RetrogeneDB ID:

retro_hsap_1898

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:18:68892929..68893954(+)
Located in intron of:ENSG00000265484
Retrocopy
information
Ensembl ID:ENSG00000263733
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:SPPL3
Ensembl ID:ENSG00000157837
Aliases:SPPL3, IMP2, MDHV1887, PRO4332, PSH1, PSL4
Description:signal peptide peptidase like 3 [Source:HGNC Symbol;Acc:30424]


Retrocopy-Parental alignment summary:






>retro_hsap_1898
GAGAGTACACAGAAAGACAATAATAGTTCTTCTGGGTCTTTCAATGGCAACAGCACCAATAATAGCATCAAATAATTGAA
TCTACCCAGGCTCTGTTCCTTCCGATTGGAGCATCTGTCTCTCTTTTATTGTTGTTTTGCTTCTTTGACTGAGCTCAAGT
AGTTTTCACAATATGTACAGCAGTTCTTACAATGATAACTTTTGCTTTTCTTCTTCTCCTGATGTGCGAGTATTTAACTA
GACTCTATTCACCTCAGAACAAGATTTCCCTGGGTTCCCCTGGATGTTTCACTGCTGCTGAGTTGTTGTTATTATCTCTG
TCTGTCGTGCTCATACTCACCTGGGTTCTCACTGGCCATTGACTTCTCATGGATGCAATGGCTGTGGGTCTCCGTCTCAC
TGTAATTTTCTTTGTCTGCCTGTTGGGCTTCAAAGTCCCCTGCCTGCTTCTCTCAGGGCTTTTAATCTATGATGTCTTTT
AGGTAGTTTTCTCAGCCTACATCTTTAATAGCAGTGTCATGGTGAATGTGGCCATGGCAGCTGGCCGAAAATCCCCTTTA
CGTTCTATCTCAGAAGCTCAGCCTGGGGCCTGGTGTTGGGCGTGATGTTCCTCGCCTGTCTCTGCCTGGAAAACTGGTCT
TCCCACGTTCTACTGGGAGCCACTTCCTCATGTTGGGCATTGGAGACATTGTTATGCCTGGTCATCTGCTATGCTTTGAC
CTTCACTATGACAATTACAAAATCAAGCCCGTGGGGACTCCTGTGGTGGCCCTGGACCTGCCAACATCTCTGGGCGCATG
CAGAAGGTCTTCTACTTTCACTGCACGCTCATGGGATACTTTGTAGATCTGCTCACGGCTACTGTGGCCTCTCACATTCA
CCAGGCCGCCCAGCCTGCCCTTCTCTGTTTGGTGCCATTTACCTTATTGCCACTCCTCATGATGGCCTATTTAAAGGGTG
ACCTCCGGTGGATGTGGTCTAAGCTATTCCACTCCAAGACCAGTAGCTCCCAATTCCTGGAAGTA

