RetrogeneDB ID:

retro_hsap_3927

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:8:4644921..4646106(+)
Located in intron of:ENSG00000183117
Retrocopy
information
Ensembl ID:ENSG00000254244
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:PAICS
Ensembl ID:ENSG00000128050
Aliases:PAICS, ADE2, ADE2H1, AIRC, PAIS
Description:phosphoribosylaminoimidazole carboxylase, phosphoribosylaminoimidazole succinocarboxamide synthetase [Source:HGNC Symbol;Acc:8587]


Retrocopy-Parental alignment summary:






>retro_hsap_3927
AAAGTCCTCCTGCAGTCCAAGGACAAGATTACAGCAGGAAATGTAGCTAGAAAGAATCACCTGGAAGGAAAAGCTGCAAT
CTCAAAGAAAATCACCAGTTGTATTTTTCAGTTATTATAGGAAGCAGGTATTAAAACTGCCTTCACCAGAAAATGTGGGG
AGACAGCTTTCATTGCACCCCAGTGCGAAATGATTCCAATTGAATGGGTTTGCAGAAGAATAGCAACTGGTTCTTTTCTC
AAAAGAAATCCTGGTGTCAAGGAAGGATATAAGTTTACCCACCTAAAGTGGAGTTGTTTTTCAAGGATGCTGCCAATAAT
GACCCACAGTGGTCTGAGGAACAGCTGATTGCTGCAAAATTTTGCTTCGCTGGACTTGTTACAGGCCAGACTGAATTGGA
TATCATGAGTCATGCTACACAGGCTATATTTGAAATGCTGGAGAAATCCTGGTTGCCCCAGAATTGTACACTGGTTGATA
TGAAGATTGAATTTGGTGTTGATGTAACCACAAAGAAATTGTTCTTGCTGATGTAATTGACAATGATTCCTGGAGACTCT
GGCCATCAGGAGATCGAAGCCAACAGAAAGACAAACAGTGTTATCGGGATCTCAAAGAAGTAACTCCTGAAGGGCTCCAA
ATGGTAAAGAAAAACTTTGAGTGGGTTGCAGAGAAAGTAGAGTTGCTTTTGAAATCAGAAAGTCAGTGCAGGGTTGTAGT
GTTGATGGGCTCTACTTCTGATCTTGGTCACTGTGAAAAAATCAAGAAGGCCTGTGGAAATTTTGGCATTCCATGTGAAC
TTTGAGTAACATCTGCGCATAAAGGACCAGATGAAACTCTGAGGGTTAAAGCTGAGTATGAAAGGGATGGCATTCCTACT
GTATTTGTGGCAGTGGCAGGCAGAAGTAATGGTTTGGGACCAGTGATGTCTGGGAACACTGCATATCCAGTTATCACCTG
TCCTCCCCTCACACCAGACTGGGGAGCTCAGGATGTGTGGTCTTCTCTTTGACTACCCAGGGTCTTGGCTGTTCAACCAC
ACTTTCTCCAGAAGGATCAGCTCAATTTACTGCTCAGATATTTGGGGTAGACAACCATTTAGTATGGAGCAAACTGTGAG
CAAGCATTTTGAACACATGTATTTCCTTGAAGCAGGCTGACAAGAAAATCAGAGAATGTAATTTA

