RetrogeneDB ID:

retro_hsap_1216

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:13:77559399..77562516(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000228002
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:DHX9
Ensembl ID:ENSG00000135829
Aliases:DHX9, DDX9, LKP, NDH2, NDHII, RHA
Description:DEAH (Asp-Glu-Ala-His) box helicase 9 [Source:HGNC Symbol;Acc:2750]


Retrocopy-Parental alignment summary:






>retro_hsap_1216
TCCTGGGACCAAGGAGCCAACTTGAAGGATTACTACTCAAGAAAGGAAGAACAAGAAGTGCAAGCGACTCTAGAGTCAGA
AGAAGTGGATTTAAATGCTGGGCTTCATGGAAACTGGACCTTGGAAAATGCTAAAACTCATCTAAACCAATATTTTCAGA
AAGAAAAAATCCAAGGAGAATATAAGTACACCCAAGTGGGTCCTGATCACAACAGGAGCTTTACTGCAGAAATAACCATT
TACATCAAGCAGCTGGGCAGAAGGATTTCTGCACATGAACATGGATCAAATAAGAAATTGGCAGCACAGTCCTGTGCCCT
GTCACTAGTCAGACAACTCTACCATCTTGGAGTGGTTGAAGCTTACTTCAGACTTACAAAGAAGGAAGGAGAGAGAGTGG
AACCTTACAAAGTAAACCTCTCTCAAGATTTAGAGCATCAGCCACAAAACATCATTTGAGAGCTAAATTTTGAGATTATG
CCCCCGCCTGAAGATCCTTCTATGCCAGTTGCACTCAACATTGGCAAATTGGCTCACTTTGAACCATCTCAGTGACAAAA
CCAAGTGGGTATAGTTCCTCGGTCACCTCCACAATCCAGATGGAATCCTTGGACTACTAGCGACATTGCTGAGGGACCTC
TGGCTTTTGCTTCTCCAGAGCAAATAAGCTTGGACCTCAAGAATGAATTGGTGTACCAGTTGGAACAGGATCATGATTTG
CCAGCAATCTTGCAGGAGCGAGAGTTACTGCCTGTGAAGAAATTTGAAAGTGAGATTCTGGAAGCAATCAGTCAAAATTC
AGTTGTCATTATTAGAGGGGCTGCTGGATGTGGTAAAACCACGCAGGTTCCCCAGTTCATTCTAGATGACTTTATCCAGA
ATGACTGACAGCAGAGTGTAACATTGTAGTAACTCAGCCCAGAAGAATCAGTGTAGTTTCCATGGCAGAGTGAGTTGCAT
TTGAGAGAGGAGAAGAGTCTGTAAAAAGCTGTGGTTACAGTGTTCAATTTGAGTCTGTACTTCCTTGTCCTCATGCCAGT
ATAATGCTTTGTACTGTAGGTGTGCTCCTAAGAAAATTAGAAGCAGGCATTTGAGGAATCAGTCATGTAATTGTAGATGA
AATACATGGAAGAGACATTAATACTGACTTCCTTTTGGTAGTACTGCGTGAAGTTGTTTCAGCTTACCCTGAAGTTCTCA
TTGTTCTTATGTCCACTTCTATTGATACCAGCATGTTGTGTGAATATTTCTTCAATTGCCCCATCATTTAAGTGTATGGG
AGGACTTACCCAGTTCAAGAATATTTTCTGGAAGACTGCATTCAGATGACCCACTTTGTTCCTTCACCGAAAACCAAGAA
GAAGGACAAGGATGATGATGGTGGTGAGGATGATGATGCAAATTGCAACTTGATCTGTGGTGATGAATATGGTCCAGAAA
CAAGGATGAGCATGTCTCAATTGAATGAAAAAGAAACTCCTTTTGAACTCGTCGAAGCTCTCTTTAAGTACATTGAAACC
CTTAATATTCCCAGAGCTGTGTTGGTATTTTTGCCTGGCTGGAATTTGATTTATACTATGCAGAAGCATTTGGAAATGAA
TCCACATTTTGGAAGCCATCAGTATCAGATTCTACCTCTGCATTCTCAGATTCCTTGACAGGAACAGCGCAAAGTGTTTG
ATCCAGTACCAGTTGGAGTAACCAAGGTTATTTTGTCCACAAATATTGCTGAAACAAGCATTATCATAAATGATGTTTAT
GTCGTTGACTCCTGCAAGCAGAAAGTGAAACTCTTTGCTACTCACAACAATATGACCAACTATGCTACAGTATGGGGATC
AAAAACAAACCTTGAACAGTGGAAAGGGCAACCTGGCCGAATACGGCCTGGATTCTGCTTTCACCTCTGCAGCCGAGCTC
GTTTTGAGAGACTTGAAACCCACATGACACCAGAGATGTTCCAAACACCATTGCATGAAGTTGCTCTTAGCATAAAACTT
CCATGTCTAGTTGGAATTGGCCAGTTTCTGGCCAAAGCAATTGAAACTCTCCCTTTGGATGCTGTGATTGAAGCAGAACA
CACTCTTAGAGAGCTTGATGCATTAGATGCCAATGATGATTTGACTCCATTGGGACGAATCCTGGCTAACCTCCTCATTG
AGCCTCGTTTTGGCAAAATGATGATAATGGTGTGTATTTTCTATGTGGGAGATGCTATCTGTACCATTCCTGCTGCTACC
TGCTTTCCAGAGCCTTTTATAAATGAAGGAAAGTGGCTGGGCTACAACCATTGAAATTTTGCTGGAAACGGATTTTCTCA
TCATGTAGCCCTTTTATCAGTATTCCAAGCCGGAGATGATACTAGAATGGGTGGAGAAGAAGCAGAAATACGTTTTTGTG
CGCACAAAAGACTTCATATGGCTACACTAAGAATGACTTGGGAAGTCAAAGTTCAGCTCAAAGAGATTCTGATTAATTCT
GGGTTTCCAGAAGATTGTTTGGTGACACAAGTGTTTACTAACACTGGACCAGATAATAATTTGGATGTTGTTATCTCTCT
TCCTGGCCTTTGGTGTGTACCCCAATGTATGCTATCATAAGGAAAAGACAAAGATTCTCACCACTGAAGGGTGTAATGCA
CTTATCCACAAATCATCTGTTAATTGTCCTTTTAGTAGCCAAGACATGAAGTACCCATCTCCCTTCTTTGCATTTGGTGA
AAAGATTCGAACTCGAGCCATCTCTGCTAAAGGCATGACTTTAGTCACCCCACTACAGTTGCTTCTCTTTGCCTCCAAGA
AAGTCCAATCTGATGGGCAGATTGTGCTTGCAGATGACTGGATTAAACTGCAAATATCTCATGAAGCTGCTGCCTGCATC
ACCGCTCTCCAGGCAGCCACTGAGGCTCTGGTTGTTGAAGTAACCAAACAACCTGCTATCATCAGCCAGTTGGACCCCGT
AAATGAAAGTATACTGAACATGATCCGTCAAATCTCTAGACCCTCAGCTGCTGATATCAACCTTATGATTGGCAGTACAT
GGTATGGAGATGGTCCAGGTCCTCCTAAGATGGCCCAATATGACAATGGAAGCGGATATAGAAGGGGAGGTTCTAGT

