RetrogeneDB ID:

retro_hsap_2866

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:3:154070375..154071801(-)
Located in intron of:ENSG00000174948
Retrocopy
information
Ensembl ID:ENSG00000240048
Aliases:DDX50P2, RH_II/GuBp2
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:DDX50
Ensembl ID:ENSG00000107625
Aliases:DDX50, GU2, GUB, RH-II/GuB, mcdrh
Description:DEAD (Asp-Glu-Ala-Asp) box polypeptide 50 [Source:HGNC Symbol;Acc:17906]


Retrocopy-Parental alignment summary:






>retro_hsap_2866
TCAAAGCAAGTATCATCCTTAGATAGTTCTACTCATAAATCAAGTGATAATAAACTAGAGGAGACCTTAACATGTGAACA
GAAAGAAAGAGCTTTCTCCTATTTCCGTATTTCTGAAGAGACTGTAAAGCTTCTGAAACATCAAAGGGTAACATATCTCT
TTCCTATTCAAGTTAGGACCTTGTCCTGTATTTGAAAGAAAAGATTTAATAGCTCGAGCATGGACAGGAACAGGAAAGAC
ATTCTTTTTTGCCATCCCCTTGATTGAAAGACTCCAAAGAAATCAAGAAACAATTTTTAAAAAGCTGCTCAACAAAGGTA
CTTGTTTTGGCTCCAGCAAGGGAACTGGCAAACCAAGTAGCCAAAGACTTCAAAGATAAAACTAGGAAACTCAGCATGGT
GTGTTTTTATGGTGCAATACCATATCAAAGCCAAATTAATCATATGCAAAATGGTATTGACATCTTGGTTGGAACCCCTG
GTCATATCAAAGATCATCTGCAGAGTGGCTGATTGGATCTTTCTAAACTGTGCCATGTTGTGCTTGATGAAGTGGATCAA
ACGTTAGATTTAGATTTTAATGAACAAGTTGAAGATGTGATTCACAAATCCTACAAAACTGAATCTGAAGACCATCCTCA
GACTTTACTTTTTTCTGCAACTTGCCCACAGTGGGTATACAAAGTTGCAAATAAATACATGAAATCCAGATATGAACAGG
TTGACCTTATTGGATAAATGACTCAAAAGGCTGCAACTACTGTGGAACACTTGGCCATTCAGTGTCATTGGTCTCAGAGG
CCAGCAGTTATTGGAGATGTCCTTCAAGTCTACAGTGGGTCTGAAGGGAGGGCTATTATTTTCTGTGAGACCAGGAAGAA
TGTAACTGAAATGGCCATGAATCCACACATAAAACAGAATGCCCAGTGTTTACATGGGGATATTGCACAGTCACAAAGAG
AAATTACACTAAAAGGCTTCAGAGAAGATAGTTTTAAAGTTTTGGTGGCAACCAATGTGGCTGCCCATAGTTTGCACATT
CCTGAAGTAGACCTGGTGATTCAACATTCTCCTCCTCAGGATGTTGAGGCCCGTATCCATCGCTCTGGATGCACAGGTAG
AGCTGGACAGGGATTTGTATATGTTTTTATCAACCAAGAGAAAGAGGTCAACTAAGATATGTGGAACAAAAAGCAAGAAT
TACTTTTAAATGTGTAGGTGTTCCTTCTACAATGGATTTAGTTAAATCTAAAAGCATGGATACCATCAGGTTTCTGACTT
CCGTTTCTTATGCTGCTGTTGATTTTTTCTGACCATCAGCTCAGAGACTGATAGAAGAGAAAGGGGCAGTGGATGCATTG
GCTGCAACTTTAGCCCACATTTCTGGTGCATCAAGTTTTGAACCACAGTCTTTGATCGCCTCTGAT

