RetrogeneDB ID:

retro_hsap_3420

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:6:7986769..7988278(+)
Located in intron of:ENSG00000259040
Retrocopy
information
Ensembl ID:ENSG00000219294
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:PIP5K1A
Ensembl ID:ENSG00000143398
Aliases:None
Description:phosphatidylinositol-4-phosphate 5-kinase, type I, alpha [Source:HGNC Symbol;Acc:8994]


Retrocopy-Parental alignment summary:






>retro_hsap_3420
ATGGCGTCGGCCTCCTCCCAACCGTCGTTGGCGGTCGGTTTTTCATCCTTTGATCCCGGGGCCCCTTCCTGTACCGCGTC
CTCAGCATCTGGAATCTTGAGCCCCACGGCATCTGAGGTGCCTTATGCCTCTGGCATGCCCATCAAGAAAACAGGCCATC
GAGGTGTCGATTCCTCAGGAGAGACAACATATAAAAAGACAACCTCAACAGCCTTGAAAGGTGCCATCCAGTTAGGCATT
ACTTACACTGTGGGGAGCCTGAGTACCAAACCAGAGCGTGATGTCCTCATGCAAGATTTCTACGTGGTGGAGAGTATCTT
CTTCCCCAGTGAAGGGAGCAACCTGACCCCTGCTCATCACTACAATGCCTTCCGTTTCAAGACCTATGCGCCGGTTGCCT
TCCGCTACTTTCGGGAGCTATTTGGTATCCCGCCCGATGATTACTTGTGCTCCCTCTGCAGTGAGCCGCTGATTGAACTC
TGTAGCTCTGGAGCTAGTGGTTCCCTGTTCTATGTGTCCAGCGACGATGAACTCATTATTAAGACACTCCAACATAAAGA
GGCGGAGTTTCTGCAGAAGCTGCTTCCAGGATACTACTTGAACCTCAGCCAGAACCCTCGGACTTTGCTGCCTAAATTCT
TTGGACTGTACTGTGTGCAGACAGGTGGCAAGAACATTCGGATTGTGGTGATGAACAATCTTTTACCAAGATCCGTCAAA
ATGCATATCAAATATGACCTCAAAGGCTCAACCTACAAACGCCGGGCTTCCCAGAAAGAGCGAGAGAAGCCTCTTCCCAC
ATTTAAAGATCTAGACTTCTTACAAGACATCCCTGATGGTCTTTTTTTGGATGCTGACACGTACAATGCTCTCTGTAAGA
CCCTGCAGCGTGACTGTTTGGTGCTGCAGAGCTTCAAGATAATGGACTATAGCCTCTGGCTGTCAATCCACAATATAGAT
CATGCACAACGAGAGCCCTTAAGCAGCGACACTCTTCAAGTGTCAATCGACACTCAAAGACTGGCTCCCCAAAAGGCTCT
GTATTCCACAGCCATGGAATTCATCCAGGGAGAGGCTCGGCTGGGCGACACCATGGAGGCCGATGACCATATGGGTGGCA
TCCCTGCTCAGAATAGTAAAGGGGAAAGGCTTCTGCTTTATATTGGCATCATTGACATTCTACAGTCTTACACGTTTCTT
AAGAAGTTGGAGCACTCTTGGAAAGCCGTGGTACATGATGGGGACGCTGTCTCAGTGCATCGCCCAGGCTTCTACGCTGA
ACGGTTCCAGCACTTCATGTGCAACGCAGTATTTAAGAAGATCCCCTTGAAGCCTTCTCCTTCCAAAAAGTTTCGGTCTG
GCTTATCTTTCTCTCTGCATACGGGCTCCAGTGGCAACTCCTGCATTACTTACCAGCCATTGGTCTCTGAGGAACACAAG
TCACAAGTGATAAAGGTGCAAGTGGAGCCAGGTGTTCACCTTGGTCGTTCTGATGTTTTACCTCAGACC

