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Record W2074261724 · doi:10.1074/jbc.m310761200

Gene Fusion and Overlapping Reading Frames in the Mammalian Genes for 4E-BP3 and MASK

2003· article· en· W2074261724 on OpenAlexaff
Francis Poulin, Andrea Brueschke, Nahum Sonenberg

Bibliographic record

VenueJournal of Biological Chemistry · 2003
Typearticle
Languageen
FieldBiochemistry, Genetics and Molecular Biology
TopicViral Infectious Diseases and Gene Expression in Insects
Canadian institutionsMcGill University
Fundersnot available
KeywordsGeneReading (process)GeneticsOpen reading frameFusion geneBiologyComputational biologyLinguisticsPhilosophy

Abstract

fetched live from OpenAlex

4E-BP3 is a member of the eukaryotic initiation factor (eIF) 4F-binding protein family of translational repressors. eIF4E-binding proteins (4E-BPs) inhibit translation initiation by sequestering eIF4E, the cap-binding protein, from eIF4G thus preventing ribosome recruitment to the mRNA. Previous analysis of 4E-BP3 expression uncovered an 8.5-kb mRNA variant of unknown origin. To study this splice variant, we determined the structure of the genomic locus encoding human 4E-BP3 (EIF4EBP3). EIF4EBP3 is located on human chromosome 5q31.3 and comprises three exons (A, B, and C) and two introns. Exon B contains the region of the open reading frame responsible for eIF4E binding. GenBank™ searches revealed multiple expressed sequence tags originating from the alternative splicing of exon B with unidentified upstream exons. Further studies revealed that the 8.5-kb transcript arises from the fusion of EIF4EBP3 with the mammalian homologue of Drosophila is for and the open reading frame of the transcript is from that of that exon B is an alternative reading fusion to that of and EIF4EBP3 for the of an alternative reading frame is for two and of the of mammalian and for the analysis of 4E-BP3 and eIF4E and of the a for the fusion 4E-BP3 is a member of the eukaryotic initiation factor (eIF) 4F-binding protein family of translational repressors. eIF4E-binding proteins (4E-BPs) inhibit translation initiation by sequestering eIF4E, the cap-binding protein, from eIF4G thus preventing ribosome recruitment to the mRNA. Previous analysis of 4E-BP3 expression uncovered an 8.5-kb mRNA variant of unknown origin. To study this splice variant, we determined the structure of the genomic locus encoding human 4E-BP3 (EIF4EBP3). EIF4EBP3 is located on human chromosome 5q31.3 and comprises three exons (A, B, and C) and two introns. Exon B contains the region of the open reading frame responsible for eIF4E binding. GenBank™ searches revealed multiple expressed sequence tags originating from the alternative splicing of exon B with unidentified upstream exons. Further studies revealed that the 8.5-kb transcript arises from the fusion of EIF4EBP3 with the mammalian homologue of Drosophila is for and the open reading frame of the transcript is from that of that exon B is an alternative reading fusion to that of and EIF4EBP3 for the of an alternative reading frame is for two and of the of mammalian and for the analysis of 4E-BP3 and eIF4E and of the a for the fusion of translation is an to the initiation the is to the mRNA of recruitment is by the structure is on eukaryotic structure is by eukaryotic initiation factor (eIF) initiation reading sequence reading of protein initiation reading sequence reading of protein a of three eIF4E, the cap-binding a and a that a the ribosome and mRNA eIF4E a translational initiation and is multiple and the of the eIF4E-binding proteins inhibit translation initiation by preventing the of eIF4E with and thus ribosome to the mRNA the the eIF4G and for eIF4E of the to eIF4E is by of with eIF4E, the with on multiple and from eIF4E to translational and 4E-BP3 the three of the mammalian family is the and is to the of the 4E-BP3 the and of to analysis of 4E-BP3 expression revealed that is expressed two of is of unknown To this we the of the human EIF4EBP3 genomic and 4E-BP3 splice by and to the 4E-BP3 exon of the exons of the exon of the 4E-BP3 exon of the and human of the and human 4E-BP3 by genomic and a from with the human 4E-BP3 a by a to the and and with and to the human and with and to the human by from the of the for the the by the of an for by of for for and for of the of with a for for and the by the of the the and a a from exon to and a to the and a fusion and a fusion and and and and from the and from the and with to the the on a and for by and the to three by and the protein the determined the protein of and with of and for by with protein to a with to protein with for and three with and to on and for for with for with and a to of with with with with of and 4E-BP3 a analysis of 4E-BP3 mRNA we that the human 4E-BP3 with two a mRNA of to the and an unidentified mRNA of To expression of the 8.5-kb variant is the we a analysis on multiple the 4E-BP3 a the and 8.5-kb expressed the To the of the 8.5-kb we the human EIF4EBP3 and human EIF4EBP3 and comprises three exons and two searches revealed that human EIF4EBP3 to by analysis that the human EIF4EBP3 is a searches of the sequence analysis that the family is of three expressed and a structure that is to the human is analysis that is located on chromosome on a that is with human chromosome sequence of the GenBank™ of the human and EIF4EBP3 genomic structure of the EIF4EBP3 locus and the region located 4E-BP3 mRNA is expressed from this locus variant two and exons with Exon is located and EIF4EBP3 and is splice variant and B, genomic structure of the and EIF4EBP3 determined from the chromosome genomic on the sequence the of of the three expressed from the two the genomic exons for and proteins of EIF4EBP3 exon with the 4E-BP3 exon and the exon with the EIF4EBP3 exons B and with the 4E-BP3 and and of 4E-BP3 mRNA the genomic structure of EIF4EBP3 to splice by and to a human analysis an and an 8.5-kb with a of exon on the to exons the exon the the 8.5-kb of transcript expression from the human and EIF4EBP3 expression of from the EIF4EBP3 locus by on of from human from the exons for the of 4E-BP3 and expression by the exons B, 4E-BP3 expression by the exon expression by the exon expression by the exon the of mRNA a human the of the 8.5-kb searches on the human of with the sequence of exon that the of 4E-BP3 two of the sequence of exons a with exon the the 4E-BP3 of to exons unidentified sequence located the exon is 4E-BP3 of from this and a the EIF4EBP3 exons and that located and upstream of exon searches the sequence of exon to splice with the sequence of exon a of that contains a exon located exon from the for exon the of upstream sequence with and and for a human multiple and revealed the and of expression to the 8.5-kb the EIF4EBP3 exons the 8.5-kb on from and with from the the for splice variant contains exons the for splice variant contains exons for splice variant is and of a of an of and a of of the is to the of the mRNA is to the of the the of a on the mRNA. is an located upstream from the for splice variant is and of a of that is to that of splice variant an of and a of the of Drosophila of splice variant a protein with a of contains two two of and and a is this is to the Drosophila protein is the the and and the of this we the protein by splice variant human of of with from and of human Drosophila human and and protein sequence is from a of and from of of the