RetrogeneDB ID:

retro_hsap_174

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:1:79214736..79216341(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000235400
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:SNW1
Ensembl ID:ENSG00000100603
Aliases:SNW1, Bx42, NCOA-62, PRPF45, Prp45, SKIIP, SKIP
Description:SNW domain containing 1 [Source:HGNC Symbol;Acc:16696]


Retrocopy-Parental alignment summary:






>retro_hsap_174
ATAGCGTTGCCAGATAAAACACCTGCACCTACTCAGTTATCTCAGGACCAGCTTGAGGCTGAAGAAAAGACAAGATCCCA
GAGATCATGGCAGACTTCATTTGTCTCTTCCGGAAGAGAACCTTCCCGGTAAAGATACCGGAAAGGCTGGACGCTTCGGT
TATTAGAGGATTTTGGAGATGGAGGTGCTTTTCCAGAAATCCATGTGGCTCAGTATCCACTGGATATGGGACGAAAGAAA
AAAATATCTAGTGCGCTGGCCATTCAGGTGGATTCTGAAGGAAAAATCAAATATGATGGAATCACTCGACAAGGACAGTC
AAAAGACAAGGTCATTTATAGCAAATACACTGTCCTGGTTCCAAAGGATGTTACGAATGCAAATGATCCAGACTTGCAAA
GGCCCGATGAAGAAGCTATAAAAGAGATAACAGAAAAGACAAGAGTAGCCTTATAAAAAGCTGTACCACAGAAGGTCACC
GCAGTCACGCCAGTTCAGGCAGCTGACAAACCGGCTCCTGCTCAGTATATCCGATACACACCATCTCAGCAAGGAGTGGC
TTTCAACTCTGGAGTTAAACAGAGGGTTAGTCGGATGGTAGAAGTGCAGAAAGATCCAACGGAGCCTCCAAGGTTCAAGA
TTAATAAGAAAATTCCCCGGGGACCACCTTCTCCTCCTGTGCCTGTCATGCATTCTCCTAGCCGAAAGATGATTGTAAGG
GAACAGCAAGAGTAAAAGTTTCCTCCTTTTATTTCTAACTGGAAAAATGCAAAGGGTTATACAATTCCATTAGACAAACG
TCTGGCTGCCGAAGGAAGAGGACTACAGACAGTACACATAAAAGAAAATGTTGCCACATTGGTGATCCTCTACATTGCTG
ATCAGAAGGCTTGTGAAGCTGTGGAAATGCGTGCCCGAGTAGAGAGAAAAATGGCTCAGAAAGAAAAGGGAAAATATGAA
GAGAAACTTAGAGAAATGGCACAGAAAGCCAGGGAGAGAAGAGCTGGGATCAAAACTCATGTGGAAAAAGAGGATAGGGA
GGCACGTGAGAGGAATGAAATCCGGCATGACAGGCGAAAAGAGAGACAGCATGACCAGAATCTTTCCAGGGCAGCTCCTG
ATAAGAGGTCGAAACTGCAGAGAAATGAAAATGGGGATATCAGTGAAGTCATTGCTCTCTGTGTTCCTAATCCTTGAACT
TCCAATGAAGGTCAGTACGACCAAAGGCTCGTCAACCAATCCAAGGGTATGGACAGTGGATTTGCAGGTGGAGAAGATGG
AATTTATAATGTTTATGATCAAGCCTAGAGAGGTGGTAAAGATATGGCCCACAGTAGTTATAGGCCCAGTAAAAATCTGG
ACAAGGACATGTATAACGATGACCTAGAACCCAGAATAAAGACCAACAGATTTGTTCCCGACAAAGAGTTTTCTGGTTCA
GGCTGTAAGCAGAGAGGCCGAGAAGGACCAGTTCAGTTTGAGGAAGATCCTTTTGGTTTGGACAAGTTTTTGGAAGAAGT
GAAACAGCACGGTGGCTCTAAAAGACCCTCAGATAGCAGCCGCCCCATGGAATATGAGCATGAAGGCAAGAAGAGGAGGA
AGGAC

