RetrogeneDB ID:

retro_hsap_236

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:1:158424040..158425060(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000236257
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:EI24
Ensembl ID:ENSG00000149547
Aliases:EI24, EPG4, PIG8, TP53I8
Description:etoposide induced 2.4 [Source:HGNC Symbol;Acc:13276]


Retrocopy-Parental alignment summary:






>retro_hsap_236
ATGGCTGACAGTGTCAAAACCTTTCTTCAGGACCTTGCCAGAGGAATCAAAGACTCCACCTGGGCTGTTTGTACCATCTC
AAAGCTAGATGCTCAAATCCAGGAAAAGAGAGAGGAGCAGCCTTGAAGAAGGGCAAGTAGTGTCTTGGCCCAAAGAAGAG
CCCAGCATATAGAGTGGAGGCAAGAGAGTGAGCCATGCGTTGTTAGTAGAATTTTCCAGCGTTGTGCTTGGAATGGTGGA
GTGTTGTTGTTCAGTCTCCTTTTGTTTTATCGAGTATTTATTCCTGTGCTTCAGTCAGTAACAGCCCAAATTATTGGTGA
TCCATCACTACATGGAGATGTTTGGTAGTGGCTGGAATTCTTCCTCAGGTCAATTTTCAATGCTCTTTGGGTGCTCCCCT
TGTTTGTGCTTAGCAAAGTAGTGAATGCCATTTGGTTCCAGGATATAGCTGACCTGACAATTGAGGTATCAGGGAGGAAG
CCTCACCCATTCCCTAGTGTCAGCAAAATAATTGCTGACATGCTCTTCAACCTTTTGCTGCAGGCTCTTTTCCCCATTCA
GGGAATGTTTGTGATTCTCTTTCTCATCCATCTTGTAGGTCAGCTGGTTAGTCTCCTGCATATGTCCCTTCTCTAGTCAC
TGTACTGCTTTGAATATCGTTGGTTCAGTAAAGGAACTGAAATACACCAGCAGTTGTCTAACATAGAGAGCAATTGGCCT
TACTACTTTGGGTTTGGTTTGCCCTTGGCTTTTCTCATAGCAATGCAGTCCTCATATACTATCAGCAGCTGCCTTTTCTC
TATCCTCTTTCCTTTATTCATTATCAGCGCCAATGAAGCAAAGACCCCTGGAAAAGCGTATCTCTTCCAGTTGTGCCTGT
TCTCCTTGGTGGTCTTCTTAAGCAACAGACTCTTCCACAAGACAGTCTACCTGCAGTCTGTCCTGAGCAGCTCCACTTCT
GCAGAGAAGTTCCCTTCACCTCATCCGTCTCTTGCCAAACTGAAGGCTACTGCAGGCCAC