ORF - retro_hsap_3420 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 89.29 %
Parental protein coverage: 91.62 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMASASSGPSSSVGFSSFDPAVPSCTLSSASGIKRPMASEVPYASGMPIKKIGHRSVDSSGETTYKKTTSS
MASASS.PS..VGFSSFDP..PSCT.SSASGI..P.ASEVPYASGMPIKK.GHR.VDSSGETTYKKTTS.
RetrocopyMASASSQPSLAVGFSSFDPGAPSCTASSASGILSPTASEVPYASGMPIKKTGHRGVDSSGETTYKKTTST
ParentalALKGAIQLGITHTVGSLSTKPERDVLMQDFYVVESIFFPSEGSNLTPAHHYNDFRFKTYAPVAFRYFREL
ALKGAIQLGIT.TVGSLSTKPERDVLMQDFYVVESIFFPSEGSNLTPAHHYN.FRFKTYAPVAFRYFREL
RetrocopyALKGAIQLGITYTVGSLSTKPERDVLMQDFYVVESIFFPSEGSNLTPAHHYNAFRFKTYAPVAFRYFREL
ParentalFGIRPDDYLYSLCSEPLIELCSSGASGSLFYVSSDDEFIIKTVQHKEAEFLQKLLPGYYMNLNQNPRTLL
FGI.PDDYL.SLCSEPLIELCSSGASGSLFYVSSDDE.IIKT.QHKEAEFLQKLLPGYY.NL.QNPRTLL
RetrocopyFGIPPDDYLCSLCSEPLIELCSSGASGSLFYVSSDDELIIKTLQHKEAEFLQKLLPGYYLNLSQNPRTLL
ParentalPKFYGLYCVQAGGKNIRIVVMNNLLPRSVKMHIKYDLKGSTYKRRASQKEREKPLPTFKDLDFLQDIPDG
PKF.GLYCVQ.GGKNIRIVVMNNLLPRSVKMHIKYDLKGSTYKRRASQKEREKPLPTFKDLDFLQDIPDG
RetrocopyPKFFGLYCVQTGGKNIRIVVMNNLLPRSVKMHIKYDLKGSTYKRRASQKEREKPLPTFKDLDFLQDIPDG
ParentalLFLDADMYNALCKTLQRDCLVLQSFKIMDYSLLMSIHNIDHAQREPLSSET-QYSVDTRRPAPQKALYST
LFLDAD.YNALCKTLQRDCLVLQSFKIMDYSL..SIHNIDHAQREPLSS.T.Q.S.DT.R.APQKALYST
RetrocopyLFLDADTYNALCKTLQRDCLVLQSFKIMDYSLWLSIHNIDHAQREPLSSDTLQVSIDTQRLAPQKALYST
ParentalAMESIQGEARRGGTMETDDHMGGIPARNSKGERLLLYIGIIDILQSYRFVKKLEHSWKALVHDGDTVSVH
AME.IQGEAR.G.TME.DDHMGGIPA.NSKGERLLLYIGIIDILQSY.F.KKLEHSWKA.VHDGD.VSVH
RetrocopyAMEFIQGEARLGDTMEADDHMGGIPAQNSKGERLLLYIGIIDILQSYTFLKKLEHSWKAVVHDGDAVSVH
ParentalRPGFYAERFQRFMCNTVFKKIPLKPSPSKKFRSGSSFSRRAGSSGNSCITYQPSVSGEHKAQVTTKAEVE
RPGFYAERFQ.FMCN.VFKKIPLKPSPSKKFRSG.SFS...GSSGNSCITYQP.VS.EHK.QV..K..VE
RetrocopyRPGFYAERFQHFMCNAVFKKIPLKPSPSKKFRSGLSFSLHTGSSGNSCITYQPLVSEEHKSQV-IKVQVE
ParentalPGVHLGRPDVLPQT
PGVHLGR.DVLPQT
RetrocopyPGVHLGRSDVLPQT

