RetrogeneDB ID:

retro_hsap_2894

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:3:182178207..182178860(-)
Located in intron of:ENSG00000241098
Retrocopy
information
Ensembl ID:ENSG00000244199
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:EIF4E
Ensembl ID:ENSG00000151247
Aliases:None
Description:eukaryotic translation initiation factor 4E [Source:HGNC Symbol;Acc:3287]


Retrocopy-Parental alignment summary:






>retro_hsap_2894
ATGGCGACTGTCGAACAGGAAACCACCCCTACTTCTAATCCTGTGACTACAGAAAAGGAGAAAACAGAATCTATTCAGGA
GGTTGCTAACCCAGAACACTATATTAAACATCCTTTACAGAACAGATGGGCCCTCTGGTTTTTTAAAAATGGTAAAAGCA
AAAACTTGGCAAGCAAACCTGTGGCTGATCTCTAAGTTTGATACTGTTTGAAGACTTTTGGGCTCTGTACAACCATATCC
AGTTGCCTAGTAATTTAATGCCTGGCTGTGACTACTGACTTTTTAAGGCTGGTATTGAGCCTATGTGGGAAGATGAGAAA
AACAAACTGGGAGGACGATGGCTAATTACATTGAACAAATAGCAGAGATGAAGTGACCTCGATTGCTTTTGGCTAGAGAC
ACTGCTGTGCCTTATTGCAGAATCTTTTGATGACTACAGCAATGATGTATGTGGTGCTGTTATTAATGTTAGAGCTAAAG
GTGATAAGATAGCAATATGGACTACTGAATGTGAAAACAGAGAAGCTGTTACACATATGGGGAGGGTATACAAGAAAAGG
TTAGGACTTCCTCGAAAGATAGTGATTGGTTATCAGTCCCACGCAGACATAGCTACTAAGAATGGCTCCACCACTGAAAA
TAGGTTTGTTGTT

ORF - retro_hsap_2894 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 88.58 %
Parental protein coverage: 100. %
Number of stop codons detected: 3
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMATVEPETTPTPNPPTTEEEKTESNQEVANPEHYIKHPLQNRWALWFFKNDKSK-TWQANLRLISKFDTV
MATVE.ETTPT.NP.TTE.EKTES.QEVANPEHYIKHPLQNRWALWFFKN.KSK.TWQANL.LISKFDTV
RetrocopyMATVEQETTPTSNPVTTEKEKTESIQEVANPEHYIKHPLQNRWALWFFKNGKSK>TWQANLWLISKFDTV
Parental-EDFWALYNHIQLSSNLMPGCDYSLFKDGIEPMWEDEKNKRGGRWLITLNKQQRRSDLDRFWLETLLCLI
.EDFWALYNHIQL.SNLMPGCDY.LFK.GIEPMWEDEKNK.GGRWLITLNK.QR.SDLD.FWLETLLCLI
Retrocopy>EDFWALYNHIQLPSNLMPGCDY*LFKAGIEPMWEDEKNKLGGRWLITLNK*QR*SDLDCFWLETLLCLI
ParentalGESFDDYSDDVCGAVVNVRAKGDKIAIWTTECENREAVTHIGRVYKERLGLPPKIVIGYQSHADTATKSG
.ESFDDYS.DVCGAV.NVRAKGDKIAIWTTECENREAVTH.GRVYK.RLGLP.KIVIGYQSHAD.ATK.G
RetrocopyAESFDDYSNDVCGAVINVRAKGDKIAIWTTECENREAVTHMGRVYKKRLGLPRKIVIGYQSHADIATKNG
ParentalSTTKNRFVV
STT.NRFVV
RetrocopySTTENRFVV

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 31 .05 RPM
bodymap2_adrenal 0 .00 RPM 45 .89 RPM
bodymap2_brain 0 .00 RPM 72 .43 RPM
bodymap2_breast 0 .00 RPM 39 .96 RPM
bodymap2_colon 0 .00 RPM 40 .30 RPM
bodymap2_heart 0 .00 RPM 19 .48 RPM
bodymap2_kidney 0 .00 RPM 41 .01 RPM
bodymap2_liver 0 .00 RPM 19 .03 RPM
bodymap2_lung 0 .00 RPM 39 .52 RPM
bodymap2_lymph_node 0 .00 RPM 37 .30 RPM
bodymap2_ovary 0 .00 RPM 52 .38 RPM
bodymap2_prostate 0 .00 RPM 39 .80 RPM
bodymap2_skeletal_muscle 0 .00 RPM 12 .82 RPM
bodymap2_testis 0 .00 RPM 51 .64 RPM
bodymap2_thyroid 0 .00 RPM 56 .91 RPM
bodymap2_white_blood_cells 0 .00 RPM 30 .22 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2894 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2894 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_2894 retrocopy 5' end.