ORF - retro_hsap_3927 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 93.23 %
Parental protein coverage: 93.18 %
Number of stop codons detected: 4
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalKVLLQSKDQITAGNAARKNHLEGKAAISNKITSCIFQLLQEAGIKTAFTRKCGETAFIAPQCEMIPIEWV
KVLLQSKD.ITAGN.ARKNHLEGKAAIS.KITSCIFQLL.EAGIKTAFTRKCGETAFIAPQCEMIPIEWV
RetrocopyKVLLQSKDKITAGNVARKNHLEGKAAISKKITSCIFQLL*EAGIKTAFTRKCGETAFIAPQCEMIPIEWV
ParentalCRRIATGSFLKRNPGVKEGYKF-YPPKVELFFKDDANNDPQWSEEQLIAAKFCFAGLLIGQTEVDIMSHA
CRRIATGSFLKRNPGVKEGYKF.YPPKVELFFKD.ANNDPQWSEEQLIAAKFCFAGL..GQTE.DIMSHA
RetrocopyCRRIATGSFLKRNPGVKEGYKF<YPPKVELFFKDAANNDPQWSEEQLIAAKFCFAGLVTGQTELDIMSHA
ParentalTQAIFEILEKSWLPQNCTLVDMKIEFGVDVTTK-EIVLADVIDNDSWRLWPSGDRSQQKDKQSYRDLKEV
TQAIFE.LEKSWLPQNCTLVDMKIEFGVDVTTK.EIVLADVIDNDSWRLWPSGDRSQQKDKQ.YRDLKEV
RetrocopyTQAIFEMLEKSWLPQNCTLVDMKIEFGVDVTTK<EIVLADVIDNDSWRLWPSGDRSQQKDKQCYRDLKEV
ParentalTPEGLQMVKKNFEWVAERVELLLKSESQCRVVVLMGSTSDLGHCEKIKKACGNFGIPCELRVTSAHKGPD
TPEGLQMVKKNFEWVAE.VELLLKSESQCRVVVLMGSTSDLGHCEKIKKACGNFGIPCEL.VTSAHKGPD
RetrocopyTPEGLQMVKKNFEWVAEKVELLLKSESQCRVVVLMGSTSDLGHCEKIKKACGNFGIPCEL*VTSAHKGPD
ParentalETLRIKAEYEGDGIPTVFVAVAGRSNGLGPVMSGNTAYPVISCPPLTPDWGVQDVWSSLRLP-SGLGCST
ETLR.KAEYE.DGIPTVFVAVAGRSNGLGPVMSGNTAYPVI.CPPLTPDWG.QDVWSSL.LP..GLGCST
RetrocopyETLRVKAEYERDGIPTVFVAVAGRSNGLGPVMSGNTAYPVITCPPLTPDWGAQDVWSSL*LP<QGLGCST
ParentalVLSPEGSAQFAAQIFGLSNHLVWSKLRASILNTWISLKQADKKIRECNL
.LSPEGSAQF.AQIFG..NHLVWSKL.ASILNT.ISLKQADKKIRECNL
RetrocopyTLSPEGSAQFTAQIFGVDNHLVWSKL*ASILNTCISLKQADKKIRECNL

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 .06 RPM 39 .04 RPM
bodymap2_adrenal 0 .00 RPM 67 .77 RPM
bodymap2_brain 0 .07 RPM 66 .24 RPM
bodymap2_breast 0 .04 RPM 43 .09 RPM
bodymap2_colon 0 .02 RPM 64 .76 RPM
bodymap2_heart 0 .00 RPM 25 .55 RPM
bodymap2_kidney 0 .06 RPM 85 .35 RPM
bodymap2_liver 0 .02 RPM 99 .70 RPM
bodymap2_lung 0 .00 RPM 38 .77 RPM
bodymap2_lymph_node 0 .00 RPM 51 .88 RPM
bodymap2_ovary 0 .00 RPM 92 .41 RPM
bodymap2_prostate 0 .00 RPM 65 .82 RPM
bodymap2_skeletal_muscle 0 .02 RPM 42 .56 RPM
bodymap2_testis 0 .00 RPM 78 .96 RPM
bodymap2_thyroid 0 .00 RPM 59 .53 RPM
bodymap2_white_blood_cells 0 .00 RPM 32 .98 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3927 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3927 retrocopy.

