RetrogeneDB ID:

retro_hsap_1566

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:15:49657321..49658881(-)
Located in intron of:ENSG00000156958
Retrocopy
information
Ensembl ID:ENSG00000259531
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:SPPL2A
Ensembl ID:ENSG00000138600
Aliases:SPPL2A, IMP3, PSL2
Description:signal peptide peptidase like 2A [Source:HGNC Symbol;Acc:30227]


Retrocopy-Parental alignment summary:






>retro_hsap_1566
ATGGGGCCGCAGCGGCGGCTGTCCCCTGCCACGGCCGCCCTGCTCTGGGGCTTCCTGCTCCAGCTGACAGCCGCTCAGGA
AGCAATCTTGCATGCGTCTGGAAATGGCACATCCAAGGACTACTGCATGCTTTATAACCCCCATTGGTCAGCTCTTCCAA
GTACCCTAGAAAATGCAACTTCCATTAGTTTGATGAATCTGACTTCCGCACCACTATGCAACCTTTCTGATGTTCCTCCT
GTTGACATAAAGAACAAAGCAGTTGTGGTGCAATGGGGCAGCTGCCATTTTCTTGAAAACACCAGAAATGCACAGAAAAG
AGGTGCTGAAGCAATGTTGGTTGTCAATAACAGTATCCTATTTCCTACCTCAGGTAACAGATCTGAATTTCCTGATGTGA
AAATACTGATTGCATTTATAAGTGACAAAGACTTTATAGATATGAAGCAGACTCTAGGAAATAACATTACTGTGAAAATG
TGTTCTCCATCGTGGCCTAACTTTGATTATACTATGGTGGTTATTTTTGTAATTGCTGTGTTCACTGTGGCATTAGGTGG
ATACTGGAGTGGACTAGTTGAATTGGAAAACTTGAAAGCAGTGACAACTGAAGATAGATAAATGAGGGAAAAAAAAGGAA
GAATATCTAACTTTTAGTCCTCTTACAGTTGTAATATTTGTAGTCATCTACTGTGTTATGATGGTCTTACTTTATTTCTT
CCACAAATGGTTAGTTTATGTTATGATAGCAATTTTCTGCATAGTATCAGCAATGAGTCTGTACAACTCTCTTGCTGCAC
TAATTCATAAGATGCCATATGGACAATGCACAATTGAGTGTCGCGGCAAAAGCATGGAAGTGAGACTTATGTTTCTCTCT
GGACTGTGCATAGCAATAGCTATTGTTTGGGCTGTGTTTCAAAATGAAGACAGGTGGGCTTGGATTTTACAAGATATCTT
GGAGATTGCTTTCTGTCTGAATTTAATTAAAACACTGAAGTTGGCCAGCTTCAAGTCATGTGTGATACTTCTAGGCCTTC
TCCTCCTCTATGATGTATTTTTTGTTTTCATAACACCATTCATCACAAAGAATGGTGAGAGTATCATGGTTAAACTTGCA
GCTGGACCTTTTGAAAATACTGAAACATTGCCAGTAGTCATCAGAGTACCAAAGCTGATCTGTTTCTCAGTAATGAGTGT
GTGCATCATGCCTGTTTCAATATTGGGCTTTGGAGACATTATTGTACAGGCCTGTTGCTTGCGTACTGTAGAAGAGTTGA
TGTTTAGACTGGTTCTTCGTATATATACTATGTTTCCTCTACAGTTGCCTATGCTATTGGCATGATACTTACATTTGTTG
TTCTGGTGCTGATGAAAAAGGGGCAACCTGCTCTCCTCTATTTAGTAACTTGCACACTTATTATTGCCTCAGTTGTTGCC
TGGAAATGTAAGGAAATGAAAAAGTTCTGGAAAGGTAACAGCTATCAGATGATGGACCATCTGTATTATGCAAAAAACGA
AGAAAACCCTGTGATGTCTGGTGAACAGATTGTCCAGCAA