ORF - retro_hsap_236 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 89.12 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 3
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalMADSVKTFLQDLARGIKDSIWGICTISKLDARIQQKREEQRRRRASSVLAQRRAQSIERKQESEPRIVSR
MADSVKTFLQDLARGIKDS.W..CTISKLDA.IQ.KREEQ..RRASSVLAQRRAQ.IE..QESEP..VSR
RetrocopyMADSVKTFLQDLARGIKDSTWAVCTISKLDAQIQEKREEQP*RRASSVLAQRRAQHIEWRQESEPCVVSR
ParentalIFQCCAWNGGVFWFSLLLFYRVFIPVLQSVTARIIGDPSLHGDVWSWLEFFLTSIFSALWVLPLFVLSKV
IFQ.CAWNGGV..FSLLLFYRVFIPVLQSVTA.IIGDPSLHGDVW.WLEFFL.SIF.ALWVLPLFVLSKV
RetrocopyIFQRCAWNGGVLLFSLLLFYRVFIPVLQSVTAQIIGDPSLHGDVW*WLEFFLRSIFNALWVLPLFVLSKV
ParentalVNAIWFQDIADLAFEVSGRKPHPFPSVSKIIADMLFNLLLQALFLIQGMFVSLFPIHLVGQLVSLLHMSL
VNAIWFQDIADL..EVSGRKPHPFPSVSKIIADMLFNLLLQALF.IQGMFV.LF.IHLVGQLVSLLHMSL
RetrocopyVNAIWFQDIADLTIEVSGRKPHPFPSVSKIIADMLFNLLLQALFPIQGMFVILFLIHLVGQLVSLLHMSL
ParentalLYSLYCFEYRWFNKGIEMHQRLSNIERNWPYYFGFGLPLAFLTAMQSSYIISGCLFSILFPLFIISANEA
L.SLYCFEYRWF.KG.E.HQ.LSNIE.NWPYYFGFGLPLAFL.AMQSSY.IS.CLFSILFPLFIISANEA
RetrocopyL*SLYCFEYRWFSKGTEIHQQLSNIESNWPYYFGFGLPLAFLIAMQSSYTISSCLFSILFPLFIISANEA
ParentalK-PGKAYLFQLRLFSLVVFLSNRLFHKTVYLQSALSSSTSAEKFPSPHPSPAKLKATAGH
K.PGKAYLFQL.LFSLVVFLSNRLFHKTVYLQS.LSSSTSAEKFPSPHPS.AKLKATAGH
RetrocopyKTPGKAYLFQLCLFSLVVFLSNRLFHKTVYLQSVLSSSTSAEKFPSPHPSLAKLKATAGH

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 .04 RPM 91 .18 RPM
bodymap2_adrenal 0 .02 RPM 70 .31 RPM
bodymap2_brain 0 .00 RPM 47 .33 RPM
bodymap2_breast 0 .00 RPM 77 .45 RPM
bodymap2_colon 0 .00 RPM 106 .21 RPM
bodymap2_heart 0 .00 RPM 55 .29 RPM
bodymap2_kidney 0 .00 RPM 89 .30 RPM
bodymap2_liver 0 .00 RPM 182 .28 RPM
bodymap2_lung 0 .00 RPM 80 .36 RPM
bodymap2_lymph_node 0 .11 RPM 60 .49 RPM
bodymap2_ovary 0 .04 RPM 95 .44 RPM
bodymap2_prostate 0 .00 RPM 104 .15 RPM
bodymap2_skeletal_muscle 0 .04 RPM 71 .95 RPM
bodymap2_testis 0 .15 RPM 70 .19 RPM
bodymap2_thyroid 0 .21 RPM 66 .96 RPM
bodymap2_white_blood_cells 0 .00 RPM 33 .94 RPM

ChIP-Seq - click to see more details

RNA Polymerase II activity near the 5' end of retro_hsap_236 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_236 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_236 retrocopy 5' end.

