FlyBase Gene Report: Dmel\Kmn1

General Information

Symbol

Dmel\Kmn1

Species

D. melanogaster

Name

kinetochore Mis12-Ndc80 network component 1

Annotation Symbol

CG1558

Feature Type

protein_coding_gene

FlyBase ID

FBgn0027259

Gene Model Status

Current

Stock Availability

8 publicly available

Gene Summary

kinetochore Mis12-Ndc80 network component 1 (Kmn1) encodes a protein involved in the movement of chromosomes during mitosis. [Date last reviewed: 2019-09-19] (FlyBase Gene Snapshot)

All Summaries

Gene Snapshot
Alliance
Auto summary
Gene Group
Interactive Fly

Also Known As

Nsl1, l(1)G0237

Key Links

Genomic Location

Cytogenetic map

10C6-10C7

Sequence location

X:11,571,383..11,572,442 [-]

Recombination map

1-35

RefSeq locus

NC_004354 REGION:11571383..11572442

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 (7 terms)

Molecular Function (0 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (0 terms)

Biological Process (4 terms)

Terms Based on Experimental Evidence (4 terms)

CV Term

Evidence

References

involved_in chromosome segregation

inferred from mutant phenotype

(Przewloka et al., 2007)

involved_in mitotic chromosome movement towards spindle pole

inferred from mutant phenotype

(Venkei et al., 2011)

involved_in mitotic metaphase chromosome alignment

inferred from mutant phenotype

(Przewloka et al., 2007)

involved_in regulation of cell cycle

inferred from mutant phenotype

(Clemente-Ruiz et al., 2014)

Terms Based on Predictions or Assertions (0 terms)

Cellular Component (3 terms)

Terms Based on Experimental Evidence (3 terms)

CV Term

Evidence

References

located_in kinetochore

inferred from direct assay

(Venkei et al., 2011, Przewloka et al., 2007, Schittenhelm et al., 2007)

part_of MIS12/MIND type complex

inferred from direct assay

(Richter et al., 2016)

part_of Ndc80 complex

inferred from direct assay

(Schittenhelm et al., 2007)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

located_in kinetochore

inferred from sequence or structural similarity with UniProtKB:Q96IY1

(Przewloka et al., 2007)

Gene Group (FlyBase)

KINETOCHORE MIS12 COMPLEX - NF1A VARIANT

KINETOCHORE MIS12 COMPLEX - NF1B VARIANT

Protein Family (UniProt)

Protein Signatures (InterPro)

Summaries

Gene Snapshot

kinetochore Mis12-Ndc80 network component 1 (Kmn1) encodes a protein involved in the movement of chromosomes during mitosis. [Date last reviewed: 2019-09-19]

Gene Group (FlyBase)

KINETOCHORE MIS12 COMPLEX - NF1A VARIANT -: The MIS12 complex is an outer kinetochore complex that bridges the inner kinetochore component CENP-C and the outer kinetochore Ndc80 complex. In Drosophila, there are two complex variants, one containing Nnf1a and one containing Nnf1b. (Adapted from FBrf0231098.)
KINETOCHORE MIS12 COMPLEX - NF1B VARIANT -: The MIS12 complex is an outer kinetochore complex that bridges the inner kinetochore component CENP-C and the outer kinetochore Ndc80 complex. In Drosophila, there are two complex variants, one containing Nnf1a and one containing Nnf1b. (Adapted from FBrf0231098.)

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\Kmn1 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 Q9VYX4)

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

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

Gene model reviewed during 5.45

Gene model reviewed during 6.05

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

Kmn1-RA

FBtr0073541

NM_132501

1002

183

Kmn1-RB

FBtr0433505

NM_001316625

668

183

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

Kmn1-PA

FBpp0073386

21.4

183

4.55

FBpp0390637

21.4

183

4.55

Q9VYX4

NP_001303554

ALI51148

Polypeptides with Identical Sequences

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

183 aa isoforms: Kmn1-PA, Kmn1-PB

Additional Polypeptide Data and Comments

Reported size (kDa)

Comments

External Data

Crossreferences

Linkouts

Sequences Consistent with the Gene Model

Nucleotide / Polypeptide Records

UniProt

Q9VYX4

Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\Kmn1 using the Feature Mapper tool.

