FB2020_06, released Dec 22, 2020

Gene: Dmel\Larp4B

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General Information
Symbol
Dmel\Larp4B
Species
D. melanogaster
Name
La-related protein 4B
Annotation Symbol
CG11505
Feature Type
protein_coding_gene
FlyBase ID
FBgn0035424
Gene Model Status
Current
Stock Availability
9 publicly available
Gene Snapshot
Contributions welcome
Other Summaries
Key Links
Genomic Location
Cytogenetic map
63C1-63C1
Sequence location
3L:3,224,838..3,236,604 [+]
Recombination map

3-7

RefSeq locus
NT_037436 REGION:3224838..3236604
Sequence
Get Decorated FASTA
Genomic Maps
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
NCBI
UCSC
Ensembl
PopFly
Function
GO Summary Ribbons
Gene Ontology (GO) Annotations (4 terms)
Molecular Function (1 term)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
enables mRNA 3'-UTR binding
inferred from sequence or structural similarity with UniProtKB:Q92615
(FlyBase Curators, 2008--)
Biological Process (2 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
involved_in negative regulation of cell growth
inferred from mutant phenotype
(Funakoshi et al., 2018)
involved_in negative regulation of translation
inferred from mutant phenotype
(Funakoshi et al., 2018)
Terms Based on Predictions or Assertions (0 terms)
Cellular Component (1 term)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
located_in cytosol
inferred from sequence or structural similarity with UniProtKB:Q92615
(FlyBase Curators, 2008--)
Gene Group (FlyBase)
Protein Family (UniProt)
-
Protein Signatures (InterPro)
Summaries
Gene Group (FlyBase)
LA-RELATED PROTEINS -
La-related proteins (LARPs) containing two RNA-binding motifs: an LA motif and an RNA recognition motif. LARPs have been shown to be involved in the post-transcriptional regulation of gene expression. (Adapted from FBrf0238226 & PMID:25488812.)
Protein Function (UniProtKB)
Probable RNA binding protein. Negatively regulates myc at the protein level, via an unknown mechanism, and may therefore have a role in growth. Has no effect on myc mRNA levels.
(UniProt, Q9I7T7)
Gene Model and Products
Number of Transcripts
3
Number of Unique Polypeptides
2

Please see the JBrowse view of Dmel\Larp4B for information on other features

To submit a correction to a gene model please use the Contact FlyBase form

Protein Domains (via Pfam)
Isoform displayed:
Pfam protein domains
InterPro name
classification
start
end
Protein Domains (via SMART)
Isoform displayed:
SMART protein domains
InterPro name
classification
start
end
Comments on Gene Model

Tissue-specific extension of 3' UTRs observed during later stages (FBrf0218523, FBrf0219848); all variants may not be annotated

Low-frequency RNA-Seq exon junction(s) not annotated.

Gene model reviewed during 5.46

Gene model reviewed during 5.56

Sequence Ontology: Class of Gene
gene_with_edited_transcript
(Graveley et al., 2011)
nuclear_gene
protein_coding_gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
Larp4B-RA
FBtr0073045
NM_168007
5172
1521
Larp4B-RB
FBtr0073046
NM_139536
9562
1531
Larp4B-RD
FBtr0308061
NM_206263
9523
1521
Additional Transcript Data and Comments
Reported size (kB)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kDa)
Length (aa)
Theoretical pI
RefSeq ID
GenBank
Larp4B-PA
FBpp0072909
160.8
1521
9.12
NP_728843
AAF47745
Larp4B-PB
FBpp0072910
162.0
1531
9.02
NP_647793
AAG22237
Larp4B-PD
FBpp0300406
160.8
1521
9.12
NP_995985
AAS64955
Polypeptides with Identical Sequences

The group(s) of polypeptides indicated below share identical sequence to each other.

1521 aa isoforms: Larp4B-PA, Larp4B-PD
Additional Polypeptide Data and Comments
Reported size (kDa)
Comments
External Data
Domain

The HTH La-type RNA-binding and RRM domains are required for its function in negatively regulating organ and cell size.

(UniProt, Q9I7T7)
Crossreferences
InterPro - A database of protein families, domains and functional sites
Linkouts
Sequences Consistent with the Gene Model
Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\Larp4B using the Feature Mapper tool.

