FB2022_02, released March 29, 2022

Gene: Dmel\loj

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General Information
Symbol
Dmel\loj
Species
D. melanogaster
Name
logjam
Annotation Symbol
CG10733
Feature Type
protein_coding_gene
FlyBase ID
FBgn0061492
Gene Model Status
Current
Stock Availability
6 publicly available
Gene Summary
logjam (loj) encodes a p24-transporter-type protein involved in oviposition. [Date last reviewed: 2019-07-11] (FlyBase Gene Snapshot)
All Summaries
Also Known As

l(3)04026, p24

Key Links
Genomic Location
Cytogenetic map
65A6-65A6
Sequence location
Recombination map
3-16
RefSeq locus
NT_037436 REGION:6094987..6096517
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 (12 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 cargo receptor activity
inferred from sequence model
(Carney and Bowen, 2004)
Biological Process (5 terms)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
involved_in oviposition
inferred from mutant phenotype
(Carney and Taylor, 2003)
Terms Based on Predictions or Assertions (4 terms)
CV Term
Evidence
References
involved_in endoplasmic reticulum to Golgi vesicle-mediated transport
inferred from biological aspect of ancestor with PANTHER:PTN000516376
(assigned by GO_Central )
(Gaudet et al., 2011)
involved_in Golgi organization
inferred from biological aspect of ancestor with PANTHER:PTN000516376
(assigned by GO_Central )
(Gaudet et al., 2011)
involved_in Golgi vesicle transport
inferred from sequence model
(Carney and Bowen, 2004)
involved_in intracellular protein transport
inferred from biological aspect of ancestor with PANTHER:PTN000516376
(assigned by GO_Central )
(Gaudet et al., 2011)
Cellular Component (6 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
located_in cis-Golgi network
inferred from direct assay
(Boltz et al., 2007)
located_in endoplasmic reticulum-Golgi intermediate compartment
inferred from direct assay
(Boltz et al., 2007)
Terms Based on Predictions or Assertions (5 terms)
CV Term
Evidence
References
is_active_in COPII-coated ER to Golgi transport vesicle
inferred from biological aspect of ancestor with PANTHER:PTN000516376
(assigned by GO_Central )
(Gaudet et al., 2011)
is_active_in endoplasmic reticulum-Golgi intermediate compartment
inferred from biological aspect of ancestor with PANTHER:PTN000516376
(assigned by GO_Central )
(Gaudet et al., 2011)
is_active_in endoplasmic reticulum
inferred from biological aspect of ancestor with PANTHER:PTN000516376
(assigned by GO_Central )
(Gaudet et al., 2011)
is_active_in Golgi apparatus
inferred from biological aspect of ancestor with PANTHER:PTN000516376
(assigned by GO_Central )
(Gaudet et al., 2011)
located_in integral component of membrane
inferred from sequence model
(Carney and Bowen, 2004)
Gene Group (FlyBase)
Protein Family (UniProt)
-
Protein Signatures (InterPro)
Summaries
Gene Snapshot
logjam (loj) encodes a p24-transporter-type protein involved in oviposition. [Date last reviewed: 2019-07-11]
Gene Group (FlyBase)
P24 TRANSPORTERS -
p24 proteins are single-pass type-I membrane proteins which are components of the COPI and COPII coated vesicles that mediate intracellular trafficking between the ER and Golgi. Their function in trafficking is unclear; they may be involved in cargo selection, quality control or vesicle formation. (Adapted from FBrf0174396 and FBrf0219054).
Gene Model and Products
Number of Transcripts
3
Number of Unique Polypeptides
1

Please see the JBrowse view of Dmel\loj 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
Structure New Section
Protein 3D structure   (Predicted by AlphaFold)   (AlphaFold entry Q9VRU2)

If you don't see the viewer to the right, refresh your browser.
Model Confidence:
  • Very high (pLDDT > 90)
  • Confident (90 > pLDDT > 70)
  • Low (70 > pLDDT > 50)
  • Very low (pLDDT < 50)

AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Some regions with low pLDDT may be unstructured in isolation.

Comments on Gene Model

Gene model reviewed during 5.45

Sequence Ontology: Class of Gene
nuclear_gene
protein_coding_gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
loj-RD
FBtr0301446
NM_168154
1179
237
loj-RE
FBtr0301447
NM_139770
1084
237
loj-RF
FBtr0301448
NM_168155
1104
237
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
loj-PD
FBpp0290661
26.9
237
6.50
NP_729140
AAF50698
loj-PE
FBpp0290662
26.9
237
6.50
NP_648027
AAN12236
loj-PF
FBpp0290663
26.9
237
6.50
NP_729141
AAN12237
Polypeptides with Identical Sequences