External Data

Crossreferences

Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.

Kmn1_1

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).

-0.32

Transcript Expression

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

epitope tag

Stage

Tissue/Position (including subcellular localization)

Reference

cell

• kinetochore

Comment: Localization observed in mitotic cells; assayed in cultured S2R+ cells

(Schittenhelm et al., 2007)

Additional Descriptive Data

Subcellular localization to kinetochores of mitotic cultured S2R+ cells assayed using the transgenic allele Kmn1^{Scer\UAS.T:AvicGFP-EGFP}.

(Schittenhelm et al., 2007)

Marker for

Subcellular Localization

CV Term

Evidence

References

located_in kinetochore

inferred from direct assay

(Venkei et al., 2011, Przewloka et al., 2007, Schittenhelm et al., 2007)

part_of MIS12/MIND type complex

inferred from direct assay

(Richter et al., 2016)

part_of Ndc80 complex

inferred from direct assay

(Schittenhelm et al., 2007)

Expression Deduced from Reporters

High-Throughput Expression Data

Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\Kmn1 in JBrowse

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

View exonic expression by developmental stage for Dmel\Kmn1

View exonic expression by tissue for Dmel\Kmn1

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

32102/tissue=All

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

FBgn0027259

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0027259

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

FBgn0027259

Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns

CG1558

Flygut - An atlas of the Drosophila adult midgut

FBgn0027259

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 ( 4 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of Kmn1

Transgenic constructs containing regulatory region of Kmn1

Aberrations (Deficiencies and Duplications) ( 3 )

Inferred from experimentation ( 3 )

Gene disrupted in

Df(1)52

(Meller and Rattner, 2002)

Gene duplicated in

Dp(1;3)DC241

(Popodi et al., 2010-, Venken et al., 2010)

Dp(1;Y)y⁺v⁺#3

(Venkei et al., 2011)

Inferred from location ( 17 )

Variants

Variant Molecular Consequences

Alleles Representing Disease-Implicated Variants

Phenotypes

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

Lethality

Allele

lethal, with Scer\GAL4^insc-Mz1407

Kmn1^GD9062

lethal (with Df(1)52)

Kmn1^G0237

lethal | embryonic stage | recessive

Kmn1^G0237

lethal | first instar larval stage | recessive

Kmn1^G0237

lethal | recessive

Kmn1^G0237

lethal - all die before end of larval stage

Kmn1^G0237

partially lethal - majority die, with Scer\GAL4^pnr-MD237

Kmn1^GD9062

viable

Kmn1^f06049

viable, with Dcr-2^UAS.cDa, Scer\GAL4^elav.PLu

Kmn1^GD9062

Sterility

Allele

fertile

Kmn1^f06049

Other Phenotypes

Allele

abnormal mitotic cell cycle | embryonic stage

Kmn1^G0237

abnormal neuroanatomy | larval stage, with Scer\GAL4^insc-Mz1407

Kmn1^GD9062

some die during larval stage

Kmn1^G0237

some die during pupal stage, with Scer\GAL4^pnr-MD237

Kmn1^GD9062

uncoordinated | larval stage

Kmn1^G0237

visible, with Scer\GAL4^pnr-MD237

Kmn1^GD9062

Phenotype manifest in

Allele

ganglion mother cell | larval stage, with Scer\GAL4^insc-Mz1407

Kmn1^GD9062

larval neuroblast | larval stage, with Scer\GAL4^insc-Mz1407

Kmn1^GD9062

mesonotum, with Scer\GAL4^pnr-MD237

Kmn1^GD9062

trichogen cell, with Scer\GAL4^pnr-MD237

Kmn1^GD9062

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) (0)

Model Organism Orthologs (via DIOPT v9.1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Rattus norvegicus (Norway rat) (0)

Mus musculus (laboratory mouse) (0)

Xenopus tropicalis (Western clawed frog) (0)

Danio rerio (Zebrafish) (0)

Caenorhabditis elegans (Nematode, roundworm) (0)

Anopheles gambiae (African malaria mosquito) (0)

Arabidopsis thaliana (thale-cress) (0)

Saccharomyces cerevisiae (Brewer's yeast) (0)

Schizosaccharomyces pombe (Fission yeast) (0)

Escherichia coli (enterobacterium) (0)

Other Organism Orthologs (via OrthoDB)

Data provided directly from OrthoDB:Kmn1. 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) (0)

Human Disease Associations

FlyBase Human Disease Model Reports

cancer, models of chromosomal instability

Disease Ontology (DO) Annotations

Models Based on Experimental Evidence ( 1 )

Allele

Disease

Evidence

References

Kmn1^KK111826

model of cancer

CEA with BacA\p35^UAS.cUa

(Clemente-Ruiz et al., 2014)

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?

