RetrogeneDB ID:

retro_hsap_4709

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:X:73350623..73351643(+)
Located in intron of:ENSG00000230590
Retrocopy
information
Ensembl ID:ENSG00000232928
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:DDX3X
Ensembl ID:ENSG00000215301
Aliases:DDX3X, DBX, DDX14, DDX3, HLP2
Description:DEAD (Asp-Glu-Ala-Asp) box helicase 3, X-linked [Source:HGNC Symbol;Acc:2745]


Retrocopy-Parental alignment summary:






>retro_hsap_4709
CCCCAACAAGAGAATTGGCTGTACAGATATGAGGAAGTCAGAAAATTTTCATACCAGCCTAGAGTTCATCCTTGTGTAGT
TTATGGTGATGCTGATATTGGTCAGCAAATTCAGGTCTTAGAACATGGATGCCACTTGTTAGTAGCCACGCCAGGAGGTC
TAGTGGATTTGATGGAAAGAGGAAAGATTGGATTAGACTTCTGCAAATACTTAGTGTTGGATGAAGCTGATAGGATGCTG
GATATGGGATTTGGACCTCAGATACATCTTATACTTGAACAAGATACTATGCCACTGAAGGGCATTCATCACATCATGAT
GTTTAGTGCTACTTTTCCTAACGAAATACAGATGCTTGCTCGTGACTTTTTGGATGAATATATCTTTTTGGCTGTAGGAA
GAGTAGGCTCTACCTCTGAGACTATCACACAGGAAGTAGTTTGGGTGGAAGAGCCAGATAAACGGTCATTTCTGCTTGAT
CTCTTAAATGCACCAGGGAAGGATTCACTGACTTTAGTGTTTGTGGAGACCAAAAAGGGAGAAGATTCTCTGGAGAATTT
CTTATACCATGAAGTATATCCTTGTACTAGTATTCATGGAGACCAATCACAGAGAGATCGAGAAGGAGGCCCTTCATCAG
TTTTGCTTGGGGAAAATCCCAATTCTAGTGGCTACAGCTGTGGCAGCATGAAGACTAGACATTTCAAATGTGAAACATGC
TTCAATTTTGATTTGCCAAGTGATATTGAAGAATATGTGCCTTGTATTGGCTGTACAGGATGTGTGGGAATCCAGGGTCT
TGCCACCTCATTCTTTAATTAAAGAAATATGAATATTACAAAGGATTTGTTGGATATTCTTATAGAAGCTAAACAAGAAG
TGCCTGCTTGGTTGGAAAATAAAGCTTATAAACACCACTACAAGGGTGGTATTCATGCATGATCTAAAAGATTCAGTGGA
GGATTTGGTGCCAGAGACTATTGACAAAGTAGTGGTTCCAGCAGTTCTGGCTTCAGTAGT

ORF - retro_hsap_4709 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 80.52 %
Parental protein coverage: 52.94 %
Number of stop codons detected: 4
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalPTRELAVQIYEEARKFSYRSRVRPCVVYGGADIGQQIRDLERGCHLLVATPGRLVDMMERGKIGLDFCKY
P..E.....YEE.RKFSY..RV.PCVVYG.ADIGQQI..LE.GCHLLVATPG.LVD.MERGKIGLDFCKY
RetrocopyPQQENWLYRYEEVRKFSYQPRVHPCVVYGDADIGQQIQVLEHGCHLLVATPGGLVDLMERGKIGLDFCKY
ParentalLVLDEADRMLDMGFEPQIRRIVEQDTMPPKGVRHTMMFSATFPKEIQMLARDFLDEYIFLAVGRVGSTSE
LVLDEADRMLDMGF.PQI..I.EQDTMP.KG..H.MMFSATFP.EIQMLARDFLDEYIFLAVGRVGSTSE
RetrocopyLVLDEADRMLDMGFGPQIHLILEQDTMPLKGIHHIMMFSATFPNEIQMLARDFLDEYIFLAVGRVGSTSE
ParentalNITQKVVWVEESDKRSFLLDLLNATGKDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDRE-E
.ITQ.VVWVEE.DKRSFLLDLLNA.GKDSLTLVFVETKKG.DSLE.FLYHE.Y.CTSIHGD.SQRDRE.E
RetrocopyTITQEVVWVEEPDKRSFLLDLLNAPGKDSLTLVFVETKKGEDSLENFLYHEVYPCTSIHGDQSQRDRE>E
ParentalALHQFRSGKSPILVATAVAARGLDISNVKHV-INFDLPSDIEEYVHRIGRTGRVGNLGLATSFFNERNIN
ALHQF..GK.PILVATAVAA..LDISNVKH...NFDLPSDIEEYV..IG.TG.VG..GLATSFFN.RN.N
RetrocopyALHQFCLGKIPILVATAVAA*RLDISNVKHA<FNFDLPSDIEEYVPCIGCTGCVGIQGLATSFFN*RNMN
ParentalITKDLLDLLVEAKQEVPSWLENMAYEHHYKGSSRGRSKSSRFSGGFGARDYRQSSGASSSSFSS
ITKDLLD.L.EAKQEVP.WLEN.AY.HHYKG.....SK..RFSGGFGARDY.QSSG.SSS.FSS
RetrocopyITKDLLDILIEAKQEVPAWLENKAYKHHYKGGIHA*SK--RFSGGFGARDY*QSSGSSSSGFSS