of B, of the of of the searches of GenBank™ a family of expressed from to the of the and the of the human a that to from a of is located on chromosome and a transcript that a protein GenBank™ human to with the and from the of and for is located on chromosome is upstream by the and by the EIF4EBP3 transcript that we splice variant from of by alternative splicing splice variant from the fusion of exons with EIF4EBP3 exons and we the protein human a protein with a of to of and the two of the from the translation of exons B, and analysis that exons B and of the transcript a reading frame that from that of 4E-BP3 the and exons of the EIF4EBP3 two To the protein that we to for reading and of and multiple by of the three to is expressed the with a expression the and of the mRNA. is to the mRNA expression is with the and the mRNA expression is with expression the and and and proteins expressed we with the two proteins and and the and for a fusion protein from the exons that the the we with of the two proteins an the and by and and the to and the and the protein and To the of and and and with and on of and of and by and by to the of proteins and the of the expression of B, of and by and by the of the of of and by and by and with and with and an of and on protein from with of a of the with an and the proteins that by and of the and by analysis the for and that of of the and we to proteins of To the expression of and we the two proteins three with revealed that and and the the structure of the encoding the translational of EIF4EBP3 with the and that a for for and for three three exons and two with the the of the is human and of the is the three the of the splice and of the exons is the exon of is the with and the exon of EIF4EBP3 is the with and is is the the from the that is the human Drosophila a and the three human located on of the mammalian family from the of an analysis of and mRNA revealed that expression and is of the that and from a is to that the expression of the mRNA for is the of the that we and a to mRNA is expressed a of and 4E-BP3 is that expression and human with a expression is expressed the and the and to the three human expression that the two mammalian and to that studies of and 4E-BP3 the to to of the of human and 4E-BP3 and to a of the for the structure of EIF4EBP3 to the of an alternative transcript that we the and that is from the fusion of EIF4EBP3 with a located the human homologue of the is an of and of on a the Drosophila is for and the human and to the structure of the thus that the transcript arises from of is the for that an exon that is located and EIF4EBP3 and To the transcript alternative splicing to the exons the and the 4E-BP3 translation initiation of the revealed that and located on the human two by on chromosome and a of from the two is a mRNA. of the GenBank™ revealed that a fusion of and EIF4EBP3 is and and is a fusion the of a for the of the and human and EIF4EBP3 and to the of a is that the of the two is by the that that to the EIF4EBP3 a protein that is to and a protein that is to of is that is a reading frame that from two proteins by the exon of and with 4E-BP3 the of to to the that the exon of EIF4EBP3 is an alternative reading frame that is that for the of the sequence from the the sequence by the alternative 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from the that is the human Drosophila a and the three human located on of the mammalian family from the of an analysis of and mRNA revealed that expression and is of the that and from a is to that the expression of the mRNA for is the of the that we and a to mRNA is expressed a of and 4E-BP3 is that expression and human with a expression is expressed the and the and to the three human expression that the two mammalian and to that studies of and 4E-BP3 the to to of the of human and 4E-BP3 and to a of the for the structure of EIF4EBP3 to the of an alternative transcript that we the and that is from the fusion of EIF4EBP3 with a located the human homologue of the is an of and of on a the Drosophila is for and the human and to the structure of the thus that the transcript arises from of is the for that an exon that is located and EIF4EBP3 and To the transcript alternative splicing to the exons the and the 4E-BP3 translation initiation of the revealed that and located on the human two by on chromosome and a of from the two is a mRNA. of the GenBank™ revealed that a fusion of and EIF4EBP3 is and and is a fusion the of a for the of the and human and EIF4EBP3 and to the of a is that the of the two is by the that that to the EIF4EBP3 a protein that is to and a protein that is to of is that is a reading frame that from two proteins by the exon of and with 4E-BP3 the of to to the that the exon of EIF4EBP3 is an alternative reading frame that is that for the of the sequence from the the sequence by the alternative reading frame with that the fusion of proteins that we that and 4E-BP3 that the two proteins the the mammalian of and the of eIF4E is by the of to is by the exons and this on eIF4E is of a fusion to that of and the of reading mammalian is for the and the the fusion and of an alternative reading frame the we uncovered a that mammalian to from the structure of the encoding the translational of EIF4EBP3 with the and that a for for and for three three exons and two with the the of the is human and of the is the three the of the splice and of the exons is the exon of is the with and the exon of EIF4EBP3 is the with and is is the the from the that is the human Drosophila a and the three human located on of the mammalian family from the of an analysis of and mRNA revealed that expression and is of the that and from a is to that the expression of the mRNA for is the of the that we and a to mRNA is expressed a of and 4E-BP3 is that expression and human with a expression is expressed the and the and to the three human expression that the two mammalian and to that studies of and 4E-BP3 the to to of the of human and 4E-BP3 and to a of the for the structure of EIF4EBP3 to the of an alternative transcript that we the and that is from the fusion of EIF4EBP3 with a located the human homologue of the is an of and of on a the Drosophila is for and the human and to the structure of the thus that the transcript arises from of is the for that an exon that is located and EIF4EBP3 and To the transcript alternative splicing to the exons the and the 4E-BP3 translation initiation of the revealed that and located on the human two by on chromosome and a of from the two is a mRNA. of the GenBank™ revealed that a fusion of and EIF4EBP3 is and and is a fusion the of a for the of the and human and EIF4EBP3 and to the of a is that the of the two is by the that that to the EIF4EBP3 a protein that is to and a protein that is to of is that is a reading frame that from two proteins by the exon of and with 4E-BP3 the of to to the that the exon of EIF4EBP3 is an alternative reading frame that is that for the of the sequence from the the sequence by the alternative reading frame with that the fusion of proteins that we that and 4E-BP3 that the two proteins the the mammalian of and the of eIF4E is by the of to is by the exons and this on eIF4E is of a fusion to that of and the of reading mammalian is for the and the the fusion and of an alternative reading frame the we uncovered a that mammalian to from for and for with for and for reading of the

Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.

How this classification was reachedexpand

Full frame distilled prediction

Teacher imitation

Not calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.

metaresearch head score (Codex)0.000
metaresearch head score (Gemma)0.000
Version: codex-gemma-dda1882f352aValidation status: machine_predicted_unvalidated
Candidate categoriesnone
Consensus categoriesnone
DomainCandidate signal: none · Consensus signal: none
Study designCandidate signal: Bench or experimental · Consensus signal: Bench or experimental
GenreCandidate signal: Empirical · Consensus signal: Empirical
Teacher disagreement score0.019
Threshold uncertainty score0.253

Codex and Gemma teacher scores by category

CategoryCodexGemma
Metaresearch0.0000.000
Meta-epidemiology (narrow)0.0000.000
Meta-epidemiology (broad)0.0000.000
Bibliometrics0.0000.000
Science and technology studies0.0000.000
Scholarly communication0.0000.000
Open science0.0000.000
Research integrity0.0000.000
Insufficient payload (model declined to judge)0.0000.000

Machine scores (provisional)

The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.

Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.

Opus teacher head0.018
GPT teacher head0.267
Teacher spread0.249 · how far apart the two teachers sit on this one work
Validation statusscore_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from it

Classification

machine, unvalidated

Machine predicted; a candidate call from one teacher head, not a consensus.

The models applied no category: nothing in the taxonomy fit this work.
Study designBench or experimental
Domainnot available
GenreEmpirical

How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".

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Citations59
Published2003
Admission routes1
Has abstractyes

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