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

Interaction Browsers

View in FlyBase Interactions Browser View in MIST tool (external link)

Please see the Physical Interaction reports below for full details

protein-protein

Physical Interaction

Assay

References

Kmn1

two hybrid

(Schittenhelm et al., 2009)

Kmn1 - Bub1

two hybrid

(Schittenhelm et al., 2009)

Kmn1 - Cenp-C

molecular sieving, cosedimentation, molecular weight estimation by staining, anti tag coimmunoprecipitation, peptide massfingerprinting, protein cross-linking with a bifunctional reagent, anti bait coimmunoprecipitation

(Liu et al., 2016, Richter et al., 2016, Lipinszki et al., 2015, Przewloka et al., 2011)

Kmn1 - Mis12

anti tag coimmunoprecipitation, peptide massfingerprinting, experimental knowledge based, mass spectrometry study of hydrogen/deuterium exchange, anti bait coimmunoprecipitation, molecular sieving, cosedimentation, molecular weight estimation by staining, pull down, protein cross-linking with a bifunctional reagent, two hybrid

(Liu et al., 2016, Richter et al., 2016, Guruharsha et al., 2011, Schittenhelm et al., 2009, Przewloka et al., 2007)

Kmn1 - Ndc80

anti tag coimmunoprecipitation, peptide massfingerprinting

(Przewloka et al., 2007)

Kmn1 - Nnf1a

two hybrid, anti tag coimmunoprecipitation, peptide massfingerprinting, pull down, anti tag western blot, anti bait coimmunoprecipitation, mass spectrometry study of hydrogen/deuterium exchange, experimental knowledge based, molecular sieving, cosedimentation, molecular weight estimation by staining, protein cross-linking with a bifunctional reagent

(Liu et al., 2016, Richter et al., 2016, Guruharsha et al., 2011, Schittenhelm et al., 2009, Przewloka et al., 2007)

Kmn1 - Nnf1b

molecular sieving, cosedimentation, molecular weight estimation by staining, pull down, anti tag western blot, protein cross-linking with a bifunctional reagent, peptide massfingerprinting

(Liu et al., 2016)

Kmn1 - Nuf2

anti tag coimmunoprecipitation, peptide massfingerprinting

(Przewloka et al., 2007, Schittenhelm et al., 2007)

Kmn1 - Spc105R

two hybrid, molecular sieving, cosedimentation, molecular weight estimation by staining

(Liu et al., 2016, Schittenhelm et al., 2009)

Kmn1 - Spc25

anti tag coimmunoprecipitation, peptide massfingerprinting

(Przewloka et al., 2007, Schittenhelm et al., 2007)

Kmn1 - fd59A

anti tag coimmunoprecipitation, peptide massfingerprinting, experimental knowledge based

(Rhee et al., 2014)

Summary of Genetic Interactions

Interaction Browsers

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

External Data

Linkouts

DroID - A comprehensive database of gene and protein interactions.

FBgn0027259

MIST (protein-protein) - An integrated Molecular Interaction Database

32102

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

FlyBase

External Links

External Data

Linkouts

Class of Gene

nuclear_gene

protein_coding_gene

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

1-35

Cytogenetic map

10C6-10C7

Sequence location

X:11,571,383..11,572,442 [-]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

10C6-10C7

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

10C1-10C2

(determined by in situ hybridisation)

(Peter et al., 2002, Schäfer et al., 1999.6.15)

Experimentally Determined Recombination Data

Location

1-35

(FlyBase, 2016)

1-36.5

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (8)