External Data
Crossreferences
Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
Linkouts
Expression Data
Expression Summary Ribbons
Colored tiles in ribbon indicate that expression data has been curated by FlyBase for that anatomical location. Colorless tiles indicate that there is no curated data for that location.
For complete stage-specific expression data, view the modENCODE Development RNA-Seq section under High-Throughput Expression below.
Transcript Expression
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
mass spectroscopy
Stage
Tissue/Position (including subcellular localization)
Reference
adult stage
adult head
(Aradska et al., 2015)
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\Larp4B in GBrowse 2
RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region
Bulk Downloads
RNA-Seq RPKM values for all genes
Reference
See Gelbart and Emmert, 2013 for analysis details and data files for all genes.
Developmental Proteome: Life Cycle
Developmental Proteome: Embryogenesis
External Data and Images
Linkouts
FLIGHT - Cell culture data for RNAi and other high-throughput technologies
FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
Flygut - An atlas of the Drosophila adult midgut
Images
FlyBase Wiki
Image Based Resources
Alleles, Insertions, and Transgenic Constructs
Classical and Insertion Alleles ( 6 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 7 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of Larp4B
Transgenic constructs containing regulatory region of Larp4B
Deletions and Duplications ( 0 )
Phenotypes
Orthologs
Downloads
Download All DIOPT Orthologs
Download All OrthoDB Orthologs
Human Orthologs (via DIOPT v8.0)
Homo sapiens (Human) (5)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
eggNOG
Hieranoid
Homologene
Inparanoid
Isobase
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
RoundUp
TreeFam
ZFIN
Alignment
Complementation?
Transgene?
Hsap\LARP4
8 of 15
Yes
Yes
1  
Hsap\LARP4B
7 of 15
No
Yes
1  
Hsap\LARP1B
1 of 15
No
No
Hsap\LARP1
1 of 15
No
No
Hsap\LARP6
1 of 15
No
No
Model Organism Orthologs (via DIOPT v8.0)
Mus musculus (laboratory mouse) (5)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
eggNOG
Hieranoid
Homologene
Inparanoid
Isobase
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
RoundUp
TreeFam
ZFIN
Alignment
Complementation?
Transgene?
Mmus\Larp4
8 of 15
Yes
Yes
Mmus\Larp4b
7 of 15
No
Yes
Mmus\Larp1b
1 of 15
No
No
Mmus\Larp1
1 of 15
No
No
Mmus\Larp6
1 of 15
No
No
Rattus norvegicus (Norway rat) (6)
Rnor\Larp4b
5 of 13
Yes
Yes
Rnor\Larp1b
1 of 13
No
No
Rnor\Larp1
1 of 13
No
No
Rnor\Larp4
1 of 13
No
Yes
Rnor\Larp6
1 of 13
No
No
Rnor\RGD1305704
1 of 13
No
Yes
Xenopus tropicalis (Western clawed frog) (6)
Xtro\larp4b
4 of 12
Yes
Yes
Xtro\larp4
4 of 12
Yes
Yes
Xtro\larp1b
1 of 12
No
No
Xtro\larp1
1 of 12
No
No
Xtro\larp6-like.1
1 of 12
No
No
Xtro\larp6
1 of 12
No
No
Danio rerio (Zebrafish) (7)
Drer\larp4aa
8 of 15
Yes
Yes
Drer\larp4b
7 of 15
No
Yes
Drer\larp4ab
6 of 15
No
Yes
Drer\larp1b
1 of 15
No
No
Drer\larp1
1 of 15
No
No
Drer\larp6a
1 of 15
No
No
Drer\LOC100332095
1 of 15
No
Yes
Caenorhabditis elegans (Nematode, roundworm) (1)
Cele\larp-5
7 of 15
Yes
Yes
Arabidopsis thaliana (thale-cress) (6)
Atha\LARP1c
2 of 9
Yes
Yes
Atha\LARP1a
1 of 9
No
No
Atha\LARP1b
1 of 9
No
Yes
Atha\LARP6a
1 of 9
No
No
Atha\LARP6b
1 of 9
No
No
Atha\LARP6c
1 of 9
No
No
Saccharomyces cerevisiae (Brewer's yeast) (3)
Scer\SLF1
2 of 15
Yes
No
Scer\SRO9
2 of 15
Yes
No
Scer\LHP1
1 of 15
No
No
Schizosaccharomyces pombe (Fission yeast) (2)
Spom\sla1
1 of 12
Yes
No
Spom\SPAC1527.03
1 of 12
Yes
No
Ortholog(s) in Drosophila Species (via OrthoDB v9.1) ( EOG091901OR )
