosikiewicz/RetrogeneDB2/BETA/retrogene_maps.php on line 3390