RetrogeneDB ID:

retro_hsap_2593

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:22:42503771..42504957(-)
Located in intron of:ENSG00000237037
Retrocopy
information
Ensembl ID:ENSG00000213790
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:OLA1
Ensembl ID:ENSG00000138430
Aliases:OLA1, DOC45, GBP45, GTBP9, GTPBP9
Description:Obg-like ATPase 1 [Source:HGNC Symbol;Acc:28833]


Retrocopy-Parental alignment summary:






>retro_hsap_2593
ATGCCCCCTCAAAAGGGAGGTGATGGAATTAAACCACCCCCAATCATTGGAAGATTTGGAACCTCACTGAAAATTGGTAT
TGTTGGATTGCCAAATGTTGGGAAATCTACTTTCTTCAATGTATTAACCAATAGTCAGGCTTCAGCAGAAAACTTCCCAT
TCTGCACTATTGATCCTAATGAGAGCAGAGTACCTGTGCCAGATGAAAGGTTTGACTTTCTTTGCCAATATCACAAACCA
GCAAGCAAAATTCCTGCCTTTCTAAATGTAGTGGATATTGCTGGCCTTGTGAAAGGAGCTCACAATGGGCAGGGCCTGGG
GAATGCTTTTTTATCTCATTTTAGTGCTTGTGATGGCATCTTTCATCTAACACGTGCTTTTGAAGATGATGATATCACAC
ATGTTGAAGAAAGTGTAGATCCTATTCGAGATATAGAAATAATACATGAAGAGCTTCAGCTTAAAGATGAGGAATGACTG
GGCCCATTATAGATAAACTAGAAAAGGTGGCTGTGAGAGGAGGAGATAAAAAACTAAAACCCAAATATGATATAATGTGC
AAAGTAAAATCCTGGGTTATAGATCAAAAGAACCTGTTCGCTTCTATCATGATTGGAATGACAAAGAGATTGAAGTGTTG
AATAAACACTTATTTTTGACTTCAAAACCAATGGTCTACTTGGTTAATCTTTCTGAAAAAGACTACATTAGAAAGAAAAA
CAAATGGCTGATAAAAATTAAAGAGTGGGTGGACAAGTATGACCCAGGTGCCTTGGTCATTCCTTTTAGTGGGGCCTTGG
AACTCAAGTTGCAAGAATTGAGTGCTGAGGAGAGACAGCAGTATCTGGAAGCGAACATGACACAAAGTGCTTTGCCAAAG
ATCATTAAGGCTGGGTTTGCAGCACTCCAACTAAAATACTTTTTCACTGCAGGCCCAGATGAAGTGCGTGCACGGACCAT
CAGGAAAGGGACTAAGGCTCCTCAGGCTGCAGGAAAGATTCACACAGATTTTGAAAAGGGATTCATTATGGCTGAAGTAA
TGAAATATGAAGATTTTAAAGAGGAAGGTTCTGAAAATGCAGTCAAGGCTGCTGGAAAGTACAGACAACAAGGCAGAAAT
TATATTGTTGAAGATGGAGATATTATCTTCTTCAAATTTAACACACCTTAACAACTGAAGAAGAAA

ORF - retro_hsap_2593 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 96.73 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMPPKKGGDGIKPPPIIGRFGTSLKIGIVGLPNVGKSTFFNVLTNSQASAENFPFCTIDPNESRVPVPDER
MPP.KGGDGIKPPPIIGRFGTSLKIGIVGLPNVGKSTFFNVLTNSQASAENFPFCTIDPNESRVPVPDER
RetrocopyMPPQKGGDGIKPPPIIGRFGTSLKIGIVGLPNVGKSTFFNVLTNSQASAENFPFCTIDPNESRVPVPDER
ParentalFDFLCQYHKPASKIPAFLNVVDIAGLVKGAHNGQGLGNAFLSHISACDGIFHLTRAFEDDDITHVEGSVD
FDFLCQYHKPASKIPAFLNVVDIAGLVKGAHNGQGLGNAFLSH.SACDGIFHLTRAFEDDDITHVE.SVD
RetrocopyFDFLCQYHKPASKIPAFLNVVDIAGLVKGAHNGQGLGNAFLSHFSACDGIFHLTRAFEDDDITHVEESVD
ParentalPIRDIEIIHEELQLKDEE-MIGPIIDKLEKVAVRGGDKKLKPEYDIMCKVKSWVIDQK-KPVRFYHDWND
PIRDIEIIHEELQLKDEE.M.GPIIDKLEKVAVRGGDKKLKP.YDIMCKVKSWVIDQK..PVRFYHDWND
RetrocopyPIRDIEIIHEELQLKDEE<MTGPIIDKLEKVAVRGGDKKLKPKYDIMCKVKSWVIDQK<EPVRFYHDWND
ParentalKEIEVLNKHLFLTSKPMVYLVNLSEKDYIRKKNKWLIKIKEWVDKYDPGALVIPFSGALELKLQELSAEE
KEIEVLNKHLFLTSKPMVYLVNLSEKDYIRKKNKWLIKIKEWVDKYDPGALVIPFSGALELKLQELSAEE
RetrocopyKEIEVLNKHLFLTSKPMVYLVNLSEKDYIRKKNKWLIKIKEWVDKYDPGALVIPFSGALELKLQELSAEE
ParentalRQKYLEANMTQSALPKIIKAGFAALQLEYFFTAGPDEVRAWTIRKGTKAPQAAGKIHTDFEKGFIMAEVM
RQ.YLEANMTQSALPKIIKAGFAALQL.YFFTAGPDEVRA.TIRKGTKAPQAAGKIHTDFEKGFIMAEVM
RetrocopyRQQYLEANMTQSALPKIIKAGFAALQLKYFFTAGPDEVRARTIRKGTKAPQAAGKIHTDFEKGFIMAEVM
ParentalKYEDFKEEGSENAVKAAGKYRQQGRNYIVEDGDIIFFKFNTPQQPKKK
KYEDFKEEGSENAVKAAGKYRQQGRNYIVEDGDIIFFKFNTP.Q.KKK
RetrocopyKYEDFKEEGSENAVKAAGKYRQQGRNYIVEDGDIIFFKFNTP*QLKKK