Organism
Common Name
Gene
AAA Syntenic Ortholog
Multiple Dmel Genes in this Orthologous Group
Drosophila suzukii
Spotted wing Drosophila
Dsuz\DS10_00007867
Drosophila simulans
Dsim\GD13743
Drosophila sechellia
Dsec\GM14551
Drosophila erecta
Dere\GG15116
Drosophila yakuba
Dyak\GE21342
Drosophila ananassae
Dana\GF10124
Drosophila pseudoobscura pseudoobscura
Dpse\GA11040
Drosophila willistoni
Dwil\GK17513
Drosophila virilis
Dvir\GJ15458
Drosophila mojavensis
Dmoj\GI12555
Drosophila grimshawi
Dgri\GH15776
Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG091504ZN )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Musca domestica
House fly
Mdoa\17016565
Glossina morsitans
Tsetse fly
Gmor\GMOY004958
Lucilia cuprina
Australian sheep blowfly
Lcup\FF38_09051
Aedes aegypti
Yellow fever mosquito
Aaeg\AAEL010841
Anopheles darlingi
American malaria mosquito
Adar\ADAC007576
Anopheles gambiae
Malaria mosquito
Agam\AGAP006460
Culex quinquefasciatus
Southern house mosquito
Cqui\CPIJ008950
Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W02O0 )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Apis florea
Little honeybee
Aflo\2938164692
Apis mellifera
Western honey bee
Amel\GB42747
Bombus impatiens
Common eastern bumble bee
Bimp\BIMP13203
Bombus terrestris
Buff-tailed bumblebee
Bter\15206529
Linepithema humile
Argentine ant
Lhum\LH18775
Megachile rotundata
Alfalfa leafcutting bee
Mrot\MROTU:002fcd
Nasonia vitripennis
Parasitic wasp
Nvit\Nasvi2EG014898
Dendroctonus ponderosae
Mountain pine beetle
Dpod\YQE_07427
Pediculus humanus
Human body louse
Phum\PHUM582400
Rhodnius prolixus
Kissing bug
Rpro\RPRC009289
Cimex lectularius
Bed bug
Clec\CLEC000197
Acyrthosiphon pisum
Pea aphid
Apim\ACYPI008653
Zootermopsis nevadensis
Nevada dampwood termite
Znev\Znev_01102
Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X02L9 )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strigamia maritima
European centipede
Smar\SMAR004843
Stegodyphus mimosarum
African social velvet spider
Smim\KFM81047.1
Tetranychus urticae
Two-spotted spider mite
Turt\tetur01g04830
Tetranychus urticae
Two-spotted spider mite
Turt\tetur08g06070
Daphnia pulex
Water flea
Dpux\DAPPUDRAFT_52327
Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( EOG091G03E9 )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strongylocentrotus purpuratus
Purple sea urchin
Spur\Sp-Larp4L
Ciona intestinalis
Vase tunicate
Cint\ENSCING00000015692
Gallus gallus
Domestic chicken
Ggal\LARP4B
Gallus gallus
Domestic chicken
Ggal\ENSGALG00000006163
Paralogs
Downloads
Download All DIOPT Paralogs
Paralogs (via DIOPT v8.0)
Drosophila melanogaster (Fruit fly) (4)
Gene Symbol
Score
Source
Compara
eggNOG
Homologene
Inparanoid
Isobase
OrthoDB
OrthoFinder
orthoMCL
Panther
RoundUp
Alignment
Achl
2 of 10
La
2 of 10
Larp7
2 of 10
larp
2 of 10
Human Disease Associations
FlyBase Human Disease Model Reports
    Disease Model Summary Ribbon
    Disease Ontology (DO) Annotations
    Models Based on Experimental Evidence ( 0 )
    Allele
    Disease
    Evidence
    References
    Potential Models Based on Orthology ( 0 )
    Human Ortholog
    Disease
    Evidence
    References
    Modifiers Based on Experimental Evidence ( 0 )
    Allele
    Disease
    Interaction
    References
    Disease Associations of Human Orthologs (via DIOPT v8.0 and OMIM)
    Note that ortholog calls supported by only 1 or 2 algorithms (DIOPT score < 3) are not shown.
    Homo sapiens (Human)
    Gene name
    Score
    OMIM
    OMIM Phenotype
    DO term
    Complementation?
    Transgene?
    LARP4; La ribonucleoprotein 4
    8 of 15
    618657
         