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

237 aa isoforms: loj-PD, loj-PE, loj-PF
Additional Polypeptide Data and Comments
Reported size (kDa)
Comments
External Data
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\loj 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
in situ
Stage
Tissue/Position (including subcellular localization)
Reference
oogenesis stage S7 -- S8 & adult stage | female
follicle cell | faint
(Boltz et al., 2007)
nurse cell | faint
(Boltz et al., 2007)
oogenesis stage S9 -- S10 & adult stage | female
follicle cell
(Boltz et al., 2007)
nurse cell
(Boltz et al., 2007)
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
immunolocalization
Stage
Tissue/Position (including subcellular localization)
Reference
adult stage
adult brain
(Saleem et al., 2012)
adult ventral nerve cord
(Saleem et al., 2012)
adult stage | female
adult fat body
(Saleem et al., 2012)
female accessory gland
(Saleem et al., 2012)
spermatheca
(Saleem et al., 2012)
egg chamber
(Saleem et al., 2012)
adult brain | restricted
(Boltz et al., 2007)
adult ventral nerve cord | restricted
(Boltz et al., 2007)
adult stage | male
adult fat body
(Saleem et al., 2012)
male accessory gland
(Saleem et al., 2012)
testis
(Saleem et al., 2012)
ejaculatory duct
(Saleem et al., 2012)
ejaculatory bulb
(Saleem et al., 2012)
seminal vesicle
(Saleem et al., 2012)
oogenesis stage S9 -- S10 & adult stage | female
follicle cell
(Boltz et al., 2007)
nurse cell
(Boltz et al., 2007)
mass spectroscopy
Stage
Tissue/Position (including subcellular localization)
Reference
adult stage
adult head
(Aradska et al., 2015)
Additional Descriptive Data

In the adult brain, a subset of neurons labelled with loj protein co-express the peptidergic marker Scer\GAL4dimm-929. In the abdominal ganglion, expression co-localises with the octopaminergic marker Scer\GAL4ptc-559.1.

(Saleem et al., 2012)
Marker for
 
Subcellular Localization
CV Term
Evidence
References
located_in cis-Golgi network
inferred from direct assay
(Boltz et al., 2007)
located_in endoplasmic reticulum-Golgi intermediate compartment
inferred from direct assay
(Boltz et al., 2007)
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\loj 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
BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species
EMBL-EBI Single Cell Expression Atlas - Single cell expression across species
FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
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, Transgenic Constructs, and Aberrations
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 loj
Transgenic constructs containing regulatory region of loj
Aberrations (Deficiencies and Duplications) ( 6 )
Alleles Representing Disease-Implicated Variants
Phenotypes
Orthologs
Downloads
Download All DIOPT 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\TMED6
12 of 15
Yes
Yes
Hsap\TMED1
1 of 15
No
No
Hsap\TMED3
1 of 15
No
No
Hsap\TMED5
1 of 15
No
No
1  
Hsap\TMED7
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\Tmed6
9 of 15
Yes
Yes
Mmus\Tmed1
1 of 15
No
No
Mmus\Tmed3
1 of 15
No
No
Mmus\Tmed5
1 of 15
No
No
Mmus\Tmed7
1 of 15
No
No
Rattus norvegicus (Norway rat) (4)
Rnor\Tmed6
9 of 13
Yes
Yes
Rnor\Tmed1
1 of 13
No
No
Rnor\Tmed3
1 of 13
No
No
Rnor\Tmed7
1 of 13
No
No
Xenopus tropicalis (Western clawed frog) (4)
Xtro\tmed6
7 of 12
Yes
Yes
Xtro\tmed1
1 of 12
No
No
Xtro\tmed5
1 of 12
No
No
Xtro\tmed7
1 of 12
No
No
Danio rerio (Zebrafish) (5)
Drer\tmed6
7 of 15
Yes
Yes
Drer\tmed1a
1 of 15
No
No
Drer\tmed3
1 of 15
No
No
Drer\tmed5
1 of 15
No
No
Drer\tmed7
1 of 15
No
No
Caenorhabditis elegans (Nematode, roundworm) (3)
Cele\C26C6.9
1 of 15
Yes
Yes
Cele\tmed-1
1 of 15
Yes
No
Cele\tmed-3
1 of 15
Yes
No
Arabidopsis thaliana (thale-cress) (2)
Atha\AT3G22845
2 of 9
Yes
No
Atha\p24beta2
2 of 9
Yes
No
Saccharomyces cerevisiae (Brewer's yeast) (4)
Scer\ERP2
3 of 15
Yes
No
Scer\ERP3
3 of 15
Yes
No
Scer\ERP4
3 of 15
Yes
No
Scer\EMP24
1 of 15
No
No
Schizosaccharomyces pombe (Fission yeast) (2)
Spom\SPAC17A5.08
2 of 12
Yes
No
Spom\emp24
1 of 12
No
No
Other Organism Orthologs (via OrthoDB)
Paralogs
Downloads
Download All DIOPT Paralogs
Paralogs (via DIOPT v8.0)
Drosophila melanogaster (Fruit fly) (8)
Gene Symbol
Score
Source
Compara
eggNOG
Homologene
Inparanoid
Isobase
OrthoDB
OrthoFinder
orthoMCL
Panther
RoundUp
Alignment
CG31787
4 of 10
opm
3 of 10
p24-1
3 of 10
bai
2 of 10
CG9308
2 of 10
CHOp24
2 of 10
eca
2 of 10
p24-2
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?
    TMED6; transmembrane p24 trafficking protein 6
    12 of 15
        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
        Interactions Browser
        Summary of Genetic Interactions
        esyN Network Diagram
        Starting gene(s)
        Interaction type
        Interacting gene(s)
        Reference
        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.
        Pathways
        Signaling Pathways (FlyBase)
        Metabolic Pathways
        External Data
        Linkouts
        Genomic Location and Detailed Mapping Data
        Chromosome (arm)
        3L
        Recombination map
        3-16
        Cytogenetic map
        65A6-65A6
        Sequence location
        FlyBase Computed Cytological Location
        Cytogenetic map
        Evidence for location
        65A6-65A6
        Limits computationally determined from genome sequence between P{PZ}vn10567 and P{PZ}loj04026
        Experimentally Determined Cytological Location
        Cytogenetic map
        Notes
        References
        65A5-65A6
        (determined by in situ hybridisation)
        (Spradling et al., 1999)
        65A5-65A6
        (BDGP Project Members, 1994-1999)
        Experimentally Determined Recombination Data
        Location

