FB2021_02, released April 13, 2021

Gene: Dmel\icln

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General Information
Symbol
Dmel\icln
Species
D. melanogaster
Name
icln
Annotation Symbol
CG4924
Feature Type
protein_coding_gene
FlyBase ID
FBgn0029079
Gene Model Status
Current
Stock Availability
2 publicly available
Gene Summary
icln (icln) encodes a cytosolic protein that functions as an assembly chaperone in the biogenesis of pre-mRNA processing small nuclear ribonucleoproteins (snRNPs) via interaction with Sm proteins. It is required in the motor system for viability and motor behaviour. [Date last reviewed: 2019-03-07] (FlyBase Gene Snapshot)
All Summaries
Also Known As

pICln

Key Links
Genomic Location
Cytogenetic map
54C12-54C12
Sequence location
2R:17,590,964..17,591,881 [+]
Recombination map
2-83
RefSeq locus
NT_033778 REGION:17590964..17591881
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 (7 terms)
Molecular Function (0 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (0 terms)
Biological Process (3 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (3 terms)
CV Term
Evidence
References
involved_in cell volume homeostasis
inferred from electronic annotation with InterPro:IPR003521
(assigned by InterPro )
(FlyBase Curators et al., 2004-)
involved_in chloride transport
inferred from electronic annotation with InterPro:IPR003521
(assigned by InterPro )
(FlyBase Curators et al., 2004-)
involved_in spliceosomal snRNP assembly
inferred from electronic annotation with InterPro:IPR003521
(assigned by InterPro )
(FlyBase Curators et al., 2004-)
Cellular Component (4 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (4 terms)
CV Term
Evidence
References
located_in cytosol
inferred from electronic annotation with InterPro:IPR003521
(assigned by InterPro )
(FlyBase Curators et al., 2004-)
part_of methylosome
inferred from electronic annotation with InterPro:IPR003521
(assigned by InterPro )
(FlyBase Curators et al., 2004-)
part_of pICln-Sm protein complex
inferred from electronic annotation with InterPro:IPR003521
(assigned by InterPro )
(FlyBase Curators et al., 2004-)
located_in plasma membrane
inferred from electronic annotation with InterPro:IPR003521
(assigned by InterPro )
(FlyBase Curators et al., 2004-)
Gene Group (FlyBase)
Protein Family (UniProt)
Belongs to the pICln (TC 1.A.47) family. (A1ZAW5)
Protein Signatures (InterPro)
Summaries
Gene Snapshot
icln (icln) encodes a cytosolic protein that functions as an assembly chaperone in the biogenesis of pre-mRNA processing small nuclear ribonucleoproteins (snRNPs) via interaction with Sm proteins. It is required in the motor system for viability and motor behaviour. [Date last reviewed: 2019-03-07]
Protein Function (UniProtKB)
Chaperone that regulates the assembly of spliceosomal U1, U2, U4 and U5 small nuclear ribonucleoproteins (snRNPs), the building blocks of the spliceosome. Thereby, plays an important role in the splicing of cellular pre-mRNAs. Most spliceosomal snRNPs contain a common set of Sm proteins SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF and SNRPG that assemble in a heptameric protein ring on the Sm site of the small nuclear RNA to form the core snRNP. In the cytosol, the Sm proteins SNRPD1, SNRPD2, SNRPE, SNRPF and SNRPG are trapped in an inactive 6S pICln-Sm complex by the chaperone CLNS1A that controls the assembly of the core snRNP. Dissociation by the SMN complex of CLNS1A from the trapped Sm proteins and their transfer to an SMN-Sm complex triggers the assembly of core snRNPs and their transport to the nucleus (By similarity).
(UniProt, A1ZAW5)
Gene Model and Products
Number of Transcripts
1
Number of Unique Polypeptides
1

Please see the JBrowse view of Dmel\icln 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

Gene model reviewed during 5.46

Sequence Ontology: Class of Gene
nuclear_gene
protein_coding_gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
icln-RA
FBtr0086832
NM_137393
832
215
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
icln-PA
FBpp0086010
23.7
215
3.72
NP_611237
AAF57826
Polypeptides with Identical Sequences

There is only one protein coding transcript and one polypeptide associated with this gene

Additional Polypeptide Data and Comments
Reported size (kDa)
Comments
External Data
Subunit Structure (UniProtKB)

Component of the methylosome, a 20S complex containing at least CLNS1A/pICln, PRMT5/SKB1 and WDR77/MEP50; may mediate SNRPD1 and SNRPD3 methylation. Forms a 6S pICln-Sm complex composed of CLNS1A/pICln, SNRPD1, SNRPD2, SNRPE, SNRPF and SNRPG; ring-like structure where CLNS1A/pICln mimics additional Sm proteins and which is unable to assemble into the core snRNP.