        LARP4B; La ribonucleoprotein 4B
        7 of 15
        616513
             
            Functional Complementation Data
            Functional complementation data is computed by FlyBase using a combination of the orthology data obtained from DIOPT and OrthoDB and the allele-level genetic interaction data curated from the literature.
            Interactions
            Summary of Physical Interactions
            esyN Network Diagram
            Show neighbor-neighbor interactions:
            Select Layout:
            Legend:
            Protein
            RNA
            Selected Interactor(s)
            Interactions Browser
            View in Interactions Browser
            Please see the Physical Interaction reports below for full details
            protein-protein
            Physical Interaction
            Assay
            References
            Larp4B - AGO1
            experimental knowledge based
            (Guruharsha et al., 2011)
            Larp4B - Atx2
            experimental knowledge based
            (Guruharsha et al., 2011)
            Larp4B - Bap60
            experimental knowledge based
            (Guruharsha et al., 2011)
            Larp4B - CG10077
            experimental knowledge based
            (Guruharsha et al., 2011)
            Larp4B - CG2017
            experimental knowledge based
            (Guruharsha et al., 2011)
            Larp4B - CG34159
            experimental knowledge based
            (Guruharsha et al., 2011)
            Larp4B - Cpsf6
            experimental knowledge based
            (Guruharsha et al., 2011)
            Larp4B - Hakai
            anti tag coimmunoprecipitation, peptide massfingerprinting, experimental knowledge based
            (Rhee et al., 2014)
            Larp4B - MED10
            experimental knowledge based
            (Guruharsha et al., 2011)
            Larp4B - MED11
            experimental knowledge based
            (Guruharsha et al., 2011)
            Larp4B - MED14
            experimental knowledge based
            (Guruharsha et al., 2011)
            Larp4B - MED17
            experimental knowledge based
            (Guruharsha et al., 2011)
            Larp4B - MED18
            experimental knowledge based
            (Guruharsha et al., 2011)
            Larp4B - MED20
            experimental knowledge based
            (Guruharsha et al., 2011)
            Larp4B - MED23
            experimental knowledge based
            (Guruharsha et al., 2011)
            Larp4B - MED27
            experimental knowledge based
            (Guruharsha et al., 2011)
            Larp4B - MED30
            experimental knowledge based
            (Guruharsha et al., 2011)
            Larp4B - MED4
            experimental knowledge based
            (Guruharsha et al., 2011)
            Larp4B - MED6
            experimental knowledge based
            (Guruharsha et al., 2011)
            Larp4B - MED7
            experimental knowledge based
            (Guruharsha et al., 2011)
            Larp4B - MED8
            experimental knowledge based
            (Guruharsha et al., 2011)
            Larp4B - Psi
            experimental knowledge based
            (Guruharsha et al., 2011)
            Larp4B - Rga
            anti tag coimmunoprecipitation, peptide massfingerprinting, experimental knowledge based
            (Rhee et al., 2014)
            Larp4B - Tdrd3
            experimental knowledge based
            (Guruharsha et al., 2011)
            Larp4B - Usp10
            experimental knowledge based
            (Guruharsha et al., 2011)
            Larp4B - boca
            experimental knowledge based
            (Guruharsha et al., 2011)
            Larp4B - brm
            experimental knowledge based
            (Guruharsha et al., 2011)
            Larp4B - csw
            anti tag coimmunoprecipitation, peptide massfingerprinting
            (Friedman et al., 2011)
            Larp4B - dsh
            experimental knowledge based
            (Guruharsha et al., 2011)
            Larp4B - ebi
            experimental knowledge based
            (Guruharsha et al., 2011)
            Larp4B - ft
            anti tag coimmunoprecipitation, peptide massfingerprinting
            (Kwon et al., 2013)
            Larp4B - ix
            experimental knowledge based
            (Guruharsha et al., 2011)
            Larp4B - kel
            proximity-dependent biotin identification, Identification by mass spectrometry
            (Mannix et al., 2019)
            Larp4B - mor
            experimental knowledge based
            (Guruharsha et al., 2011)
            Larp4B - osa
            experimental knowledge based
            (Guruharsha et al., 2011)
            Larp4B - tyf
            experimental knowledge based
            (Guruharsha et al., 2011)
            Summary of Genetic Interactions
            esyN Network Diagram
            esyN Network Key:
            Suppression
            Enhancement
            View in Interactions Browser
            Please look at the allele data for full details of the genetic interactions
            Starting gene(s)
            Interaction type
            Interacting gene(s)
            Reference
            Larp4B
            suppressible
            Myc
            (Funakoshi et al., 2018)
            Starting gene(s)
            Interaction type
            Interacting gene(s)
            Reference
            External Data
            Linkouts
            BioGRID - A database of protein and genetic interactions.
            DroID - A comprehensive database of gene and protein interactions.
            InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
            MIST (protein-protein) - An integrated Molecular Interaction Database
            Pathways
            Signaling Pathways (FlyBase)
            Metabolic Pathways
            External Data
            Linkouts
            Genomic Location and Detailed Mapping Data
            Chromosome (arm)
            3L
            Recombination map