ORF - retro_hsap_1216 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 89.56 %
Parental protein coverage: 82.05 %
Number of stop codons detected: 7
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalTWDRGANLKDYYSRKEEQEVQATLESEEVDLNAGLHGNWTLENAKARLNQYFQKEKIQGEYKYTQVGPDH
.WD.GANLKDYYSRKEEQEVQATLESEEVDLNAGLHGNWTLENAK..LNQYFQKEKIQGEYKYTQVGPDH
RetrocopySWDQGANLKDYYSRKEEQEVQATLESEEVDLNAGLHGNWTLENAKTHLNQYFQKEKIQGEYKYTQVGPDH
ParentalNRSFIAEMTIYIKQLGRRIFAREHGSNKKLAAQSCALSLVRQLYHLGVVEAYSGLTKKKEGETVEPYKVN
NRSF.AE.TIYIKQLGRRI.A.EHGSNKKLAAQSCALSLVRQLYHLGVVEAY..LTKK.EGE.VEPYKVN
RetrocopyNRSFTAEITIYIKQLGRRISAHEHGSNKKLAAQSCALSLVRQLYHLGVVEAYFRLTKK-EGERVEPYKVN
ParentalLSQDLEHQLQNIIQELNLEILPPPEDPSVPVALNIGKLAQFEPSQRQNQVGVVPWSPPQSNWNPWTSSNI
LSQDLEHQ.QNII.ELN.EI.PPPEDPS.PVALNIGKLA.FEPSQ.QNQVG.VP.SPPQS.WNPWT.S.I
RetrocopyLSQDLEHQPQNII*ELNFEIMPPPEDPSMPVALNIGKLAHFEPSQ*QNQVGIVPRSPPQSRWNPWTTSDI
ParentalDEGPLAFATPEQISMDLKNELMYQLEQDHDLQAILQERELLPVKKFESEILEAISQNSVVIIRGATGCGK
.EGPLAFA.PEQIS.DLKNEL.YQLEQDHDL.AILQERELLPVKKFESEILEAISQNSVVIIRGA.GCGK
RetrocopyAEGPLAFASPEQISLDLKNELVYQLEQDHDLPAILQERELLPVKKFESEILEAISQNSVVIIRGAAGCGK
ParentalTTQVPQFILDDFIQND-RAAECNIVVTQPRRISAVSVAERVAFERGEEPGKSCGYSVRFESILPRPHASI
TTQVPQFILDDFIQND...AECNIVVTQPRRIS.VS.AE.VAFERGEE..KSCGYSV.FES.LP.PHASI
RetrocopyTTQVPQFILDDFIQND<LTAECNIVVTQPRRISVVSMAE*VAFERGEESVKSCGYSVQFESVLPCPHASI
ParentalMFCTVGVLLRKLEAGIRGISHVIVDEIHERDINTDFLLVVLRDVVQAYPEVRIVLMSATIDTSMFCEYFF
M.CTVGVLLRKLEAGI.GISHVIVDEIH.RDINTDFLLVVLR.VV.AYPEV.IVLMS..IDTSM.CEYFF
RetrocopyMLCTVGVLLRKLEAGI*GISHVIVDEIHGRDINTDFLLVVLREVVSAYPEVLIVLMSTSIDTSMLCEYFF
ParentalNCPIIEVYGRTYPVQEYFLEDCIQMTHFVPPPKDKKKKDKDDDGGEDDDANCNLICGDEYGPETRLSMSQ
NCPII.VYGRTYPVQEYFLEDCIQMTHFVP.PK.KKK.DKDDDGGEDDDANCNLICGDEYGPETR.SMSQ
RetrocopyNCPII*VYGRTYPVQEYFLEDCIQMTHFVPSPKTKKK-DKDDDGGEDDDANCNLICGDEYGPETRMSMSQ
