RetrogeneDB ID:

retro_hsap_2912

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:4:13338105..13340247(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000205940
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:HSP90AB1
Ensembl ID:ENSG00000096384
Aliases:HSP90AB1, D6S182, HSP84, HSP90B, HSPC2, HSPCB
Description:heat shock protein 90kDa alpha (cytosolic), class B member 1 [Source:HGNC Symbol;Acc:5258]


Retrocopy-Parental alignment summary:






>retro_hsap_2912
ATGCCTGAGGAAGTGCACCTTGGAGAGAAGGAGGTGGAGACTTTTGCCTTTCAGGCAGAAATTGCCCAACTCATGTCTCT
TATCATCAATACCTTCTATTCCAACAAGGAGATTTTCCTTTGGGAGTTGATCTCTAATGCTTCTGATGCCTTGGACAAGA
TTCGCTATGAAAGCCTAACAGACCCTTCCAAGTTGGACAGTGGTAAAGAGCTGAAAATTGACATCATCCCCAATACTCAG
GAACATACCCTGACTTTGGTAGACACAGGCATTGGCATGACCAAAGCTGATCTCATAAATAATTTGGGAACCATTGCCAA
GTTTCGTACGAAAGCATTCATGGAGGCTTTTTAGGCTGGCGCAGACATCTCCATGATTGGGCAATTTGGTATTGGCTTTT
ATTCTGCCTACCTGGTAGCAGAGAAAGTGGTTGTGATCACAAAGCCCAATGATGATGGCATGCCTGAGAGTCTTCTGCTG
GAGGTTCCTTCACTGTGTGTGCTGACCATGGTGAGCCTATTGGTAGGGGTACCAAAGTGATCCTCCACCTTAAAGAAGAT
CAGACAGAGTACTTAGAAGAGATGCAGGTCAAAGAAGTAGTGGAGAAGCACTCTCAGTTCCTAGGCTATCCCATCACCCT
TTATCTGGAGAAGGAACGAGAGAAAGAAATTAGTGATGGTAAGGCAGAGGAAGAGAAAGGTGAGAAAGAAGAGGAAAATA
AAGATGACGAAGAAAAGCCCAAGATCGAAGATGTGGGTTCAGATGAGGAGGATGACAGTGGTAAGGATAAGAAGAAGAAA
ACTAAGAAGATCAAAGAGAAATACATTGATCAGGAAGAACTAAACAAGACCAAGCCTATTTGGACCAGAAACACTGAAGA
CATCACCCAAGAGGAGTATGGAGAATTCTATAAGAGCCTCACCAATGACTGGAAAGACCACTTGGCAGTCAGGTACTTTT
CTGTAGAAGGTCAGTTGGAATTCAGGGCATTGCTATTCATTCCTCCTTAGGCTCCCTTTCATCTTTTTGAGAACAAGAAG
AAAAAGAACAACATCAAACTCTATGTCCATCGTGTGTTCATCAGGGACAGCTGTGTTGAGTTGATACCAGAGTGTCTCAA
CTTTATCCGTGGTGTGGTTGACTCTGAGGATTTCCCCTGAACATCTCCTGAGAAATGCTCCAGCAGAGCAAAATCTTCAA
AGTCATTCACAGAAACATTGTTAAGAAGTGCCTTGAGCTCTTCACTGAGCTGGTGGAAGACAAGGAGAATTACAAGAAAT
TCTATGAGGCATTCTCTAAAAATCTCAAGCTTGGAATCCACAAGGACTCCACTAACTGATGCCACCCGTCTGAGCTGCTG
TGTTATCACACCTCCCAGTCTGGAGATGAGATGATATCTTTGTTAGAGTATGTTTCTCGCATGAAGGAGATACAGAAGTC
CATCTATTACATCACTGGTGAGAGCAAAGAGCAGGTTGCCAACTCAGCTTTTGTGGAGCAAGTATGGAAGCGGGACTCCA
GGGTGGTATATATGACCGAGCCCATTGATGGCTACGTGTGCAGCAACTCAAGGAGTTTGATGGGAAGAGCCTGGTCTCAG
TTACCAAGGAGGGCCTGGAGCTACCTGAGGATGGGGAGGAGAAGAAGAGAATGGAAGAGAGGAAGGCAAAGTTTGAGAAC
CTCTGCAAGTTCATGAAAGAAACTTTAGATAAGAAGGTTGAGATGGTGACAGTCTCCAACAGGCTTGTGTCTTCATCCTG
CTGCATTGTGACCAGCACCTACAGCTGGACAGCCAATATGGAGCAGATCATGAAAGCCTAGGCACTTCGGGTCACCTCCA
CCGTGGGCTATATGATGGCCAAAAAGCACCTGGAGATCAACCCCAACCACCCCATTGTGGAGACGCTGCGGCAGAAGGCT
GAGACACACAAGAATGACAAGGCAGTCAAGGACCTGGTGGTGCTGCCGTTAGAAACTGCCTTGCTGTCTTCTGGCTTTTC
CCTTGAGGATCCCCAGACCCATTCCAACCACATCTACTGCATGATCAAGCTAGGTCTAGGTATCGATGAAGATTAAGTGA
CAGCAGAGGAACACAGTGCTGTGGTTCCTGATGAGATCACCCCTCTTGAGGGTGACGAGGAT