ORF - retro_hsap_174 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 86.19 %
Parental protein coverage: 100. %
Number of stop codons detected: 5
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMALTSFLPAPTQLSQDQLEAEEKARSQRSRQTSLVSSRREPPPYGYRKGWIPRLLEDFGDGGAFPEIHVA
.AL....PAPTQLSQDQLEAEEK.RSQRS.QTS.VSS.REP....YRKGW..RLLEDFGDGGAFPEIHVA
RetrocopyIALPDKTPAPTQLSQDQLEAEEKTRSQRSWQTSFVSSGREPSR*RYRKGWTLRLLEDFGDGGAFPEIHVA
ParentalQYPLDMGRKKKMSNALAIQVDSEGKIKYDAIARQGQSKDKVIYSKYTDLVPKEVMNADDPDLQRPDEEAI
QYPLDMGRKKK.S.ALAIQVDSEGKIKYD.I.RQGQSKDKVIYSKYT.LVPK.V.NA.DPDLQRPDEEAI
RetrocopyQYPLDMGRKKKISSALAIQVDSEGKIKYDGITRQGQSKDKVIYSKYTVLVPKDVTNANDPDLQRPDEEAI
ParentalKEITEKTRVALEKSVSQKVAAAMPVRAADKLAPAQYIRYTPSQQGVAFNSGAKQRVIRMVEMQKDPMEPP
KEITEKTRVAL.K.V.QKV.A..PV.AADK.APAQYIRYTPSQQGVAFNSG.KQRV.RMVE.QKDP.EPP
RetrocopyKEITEKTRVAL*KAVPQKVTAVTPVQAADKPAPAQYIRYTPSQQGVAFNSGVKQRVSRMVEVQKDPTEPP
ParentalRFKINKKIPRGPPSPPAPVMHSPSRKMTVKEQQEWKIPPCISNWKNAKGYTIPLDKRLAADGRGLQTVHI
RFKINKKIPRGPPSPP.PVMHSPSRKM.V.EQQE.K.PP.ISNWKNAKGYTIPLDKRLAA.GRGLQTVHI
RetrocopyRFKINKKIPRGPPSPPVPVMHSPSRKMIVREQQE*KFPPFISNWKNAKGYTIPLDKRLAAEGRGLQTVHI
ParentalNENFAKLAEALYIADRKAREAVEMRAQVERKMAQKEKEKHEEKLREMAQKARERRAGIKTHVEKEDGEAR
.EN.A.L...LYIAD.KA.EAVEMRA.VERKMAQKEK.K.EEKLREMAQKARERRAGIKTHVEKED.EAR
RetrocopyKENVATLV-ILYIADQKACEAVEMRARVERKMAQKEKGKYEEKLREMAQKARERRAGIKTHVEKEDREAR
ParentalERDEIRHDRRKERQHDRNLSRAAPDKRSKLQRNENRDISEVIALGVPNPRTSNEVQYDQRLFNQSKGMDS
ER.EIRHDRRKERQHD.NLSRAAPDKRSKLQRNEN.DISEVIAL.VPNP.TSNE.QYDQRL.NQSKGMDS
RetrocopyERNEIRHDRRKERQHDQNLSRAAPDKRSKLQRNENGDISEVIALCVPNP*TSNEGQYDQRLVNQSKGMDS
ParentalGFAGGEDEIYNVYDQAWRGGKDMAQSIYRPSKNLDKDMYGDDLEARIKTNRFVPDKEFSGSDRRQRGREG
GFAGGED.IYNVYDQA.RGGKDMA.S.YRPSKNLDKDMY.DDLE.RIKTNRFVPDKEFSGS...QRGREG
RetrocopyGFAGGEDGIYNVYDQA*RGGKDMAHSSYRPSKNLDKDMYNDDLEPRIKTNRFVPDKEFSGSGCKQRGREG
ParentalPVQFEEDPFGLDKFLEEAKQHGGSKRPSDSSRPKEHEHEGKKRRKE
PVQFEEDPFGLDKFLEE.KQHGGSKRPSDSSRP.E.EHEGKKRRK.
RetrocopyPVQFEEDPFGLDKFLEEVKQHGGSKRPSDSSRPMEYEHEGKKRRKD