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 35 .38 RPM
bodymap2_adrenal 0 .08 RPM 65 .85 RPM
bodymap2_brain 0 .09 RPM 34 .90 RPM
bodymap2_breast 0 .00 RPM 40 .88 RPM
bodymap2_colon 0 .00 RPM 27 .28 RPM
bodymap2_heart 0 .00 RPM 35 .39 RPM
bodymap2_kidney 0 .02 RPM 44 .19 RPM
bodymap2_liver 0 .00 RPM 19 .26 RPM
bodymap2_lung 0 .00 RPM 58 .79 RPM
bodymap2_lymph_node 0 .09 RPM 44 .62 RPM
bodymap2_ovary 0 .12 RPM 58 .52 RPM
bodymap2_prostate 0 .00 RPM 46 .56 RPM
bodymap2_skeletal_muscle 0 .00 RPM 30 .17 RPM
bodymap2_testis 2 .32 RPM 72 .26 RPM
bodymap2_thyroid 0 .04 RPM 46 .57 RPM
bodymap2_white_blood_cells 0 .00 RPM 50 .09 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3420 was not detected

EST - click to see more details

8 EST(s) were mapped to retro_hsap_3420 retrocopy
EST ID Start End Identity Match Mis-match Score
CD557555 7987228 7987433 99.6 201 1 199
CV024289 7986769 7987393 99.7 622 2 620
DB099491 7986729 7987325 99.9 595 1 594
DB448145 7986740 7987177 99.1 436 1 434
DB454864 7986741 7987239 99.8 497 1 496
HY002949 7986744 7987293 99.3 544 4 540
HY023811 7986747 7987218 99.2 465 4 461
HY046127 7986744 7987232 99.8 487 1 486

TSS - click to see more details

No TSS is located nearby retro_hsap_3420 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3420 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3420 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2324
Macaca mulatta retro_mmul_1748
Parental genes homology:
Parental genes homology involve 6 parental genes, and 12 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG00000143398 2 retrocopies
retro_hsap_3420 , retro_hsap_716,
Macaca mulatta ENSMMUG000000052281 retrocopy
retro_mmul_1748,
Nomascus leucogenys ENSNLEG000000101302 retrocopies
retro_nleu_468, retro_nleu_5,
Otolemur garnettii ENSOGAG000000028461 retrocopy
retro_ogar_1855,
Pongo abelii ENSPPYG000000008724 retrocopies
retro_pabe_3037, retro_pabe_3112, retro_pabe_59, retro_pabe_619,
Pan troglodytes ENSPTRG000000012822 retrocopies
retro_ptro_2324, retro_ptro_511,

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

Indel association:

The presence of retro_hsap_3420 across human populations is associated with 1 indel. The percentage values indicate the frequencies of retro_hsap_3420 presence in various populations. Based on Kabza et al. 2015 (PubMed).


# Indel coordinates AFR, African AMR, Ad Mixed American EUR, European EAS, East Asian
ASW YRI LWK MXL PUR CLM CEU IBS GBR FIN TSI JPT CHB CHS
1. 6:7984273..7987010 100 100 100 100 100 100 100 100 100 99.46 100 100 100 100

Indel #1, located at the genomic coordinates 6:7984273..7987010.

image/svg+xml Mexican Ancestryfrom Los Angeles USA MXL 100 % Puerto Ricansfrom Puerto Rico PUR 100 % Colombians fromMedellin, Colombia CLM 100 % Americans of AfricanAncestry in SW USA ASW 100 % Yoruba in Ibadan,Nigeria YRI 100 % Luhya in Webuye,Kenya LWK 100 % Utah Residents (CEPH)with Northern andWestern European Ancestry CEU 100 % Iberian Populationin Spain IBS 100 % British in Englandand Scotland GBR 100 % Finnish in Finland FIN 99.46 % Toscani in Italia TSI 100 % Han Chinese in Bejing,China CHB 100 % Japanese in Tokyo,Japan 100 % Southern Han Chinese CHS 100 % JPT EUROPE AMERICAS AFRICA EAST ASIA




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