ORF - retro_hsap_1566 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 88.89 %
Parental protein coverage: 100. %
Number of stop codons detected: 2
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMGPQRRLSPAGAALLWGFLLQLTAAQEAILHASGNGTTKDYCMLYNPYWTALPSTLENATSISLMNLTST
MGPQRRLSPA.AALLWGFLLQLTAAQEAILHASGNGT.KDYCMLYNP.W.ALPSTLENATSISLMNLTS.
RetrocopyMGPQRRLSPATAALLWGFLLQLTAAQEAILHASGNGTSKDYCMLYNPHWSALPSTLENATSISLMNLTSA
ParentalPLCNLSDIPPVGIKSKAVVVPWGSCHFLEKARIAQKGGAEAMLVVNNSVLFPPSGNRSEFPDVKILIAFI
PLCNLSD.PPV.IK.KAVVV.WGSCHFLE..R.AQK.GAEAMLVVNNS.LFP.SGNRSEFPDVKILIAFI
RetrocopyPLCNLSDVPPVDIKNKAVVVQWGSCHFLENTRNAQKRGAEAMLVVNNSILFPTSGNRSEFPDVKILIAFI
ParentalSYKDFRDMNQTLGDNITVKMYSPSWPNFDYTMVVIFVIAVFTVALGGYWSGLVELENLKAVTTEDREMR-
S.KDF.DM.QTLG.NITVKM.SPSWPNFDYTMVVIFVIAVFTVALGGYWSGLVELENLKAVTTEDR.MR.
RetrocopySDKDFIDMKQTLGNNITVKMCSPSWPNFDYTMVVIFVIAVFTVALGGYWSGLVELENLKAVTTEDR*MR>
ParentalKKKEEYLTFSPLTVVIFVVICCVMMVLLYFFYKWLVYVMIAIFCIASAMSLYNCLAALIHKIPYGQCTIA
...EEYLTFSPLTVVIFVVI.CVMMVLLYFF.KWLVYVMIAIFCI.SAMSLYN.LAALIHK.PYGQCTI.
RetrocopyXXXEEYLTFSPLTVVIFVVIYCVMMVLLYFFHKWLVYVMIAIFCIVSAMSLYNSLAALIHKMPYGQCTIE
ParentalCRGKNMEVRLIFLSGLCIAVAVVWAVFRNEDRWAWILQDILGIAFCLNLIKTLKLPNFKSCVILLGLLLL
CRGK.MEVRL.FLSGLCIA.A.VWAVF.NEDRWAWILQDIL.IAFCLNLIKTLKL..FKSCVILLGLLLL
RetrocopyCRGKSMEVRLMFLSGLCIAIAIVWAVFQNEDRWAWILQDILEIAFCLNLIKTLKLASFKSCVILLGLLLL
ParentalYDVFFVFITPFITKNGESIMVELAAGPFGNNEKLPVVIRVPKLIYFSVMSVCLMPVSILGFGDIIV-PGL
YDVFFVFITPFITKNGESIMV.LAAGPF.N.E.LPVVIRVPKLI.FSVMSVC.MPVSILGFGDIIV..GL
RetrocopyYDVFFVFITPFITKNGESIMVKLAAGPFENTETLPVVIRVPKLICFSVMSVCIMPVSILGFGDIIV<TGL
ParentalLIAYCRRFDVQTGSSYIYYVSSTVAYAIGMILTFVVLVLMKKGQPALLYLVPCTLITASVVAWRRKEMKK
L.AYCRR.DV.TGSSYIYYVSSTVAYAIGMILTFVVLVLMKKGQPALLYLV.CTLI.ASVVAW..KEMKK
RetrocopyLLAYCRRVDV*TGSSYIYYVSSTVAYAIGMILTFVVLVLMKKGQPALLYLVTCTLIIASVVAWKCKEMKK
ParentalFWKGNSYQMMDHLDCATNEENPVISGEQIVQQ
FWKGNSYQMMDHL..A.NEENPV.SGEQIVQQ
RetrocopyFWKGNSYQMMDHLYYAKNEENPVMSGEQIVQQ