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 75 .75 RPM
bodymap2_adrenal 0 .10 RPM 66 .69 RPM
bodymap2_brain 0 .38 RPM 55 .32 RPM
bodymap2_breast 0 .02 RPM 58 .70 RPM
bodymap2_colon 0 .46 RPM 66 .28 RPM
bodymap2_heart 0 .00 RPM 30 .77 RPM
bodymap2_kidney 0 .43 RPM 44 .53 RPM
bodymap2_liver 0 .00 RPM 22 .07 RPM
bodymap2_lung 0 .00 RPM 64 .21 RPM
bodymap2_lymph_node 0 .11 RPM 54 .18 RPM
bodymap2_ovary 0 .12 RPM 85 .28 RPM
bodymap2_prostate 0 .00 RPM 71 .17 RPM
bodymap2_skeletal_muscle 0 .04 RPM 55 .13 RPM
bodymap2_testis 0 .83 RPM 127 .22 RPM
bodymap2_thyroid 0 .09 RPM 87 .38 RPM
bodymap2_white_blood_cells 0 .02 RPM 91 .78 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_174 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_174 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_174 retrocopy 5' end.

Lab - click to see more details

retro_hsap_174 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_174 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_165
Gorilla gorilla retro_ggor_257
Pongo abelii retro_pabe_454
Callithrix jacchus retro_cjac_2932
Parental genes homology:
Parental genes homology involve 18 parental genes, and 27 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000039762 retrocopies
retro_amel_163, retro_amel_912,
Canis familiaris ENSCAFG000000304091 retrocopy
retro_cfam_195,
Dipodomys ordii ENSDORG000000123803 retrocopies
retro_dord_693, retro_dord_781, retro_dord_782,
Felis catus ENSFCAG000000016371 retrocopy
retro_fcat_635,
Homo sapiens ENSG00000100603 1 retrocopy
retro_hsap_174 ,
Gorilla gorilla ENSGGOG000000260161 retrocopy
retro_ggor_257,
Loxodonta africana ENSLAFG000000034822 retrocopies
retro_lafr_474, retro_lafr_787,
Myotis lucifugus ENSMLUG000000052282 retrocopies
retro_mluc_387, retro_mluc_805,
Monodelphis domestica ENSMODG000000052521 retrocopy
retro_mdom_1841,
Mustela putorius furoENSMPUG000000087241 retrocopy
retro_mputfur_551,
Mus musculus ENSMUSG000000210392 retrocopies
retro_mmus_1022, retro_mmus_387,
Nomascus leucogenys ENSNLEG000000167711 retrocopy
retro_nleu_982,
Ochotona princeps ENSOPRG000000075681 retrocopy
retro_opri_737,
Pongo abelii ENSPPYG000000060311 retrocopy
retro_pabe_454,
Pan troglodytes ENSPTRG000000065871 retrocopy
retro_ptro_165,
Sorex araneus ENSSARG000000022793 retrocopies
retro_sara_403, retro_sara_568, retro_sara_727,
Taeniopygia guttata ENSTGUG000000123402 retrocopies
retro_tgut_15, retro_tgut_30,
Tarsius syrichta ENSTSYG000000109511 retrocopy
retro_tsyr_1871,

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 = 0.13 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 .04 RPM
CEU_NA12751 0 .02 RPM
CEU_NA12760 0 .13 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .00 RPM
CEU_NA12873 0 .03 RPM
FIN_HG00183 0 .03 RPM
FIN_HG00277 0 .00 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .03 RPM
FIN_HG00328 0 .02 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .00 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .03 RPM
FIN_HG00378 0 .00 RPM
GBR_HG00099 0 .00 RPM
GBR_HG00111 0 .02 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 .03 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 .03 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .06 RPM
YRI_NA18870 0 .00 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .00 RPM
YRI_NA19093 0 .00 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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