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 .60 RPM 59 .18 RPM
bodymap2_adrenal 0 .49 RPM 59 .57 RPM
bodymap2_brain 0 .75 RPM 133 .23 RPM
bodymap2_breast 0 .49 RPM 72 .59 RPM
bodymap2_colon 0 .73 RPM 87 .88 RPM
bodymap2_heart 0 .59 RPM 51 .82 RPM
bodymap2_kidney 0 .35 RPM 73 .99 RPM
bodymap2_liver 0 .27 RPM 34 .71 RPM
bodymap2_lung 0 .60 RPM 41 .77 RPM
bodymap2_lymph_node 0 .69 RPM 48 .96 RPM
bodymap2_ovary 0 .79 RPM 59 .76 RPM
bodymap2_prostate 2 .34 RPM 83 .02 RPM
bodymap2_skeletal_muscle 1 .44 RPM 104 .11 RPM
bodymap2_testis 0 .89 RPM 94 .27 RPM
bodymap2_thyroid 0 .26 RPM 75 .31 RPM
bodymap2_white_blood_cells 1 .20 RPM 65 .44 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2593 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2593 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_109359985 libraries763 libraries81 libraries0 libraries0 libraries

The graphical summary, for retro_hsap_2593 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_2593 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2593 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1517
Gorilla gorilla retro_ggor_1623
Pongo abelii retro_pabe_1912
Parental genes homology:
Parental genes homology involve 15 parental genes, and 18 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000069701 retrocopy
retro_btau_1737,
Choloepus hoffmanni ENSCHOG000000050441 retrocopy
retro_chof_1295,
Callithrix jacchus ENSCJAG000000078771 retrocopy
retro_cjac_2875,
Dipodomys ordii ENSDORG000000086811 retrocopy
retro_dord_556,
Homo sapiens ENSG00000138430 1 retrocopy
retro_hsap_2593 ,
Gorilla gorilla ENSGGOG000000222151 retrocopy
retro_ggor_1623,
Myotis lucifugus ENSMLUG000000251961 retrocopy
retro_mluc_626,
Monodelphis domestica ENSMODG000000092961 retrocopy
retro_mdom_1428,
Nomascus leucogenys ENSNLEG000000058171 retrocopy
retro_nleu_1526,
Otolemur garnettii ENSOGAG000000165571 retrocopy
retro_ogar_1697,
Pongo abelii ENSPPYG000000129432 retrocopies
retro_pabe_1912, retro_pabe_928,
Pan troglodytes ENSPTRG000000126501 retrocopy
retro_ptro_1517,
Sorex araneus ENSSARG000000107431 retrocopy
retro_sara_545,
Tarsius syrichta ENSTSYG000000055172 retrocopies
retro_tsyr_1845, retro_tsyr_394,
Vicugna pacos ENSVPAG000000096602 retrocopies
retro_vpac_52, retro_vpac_613,

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 = 0.58 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .17 RPM
CEU_NA11843 0 .20 RPM
CEU_NA11930 0 .33 RPM
CEU_NA12004 0 .11 RPM
CEU_NA12400 0 .21 RPM
CEU_NA12751 0 .10 RPM
CEU_NA12760 0 .40 RPM
CEU_NA12827 0 .28 RPM
CEU_NA12872 0 .16 RPM
CEU_NA12873 0 .16 RPM
FIN_HG00183 0 .49 RPM
FIN_HG00277 0 .30 RPM
FIN_HG00315 0 .08 RPM
FIN_HG00321 0 .21 RPM
FIN_HG00328 0 .12 RPM
FIN_HG00338 0 .09 RPM
FIN_HG00349 0 .26 RPM
FIN_HG00375 0 .22 RPM
FIN_HG00377 0 .10 RPM
FIN_HG00378 0 .11 RPM
GBR_HG00099 0 .26 RPM
GBR_HG00111 0 .13 RPM
GBR_HG00114 0 .11 RPM
GBR_HG00119 0 .10 RPM
GBR_HG00131 0 .17 RPM
GBR_HG00133 0 .14 RPM
GBR_HG00134 0 .11 RPM
GBR_HG00137 0 .14 RPM
GBR_HG00142 0 .06 RPM
GBR_HG00143 0 .06 RPM
TSI_NA20512 0 .08 RPM
TSI_NA20513 0 .17 RPM
TSI_NA20518 0 .58 RPM
TSI_NA20532 0 .17 RPM
TSI_NA20538 0 .32 RPM
TSI_NA20756 0 .12 RPM
TSI_NA20765 0 .17 RPM
TSI_NA20771 0 .14 RPM
TSI_NA20786 0 .13 RPM
TSI_NA20798 0 .06 RPM
YRI_NA18870 0 .27 RPM
YRI_NA18907 0 .10 RPM
YRI_NA18916 0 .11 RPM
YRI_NA19093 0 .08 RPM
YRI_NA19099 0 .13 RPM
YRI_NA19114 0 .18 RPM
YRI_NA19118 0 .17 RPM
YRI_NA19213 0 .14 RPM
YRI_NA19214 0 .05 RPM
YRI_NA19223 0 .06 RPM

Indel association:

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



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