(UniProt, A1ZAW5)
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\icln 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
wandering third instar larval stage
wing pouch | restricted
(Molnar et al., 2012)
wing hinge primordium | restricted
(Molnar et al., 2012)
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
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\icln 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, Transgenic Constructs, and Aberrations
Classical and Insertion Alleles ( 0 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 5 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of icln
Transgenic constructs containing regulatory region of icln
Aberrations (Deficiencies and Duplications) ( 1 )
Inferred from experimentation ( 1 )
Gene disrupted in
Df(2R)Exel7149
(Ryder, 2004.4.26)
Inferred from location ( 0 )
Phenotypes
For more details about a specific phenotype click on the relevant allele symbol.
Lethality
Allele
lethal, with Dcr-2UAS.cUa, Scer\GAL4Mef2.PR
lethal, with Scer\GAL4c179
lethal, with Scer\GAL4da.PU
lethal, with Scer\GAL4G7
lethal, with Scer\GAL4how-24B
lethal, with Scer\GAL4Mef2.PR
partially lethal, with Scer\GAL4Mef2.PR
partially lethal - majority die, with Dcr-2UAS.cUa, Scer\GAL4RapGAP1-OK6
partially lethal - majority die, with Scer\GAL4c179
partially lethal - majority die, with Scer\GAL4G7
partially lethal - majority die, with Scer\GAL4how-24B
viable, with Dcr-2UAS.cDa, Scer\GAL4e22c, Scer\GAL4sqh.PW
viable, with Dcr-2UAS.cDa, Scer\GAL4elav.PLu
viable, with Dcr-2UAS.cUa, Scer\GAL4elav.PU
viable, with Dcr-2UAS.cUa, Scer\GAL4Mef2.PR
viable, with Dcr-2UAS.cUa, Scer\GAL4RapGAP1-OK6
viable, with Scer\GAL4elav.PU
viable, with Scer\GAL4G7
viable, with Scer\GAL4Mef2.PR
viable, with Scer\GAL4pnr-MD237
viable, with Scer\GAL4RapGAP1-OK6
viable, with Scer\GAL4tin.CΔ4
Other Phenotypes
Allele
abnormal body size | pupal stage, with Scer\GAL4how-24B
abnormal flight, with Dcr-2UAS.cUa, Scer\GAL4Mef2.PR
abnormal flight, with Scer\GAL4Mef2.PR
abnormal locomotor behavior | adult stage, with Dcr-2UAS.cUa, Scer\GAL4Mef2.PR
abnormal locomotor behavior | adult stage, with Scer\GAL4Mef2.PR
flightless, with Scer\GAL4Mef2.PR
visible | adult stage, with Scer\GAL4Mef2.PR
Phenotype manifest in
Allele
wing blade, with Scer\GAL4Mef2.PR
Orthologs
Downloads
Download All DIOPT Orthologs
Download All OrthoDB Orthologs
Human Orthologs (via DIOPT v8.0)
Homo sapiens (Human) (1)
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\CLNS1A
12 of 15
Yes
Yes
Model Organism Orthologs (via DIOPT v8.0)
Mus musculus (laboratory mouse) (1)
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\Clns1a
11 of 15
Yes
Yes
Rattus norvegicus (Norway rat) (1)
Rnor\Clns1a
10 of 13
Yes
Yes
Xenopus tropicalis (Western clawed frog) (1)
Xtro\clns1a
6 of 12
Yes
Yes
Danio rerio (Zebrafish) (1)
Drer\clns1a
8 of 15
Yes
Yes
Caenorhabditis elegans (Nematode, roundworm) (2)
Cele\icln-1
11 of 15
Yes
Yes
Cele\icl-1
1 of 15
No
Yes
Arabidopsis thaliana (thale-cress) (1)
Atha\AT5G62290
5 of 9
Yes
Yes
Saccharomyces cerevisiae (Brewer's yeast) (1)
Scer\LOT5
1 of 15
Yes
Yes
Schizosaccharomyces pombe (Fission yeast) (1)
Spom\SPAC1610.01
2 of 12
Yes
Yes
Ortholog(s) in Drosophila Species (via OrthoDB v9.1) ( EOG09190G3O )
Organism
Common Name
Gene
AAA Syntenic Ortholog
Multiple Dmel Genes in this Orthologous Group
Drosophila suzukii
Spotted wing Drosophila
Dsuz\DS10_00003594
Drosophila simulans
Dsim\GD11295
Drosophila sechellia
Dsec\GM21806
Drosophila erecta
Dere\GG21803
Drosophila yakuba
Dyak\icln
Drosophila ananassae
Dana\GF11656
Drosophila pseudoobscura pseudoobscura
Dpse\GA18528
Drosophila persimilis
Dper\GL16784
Drosophila willistoni
Dwil\GK10720
Drosophila virilis
Dvir\GJ21819
Drosophila mojavensis
Dmoj\GI18789
Drosophila grimshawi
Dgri\GH20074
Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG09150CEA )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Musca domestica
House fly
Mdoa\17005753
Glossina morsitans
Tsetse fly
Gmor\GMOY004857
Lucilia cuprina
Australian sheep blowfly
Lcup\FF38_10748
Aedes aegypti
Yellow fever mosquito
Aaeg\AAEL010245
Anopheles darlingi
American malaria mosquito
Adar\ADAC006893
Anopheles gambiae
Malaria mosquito
Agam\AGAP011245
Culex quinquefasciatus
Southern house mosquito
Cqui\CPIJ005015
Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W0MCX )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Bombyx mori
Silkmoth
Bmor\BGIBMGA000155
Danaus plexippus
Monarch butterfly
Dple\DPOGS207915-PA
Heliconius melpomene
Postman butterfly
Hmel\HMEL003794
Apis florea
Little honeybee
Aflo\2770405380
Apis mellifera
Western honey bee
Amel\GB43429
Bombus impatiens
Common eastern bumble bee