TSS - click to see more details



TSS No. TSS Name TSS expression level (Expr) in TPM range:
no expression 0 < Expr ≤ 1 1 < Expr ≤ 5 5 < Expr ≤ 10 Expr > 10
TSS #1 TSS_184978227 libraries151 libraries701 libraries365 libraries385 libraries

The graphical summary, for retro_hsap_3927 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1829 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Display detail expression values in each library
... or ...
Directly download all expression values

Lab - click to see more details

retro_hsap_3927 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3927 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2670
Gorilla gorilla retro_ggor_2643
Parental genes homology:
Parental genes homology involve 15 parental genes, and 29 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000105771 retrocopy
retro_btau_508,
Cavia porcellus ENSCPOG000000107491 retrocopy
retro_cpor_969,
Dasypus novemcinctus ENSDNOG000000134131 retrocopy
retro_dnov_284,
Echinops telfairi ENSETEG000000152422 retrocopies
retro_etel_1918, retro_etel_341,
Homo sapiens ENSG00000128050 3 retrocopies
retro_hsap_3802, retro_hsap_3915, retro_hsap_3927 ,
Gorilla gorilla ENSGGOG000000243921 retrocopy
retro_ggor_2643,
Mus musculus ENSMUSG000000292476 retrocopies
retro_mmus_1748, retro_mmus_2750, retro_mmus_2858, retro_mmus_3126, retro_mmus_653, retro_mmus_971,
Nomascus leucogenys ENSNLEG000000087862 retrocopies
retro_nleu_1274, retro_nleu_2156,
Otolemur garnettii ENSOGAG000000035752 retrocopies
retro_ogar_2138, retro_ogar_865,
Procavia capensis ENSPCAG000000085311 retrocopy
retro_pcap_172,
Pan troglodytes ENSPTRG000000160812 retrocopies
retro_ptro_2662, retro_ptro_2670,
Rattus norvegicus ENSRNOG000000021013 retrocopies
retro_rnor_1891, retro_rnor_2768, retro_rnor_804,
Tupaia belangeri ENSTBEG000000067511 retrocopy
retro_tbel_3697,
Tarsius syrichta ENSTSYG000000104972 retrocopies
retro_tsyr_2170, retro_tsyr_329,
Drosophila melanogaster FBgn00205131 retrocopy
retro_dmel_82,

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 = 0.47 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .09 RPM
CEU_NA11843 0 .14 RPM
CEU_NA11930 0 .23 RPM
CEU_NA12004 0 .04 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .07 RPM
CEU_NA12760 0 .09 RPM
CEU_NA12827 0 .05 RPM
CEU_NA12872 0 .14 RPM
CEU_NA12873 0 .06 RPM
FIN_HG00183 0 .11 RPM
FIN_HG00277 0 .11 RPM
FIN_HG00315 0 .11 RPM
FIN_HG00321 0 .15 RPM
FIN_HG00328 0 .07 RPM
FIN_HG00338 0 .11 RPM
FIN_HG00349 0 .20 RPM
FIN_HG00375 0 .20 RPM
FIN_HG00377 0 .20 RPM
FIN_HG00378 0 .19 RPM
GBR_HG00099 0 .20 RPM
GBR_HG00111 0 .11 RPM
GBR_HG00114 0 .16 RPM
GBR_HG00119 0 .10 RPM
GBR_HG00131 0 .09 RPM
GBR_HG00133 0 .07 RPM
GBR_HG00134 0 .22 RPM
GBR_HG00137 0 .14 RPM
GBR_HG00142 0 .25 RPM
GBR_HG00143 0 .13 RPM
TSI_NA20512 0 .08 RPM
TSI_NA20513 0 .17 RPM
TSI_NA20518 0 .47 RPM
TSI_NA20532 0 .24 RPM
TSI_NA20538 0 .09 RPM
TSI_NA20756 0 .17 RPM
TSI_NA20765 0 .10 RPM
TSI_NA20771 0 .11 RPM
TSI_NA20786 0 .13 RPM
TSI_NA20798 0 .09 RPM
YRI_NA18870 0 .10 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .08 RPM
YRI_NA19093 0 .08 RPM
YRI_NA19099 0 .11 RPM
YRI_NA19114 0 .16 RPM
YRI_NA19118 0 .08 RPM
YRI_NA19213 0 .07 RPM
YRI_NA19214 0 .00 RPM
YRI_NA19223 0 .10 RPM

Indel association:

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





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