RetrogeneDB ID:

retro_hsap_867

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:11:35988559..35990199(-)
Located in intron of:ENSG00000179241
Retrocopy
information
Ensembl ID:ENSG00000254672
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:WEE2
Ensembl ID:ENSG00000263042
Aliases:None
Description:WEE1 homolog 2 (S. pombe) [Source:HGNC Symbol;Acc:19684]


Retrocopy-Parental alignment summary:






>retro_hsap_867
GAAGAGACTCAGAATGTAGGGCAAAAGAAAGCACAGGGAAGCAGGGAGGCCCAGAGCCAGATCCCAGAGAAGAGTGAAGT
GCAGAATTCAGAGGCAATGCTTACATTGCCCAGGACTCCTCTCAGTAACGTGCATGAACTCAACACACCTCGGGAAAAAG
AAAAAGAAGATCCAGATCAGATTTTGAGGACTCCAGTGTCACACCTTCTCAAATATCCTGAGACACCAGGCCAACCAGGC
AACAGGAACAAGCAGCCACATGGTGCCAGCCCCTCTACTCCCAAAAGCCCGCTGAGCCAGACGTTATTTCTCCAACAGCA
AAGCCTCCTTCCAGAGGCTCTAAGCATTTGATGCTCACATCCACTCCTCCCAAGGATGAGATGACCTCACTGGCTCTGGT
CAATACTAATCCCTTCACCCCAAAGTCCTATAGAAAATTATTCCTTCAATCCAGTGTCAAGAGGAAAATTCGAGATGATC
TTGAGGAAGCTGGTCCAGAGGAAGGCAAGGAAGAACAAGGGCTGCCTGCTGAGACATGTGTTCTATGAGAAACCAACATG
GCTTCCTACTATAAAAAAGAATGCTCGGAGGTAGAAAAAATTGGGGTTGGTGAATTTGGTACAGTCTACAAGTGCATTAA
AAGCCTGGATAGAAGTGTTTATGCAATAAAGCACTATATGAAAACTTTTTCAGGATTTCACCTGAGAATTTGGCTTTGCG
TGAAGTTTATGCTCATACAGTGTTTGGACATCACCCCACCTGGTACATTACTACCCCTTACAGGCAGAAGATAACCATAT
GATCATTCAGAATGGATACTGCAATGGCAGGAGCTTGCAGGCTGCTATATCTGAAAACACTAAGTCTACTAATCACTTCC
AAGAGCCAAAACTCAAGGACATCCTTCTACAGATTTCCCTTGAACTTAAATACAGCCACAACTCTGGCATGGTGCACCCG
GACATGAAACCTTGTAAAACCTTCCTTTGTCACAAGATGCAAAGTGACTCCTCTGGAGTCACAGAAGTTGAAAATGAAGC
TGATTAGTTTCTCTCTGCCCATGTGATATATAAAATTGGTGACCTAGGCCATGTGACATCAATAAGCAAACTCAAAGTGG
AAAAAGCAGATAGTTGCTGCCTAGCAAATGAGATTTTGCAAGAGGATTATTAGTACCTTCCCAAAGCAGACCTATTTGCC
TTGGGATTAATCACTGCAATGGCTGAAGGAGTAAGGACATTACCCATCAACAGTGCTGCAAGGCACCATAACCATGAGAG
TAACTTCCCAGACATTCCTCAGGAGCTCTCAGAAGACTTTTACAGTCTGCTCAAGCACATGATCCACCCTGATCCAGGAG
AGAGACCTTCTGCAGCAGCTCTGGTCAGAAATTGGCCCTGGCCCTCCCTGGGGAAAGCAGAAGAGCTCTAGCAGCAGCTG
AATTTGGAAAAGTCCAAGACAGCTGCACTGGAAAGGGAACTAAGGGAAGCCCAGCAGGCCCAGTCCCTGCAGGGAGACTT
CCATCATGGTGACCCTCGGGTCTTTGGGACCACACGGGATCAGAAAACACCAAATGCCTGGTAGGAGGAAAGAGTGCAAG
GTCTTCAAGCTTTACCTCAGGACAGCATGAGCCTCTGAAC

