FlyBase Gene Report: Dmel\Sdic3

General Information

Symbol

Dmel\Sdic3

Species

D. melanogaster

Name

Sperm-specific dynein intermediate chain 3

Annotation Symbol

CG32823

Feature Type

protein_coding_gene

FlyBase ID

FBgn0052823

Gene Model Status

Current

Stock Availability

1 publicly available

Gene Summary

Contribute a Gene Snapshot for this gene.

All Summaries

Alliance
Auto summary
Gene Group
Interactive Fly

Also Known As

Sdic:CG32823

Key Links

Genomic Location

Cytogenetic map

19C1-19C1

Sequence location

X:20,189,440..20,194,227 [-]

Recombination map

1-64

RefSeq locus

NC_004354 REGION:20189440..20194227

Sequence

Get Decorated FASTA

Genomic Maps

JBrowse

Other Genome Views

The following external sites may use different assemblies or annotations than FlyBase.

Function

Gene Ontology (GO) Annotations (5 terms)

Molecular Function (2 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

enables dynein heavy chain binding

inferred from biological aspect of ancestor with PANTHER:PTN000277823

(GO Reference Genome Project, 2011-)

enables dynein light chain binding

inferred from biological aspect of ancestor with PANTHER:PTN000277823

(GO Reference Genome Project, 2011-)

Biological Process (2 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

involved_in microtubule-based movement

inferred from electronic annotation with InterPro:IPR025956

(InterPro Project Members, 2004-)

involved_in transport along microtubule

inferred from biological aspect of ancestor with PANTHER:PTN000277824

(GO Reference Genome Project, 2011-)

Cellular Component (1 term)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

part_of cytoplasmic dynein complex

inferred from biological aspect of ancestor with PANTHER:PTN000277824

(GO Reference Genome Project, 2011-)

inferred from electronic annotation with InterPro:IPR025956

(InterPro Project Members, 2004-)

Gene Group (FlyBase)

SPERM-SPECIFIC DYNEIN INTERMEDIATE CHAINS

Protein Family (UniProt)

Protein Signatures (InterPro)

Summaries

Gene Group (FlyBase)

SPERM-SPECIFIC DYNEIN INTERMEDIATE CHAINS -: The sperm-specific dynein intermediate chains (Sdic) are encoded as a multigene family. Present only in Drosophila melanogaster, the Sdic cluster was recently evolutionary derived from the cytoplasmic dynein intermediate chain gene sw. The protein encoded by Sdic genes lacks the N-terminal region of sw, a region that contains a coiled-coil domain and a serine-rich domain which are essential for cytoplasmic dynein intermediate chain function. (Adapted from FBrf0195004).

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\Sdic3 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

Protein 3D structure (Predicted by AlphaFold) (AlphaFold entry Q8IRZ3)

If you don't see a structure in the viewer, 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.

Experimentally Determined Structures

Crossreferences

Comments on Gene Model

Gene model reviewed during 5.56

Gene model reviewed during 5.50

Sdic/Cdic-related; one of at least 3 copies produced by duplication and expansion events.

Gene model reviewed during 5.55

Gene model reviewed during 6.01

Sequence Ontology: Class of Gene

gene_array_member

nuclear_gene

protein_coding_gene

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

Sdic3-RE

FBtr0346675

NM_001298554

1964

533

Sdic3-RF

FBtr0346676

NM_001298553

2200

533

Sdic3-RG

FBtr0346677

NM_167693

2361

533

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

UniProt

RefSeq ID

GenBank

Sdic3-PE

FBpp0312288

59.1

533

5.04

FBpp0312289

59.1

533

5.04

FBpp0312290

59.1

533

5.04

Q8IRZ3

NP_728323

AAN08994

Polypeptides with Identical Sequences

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

533 aa isoforms: Sdic3-PE, Sdic3-PF, Sdic3-PG

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

Nucleotide / Polypeptide Records

UniProt

Q8IRZ3

Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\Sdic3 using the Feature Mapper tool.

External Data

Crossreferences

Linkouts

Expression Data

Testis-specificity index

The testis specificity index was calculated from modENCODE tissue expression data by Vedelek et al., 2018 to indicate the degree of testis enrichment compared to other tissues. Scores range from -2.52 (underrepresented) to 5.2 (very high testis bias).