            3-7

            Cytogenetic map
            63C1-63C1
            Sequence location
            3L:3,224,838..3,236,604 [+]
            FlyBase Computed Cytological Location
            Cytogenetic map
            Evidence for location
            63C1-63C1
            Limits computationally determined from genome sequence between P{PZ}l(3)0680306803 and P{PZ}kst01318
            Experimentally Determined Cytological Location
            Cytogenetic map
            Notes
            References
            Experimentally Determined Recombination Data
            Location

            3-7

            (FlyBase, 2016)

            3-6.6

            (Comeron et al., 2012)
            Left of (cM)
            Right of (cM)
            Notes
            Stocks and Reagents
            Stocks (9)
            Genomic Clones (17)
             

            Please Note FlyBase no longer curates genomic clone accessions so this list may not be complete

            cDNA Clones (16)
             

            Please Note This section lists cDNAs and ESTs that fall within the genomic extent of the gene model, which may include cDNAs and ESTs of genes within introns, or of overlapping genes. Please see GBrowse for alignment of the cDNAs and ESTs to the gene model.

            cDNA clones, fully sequenced
            BDGP DGC clones
            Other clones
              Drosophila Genomics Resource Center cDNA clones

              For each fully sequenced cDNA the DGRC maintains various forms of the cDNA (e.g tagged or untagged) in several different host vectors for subsequent cloning and expression in Drosophila and Drosophila cell lines.

              cDNA Clones, End Sequenced (ESTs)
              BDGP DGC clones
              Other clones
              RNAi and Array Information
              Linkouts
              DRSC - Results frm RNAi screens
              GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
              Antibody Information
              Laboratory Generated Antibodies
               
              Commercially Available Antibodies
               
              Other Information
              Relationship to Other Genes
              Source for database identify of

              Source for identity of: Larp4B CG11505

              (Funakoshi et al., 2018)
              Source for database merge of
              Additional comments
              Other Comments
              Origin and Etymology
              Discoverer
              Etymology
              Identification
              External Crossreferences and Linkouts ( 39 )
              Sequence Crossreferences
              NCBI Gene - Gene integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes, and links to genome-, phenotype-, and locus-specific resources worldwide.
              GenBank Nucleotide - A collection of sequences from several sources, including GenBank, RefSeq, TPA, and PDB.
              GenBank Protein - A collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB.
              RefSeq - A comprehensive, integrated, non-redundant, well-annotated set of reference sequences including genomic, transcript, and protein.
              UniProt/Swiss-Prot - Manually annotated and reviewed records of protein sequence and functional information
              Other crossreferences
              Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones
              Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
              Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
              Flygut - An atlas of the Drosophila adult midgut
              GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
              InterPro - A database of protein families, domains and functional sites
              KEGG Genes - Molecular building blocks of life in the genomic space.
              modMine - A data warehouse for the modENCODE project
              Linkouts
              BioGRID - A database of protein and genetic interactions.
              DroID - A comprehensive database of gene and protein interactions.
              DRSC - Results frm RNAi screens
              FLIGHT - Cell culture data for RNAi and other high-throughput technologies
              FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
              FlyCyc Genes - Genes from a BioCyc PGDB for Dmel
              FlyMine - An integrated database for Drosophila genomics
              InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
              MIST (protein-protein) - An integrated Molecular Interaction Database
              Synonyms and Secondary IDs (4)
              Datasets (0)
              Study focus (0)
              Experimental Role
              Project
              Project Type
              Title
              References (40)