        3-16

        (FlyBase, 2016)

        3-14.3

        (Comeron et al., 2012)
        Left of (cM)
        Right of (cM)
        Notes
        Stocks and Reagents
        Stocks (6)
        Genomic Clones (19)
        cDNA Clones (36)
         

        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
           

          polyclonal

          (Boltz et al., 2007)
          Commercially Available Antibodies
           
          Other Information
          Relationship to Other Genes
          Source for database identify of
          Source for database merge of

          Source for merge of: loj CG10733 l(3)04026

          (Carney and Taylor, 2003)
          Additional comments
          Other Comments

          Identification: In a screen for genes involved in female-specific reproductive behaviors.

          (Carney and Taylor, 2002)

          Mutations in loj cause the loss of oviposition behavior and the retention of mature eggs in the oviducts and uteruses of mated mutant females.

          (Carney and Taylor, 2002)
          Origin and Etymology
          Discoverer
          Etymology

          The gene is named "logjam" after the mutant phenotype; in mutant females, one or more mature eggs become lodged within the genital tract, causing a "logjam" of eggs within the female and preventing the release of eggs.

          (Carney and Taylor, 2003)
          Identification
          External Crossreferences and Linkouts ( 47 )
          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/GCRP - The gene-centric reference proteome (GCRP) provides a 1:1 mapping between genes and UniProt accessions in which a single 'canonical' isoform represents the product(s) of each protein-coding gene.
          UniProt/TrEMBL - Automatically annotated and unreviewed records of protein sequence and functional information
          Other crossreferences
          AlphaFold DB - AlphaFold provides open access to protein structure predictions for the human proteome and other key proteins of interest, to accelerate scientific research.
          BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
          Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones
          DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species
          EMBL-EBI Single Cell Expression Atlas - Single cell expression across species
          Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
          FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
          FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
          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.
          MARRVEL_MODEL - MARRVEL (model organism gene)
          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
          FlyCyc Genes - Genes from a BioCyc PGDB for Dmel
          FlyMine - An integrated database for Drosophila genomics
          Synonyms and Secondary IDs (8)
          Datasets (8)
          Study focus (0)
          Experimental Role
          Project
          Project Type
          Title
          Study result (8)
          Result
          Result Type
          Title
          scRNAseq_2020_Cattenoz_NI_seq_clustering
          Clustering analysis of hemocytes from non-infested third instar larvae
          scRNAseq_2020_Cattenoz_WI_seq_clustering
          Clustering analysis of hemocytes from wasp-infested third instar larvae
          scRNAseq_2020_Cho_NI72LG_seq_clustering
          Clustering analysis of lymph gland cells from non-infested larvae at 72 h after egg-laying
          scRNAseq_2020_Cho_NI96LG_seq_clustering
          Clustering analysis of lymph gland cells from non-infested larvae at 96 h after egg-laying
          scRNAseq_2020_Cho_NI120LG_seq_clustering
          Clustering analysis of lymph gland cells from non-infested larvae at 120 h after egg-laying
          scRNAseq_2020_Cho_WI96LG_seq_clustering
          Clustering analysis of lymph gland cells from wasp-infested larvae at 96 h after egg-laying
          scRNAseq_2020_Cho_NI96HL_seq_clustering
          Clustering analysis of circulating hemocytes from non-infested larvae at 96 h after egg-laying
          scRNAseq_2020_Cho_NI120HL_seq_clustering
          Clustering analysis of circulating hemocytes from non-infested larvae at 120 h after egg-laying
          References (54)