RetrogeneDB ID:

retro_hsap_271

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:1:182305142..182305472(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000231684
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:EIF1
Ensembl ID:ENSG00000173812
Aliases:None
Description:eukaryotic translation initiation factor 1 [Source:HGNC Symbol;Acc:3249]


Retrocopy-Parental alignment summary:






>retro_hsap_271
GCTATCCAGAACCTCCACTCTTTCGACCCCTTTGCTGATGCAAGTAAGGGTGATGACCTGCTTCCTGCTGGCACTGAGGA
TTATATCCATATAAGAATTCAACAGAGAAATGGCAGGAAGACCCTTACTACTGTCCAAGGGATTGCTGATGATTATGATA
AAAAGAAACTAGTGAAGGCATTTAAGAATTTTGCCTGCAATGGTACTGTAATTGAGCATCCAGAGTATGGAGAAGTAATT
CAGCCTCAGGGTGACCAATGCAATAACATATGCCAGTTCCTCGTAGAGCTTGGACTGGCTAAGGACGATCAGCTGAAGGT
TCATGTGTTT

ORF - retro_hsap_271 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 93.69 %
Parental protein coverage: 91.74 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalAIQNLHSFDPFADASKGDDLLPAGTEDYIHIRIQQRNGRKTLTTVQGIADDYDKKKLVKAFKKKFACNGT
AIQNLHSFDPFADASKGDDLLPAGTEDYIHIRIQQRNGRKTLTTVQGIADDYDKKKLVKAFK..FACNGT
RetrocopyAIQNLHSFDPFADASKGDDLLPAGTEDYIHIRIQQRNGRKTLTTVQGIADDYDKKKLVKAFK-NFACNGT
ParentalVIEHPEYGEVIQLQGDQRKNICQFLVEIGLAKDDQLKVHGF
VIEHPEYGEVIQ.QGDQ..NICQFLVE.GLAKDDQLKVH.F
RetrocopyVIEHPEYGEVIQPQGDQCNNICQFLVELGLAKDDQLKVHVF

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 .10 RPM 610 .13 RPM
bodymap2_adrenal 0 .04 RPM 472 .35 RPM
bodymap2_brain 0 .02 RPM 366 .37 RPM
bodymap2_breast 0 .02 RPM 507 .11 RPM
bodymap2_colon 0 .02 RPM 793 .56 RPM
bodymap2_heart 0 .00 RPM 468 .08 RPM
bodymap2_kidney 0 .04 RPM 444 .80 RPM
bodymap2_liver 0 .00 RPM 238 .00 RPM
bodymap2_lung 0 .00 RPM 868 .46 RPM
bodymap2_lymph_node 0 .00 RPM 546 .24 RPM
bodymap2_ovary 0 .04 RPM 617 .73 RPM
bodymap2_prostate 0 .00 RPM 836 .72 RPM
bodymap2_skeletal_muscle 0 .04 RPM 1266 .04 RPM
bodymap2_testis 0 .06 RPM 498 .51 RPM
bodymap2_thyroid 0 .00 RPM 467 .41 RPM
bodymap2_white_blood_cells 0 .00 RPM 676 .16 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_271 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_271 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_271 retrocopy 5' end.