Bimp\BIMP20288
Bombus terrestris
Buff-tailed bumblebee
Bter\15214680
Linepithema humile
Argentine ant
Lhum\LH14259
Megachile rotundata
Alfalfa leafcutting bee
Mrot\MROTU:001d97
Nasonia vitripennis
Parasitic wasp
Nvit\Nasvi2EG009342
Dendroctonus ponderosae
Mountain pine beetle
Dpod\YQE_02280
Tribolium castaneum
Red flour beetle
Tcas\TC003587
Pediculus humanus
Human body louse
Phum\PHUM091620
Rhodnius prolixus
Kissing bug
Rpro\RPRC003753
Cimex lectularius
Bed bug
Clec\CLEC010650
Acyrthosiphon pisum
Pea aphid
Apim\ACYPI086593
Zootermopsis nevadensis
Nevada dampwood termite
Znev\Znev_04145
Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X0ML1 )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strigamia maritima
European centipede
Smar\SMAR005360
Ixodes scapularis
Black-legged tick
Isca\ISCW002915
Stegodyphus mimosarum
African social velvet spider
Smim\KFM68143.1
Daphnia pulex
Water flea
Dpux\DAPPUDRAFT_308065
Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( None identified )
No non-Arthropod Metazoa orthologies identified
Paralogs
Downloads
Download All DIOPT Paralogs
Paralogs (via DIOPT v8.0)
Drosophila melanogaster (Fruit fly) (0)
No records found.
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?
    CLNS1A; chloride nucleotide-sensitive channel 1A
    12 of 15
    602158
        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
        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
        icln
        enhanceable
        Gem3
        (Borg et al., 2016)
        icln
        suppressible
        Gem3
        (Borg et al., 2016)
        Starting gene(s)
        Interaction type
        Interacting gene(s)
        Reference
        External Data
        Subunit Structure (UniProtKB)
        Component of the methylosome, a 20S complex containing at least CLNS1A/pICln, PRMT5/SKB1 and WDR77/MEP50; may mediate SNRPD1 and SNRPD3 methylation. Forms a 6S pICln-Sm complex composed of CLNS1A/pICln, SNRPD1, SNRPD2, SNRPE, SNRPF and SNRPG; ring-like structure where CLNS1A/pICln mimics additional Sm proteins and which is unable to assemble into the core snRNP.
        (UniProt, A1ZAW5 )
        Linkouts
        DroID - A comprehensive database of gene and protein interactions.
        InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
        MIST (genetic) - An integrated Molecular Interaction Database
        MIST (protein-protein) - An integrated Molecular Interaction Database
        Pathways
        Signaling Pathways (FlyBase)
        Metabolic Pathways
        External Data
        Linkouts
        KEGG Pathways - Wiring diagrams of molecular interactions, reactions and relations.
        Genomic Location and Detailed Mapping Data
        Chromosome (arm)
        2R
        Recombination map
        2-83
        Cytogenetic map
        54C12-54C12
        Sequence location
        2R:17,590,964..17,591,881 [+]
        FlyBase Computed Cytological Location
        Cytogenetic map
        Evidence for location
        54C12-54C12
        Limits computationally determined from genome sequence between P{EP}MESR4EP386&P{EP}POSHEP1206 and P{PZ}l(2)1050510505
        Experimentally Determined Cytological Location
        Cytogenetic map
        Notes
        References
        Experimentally Determined Recombination Data
        Location

        2-83

        (FlyBase, 2016)

        2-86.2

        (Comeron et al., 2012)
        Left of (cM)
        Right of (cM)
        Notes
        Stocks and Reagents
        Stocks (2)
        Genomic Clones (17)
         

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

        cDNA Clones (66)
         

        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 database merge of

        Source for merge of: icln CG4924

        (Bayraktaroglu, 2000.8.7)
        Additional comments
        Other Comments
        Origin and Etymology
        Discoverer
        Etymology
        Identification
        External Crossreferences and Linkouts ( 31 )
        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
        iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)
        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
        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.
        KEGG Pathways - Wiring diagrams of molecular interactions, reactions and relations.
        MIST (genetic) - An integrated Molecular Interaction Database
        MIST (protein-protein) - An integrated Molecular Interaction Database
        Synonyms and Secondary IDs (3)
        Datasets (0)
        Study focus (0)
        Experimental Role
        Project
        Project Type
        Title
        References (31)