Lab - click to see more details

retro_hsap_236 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_236 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_206
Pongo abelii retro_pabe_416
Parental genes homology:
Parental genes homology involve 26 parental genes, and 69 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000009902 retrocopies
retro_amel_1449, retro_amel_1681,
Bos taurus ENSBTAG000000072022 retrocopies
retro_btau_1242, retro_btau_443,
Canis familiaris ENSCAFG000000108981 retrocopy
retro_cfam_1829,
Choloepus hoffmanni ENSCHOG000000126693 retrocopies
retro_chof_1433, retro_chof_1994, retro_chof_804,
Cavia porcellus ENSCPOG000000072722 retrocopies
retro_cpor_132, retro_cpor_929,
Dasypus novemcinctus ENSDNOG000000023624 retrocopies
retro_dnov_1083, retro_dnov_1421, retro_dnov_2143, retro_dnov_2345,
Equus caballus ENSECAG000000158611 retrocopy
retro_ecab_1022,
Erinaceus europaeus ENSEEUG000000032741 retrocopy
retro_eeur_435,
Felis catus ENSFCAG000000151001 retrocopy
retro_fcat_1754,
Homo sapiens ENSG00000149547 3 retrocopies
retro_hsap_236 , retro_hsap_2782, retro_hsap_3804,
Loxodonta africana ENSLAFG0000001088815 retrocopies
retro_lafr_262, retro_lafr_263, retro_lafr_264, retro_lafr_265, retro_lafr_394, retro_lafr_395, retro_lafr_396, retro_lafr_397, retro_lafr_398, retro_lafr_399, retro_lafr_566, retro_lafr_589, retro_lafr_626, retro_lafr_627, retro_lafr_999,
Microcebus murinus ENSMICG000000030233 retrocopies
retro_mmur_398, retro_mmur_498, retro_mmur_632,
Myotis lucifugus ENSMLUG000000015831 retrocopy
retro_mluc_1249,
Macaca mulatta ENSMMUG000000100093 retrocopies
retro_mmul_1443, retro_mmul_1653, retro_mmul_2244,
Nomascus leucogenys ENSNLEG000000074513 retrocopies
retro_nleu_2149, retro_nleu_684, retro_nleu_853,
Oryctolagus cuniculus ENSOCUG000000146701 retrocopy
retro_ocun_1578,
Otolemur garnettii ENSOGAG000000018386 retrocopies
retro_ogar_1055, retro_ogar_1379, retro_ogar_2700, retro_ogar_2701, retro_ogar_659, retro_ogar_799,
Ochotona princeps ENSOPRG000000134912 retrocopies
retro_opri_106, retro_opri_1130,
Procavia capensis ENSPCAG000000127621 retrocopy
retro_pcap_452,
Pongo abelii ENSPPYG000000040333 retrocopies
retro_pabe_2234, retro_pabe_3107, retro_pabe_416,
Pan troglodytes ENSPTRG000000044444 retrocopies
retro_ptro_1202, retro_ptro_1883, retro_ptro_206, retro_ptro_2581,
Pteropus vampyrus ENSPVAG000000045321 retrocopy
retro_pvam_1124,
Rattus norvegicus ENSRNOG000000303911 retrocopy
retro_rnor_2605,
Sarcophilus harrisii ENSSHAG000000173331 retrocopy
retro_shar_433,
Ictidomys tridecemlineatus ENSSTOG000000042992 retrocopies
retro_itri_1343, retro_itri_1373,
Tarsius syrichta ENSTSYG000000047472 retrocopies
retro_tsyr_1238, retro_tsyr_1423,

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 = 0.48 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .19 RPM
CEU_NA11843 0 .20 RPM
CEU_NA11930 0 .20 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .39 RPM
CEU_NA12751 0 .02 RPM
CEU_NA12760 0 .31 RPM
CEU_NA12827 0 .19 RPM
CEU_NA12872 0 .03 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .00 RPM
FIN_HG00277 0 .18 RPM
FIN_HG00315 0 .06 RPM
FIN_HG00321 0 .03 RPM
FIN_HG00328 0 .17 RPM
FIN_HG00338 0 .43 RPM
FIN_HG00349 0 .48 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .10 RPM
FIN_HG00378 0 .02 RPM
GBR_HG00099 0 .20 RPM
GBR_HG00111 0 .00 RPM
GBR_HG00114 0 .18 RPM
GBR_HG00119 0 .02 RPM
GBR_HG00131 0 .34 RPM
GBR_HG00133 0 .10 RPM
GBR_HG00134 0 .35 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .17 RPM
GBR_HG00143 0 .22 RPM
TSI_NA20512 0 .28 RPM
TSI_NA20513 0 .19 RPM
TSI_NA20518 0 .03 RPM
TSI_NA20532 0 .00 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .17 RPM
TSI_NA20765 0 .00 RPM
TSI_NA20771 0 .00 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .41 RPM
YRI_NA18870 0 .07 RPM
YRI_NA18907 0 .17 RPM
YRI_NA18916 0 .19 RPM
YRI_NA19093 0 .16 RPM
YRI_NA19099 0 .03 RPM
YRI_NA19114 0 .10 RPM
YRI_NA19118 0 .17 RPM
YRI_NA19213 0 .22 RPM
YRI_NA19214 0 .02 RPM
YRI_NA19223 0 .34 RPM

Indel association:

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



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