Lab - click to see more details

retro_hsap_271 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_271 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_227
Gorilla gorilla retro_ggor_318
Parental genes homology:
Parental genes homology involve 24 parental genes, and 117 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000056209 retrocopies
retro_amel_1335, retro_amel_335, retro_amel_567, retro_amel_575, retro_amel_587, retro_amel_666, retro_amel_782, retro_amel_798, retro_amel_823,
Bos taurus ENSBTAG000000022821 retrocopy
retro_btau_63,
Canis familiaris ENSCAFG000000295844 retrocopies
retro_cfam_1465, retro_cfam_1479, retro_cfam_359, retro_cfam_655,
Callithrix jacchus ENSCJAG000000121206 retrocopies
retro_cjac_1237, retro_cjac_2089, retro_cjac_346, retro_cjac_3815, retro_cjac_600, retro_cjac_84,
Cavia porcellus ENSCPOG000000143503 retrocopies
retro_cpor_42, retro_cpor_613, retro_cpor_643,
Dasypus novemcinctus ENSDNOG0000000785611 retrocopies
retro_dnov_1098, retro_dnov_1110, retro_dnov_1368, retro_dnov_148, retro_dnov_1516, retro_dnov_1668, retro_dnov_1807, retro_dnov_2062, retro_dnov_2209, retro_dnov_402, retro_dnov_421,
Dipodomys ordii ENSDORG000000138534 retrocopies
retro_dord_349, retro_dord_350, retro_dord_663, retro_dord_753,
Felis catus ENSFCAG000000244552 retrocopies
retro_fcat_1555, retro_fcat_74,
Homo sapiens ENSG00000173812 2 retrocopies
retro_hsap_1659, retro_hsap_271 ,
Gorilla gorilla ENSGGOG000000272012 retrocopies
retro_ggor_1251, retro_ggor_318,
Macropus eugenii ENSMEUG000000153606 retrocopies
retro_meug_1513, retro_meug_1635, retro_meug_2189, retro_meug_315, retro_meug_749, retro_meug_821,
Myotis lucifugus ENSMLUG000000050773 retrocopies
retro_mluc_233, retro_mluc_305, retro_mluc_330,
Mustela putorius furoENSMPUG000000108836 retrocopies
retro_mputfur_1019, retro_mputfur_1072, retro_mputfur_1239, retro_mputfur_1299, retro_mputfur_41, retro_mputfur_752,
Nomascus leucogenys ENSNLEG000000110133 retrocopies
retro_nleu_1482, retro_nleu_2005, retro_nleu_92,
Otolemur garnettii ENSOGAG000000315776 retrocopies
retro_ogar_1349, retro_ogar_1701, retro_ogar_1940, retro_ogar_2645, retro_ogar_2899, retro_ogar_856,
Pongo abelii ENSPPYG000000296671 retrocopy
retro_pabe_127,
Pan troglodytes ENSPTRG000000091753 retrocopies
retro_ptro_1261, retro_ptro_227, retro_ptro_2923,
Pteropus vampyrus ENSPVAG000000106294 retrocopies
retro_pvam_1152, retro_pvam_471, retro_pvam_665, retro_pvam_923,
Rattus norvegicus ENSRNOG0000003376515 retrocopies
retro_rnor_1088, retro_rnor_1347, retro_rnor_1518, retro_rnor_1744, retro_rnor_1971, retro_rnor_2067, retro_rnor_2171, retro_rnor_2203, retro_rnor_2532, retro_rnor_2548, retro_rnor_2579, retro_rnor_45, retro_rnor_532, retro_rnor_571, retro_rnor_65,
Sorex araneus ENSSARG000000062871 retrocopy
retro_sara_36,
Sarcophilus harrisii ENSSHAG000000057291 retrocopy
retro_shar_42,
Sus scrofa ENSSSCG000000174306 retrocopies
retro_sscr_1114, retro_sscr_1126, retro_sscr_1192, retro_sscr_394, retro_sscr_402, retro_sscr_922,
Ictidomys tridecemlineatus ENSSTOG0000000271915 retrocopies
retro_itri_1082, retro_itri_1184, retro_itri_1369, retro_itri_1398, retro_itri_1401, retro_itri_1716, retro_itri_1784, retro_itri_1846, retro_itri_220, retro_itri_285, retro_itri_526, retro_itri_606, retro_itri_688, retro_itri_702, retro_itri_977,
Tursiops truncatus ENSTTRG000000171353 retrocopies
retro_ttru_1664, retro_ttru_224, retro_ttru_315,

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 = 0.12 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .02 RPM
CEU_NA11843 0 .06 RPM
CEU_NA11930 0 .03 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .04 RPM
CEU_NA12751 0 .07 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .05 RPM
CEU_NA12872 0 .03 RPM
CEU_NA12873 0 .06 RPM
FIN_HG00183 0 .05 RPM
FIN_HG00277 0 .00 RPM
FIN_HG00315 0 .08 RPM
FIN_HG00321 0 .09 RPM
FIN_HG00328 0 .02 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .03 RPM
FIN_HG00375 0 .05 RPM
FIN_HG00377 0 .03 RPM
FIN_HG00378 0 .06 RPM
GBR_HG00099 0 .00 RPM
GBR_HG00111 0 .06 RPM
GBR_HG00114 0 .00 RPM
GBR_HG00119 0 .05 RPM
GBR_HG00131 0 .03 RPM
GBR_HG00133 0 .00 RPM
GBR_HG00134 0 .02 RPM
GBR_HG00137 0 .05 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .06 RPM
TSI_NA20513 0 .00 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .03 RPM
TSI_NA20538 0 .05 RPM
TSI_NA20756 0 .12 RPM
TSI_NA20765 0 .00 RPM
TSI_NA20771 0 .03 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .03 RPM
YRI_NA18870 0 .03 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .02 RPM
YRI_NA19093 0 .05 RPM
YRI_NA19099 0 .05 RPM
YRI_NA19114 0 .05 RPM
YRI_NA19118 0 .00 RPM
YRI_NA19213 0 .05 RPM
YRI_NA19214 0 .02 RPM
YRI_NA19223 0 .02 RPM

Indel association:

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



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