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 .08 RPM 56 .93 RPM
bodymap2_adrenal 0 .02 RPM 60 .45 RPM
bodymap2_brain 0 .00 RPM 15 .45 RPM
bodymap2_breast 0 .06 RPM 60 .16 RPM
bodymap2_colon 0 .00 RPM 34 .98 RPM
bodymap2_heart 0 .06 RPM 57 .41 RPM
bodymap2_kidney 0 .62 RPM 72 .73 RPM
bodymap2_liver 0 .08 RPM 49 .39 RPM
bodymap2_lung 0 .00 RPM 45 .38 RPM
bodymap2_lymph_node 0 .22 RPM 28 .93 RPM
bodymap2_ovary 0 .21 RPM 38 .65 RPM
bodymap2_prostate 0 .12 RPM 32 .72 RPM
bodymap2_skeletal_muscle 0 .16 RPM 158 .58 RPM
bodymap2_testis 0 .00 RPM 34 .88 RPM
bodymap2_thyroid 0 .04 RPM 74 .76 RPM
bodymap2_white_blood_cells 0 .00 RPM 63 .24 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_1566 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_1566 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_1566 retrocopy 5' end.

Lab - click to see more details

retro_hsap_1566 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1566 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1054
Gorilla gorilla retro_ggor_1191
Pongo abelii retro_pabe_1293
Parental genes homology:
Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species Parental gene accession Retrocopies number
Dipodomys ordii ENSDORG000000089461 retrocopy
retro_dord_754,
Homo sapiens ENSG00000138600 1 retrocopy
retro_hsap_1566 ,
Homo sapiens ENSG000001578371 retrocopy
retro_hsap_1898,
Gorilla gorilla ENSGGOG000000131541 retrocopy
retro_ggor_1191,
Pongo abelii ENSPPYG000000064721 retrocopy
retro_pabe_1293,
Pan troglodytes ENSPTRG000000070701 retrocopy
retro_ptro_1054,
Rattus norvegicus ENSRNOG000000116521 retrocopy
retro_rnor_1750,

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 = 0.11 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .06 RPM
CEU_NA11843 0 .03 RPM
CEU_NA11930 0 .07 RPM
CEU_NA12004 0 .11 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .07 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .05 RPM
CEU_NA12872 0 .03 RPM
CEU_NA12873 0 .06 RPM
FIN_HG00183 0 .05 RPM
FIN_HG00277 0 .00 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .03 RPM
FIN_HG00328 0 .05 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .06 RPM
FIN_HG00375 0 .07 RPM
FIN_HG00377 0 .05 RPM
FIN_HG00378 0 .02 RPM
GBR_HG00099 0 .03 RPM
GBR_HG00111 0 .00 RPM
GBR_HG00114 0 .03 RPM
GBR_HG00119 0 .05 RPM
GBR_HG00131 0 .09 RPM
GBR_HG00133 0 .02 RPM
GBR_HG00134 0 .04 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .03 RPM
GBR_HG00143 0 .03 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .05 RPM
TSI_NA20518 0 .03 RPM
TSI_NA20532 0 .03 RPM
TSI_NA20538 0 .09 RPM
TSI_NA20756 0 .06 RPM
TSI_NA20765 0 .06 RPM
TSI_NA20771 0 .00 RPM
TSI_NA20786 0 .03 RPM
TSI_NA20798 0 .03 RPM
YRI_NA18870 0 .00 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .00 RPM
YRI_NA19093 0 .05 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .06 RPM
YRI_NA19213 0 .00 RPM
YRI_NA19214 0 .00 RPM
YRI_NA19223 0 .08 RPM

Indel association:

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



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