ParentalLNEKETPFELIEALLKYIETLNVPGAVLVFLPGWNLIYTMQKHLEMNPHFGSHRYQILPLHSQIPREEQR
LNEKETPFEL.EAL.KYIETLN.P.AVLVFLPGWNLIYTMQKHLEMNPHFGSH.YQILPLHSQIP..EQR
RetrocopyLNEKETPFELVEALFKYIETLNIPRAVLVFLPGWNLIYTMQKHLEMNPHFGSHQYQILPLHSQIP*QEQR
ParentalKVFDPVPVGVTKVILSTNIAETSITINDVVYVIDSCKQKVKLFTAHNNMTNYATVWASKTNLEQRKGRAG
KVFDPVPVGVTKVILSTNIAETSI.INDV.YV.DSCKQKVKLF..HNNMTNYATVW.SKTNLEQ.KG..G
RetrocopyKVFDPVPVGVTKVILSTNIAETSIIINDV-YVVDSCKQKVKLFATHNNMTNYATVWGSKTNLEQWKGQPG
ParentalRVRPGFCFHLCSRARFERLETHMTPEMFRTPLHEIALSIKLLRLGGIGQFLAKAIEPPPLDAVIEAEHTL
R.RPGFCFHLCSRARFERLETHMTPEMF.TPLHE.ALSIKL..L.GIGQFLAKAIE..PLDAVIEAEHTL
RetrocopyRIRPGFCFHLCSRARFERLETHMTPEMFQTPLHEVALSIKLPCLVGIGQFLAKAIETLPLDAVIEAEHTL
ParentalRELDALDANDELTPLGRILAKLPIEPRFGKMMIMGCIFYVGDAICTIAAATCFPEPFINEGKRLGYIHRN
RELDALDAND.LTPLGRILA.L.IEPRFGKMMIM.CIFYVGDAICTI.AATCFPEPFINEGK.LGY.H.N
RetrocopyRELDALDANDDLTPLGRILANLLIEPRFGKMMIMVCIFYVGDAICTIPAATCFPEPFINEGKWLGYNH*N
ParentalFAGNRFSDHVALLSVFQAWDDARMGGEEAEIRFCEHKRLNMATLRMTWEAKVQLKEILINSGFPEDCLLT
FAGN.FS.HVALLSVFQA.DD.RMGGEEAEIRFC.HKRL.MATLRMTWE.KVQLKEILINSGFPEDCL.T
RetrocopyFAGNGFSHHVALLSVFQAGDDTRMGGEEAEIRFCAHKRLHMATLRMTWEVKVQLKEILINSGFPEDCLVT
ParentalQVFTNTGPDNNLDVVISL-LAFGVYPNVCYHKEKRKILTTEGRNALIHKSSVNCPFSSQDMKYPSPFFVF
QVFTNTGPDNNLDVVISL.LAFGVYPNVCYHKEK.KILTTEG.NALIHKSSVNCPFSSQDMKYPSPFF.F
RetrocopyQVFTNTGPDNNLDVVISL>LAFGVYPNVCYHKEKTKILTTEGCNALIHKSSVNCPFSSQDMKYPSPFFAF
ParentalGEKIRTRAISAKGMTLVTPLQLLLFASKKVQSDGQIVLVDDWIKLQISHEAAACITGLRAAMEALVVEVT
GEKIRTRAISAKGMTLVTPLQLLLFASKKVQSDGQIVL.DDWIKLQISHEAAACIT.L.AA.EALVVEVT
RetrocopyGEKIRTRAISAKGMTLVTPLQLLLFASKKVQSDGQIVLADDWIKLQISHEAAACITALQAATEALVVEVT
ParentalKQPAIISQLDPVNERMLNMIRQISRPSAAGINLMIGSTRYGDGPRPPKMARYDNGSGYRRGGSS
KQPAIISQLDPVNE..LNMIRQISRPSAA.INLMIGST.YGDGP.PPKMA.YDNGSGYRRGGSS
RetrocopyKQPAIISQLDPVNESILNMIRQISRPSAADINLMIGSTWYGDGPGPPKMAQYDNGSGYRRGGSS