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 .06 RPM 749 .34 RPM
bodymap2_adrenal 0 .61 RPM 387 .77 RPM
bodymap2_brain 0 .14 RPM 387 .39 RPM
bodymap2_breast 0 .06 RPM 489 .69 RPM
bodymap2_colon 0 .00 RPM 450 .80 RPM
bodymap2_heart 0 .02 RPM 286 .44 RPM
bodymap2_kidney 0 .08 RPM 352 .11 RPM
bodymap2_liver 0 .04 RPM 179 .78 RPM
bodymap2_lung 0 .12 RPM 407 .89 RPM
bodymap2_lymph_node 0 .00 RPM 541 .21 RPM
bodymap2_ovary 0 .13 RPM 482 .67 RPM
bodymap2_prostate 0 .07 RPM 318 .38 RPM
bodymap2_skeletal_muscle 0 .02 RPM 265 .76 RPM
bodymap2_testis 0 .00 RPM 314 .49 RPM
bodymap2_thyroid 0 .13 RPM 582 .19 RPM
bodymap2_white_blood_cells 0 .00 RPM 549 .23 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_4709 was not detected

EST - click to see more details

2 EST(s) were mapped to retro_hsap_4709 retrocopy
EST ID Start End Identity Match Mis-match Score
BG572523 73350959 73351164 95.2 198 7 190
BQ342791 73350850 73351114 97.8 258 6 252

TSS - click to see more details

No TSS is located nearby retro_hsap_4709 retrocopy 5' end.

Lab - click to see more details

retro_hsap_4709 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4709 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 11 parental genes, and 14 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000359071 retrocopy
retro_btau_1846,
Callithrix jacchus ENSCJAG000000090502 retrocopies
retro_cjac_1428, retro_cjac_4062,
Cavia porcellus ENSCPOG000000135572 retrocopies
retro_cpor_326, retro_cpor_53,
Equus caballus ENSECAG000000099011 retrocopy
retro_ecab_413,
Homo sapiens ENSG00000215301 1 retrocopy
retro_hsap_4709 ,
Macaca mulatta ENSMMUG000000175692 retrocopies
retro_mmul_1898, retro_mmul_2504,
Mus musculus ENSMUSG000000007871 retrocopy
retro_mmus_205,
Ornithorhynchus anatinus ENSOANG000000112741 retrocopy
retro_oana_64,
Pongo abelii ENSPPYG000000202571 retrocopy
retro_pabe_3657,
Pan troglodytes ENSPTRG000000224881 retrocopy
retro_ptro_3130,
Rattus norvegicus ENSRNOG000000233831 retrocopy
retro_rnor_1415,

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 = 0.1 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .03 RPM
CEU_NA11930 0 .10 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 .05 RPM
FIN_HG00277 0 .04 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .03 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 .03 RPM
GBR_HG00111 0 .04 RPM
GBR_HG00114 0 .00 RPM
GBR_HG00119 0 .05 RPM
GBR_HG00131 0 .06 RPM
GBR_HG00133 0 .05 RPM
GBR_HG00134 0 .00 RPM
GBR_HG00137 0 .03 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .03 RPM
TSI_NA20513 0 .07 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .07 RPM
TSI_NA20538 0 .05 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .02 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 .02 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .02 RPM
YRI_NA19213 0 .02 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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