RetrogeneDB ID:

retro_hsap_878

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:11:58009875..58010428(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000254589
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:EIF4A2
Ensembl ID:ENSG00000156976
Aliases:EIF4A2, BM-010, DDX2B, EIF4A, EIF4F, eIF-4A-II, eIF4A-II
Description:eukaryotic translation initiation factor 4A2 [Source:HGNC Symbol;Acc:3284]


Retrocopy-Parental alignment summary:






>retro_hsap_878
ATGTTTGTGGTTTTGAGAAGCCTCCAGCTATTCAGCCCAGAGCTATTGTTCCTTGTATTAAAGATCCAAAACGTAATTCT
GGCACTTGGAGACTATATGGGAGAAACTTGTCGTGCCTGTATTGGTGGAACAAATGTTCAAAATTAAATGCAAAAACTGT
AGGCAGAAGCACCACATACTGTTGCTAGTACACCATGGAGAGTGTTTGATATGCTAAACATAAGATATTTTTCTCCAAGG
TGGATCAAAATGTTTGTTTTGGATGATGCAGATGAAATGTTGAGCTGAGGGTTTAAGGATGAAATCTATGAGATTTTCCA
AAAATTAAATAGAAGTATTCAGGTTGTGTTGCTTTCTGCCACAATGCCAACTGATGTGTTGGAAGTGACCAAAAAAATTC
ATGAGAGATCCAGTTTAAATTCTGGTGAAAAAGGAAGAAGGAATCAAACAGTTTTACATTAATGTTGAAAGAGAGGAATG
GAAGTTGACTACACTTTGTGACTTGTACGAGACACTGACTATTATGCAGGCTGTCATTTTTCCCAATGCAAGG

ORF - retro_hsap_878 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 82.54 %
Parental protein coverage: 60.26 %
Number of stop codons detected: 4
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMLTVLRSLPLFSRELLFPVLKIQKVILALGDYMGATCHACIGGTNVRNEMQKLQAEAPHIVVGTPGRVFD
M..VLRSL.LFS.ELLF.VLKIQ.VILALGDYMG.TC.ACIGGTNV.N.MQKL.AEAPH.V..TP.RVFD
RetrocopyMFVVLRSLQLFSPELLFLVLKIQNVILALGDYMGETCRACIGGTNVQN*MQKL*AEAPHTVASTPWRVFD
ParentalMLNRRYLSPKWIKMFVLDEADEMLSRGFKDQIYEIFQKLNTSIQVVLLSATMPTDVLEVTKK-FMRDPIR
MLN.RY.SP.WIKMFVLD.ADEMLS.GFKD.IYEIFQKLN.SIQVVLLSATMPTDVLEVTKK.FMRDP..
RetrocopyMLNIRYFSPRWIKMFVLDDADEMLS*GFKDEIYEIFQKLNRSIQVVLLSATMPTDVLEVTKK>FMRDPV*
ParentalILVKKEELTLEGIKQFYINVEREEWKLDTLCDLYETLTITQAVIFLNTR
ILVKKEE....GIKQFYINVEREEWKL.TLCDLYETLTI.QAVIF.N.R
RetrocopyILVKKEE----GIKQFYINVEREEWKLTTLCDLYETLTIMQAVIFPNAR

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 203 .43 RPM
bodymap2_adrenal 0 .00 RPM 423 .29 RPM
bodymap2_brain 0 .00 RPM 1018 .52 RPM
bodymap2_breast 0 .00 RPM 317 .26 RPM
bodymap2_colon 0 .00 RPM 1022 .71 RPM
bodymap2_heart 0 .00 RPM 263 .13 RPM
bodymap2_kidney 0 .00 RPM 383 .66 RPM
bodymap2_liver 0 .00 RPM 114 .05 RPM
bodymap2_lung 0 .02 RPM 530 .19 RPM
bodymap2_lymph_node 0 .00 RPM 664 .69 RPM
bodymap2_ovary 0 .00 RPM 698 .82 RPM
bodymap2_prostate 0 .00 RPM 806 .01 RPM
bodymap2_skeletal_muscle 0 .00 RPM 578 .94 RPM
bodymap2_testis 0 .00 RPM 536 .84 RPM
bodymap2_thyroid 0 .00 RPM 856 .03 RPM
bodymap2_white_blood_cells 0 .00 RPM 366 .33 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_878 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_878 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_878 retrocopy 5' end.

Lab - click to see more details

retro_hsap_878 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_878 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pongo abelii retro_pabe_677
Parental genes homology:
Parental genes homology involve 22 parental genes, and 59 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000147242 retrocopies
retro_btau_258, retro_btau_522,
Canis familiaris ENSCAFG000000136591 retrocopy
retro_cfam_378,
Cavia porcellus ENSCPOG000000111831 retrocopy
retro_cpor_639,
Dasypus novemcinctus ENSDNOG000000115025 retrocopies
retro_dnov_1264, retro_dnov_2018, retro_dnov_2066, retro_dnov_648, retro_dnov_869,
Echinops telfairi ENSETEG000000185653 retrocopies
retro_etel_1174, retro_etel_2164, retro_etel_451,
Homo sapiens ENSG00000156976 2 retrocopies
retro_hsap_593, retro_hsap_878 ,
Homo sapiens ENSG0000016196010 retrocopies
retro_hsap_1004, retro_hsap_1182, retro_hsap_1252, retro_hsap_1270, retro_hsap_1796, retro_hsap_2520, retro_hsap_4836, retro_hsap_4873, retro_hsap_4931, retro_hsap_610,
Gorilla gorilla ENSGGOG000000058672 retrocopies
retro_ggor_525, retro_ggor_712,
Macropus eugenii ENSMEUG000000117371 retrocopy
retro_meug_237,
Microcebus murinus ENSMICG000000073771 retrocopy
retro_mmur_525,
Macaca mulatta ENSMMUG000000037022 retrocopies
retro_mmul_1055, retro_mmul_2450,
Nomascus leucogenys ENSNLEG000000066331 retrocopy
retro_nleu_2589,
Oryctolagus cuniculus ENSOCUG000000050113 retrocopies
retro_ocun_392, retro_ocun_696, retro_ocun_763,
Otolemur garnettii ENSOGAG000000107292 retrocopies
retro_ogar_2830, retro_ogar_943,
Ochotona princeps ENSOPRG000000041701 retrocopy
retro_opri_498,
Pongo abelii ENSPPYG000000143842 retrocopies
retro_pabe_596, retro_pabe_677,
Pan troglodytes ENSPTRG000000157181 retrocopy
retro_ptro_437,
Rattus norvegicus ENSRNOG000000018152 retrocopies
retro_rnor_1163, retro_rnor_2340,
Ictidomys tridecemlineatus ENSSTOG000000126011 retrocopy
retro_itri_858,
Tupaia belangeri ENSTBEG0000000226811 retrocopies
retro_tbel_114, retro_tbel_1488, retro_tbel_1500, retro_tbel_2048, retro_tbel_2524, retro_tbel_2729, retro_tbel_2733, retro_tbel_3159, retro_tbel_3793, retro_tbel_4599, retro_tbel_841,
Takifugu rubripes ENSTRUG000000056602 retrocopies
retro_trub_14, retro_trub_6,
Tarsius syrichta ENSTSYG000000130503 retrocopies
retro_tsyr_1905, retro_tsyr_903, retro_tsyr_935,

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 = 0.05 RPM Legend:


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