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

Bloomington

91744

w^*; P{EGFP-Kmn1}II.1

11877

w^67c23 P{lacW}Kmn1^G0237/FM7c

91745

w^*; P{EGFP-Kmn1}III.1/TM3, Ser¹

22040

w^67c23 P{Mae-UAS.6.11}Kmn1^GG01714

22295

y¹ w^67c23 P{EPgy2}Kmn1^EY18911

Kyoto

111824

y¹ w^* P{lacW}Kmn1^G0237 P{neoFRT}19A/FM7c; P{ey-FLP.N}5

VDRC

v106889

P{KK111826}VIE-260B

v19529

w¹¹¹⁸; P{GD9062}v19529

Genomic Clones (8)

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

cDNA Clones (6)

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

RE03006

Other clones

DPiM_RE03006

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.

FBgn0027259

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

SD07129

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0027259

Antibody Information

Laboratory Generated Antibodies

polyclonal

(Venkei et al., 2011)

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

Other Comments

Relationship to Other Genes

Source for database merge of

Source for merge of: l(1)G0237 CG1558

(Meller and Rattner, 2002)

Source for merge of: l(1)G0237 anon-WO03040301.201

(FlyBase, 1996-)

Additional comments

"l(1)G0444" may affect "CG1558".

(Peter et al., 2002)

Source for merge of l(1)G0237 anon-WO03040301.201 was sequence comparison ( date:051113 ).

(FlyBase, 1996-)

Nomenclature History

Source for database identify of

Source for identity of: Kmn1 l(1)G0237

(Schittenhelm et al., 2007)

Nomenclature comments

Etymology

Synonyms and Secondary IDs (12)

Reported As

Symbol Synonym

CG1558

(Palu and Thummel, 2016, Hosono et al., 2015, Lipinszki et al., 2015, Keleman et al., 2009.8.5, Schittenhelm et al., 2009, González et al., 2008, Przewloka et al., 2007, Schittenhelm et al., 2007, Williams et al., 2007, Asha et al., 2003, Dimova et al., 2003, Peter et al., 2002)

CT4038

(Meller and Rattner, 2002)

Kmn1

(Isaacson et al., 2024, Vesala et al., 2024, Ai et al., 2020, Rech et al., 2019, Rotelli et al., 2019, Das et al., 2016, Liu et al., 2016, Van Bortle et al., 2015, Mateo et al., 2014, Kalajdzic et al., 2012, Korenjak et al., 2012, Neumüller et al., 2011, González et al., 2010, Popodi et al., 2010-, Venken et al., 2010, González et al., 2008, Schittenhelm et al., 2007)

NSL1

(Kyriacou and Heun, 2023)

Nsl1

(Lipinszki et al., 2015, Clemente-Ruiz et al., 2014, Morais da Silva et al., 2013, Venkei et al., 2012, Przewloka et al., 2011, Venkei et al., 2011, Schittenhelm et al., 2010, Schittenhelm et al., 2009, Somma et al., 2008)

anon-WO03040301.201

dmNsl1R

(Przewloka et al., 2007)

l(1)G0237

(Straub et al., 2008, Zraly et al., 2006, Lipatov et al., 2005)

nsl1

(Morais da Silva et al., 2013)

Name Synonyms

Nsl1-related protein

(Przewloka et al., 2007)

kinetochore Mis12-Ndc80 network component 1

(Schittenhelm et al., 2007)

l(1)G0237

(Lipatov et al., 2005)

lethal (1) G0237

Secondary FlyBase IDs

FBgn0030312
FBgn0066829

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 33 )

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.

32102

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.

Q9VYX4

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

Q9VYX4

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.

Q9VYX4

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

32102/tissue=All

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

FBgn0027259

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

FBgn0027259

FlyMine - An integrated database for Drosophila genomics

FBgn0027259

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

dme:Dmel_CG1558

MARRVEL_MODEL - MARRVEL (model organism gene)

32102

Linkouts

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

FBgn0027259

DroID - A comprehensive database of gene and protein interactions.

FBgn0027259

DRSC - Results frm RNAi screens

FBgn0027259

Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.

Kmn1_1

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0027259

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0027259

Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns

CG1558

Flygut - An atlas of the Drosophila adult midgut

FBgn0027259

MIST (protein-protein) - An integrated Molecular Interaction Database

32102

References (69)

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

-0.32

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