ORF - retro_hsap_2912 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 84.7 %
Parental protein coverage: 98.9 %
Number of stop codons detected: 7
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalMPEEVHHGEEEVETFAFQAEIAQLMSLIINTFYSNKEIFLRELISNASDALDKIRYESLTDPSKLDSGKE
MPEEVH.GE.EVETFAFQAEIAQLMSLIINTFYSNKEIFL.ELISNASDALDKIRYESLTDPSKLDSGKE
RetrocopyMPEEVHLGEKEVETFAFQAEIAQLMSLIINTFYSNKEIFLWELISNASDALDKIRYESLTDPSKLDSGKE
ParentalLKIDIIPNPQERTLTLVDTGIGMTKADLINNLGTIAKSGTKAFMEALQAGADISMIGQFGVGFYSAYLVA
LKIDIIPN.QE.TLTLVDTGIGMTKADLINNLGTIAK..TKAFMEA..AGADISMIGQFG.GFYSAYLVA
RetrocopyLKIDIIPNTQEHTLTLVDTGIGMTKADLINNLGTIAKFRTKAFMEAF*AGADISMIGQFGIGFYSAYLVA
ParentalEKVVVITKHNDDEQ-YAWESSAGGSFTVRADHGEPIGRGTKVILHLKEDQTEYLEERRVKEVVKKHSQFI
EKV.V......D....A.ESSAGGSFTV.ADHGEPIGRGTKVILHLKEDQTEYLEE..VKEVV.KHSQF.
RetrocopyEKV-VVITKPNDDG<HA*ESSAGGSFTVCADHGEPIGRGTKVILHLKEDQTEYLEEMQVKEVVEKHSQFL
ParentalGYPITLYLEKEREKEISDDEAEEEKGEKEEEDKDDEEKPKIEDVGSDEEDDSGKDKKKKTKKIKEKYIDQ
GYPITLYLEKEREKEISD...................KPKIEDVGSDEEDDSGKDKKKKTKKIKEKYIDQ
RetrocopyGYPITLYLEKEREKEISDGKXXXXXXXXXXXXXXXXXKPKIEDVGSDEEDDSGKDKKKKTKKIKEKYIDQ
ParentalEELNKTKPIWTRNPDDITQEEYGEFYKSLTNDWEDHLAVKHFSVEGQLEFRALLFIPRRAPFDLFENKKK
EELNKTKPIWTRN..DITQEEYGEFYKSLTNDW.DHLAV..FSVEGQLEFRALLFIP..APF.LFENKKK
RetrocopyEELNKTKPIWTRNTEDITQEEYGEFYKSLTNDWKDHLAVRYFSVEGQLEFRALLFIPP*APFHLFENKKK
ParentalKNNIKLYVRRVFIMDSCDELIPEYLNFIRGVVDSED-LPLNISREMLQQSKILKVIRKNIVKKCLELFSE
KNNIKLYV.RVFI.DSC.ELIPE.LNFIRGVVDSED..PLNIS.EMLQQSKI.KVI..NIVKKCLELF.E
RetrocopyKNNIKLYVHRVFIRDSCVELIPECLNFIRGVVDSED<FPLNIS*EMLQQSKIFKVIHRNIVKKCLELFTE
ParentalLAEDKENYKKFYEAFSKNLKLGIHEDSTNRRRLSELLRYHTSQSGDEMTSLSEYVSRMKETQKSIYYITG
L.EDKENYKKFYEAFSKNLKLGIH.DSTN....SELL.YHTSQSGDEM.SL.EYVSRMKE.QKSIYYITG
RetrocopyLVEDKENYKKFYEAFSKNLKLGIHKDSTN*CHPSELLCYHTSQSGDEMISLLEYVSRMKEIQKSIYYITG
ParentalESKEQVANSAFVERVRKRGFEVVYMTEPIDEYC-VQQLKEFDGKSLVSVTKEGLELPEDEEEKKKMEESK
ESKEQVANSAFVE.V.KR...VVYMTEPID.Y..VQQLKEFDGKSLVSVTKEGLELPED.EEKK.MEE.K
RetrocopyESKEQVANSAFVEQVWKRDSRVVYMTEPIDGYV<VQQLKEFDGKSLVSVTKEGLELPEDGEEKKRMEERK
ParentalAKFENLCKLMKEILDKKVEKVTISNRLVSSPCCIVTSTYGWTANMERIMKAQALRDNSTMGYMMAKKHLE
AKFENLCK.MKE.LDKKVE.VT.SNRLVSS.CCIVTSTY.WTANME.IMKA.ALR..ST.GYMMAKKHLE
RetrocopyAKFENLCKFMKETLDKKVEMVTVSNRLVSSSCCIVTSTYSWTANMEQIMKA*ALRVTSTVGYMMAKKHLE
ParentalINPDHPIVETLRQKAEADKNDKAVKDLVVLLFETALLSSGFSLEDPQTHSNRIYRMIKLGLGIDEDEVAA
INP.HPIVETLRQKAE..KNDKAVKDLVVL..ETALLSSGFSLEDPQTHSN.IY.MIKLGLGIDED.V.A
RetrocopyINPNHPIVETLRQKAETHKNDKAVKDLVVLPLETALLSSGFSLEDPQTHSNHIYCMIKLGLGIDED*VTA
ParentalEEPNAAVPDEIPPLEGDED
EE..A.VPDEI.PLEGDED
RetrocopyEEHSAVVPDEITPLEGDED