NA

Transcript Expression

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

JBrowse - Visual display of RNA-Seq signals

View Dmel\Sdic3 in JBrowse

RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region

View exonic expression by developmental stage for Dmel\Sdic3

View exonic expression by tissue for Dmel\Sdic3

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

DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species

318231/tissue=All

EMBL-EBI Single Cell Expression Atlas - Single cell expression across species

FBgn0052823

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0052823

FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data

FBgn0052823

Flygut - An atlas of the Drosophila adult midgut

FBgn0052823

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 1 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 0 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of Sdic3

Transgenic constructs containing regulatory region of Sdic3

Aberrations (Deficiencies and Duplications) ( 0 )

Inferred from experimentation ( 0 )

Inferred from location ( 0 )

Variants

Variant Molecular Consequences

Alleles Representing Disease-Implicated Variants

Phenotypes

For more details about a specific phenotype click on the relevant allele symbol.

Phenotype manifest in

Allele

Orthologs

Downloads

Download All DIOPT Orthologs

Human Orthologs (via DIOPT v9.1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Homo sapiens (Human) (22)

Hsap\DYNC1I1

12 of 14

Yes

Hsap\DYNC1I2

12 of 14

Yes

2 of 14

2 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Model Organism Orthologs (via DIOPT v9.1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Rattus norvegicus (Norway rat) (13)

Rnor\Dync1i2

13 of 14

Yes

12 of 14

2 of 14

2 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Mus musculus (laboratory mouse) (14)

Mmus\Dync1i2

13 of 14

Yes

12 of 14

2 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Xenopus tropicalis (Western clawed frog) (19)

Xtro\dync1i2

7 of 13

Yes

Xtro\dync1i1

6 of 13

Xtro\dnai4

2 of 13

Xtro\dync2i2

2 of 13

Yes

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Yes

Danio rerio (Zebrafish) (19)

Drer\dync1i2b

12 of 14

Yes

11 of 14

11 of 14

2 of 14

2 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Yes

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Caenorhabditis elegans (Nematode, roundworm) (11)

Cele\dyci-1

13 of 14

Yes

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Anopheles gambiae (African malaria mosquito) (16)

Agam\AgaP_AGAP000320

8 of 12

Yes

2 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

Arabidopsis thaliana (thale-cress) (20)

Atha\AT1G11160

1 of 13

Yes

Atha\AT1G18830

1 of 13

Yes

Atha\AT1G52360

1 of 13

Yes

Atha\AT1G71840

1 of 13

Yes

Atha\AT1G79990

1 of 13

Yes

Atha\AT2G30050

1 of 13

Yes

Atha\AT2G43770

1 of 13

Yes

Atha\AT3G15980

1 of 13

Yes

Atha\AT3G27640

1 of 13

Yes

Atha\AT4G35370

1 of 13

Yes

Atha\ATARCA

1 of 13

Yes

Atha\DDB2

1 of 13

Yes

Atha\FY

1 of 13

Yes

Atha\HOS15

1 of 13

Yes

Atha\MSI2

1 of 13

Yes

Atha\PWP2

1 of 13

Yes

Atha\SMU1

1 of 13

Yes

Atha\TAF5

1 of 13

Yes

Atha\TOZ

1 of 13

Yes

Atha\VIP3

1 of 13

Yes

Saccharomyces cerevisiae (Brewer's yeast) (5)

Scer\PAC11

3 of 13

Yes

1 of 13

1 of 13

1 of 13

1 of 13

Schizosaccharomyces pombe (Fission yeast) (2)

Spom\dic1

9 of 12

Yes

Spom\SPAC343.17c

1 of 12

Escherichia coli (enterobacterium) (0)

Other Organism Orthologs (via OrthoDB)

Data provided directly from OrthoDB:Sdic3. Refer to their site for version information.

Paralogs

Downloads

Download All DIOPT Paralogs

Paralogs (via DIOPT v9.1)

Gene Symbol

Score

Source

Alignment

Drosophila melanogaster (Fruit fly) (27)

12 of 13

12 of 13

12 of 13

11 of 13

3 of 13

3 of 13

3 of 13

3 of 13

3 of 13

3 of 13

mmm

3 of 13

2 of 13

2 of 13

2 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Nle

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Human Disease Associations

FlyBase Human Disease Model Reports

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 v9.1 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?