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 101 .20 RPM
bodymap2_adrenal 0 .00 RPM 159 .85 RPM
bodymap2_brain 0 .09 RPM 130 .12 RPM
bodymap2_breast 0 .00 RPM 100 .00 RPM
bodymap2_colon 0 .00 RPM 119 .46 RPM
bodymap2_heart 0 .00 RPM 74 .64 RPM
bodymap2_kidney 0 .15 RPM 194 .60 RPM
bodymap2_liver 0 .00 RPM 50 .82 RPM
bodymap2_lung 0 .00 RPM 112 .94 RPM
bodymap2_lymph_node 0 .02 RPM 157 .35 RPM
bodymap2_ovary 0 .10 RPM 244 .57 RPM
bodymap2_prostate 0 .17 RPM 178 .67 RPM
bodymap2_skeletal_muscle 0 .00 RPM 76 .13 RPM
bodymap2_testis 0 .08 RPM 232 .99 RPM
bodymap2_thyroid 0 .00 RPM 179 .29 RPM
bodymap2_white_blood_cells 0 .00 RPM 237 .04 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_1216 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_1216 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_34394785 libraries788 libraries248 libraries7 libraries1 library
TSS #2 TSS_343951383 libraries412 libraries34 libraries0 libraries0 libraries

The graphical summary, for retro_hsap_1216 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_1216 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1216 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_833
Gorilla gorilla retro_ggor_947
Parental genes homology:
Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG00000135829 1 retrocopy
retro_hsap_1216 ,
Gorilla gorilla ENSGGOG000000135331 retrocopy
retro_ggor_947,
Pan troglodytes ENSPTRG000000017591 retrocopy
retro_ptro_833,

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 = 0.15 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .10 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .10 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .03 RPM
CEU_NA12873 0 .10 RPM
FIN_HG00183 0 .00 RPM
FIN_HG00277 0 .15 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .03 RPM
FIN_HG00328 0 .07 RPM
FIN_HG00338 0 .02 RPM
FIN_HG00349 0 .03 RPM
FIN_HG00375 0 .02 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .04 RPM
GBR_HG00099 0 .00 RPM
GBR_HG00111 0 .02 RPM
GBR_HG00114 0 .05 RPM
GBR_HG00119 0 .05 RPM
GBR_HG00131 0 .03 RPM
GBR_HG00133 0 .02 RPM
GBR_HG00134 0 .07 RPM
GBR_HG00137 0 .03 RPM
GBR_HG00142 0 .03 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .03 RPM
TSI_NA20513 0 .00 RPM
TSI_NA20518 0 .08 RPM
TSI_NA20532 0 .00 RPM
TSI_NA20538 0 .05 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .02 RPM
TSI_NA20771 0 .03 RPM
TSI_NA20786 0 .05 RPM
TSI_NA20798 0 .03 RPM
YRI_NA18870 0 .03 RPM
YRI_NA18907 0 .07 RPM
YRI_NA18916 0 .00 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .08 RPM
YRI_NA19114 0 .10 RPM
YRI_NA19118 0 .02 RPM
YRI_NA19213 0 .02 RPM
YRI_NA19214 0 .02 RPM
YRI_NA19223 0 .06 RPM

Indel association:

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





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