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 .02 RPM 954 .68 RPM
bodymap2_adrenal 0 .33 RPM 827 .93 RPM
bodymap2_brain 0 .12 RPM 1363 .37 RPM
bodymap2_breast 0 .10 RPM 831 .55 RPM
bodymap2_colon 0 .19 RPM 2204 .15 RPM
bodymap2_heart 0 .83 RPM 593 .10 RPM
bodymap2_kidney 0 .31 RPM 911 .35 RPM
bodymap2_liver 0 .02 RPM 294 .49 RPM
bodymap2_lung 0 .11 RPM 1498 .12 RPM
bodymap2_lymph_node 0 .88 RPM 1394 .39 RPM
bodymap2_ovary 0 .67 RPM 2074 .32 RPM
bodymap2_prostate 0 .62 RPM 1329 .78 RPM
bodymap2_skeletal_muscle 0 .18 RPM 1193 .65 RPM
bodymap2_testis 0 .23 RPM 1191 .52 RPM
bodymap2_thyroid 0 .02 RPM 2048 .01 RPM
bodymap2_white_blood_cells 0 .37 RPM 545 .45 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2912 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2912 retrocopy.

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_139741751 libraries834 libraries242 libraries1 library1 library

The graphical summary, for retro_hsap_2912 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_2912 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2912 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1968
Pongo abelii retro_pabe_2425
Macaca mulatta retro_mmul_1869
Parental genes homology:
Parental genes homology involve 8 parental genes, and 18 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG000000808242 retrocopies
retro_hsap_237, retro_hsap_859,
Homo sapiens ENSG00000096384 2 retrocopies
retro_hsap_2912 , retro_hsap_2958,
Homo sapiens ENSG000001665982 retrocopies
retro_hsap_1530, retro_hsap_184,
Macropus eugenii ENSMEUG000000137351 retrocopy
retro_meug_1896,
Myotis lucifugus ENSMLUG000000052392 retrocopies
retro_mluc_1604, retro_mluc_865,
Macaca mulatta ENSMMUG000000226862 retrocopies
retro_mmul_1319, retro_mmul_1869,
Rattus norvegicus ENSRNOG000000198346 retrocopies
retro_rnor_1561, retro_rnor_1562, retro_rnor_1787, retro_rnor_597, retro_rnor_598, retro_rnor_87,
Tursiops truncatus ENSTTRG000000069241 retrocopy
retro_ttru_292,

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 = 0.33 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .17 RPM
CEU_NA11843 0 .03 RPM
CEU_NA11930 0 .26 RPM
CEU_NA12004 0 .19 RPM
CEU_NA12400 0 .14 RPM
CEU_NA12751 0 .22 RPM
CEU_NA12760 0 .09 RPM
CEU_NA12827 0 .33 RPM
CEU_NA12872 0 .16 RPM
CEU_NA12873 0 .16 RPM
FIN_HG00183 0 .14 RPM
FIN_HG00277 0 .11 RPM
FIN_HG00315 0 .11 RPM
FIN_HG00321 0 .03 RPM
FIN_HG00328 0 .24 RPM
FIN_HG00338 0 .28 RPM
FIN_HG00349 0 .23 RPM
FIN_HG00375 0 .24 RPM
FIN_HG00377 0 .08 RPM
FIN_HG00378 0 .19 RPM
GBR_HG00099 0 .15 RPM
GBR_HG00111 0 .19 RPM
GBR_HG00114 0 .03 RPM
GBR_HG00119 0 .10 RPM
GBR_HG00131 0 .11 RPM
GBR_HG00133 0 .12 RPM
GBR_HG00134 0 .20 RPM
GBR_HG00137 0 .11 RPM
GBR_HG00142 0 .28 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .06 RPM
TSI_NA20513 0 .17 RPM
TSI_NA20518 0 .19 RPM
TSI_NA20532 0 .20 RPM
TSI_NA20538 0 .28 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .33 RPM
TSI_NA20771 0 .11 RPM
TSI_NA20786 0 .10 RPM
TSI_NA20798 0 .12 RPM
YRI_NA18870 0 .14 RPM
YRI_NA18907 0 .17 RPM
YRI_NA18916 0 .17 RPM
YRI_NA19093 0 .03 RPM
YRI_NA19099 0 .13 RPM
YRI_NA19114 0 .24 RPM
YRI_NA19118 0 .15 RPM
YRI_NA19213 0 .19 RPM
YRI_NA19214 0 .25 RPM
YRI_NA19223 0 .30 RPM

Indel association:

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





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