DYNC1I1; dynein cytoplasmic 1 intermediate chain 1

12 of 14

603772

DYNC1I2; dynein cytoplasmic 1 intermediate chain 2

12 of 14

603331

NEURODEVELOPMENTAL DISORDER WITH MICROCEPHALY AND STRUCTURAL BRAIN ANOMALIES; NEDMIBA

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.

76828

DroID - A comprehensive database of gene and protein interactions.

FBgn0052823

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

External Data

Linkouts

KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

1-64

Cytogenetic map

19C1-19C1

Sequence location

X:20,189,440..20,194,227 [-]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

19C1-19C1

Limits computationally determined from genome sequence between P{EP}amn^EP1639&P{EP}amn^EP367 and P{EP}CG1702^EP1525

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

Experimentally Determined Recombination Data

Location

1-64

(FlyBase, 2016)

1-63.8

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (1)

Aberrations including deletions of this gene Aberrations including duplications of this gene

Bloomington

32743

y¹ w^* Mi{MIC}Sdic1^MI01210 Sdic2^MI01210 Sdic4^MI01210

Genomic Clones (8)

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

cDNA Clones (80)

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 JBrowse for alignment of the cDNAs and ESTs to the gene model.

cDNA clones, fully sequenced

BDGP DGC clones

Other clones

FI21737

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.

FBgn0052823

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0052823

Antibody Information

Laboratory Generated Antibodies

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

Other Comments

Sequence of transcript(s) changed in r6 genomic release relative to r5 release.

(FlyBase Genome Annotators, 2014)

New annotation (CG32823) in release 3 of the genome annotation.

(FlyBase Genome Annotators, 2002-2003)

The Sdic transcription unit is tandemly duplicated approximately 10 times. The tandem repeat region is flanked at its 5' end by sw and at its 3' end by AnnX. The repeating unit is formed from a fusion of the central region of AnnX with the 3' region of sw.

(Nurminsky et al., 1998)

Relationship to Other Genes

Source for database merge of

Member gene of

Sdic

Additional comments

Nomenclature History

Source for database identify of

Source for identity of: Sdic3 Sdic:CG32823

(Ponce and Hartl, 2006)

Nomenclature comments

Etymology

Synonyms and Secondary IDs (5)

Reported As

Symbol Synonym

CG32823

(National Institute of Genetics Fly Stocks, 2023-, Chen et al., 2012, Zhan et al., 2011, Zhang et al., 2010)

Sdic

(Jayaswal et al., 2018)

Sdic3

(Clifton et al., 2023, Clifton et al., 2017, FlyBase Genome Annotators, 2014, Vartiainen et al., 2014, Yeh et al., 2012, Yeh et al., 2012, Ponce, 2009, Ponce, 2007, Ponce and Hartl, 2006)

Sdic:CG32823

Name Synonyms

Sdic:CG32823

Sperm-specific dynein intermediate chain 3

Secondary FlyBase IDs

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 34 )

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.

318231

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.

Q8IRZ3

UniProt/TrEMBL - Automatically annotated and unreviewed records of protein sequence and functional information

Q8IRZ3

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.

Q8IRZ3

DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species

318231/tissue=All

EMBL-EBI Single Cell Expression Atlas - Single cell expression across species

FBgn0052823

FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data

FBgn0052823

FlyMine - An integrated database for Drosophila genomics

FBgn0052823

InterPro - A database of protein families, domains and functional sites

KEGG Genes - Molecular building blocks of life in the genomic space.

dme:Dmel_CG32823

MARRVEL_MODEL - MARRVEL (model organism gene)

318231

Linkouts

BioGRID - A database of protein and genetic interactions.

76828

Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones

FBgn0052823

DroID - A comprehensive database of gene and protein interactions.

FBgn0052823

DRSC - Results frm RNAi screens

FBgn0052823

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0052823

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0052823

Flygut - An atlas of the Drosophila adult midgut

FBgn0052823

FlyMet - A comprehensive tissue-specific metabolomics resource for Drosophila.

FBgn0052823

KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.

References (25)

The following external sites may use different assemblies or annotations than FlyBase.

NA

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