ORF - retro_hsap_1898 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 78.26 %
Parental protein coverage: 89.06 %
Number of stop codons detected: 3
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalQDKEKDSNSSSGSFNGNSTNNSI-QTIDSTQALFLPIGASVSLLVMFFFFDSVQVVFTICTAVLATIAFA
....KD.NSSSGSFNGNSTNNSI.Q.I.STQALFLPIGASVSLL..F.FFD..QVVFTICTAVL..I.FA
RetrocopyESTQKDNNSSSGSFNGNSTNNSI<QIIESTQALFLPIGASVSLLLLFCFFD*AQVVFTICTAVLTMITFA
ParentalFLLLPMCQYLTRPCSPQNKISFGCCGRFTAAELLSFSLSVMLVLIWVLTGHWLLMDALAMGLCVAMIAFV
FLLL.MC.YLTR..SPQNKIS.G..G.FTAAELL..SLSV.L.L.WVLTGH.LLMDA.A.GL....I.FV
RetrocopyFLLLLMCEYLTRLYSPQNKISLGSPGCFTAAELLLLSLSVVLILTWVLTGH*LLMDAMAVGLRLTVIFFV
ParentalRLPSLKVSCLLLSGLLIYDVFWVFFSAYIFNSNVMVKVAT-QPADNPLDVLSRKLHLGPNVGRDVPRLSL
.L...KV.CLLLSGLLIYDVF.V.FSAYIFNS.VMV.VA..Q.A.NPL.VLS.KL.LGP.VGRDVPRLSL
RetrocopyCLLGFKVPCLLLSGLLIYDVF*VVFSAYIFNSSVMVNVAM>QLAENPLYVLSQKLSLGPGVGRDVPRLSL
ParentalPGKLVFPSSTGSHFSMLGIGDIVMPGLLLCFVLRYDNYK-KQASGDSCGAPGPANISGRMQKVSYFHCTL
PGKLVFP.STGSHF.MLGIGDIVMPG.LLCF.L.YDNYK..QA.GDSCG.PGPANISGRMQKV.YFHCTL
RetrocopyPGKLVFPRSTGSHFLMLGIGDIVMPGHLLCFDLHYDNYK<NQARGDSCGGPGPANISGRMQKVFYFHCTL
ParentalIGYFVGLLTATVASRIHRAAQPALLYLVPFTLLPLLTMAYLKGDLRRMWSEPFHSKSSSSRFLEV
.GYFV.LLTATVAS.IH.AAQPALL.LVPFTLLPLL.MAYLKGDLR.MWS..FHSK.SSS.FLEV
RetrocopyMGYFVDLLTATVASHIHQAAQPALLCLVPFTLLPLLMMAYLKGDLRWMWSKLFHSKTSSSQFLEV

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 .00 RPM 44 .07 RPM
bodymap2_adrenal 0 .00 RPM 49 .58 RPM
bodymap2_brain 0 .00 RPM 40 .55 RPM
bodymap2_breast 0 .00 RPM 44 .98 RPM
bodymap2_colon 0 .00 RPM 31 .27 RPM
bodymap2_heart 0 .00 RPM 24 .18 RPM
bodymap2_kidney 0 .00 RPM 43 .62 RPM
bodymap2_liver 0 .00 RPM 16 .14 RPM
bodymap2_lung 0 .00 RPM 29 .48 RPM
bodymap2_lymph_node 0 .00 RPM 45 .21 RPM
bodymap2_ovary 0 .00 RPM 75 .45 RPM
bodymap2_prostate 0 .00 RPM 58 .78 RPM
bodymap2_skeletal_muscle 0 .00 RPM 22 .92 RPM
bodymap2_testis 0 .00 RPM 82 .41 RPM
bodymap2_thyroid 0 .00 RPM 65 .44 RPM
bodymap2_white_blood_cells 0 .00 RPM 59 .22 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_1898 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_1898 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_1898 retrocopy 5' end.

Lab - click to see more details

retro_hsap_1898 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1898 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1275
Gorilla gorilla retro_ggor_1392
Pongo abelii retro_pabe_1578
Parental genes homology:
Parental genes homology involve 10 parental genes, and 11 retrocopies.

Species Parental gene accession Retrocopies number
Dasypus novemcinctus ENSDNOG000000165891 retrocopy
retro_dnov_175,
Homo sapiens ENSG000001386001 retrocopy
retro_hsap_1566,
Homo sapiens ENSG00000157837 1 retrocopy
retro_hsap_1898 ,
Gorilla gorilla ENSGGOG000000162451 retrocopy
retro_ggor_1392,
Myotis lucifugus ENSMLUG000000127541 retrocopy
retro_mluc_672,
Macaca mulatta ENSMMUG000000206501 retrocopy
retro_mmul_1359,
Pongo abelii ENSPPYG000000050412 retrocopies
retro_pabe_1578, retro_pabe_1579,
Pan troglodytes ENSPTRG000000055481 retrocopy
retro_ptro_1275,
Rattus norvegicus ENSRNOG000000011781 retrocopy
retro_rnor_2157,
Sarcophilus harrisii ENSSHAG000000153261 retrocopy
retro_shar_660,

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 .00 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 .03 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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