Lab - click to see more details

retro_hsap_2894 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2894 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1957
Gorilla gorilla retro_ggor_2005
Pongo abelii retro_pabe_2396
Macaca mulatta retro_mmul_1451
Parental genes homology:
Parental genes homology involve 24 parental genes, and 80 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG000000094509 retrocopies
retro_chof_1177, retro_chof_1219, retro_chof_124, retro_chof_1319, retro_chof_1551, retro_chof_200, retro_chof_604, retro_chof_918, retro_chof_992,
Callithrix jacchus ENSCJAG000000071512 retrocopies
retro_cjac_1373, retro_cjac_2097,
Cavia porcellus ENSCPOG000000053834 retrocopies
retro_cpor_1033, retro_cpor_1480, retro_cpor_169, retro_cpor_501,
Dasypus novemcinctus ENSDNOG000000137125 retrocopies
retro_dnov_1722, retro_dnov_2378, retro_dnov_2570, retro_dnov_353, retro_dnov_638,
Echinops telfairi ENSETEG000000073473 retrocopies
retro_etel_1285, retro_etel_1449, retro_etel_499,
Homo sapiens ENSG000001359301 retrocopy
retro_hsap_2689,
Homo sapiens ENSG00000151247 4 retrocopies
retro_hsap_1843, retro_hsap_2409, retro_hsap_2894 , retro_hsap_3935,
Gorilla gorilla ENSGGOG000000047183 retrocopies
retro_ggor_1497, retro_ggor_2005, retro_ggor_2160,
Macropus eugenii ENSMEUG000000111043 retrocopies
retro_meug_2087, retro_meug_2114, retro_meug_428,
Microcebus murinus ENSMICG000000014821 retrocopy
retro_mmur_1195,
Myotis lucifugus ENSMLUG000000050353 retrocopies
retro_mluc_1519, retro_mluc_24, retro_mluc_474,
Macaca mulatta ENSMMUG000000110662 retrocopies
retro_mmul_1451, retro_mmul_601,
Monodelphis domestica ENSMODG000000207161 retrocopy
retro_mdom_701,
Mustela putorius furoENSMPUG000000020411 retrocopy
retro_mputfur_37,
Mus musculus ENSMUSG000000281566 retrocopies
retro_mmus_1059, retro_mmus_1478, retro_mmus_1872, retro_mmus_2362, retro_mmus_3462, retro_mmus_868,
Oryctolagus cuniculus ENSOCUG000000014563 retrocopies
retro_ocun_1760, retro_ocun_596, retro_ocun_810,
Otolemur garnettii ENSOGAG000000011311 retrocopy
retro_ogar_259,
Pongo abelii ENSPPYG000000149443 retrocopies
retro_pabe_1774, retro_pabe_2396, retro_pabe_3244,
Pan troglodytes ENSPTRG000000163014 retrocopies
retro_ptro_1159, retro_ptro_1386, retro_ptro_1957, retro_ptro_2672,
Rattus norvegicus ENSRNOG0000001318311 retrocopies
retro_rnor_1437, retro_rnor_1534, retro_rnor_1544, retro_rnor_1545, retro_rnor_1853, retro_rnor_1854, retro_rnor_2017, retro_rnor_2159, retro_rnor_653, retro_rnor_781, retro_rnor_783,
Sorex araneus ENSSARG000000078211 retrocopy
retro_sara_285,
Ictidomys tridecemlineatus ENSSTOG000000022305 retrocopies
retro_itri_1548, retro_itri_1549, retro_itri_1818, retro_itri_1819, retro_itri_1863,
Tarsius syrichta ENSTSYG000000108623 retrocopies
retro_tsyr_1077, retro_tsyr_1442, retro_tsyr_2169,
Drosophila melanogaster FBgn00357091 retrocopy
retro_dmel_68,

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 = 0.02 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .02 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .00 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .00 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .00 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .00 RPM
FIN_HG00277 0 .00 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .00 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .00 RPM
GBR_HG00099 0 .00 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 .00 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .00 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .00 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .00 RPM
TSI_NA20771 0 .00 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .00 RPM
YRI_NA18870 0 .00 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .00 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .00 RPM
YRI_NA19213 0 .00 RPM
YRI_NA19214 0 .00 RPM
YRI_NA19223 0 .00 RPM

Indel association:

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



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