ORF - retro_hsap_867 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 72.38 %
Parental protein coverage: 96.65 %
Number of stop codons detected: 4
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalEETEIEGQKKVEESREASSQTPEKGEVQDSEAKGTPPWTPLSNVHELDTSSEKDKESPDQILRTPVSHPL
EET...GQKK...SREA.SQ.PEK.EVQ.SEA..T.P.TPLSNVHEL.T..EK.KE.PDQILRTPVSH.L
RetrocopyEETQNVGQKKAQGSREAQSQIPEKSEVQNSEAMLTLPRTPLSNVHELNTPREKEKEDPDQILRTPVSHLL
ParentalKCPETPAQPDSRSKLLPSDSPSTPKTMLSRL-VISPTGKLPSRGPKHLKLTPAPLKDEMTSLALVNINPF
K.PETP.QP..R.K.....SPSTPK..LS...VISPT.K.PSRG.KHL.LT..P.KDEMTSLALVN.NPF
RetrocopyKYPETPGQPGNRNKQPHGASPSTPKSPLSQT<VISPTAKPPSRGSKHLMLTSTPPKDEMTSLALVNTNPF
ParentalTPESYKKLFLQSGGKRKIRGDLEEAGPEEGKG--GLPAKRCVLRETNMASRYEKEFLEVEKIGVGEFGTV
TP.SY.KLFLQS..KRKIR.DLEEAGPEEGK...GLPA..CVL.ETNMAS.Y.KE..EVEKIGVGEFGTV
RetrocopyTPKSYRKLFLQSSVKRKIRDDLEEAGPEEGKEEQGLPAETCVL*ETNMASYYKKECSEVEKIGVGEFGTV
ParentalYKCIKRLDGCVYAIKRSMKTFT-ELSNENSALHEVYAHAVLGHHP-HVVRYYSSWAEDDHMIIQNEYCNG
YKCIK.LD..VYAIK..MKTF....S.EN.AL.EVYAH.V.GHHP.H.V.YY...AED.HMIIQN.YCNG
RetrocopyYKCIKSLDRSVYAIKHYMKTFS<RISPENLALREVYAHTVFGHHP<HLVHYYPLQAEDNHMIIQNGYCNG
ParentalGSLQAAISENTKSGNHFEEPKLKDILLQISLGLNYIHNSSMVHLDIKPSNIFICHKMQSESSGVIEEVEN
.SLQAAISENTKS.NHF.EPKLKDILLQISL.L.Y.HNS.MVH.D.KP...F.CHKMQS.SSGV.E.VEN
RetrocopyRSLQAAISENTKSTNHFQEPKLKDILLQISLELKYSHNSGMVHPDMKPCKTFLCHKMQSDSSGVTE-VEN
ParentalEADWFLSANVMYKIGDLGHATSINKPKVEEGDSRFLANEILQEDYRHLPKADIFALGLTIAVAAGAESLP
EAD.FLSA.V.YKIGDLGH.TSI.K.KVE..DS..LANEILQEDY..LPKAD.FALGL..A.A.G...LP
RetrocopyEAD*FLSAHVIYKIGDLGHVTSISKLKVEKADSCCLANEILQEDY*YLPKADLFALGLITAMAEGVRTLP
ParentalTNGAAWHHIRKGNFPDVPQELSESFSSLLKNMIQPDAEQRPSAAALARNTVLRPSLGKTEELQQQLNLEK
.N.AA.HH....NFPD.PQELSE.F.SLLK.MI.PD...RPSAAAL.RN....PSLGK.EEL.QQLNLEK
RetrocopyINSAARHHNHESNFPDIPQELSEDFYSLLKHMIHPDPGERPSAAALVRNWPW-PSLGKAEEL*QQLNLEK
ParentalFKTATLERELREAQQAQSPQGYTHHGDTGVSGT-HTGSRSTKRLVGGKSARSSSFTSGEREPLH
.KTA.LERELREAQQAQS.QG..HHGD..V.GT.HTGS..TK.LVGGKSARSSSFTSG..EPL.
RetrocopySKTAALERELREAQQAQSLQGDFHHGDPRVFGT<HTGSENTKCLVGGKSARSSSFTSGQHEPLN

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 0 .00 RPM
bodymap2_adrenal 0 .02 RPM 0 .00 RPM
bodymap2_brain 0 .05 RPM 0 .00 RPM
bodymap2_breast 0 .08 RPM 0 .00 RPM
bodymap2_colon 0 .00 RPM 0 .00 RPM
bodymap2_heart 0 .04 RPM 0 .00 RPM
bodymap2_kidney 0 .00 RPM 0 .00 RPM
bodymap2_liver 0 .00 RPM 0 .00 RPM
bodymap2_lung 0 .00 RPM 0 .00 RPM
bodymap2_lymph_node 0 .00 RPM 0 .00 RPM
bodymap2_ovary 0 .13 RPM 0 .00 RPM
bodymap2_prostate 0 .00 RPM 0 .00 RPM
bodymap2_skeletal_muscle 0 .00 RPM 0 .00 RPM
bodymap2_testis 0 .00 RPM 0 .00 RPM
bodymap2_thyroid 0 .00 RPM 0 .00 RPM
bodymap2_white_blood_cells 0 .00 RPM 0 .00 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_867 was not detected

EST - click to see more details

1 EST(s) were mapped to retro_hsap_867 retrocopy
EST ID Start End Identity Match Mis-match Score
AA386311 35988549 35988846 100 295 0 295

TSS - click to see more details

No TSS is located nearby retro_hsap_867 retrocopy 5' end.

Lab - click to see more details

retro_hsap_867 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_867 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_601
Gorilla gorilla retro_ggor_705
Pongo abelii retro_pabe_684
Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG00000263042 1 retrocopy
retro_hsap_867 ,

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 = 0.03 RPM Legend:


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 .03 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

Indel association:

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



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