ORF - retro_hsap_2866 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 82.08 %
Parental protein coverage: 64.72 %
Number of stop codons detected: 4
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalSKRVSSLDTSTHKSSDNKLEETLTREQKEGAFSNFPISEETIKLLKGRGVTYLFPIQVKTFGPVYEGKDL
SK.VSSLD.STHKSSDNKLEETLT.EQKE.AFS.F.ISEET.KLLK...VTYLFPIQV.T.......K..
RetrocopySKQVSSLDSSTHKSSDNKLEETLTCEQKERAFSYFRISEETVKLLKHQRVTYLFPIQVRTLSCI*K-KRF
ParentalIAQARTGTGKTFSFAIPL-IERLQRNQETI-KKSRSPKVLVLAPTRELANQVAKDFKDITRKLSVACFYG
.........K...F..PL.IERLQRNQETI..KS.S.KVLVLAP.RELANQVAKDFKD.TRKLS..CFYG
RetrocopyNSSSMDRNRKDILFCHPL>IERLQRNQETI>LKSCSTKVLVLAPARELANQVAKDFKDKTRKLSMVCFYG
ParentalGTSYQSQINHIRNGIDILVGTPGRIKDHLQSGRLDLSKLRHVVLDEVDQMLDLGFAEQVEDIIHESYKTD
...YQSQINH..NGIDILVGTPG.IKDHLQSG.LDLSKL.HVVLDEVDQ.LDL.F.EQVED.IH.SYKT.
RetrocopyAIPYQSQINHMQNGIDILVGTPGHIKDHLQSG*LDLSKLCHVVLDEVDQTLDLDFNEQVEDVIHKSYKTE
ParentalSEDNPQTLLFSATCPQWVYKVAKKYMKSRYEQVDLVGKMTQKAATTVEHLAIQCHWSQRPAVIGDVLQVY
SED.PQTLLFSATCPQWVYKVA.KYMKSRYEQVDL.G.MTQKAATTVEHLAIQCHWSQRPAVIGDVLQVY
RetrocopySEDHPQTLLFSATCPQWVYKVANKYMKSRYEQVDLIG*MTQKAATTVEHLAIQCHWSQRPAVIGDVLQVY
ParentalSGSEGRAIIFCETKKNVTEMAMNPHIKQNAQCLHGDIAQSQREITLKGFREGSFKVLVATNVAARGLDIP
SGSEGRAIIFCET.KNVTEMAMNPHIKQNAQCLHGDIAQSQREITLKGFRE.SFKVLVATNVAA..L.IP
RetrocopySGSEGRAIIFCETRKNVTEMAMNPHIKQNAQCLHGDIAQSQREITLKGFREDSFKVLVATNVAAHSLHIP
ParentalEVDLVIQSSPPQDVESYIHRSGRTGRAGRTGICICF-YQPRERGQLRYVEQKAGITFKRVGVPSTMDLVK
EVDLVIQ.SPPQDVE..IHRSG.TGRAG..G....F.YQPRERGQLRYVEQKA.ITFK.VGVPSTMDLVK
RetrocopyEVDLVIQHSPPQDVEARIHRSGCTGRAGQ-GFVYVF<YQPRERGQLRYVEQKARITFKCVGVPSTMDLVK
ParentalSKSMDAIRSLASVSYAAVDFFRPSAQRLIEEKGAVDALAAALAHISGASSFEPRSLITSD
SKSMD.IR.L.SVSYAAVDFF.PSAQRLIEEKGAVDALAA.LAHISGASSFEP.SLI.SD
RetrocopySKSMDTIRFLTSVSYAAVDFF*PSAQRLIEEKGAVDALAATLAHISGASSFEPQSLIASD

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 .04 RPM 40 .03 RPM
bodymap2_adrenal 0 .08 RPM 49 .29 RPM
bodymap2_brain 0 .00 RPM 21 .85 RPM
bodymap2_breast 0 .00 RPM 39 .11 RPM
bodymap2_colon 0 .00 RPM 73 .42 RPM
bodymap2_heart 0 .02 RPM 23 .37 RPM
bodymap2_kidney 0 .00 RPM 37 .02 RPM
bodymap2_liver 0 .00 RPM 9 .93 RPM
bodymap2_lung 0 .00 RPM 34 .60 RPM
bodymap2_lymph_node 0 .00 RPM 33 .37 RPM
bodymap2_ovary 0 .02 RPM 79 .40 RPM
bodymap2_prostate 0 .00 RPM 74 .58 RPM
bodymap2_skeletal_muscle 0 .04 RPM 45 .49 RPM
bodymap2_testis 0 .00 RPM 78 .09 RPM
bodymap2_thyroid 0 .00 RPM 59 .94 RPM
bodymap2_white_blood_cells 0 .00 RPM 48 .55 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2866 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2866 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_2866 retrocopy 5' end.

Lab - click to see more details

retro_hsap_2866 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2866 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1938
Pongo abelii retro_pabe_2369
Parental genes homology:
Parental genes homology involve 9 parental genes, and 15 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000188441 retrocopy
retro_cjac_1298,
Homo sapiens ENSG000000800071 retrocopy
retro_hsap_76,
Homo sapiens ENSG00000107625 2 retrocopies
retro_hsap_2089, retro_hsap_2866 ,
Macaca mulatta ENSMMUG000000010061 retrocopy
retro_mmul_982,
Mus musculus ENSMUSG000000200761 retrocopy
retro_mmus_3362,
Nomascus leucogenys ENSNLEG000000116312 retrocopies
retro_nleu_1300, retro_nleu_609,
Otolemur garnettii ENSOGAG000000018442 retrocopies
retro_ogar_1492, retro_ogar_555,
Pongo abelii ENSPPYG000000023903 retrocopies
retro_pabe_2007, retro_pabe_2369, retro_pabe_2418,
Pan troglodytes ENSPTRG000000025622 retrocopies
retro_ptro_1536, retro_ptro_1938,

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 = 0.07 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .02 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .07 RPM
CEU_NA12004 0 .04 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 .03 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .02 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .00 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .02 RPM
GBR_HG00099 0 .06 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 .05 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .03 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .05 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .00 RPM
TSI_NA20538 0 .05 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .00 RPM
TSI_NA20771 0 .03 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .03 RPM
YRI_NA18870 0 .03 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .00 RPM
YRI_NA19093 0 .03 RPM
YRI_NA19099 0 .05 RPM
YRI_NA19114 0 .03 RPM
YRI_NA19118 0 .00 RPM
YRI_NA19213 0 .00 RPM
YRI_NA19214 0 .02 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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