kn knot [Drosophila melanogaster (fruit fly)] - Gene

Summary

Official Symbol: knprovided by FlyBase
Official Full Name: knotprovided by FlyBase
Primary source: FLYBASE:FBgn0001319
Locus tag: Dmel_CG10197
See related: AllianceGenome:FB:FBgn0001319
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Drosophila melanogaster
Lineage: Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Ephydroidea; Drosophilidae; Drosophila; Sophophora
Also known as: CG10197; coe; col; Col; Col/Kn; collier; Collier; DmCOE; Dmel\CG10197; Kn; Kn/Col; Knot
Summary: Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Involved in several processes, including determination of muscle attachment site; larval somatic muscle development; and regionalization. Is expressed in several structures, including anterior-posterior subdivision of organism; embryonic myoblast; larval neurons; larval somatic muscle cell; and visceral mesoderm derivative. Human ortholog(s) of this gene implicated in hypotonia, ataxia, and delayed development syndrome. Orthologous to several human genes including EBF1 (EBF transcription factor 1) and EBF3 (EBF transcription factor 3). [provided by Alliance of Genome Resources, Dec 2024]
Orthologs: all
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Genomic context

Location:: 51C2-51C3; 2-72 cM

Exon count:: 14

Annotation release	Status	Assembly	Chr	Location
Release 6.54	current	Release 6 plus ISO1 MT (GCF_000001215.4)	2R	NT_033778.4 (14772650..14807061, complement)
Release 5.57	previous assembly	Release 5 (GCF_000001215.2)	2R	NT_033778.3 (10660155..10694566, complement)

Chromosome 2R - NT_033778.4 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Ubx-Collier signaling cascade maintains blood progenitors in the posterior lobes of the Drosophila larval lymph gland.
Title: Ubx-Collier signaling cascade maintains blood progenitors in the posterior lobes of the Drosophila larval lymph gland.
Intrinsic control of muscle attachment sites matching.
Title: Intrinsic control of muscle attachment sites matching.
These analyses identified a host of putative Cut and/or Knot effector molecules, and a subset of these putative TF targets converge on modulating dendritic cytoskeletal architecture, which are grouped into three major phenotypic categories, based upon neuromorphometric analyses: complexity enhancer, complexity shifter, and complexity suppressor
Title: Dendritic Cytoskeletal Architecture Is Modulated by Combinatorial Transcriptional Regulation in Drosophila melanogaster.
two independent sites of Collier/Early B Cell Factor expression, hematopoietic progenitors and the PSC, achieve control of hematopoiesis
Title: Two Independent Functions of Collier/Early B Cell Factor in the Control of Drosophila Blood Cell Homeostasis.
Col direct control of expression of the transcription regulators apterous and eyes-absent is critical to specifying neuronal identities. cross-regulation between col and eya in muscle progenitor cells is required for specification of muscle identity
Title: Genome-Wide Mapping of Collier In Vivo Binding Sites Highlights Its Hierarchical Position in Different Transcription Regulatory Networks.
Col expression is required in the prohemocytes to prevent their differentiation.
Title: The EBF transcription factor Collier directly promotes Drosophila blood cell progenitor maintenance independently of the niche.
The transcription factors Abrupt (Ab) and Knot (Kn) act as selectors of distinct dendritic arbor morphologies in two classes of Drosophila sensory neurons, termed class I and class IV, respectively.
Title: Sensory-neuron subtype-specific transcriptional programs controlling dendrite morphogenesis: genome-wide analysis of Abrupt and Knot/Collier.
Data show that the three dorso-lateral (DL) progenitors which express Nautilus and Collier are specified in a fixed temporal sequence and that each expresses additionally other, distinct identity transcription factors (iTFs).
Title: Combinatorial coding of Drosophila muscle shape by Collier and Nautilus.
Collier controls hemocyte homeostasis via coordinate regulation of PSC cell number and PSC signaling to prohemocytes.
Title: Size control of the Drosophila hematopoietic niche by bone morphogenetic protein signaling reveals parallels with mammals.
Second order regulator Collier directly controls intercalary-specific segment polarity gene expression.
Title: Second order regulator Collier directly controls intercalary-specific segment polarity gene expression.

Submit: New GeneRIF Correction See all GeneRIFs (17)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Homology

NCBI Orthologs

Orthologs from OrthoDB

Gene Ontology Provided by FlyBase

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription factor activity	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
involved_in anterior head segmentation	TAS Traceable Author Statement more info	PubMed
involved_in blastoderm segmentation	TAS Traceable Author Statement more info	PubMed
involved_in dendrite morphogenesis	IGI Inferred from Genetic Interaction more info	PubMed
involved_in dendrite morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in determination of muscle attachment site	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in embryonic development via the syncytial blastoderm	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in head segmentation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in imaginal disc-derived wing morphogenesis	TAS Traceable Author Statement more info	PubMed
involved_in imaginal disc-derived wing vein specification	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in innate immune response	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in larval somatic muscle development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in muscle cell fate specification	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in posterior head segmentation	TAS Traceable Author Statement more info	PubMed
involved_in regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in regulation of DNA-templated transcription	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of DNA-templated transcription	TAS Traceable Author Statement more info	PubMed
involved_in regulation of dendrite morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of gene expression	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of lamellocyte differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in response to symbiont	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in segment polarity determination	IDA Inferred from Direct Assay more info	PubMed
involved_in specification of segmental identity, intercalary segment	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in ventral cord development	HMP more info	PubMed

General protein information

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Preferred Names: knot

Names: CG10197-PA; CG10197-PB; CG10197-PC; CG10197-PD; CG10197-PE; Collier-Knot; KNOT; colier; collier; collier/knot; early B cell factor; kn-PA; kn-PB; kn-PC; kn-PD; kn-PE; knotted

NCBI Reference Sequences (RefSeq)

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Genome Annotation

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference assembly

Genomic

NT_033778.4 Reference assembly

Range

14772650..14807061 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001103847.2 → NP_001097317.1 knot, isoform C [Drosophila melanogaster]

See identical proteins and their annotated locations for NP_001097317.1

Status: REVIEWED

UniProtKB/TrEMBL

A8DYD9

Conserved Domains (3) summary

cd11606
Location:184 → 395

COE_DBD; Colier/Olf/Early B-cell factor (EBF) DNA Binding Domain

cd01175
Location:431 → 515

IPT_COE; IPT domain of the COE family (Col/Olf-1/EBF) of non-basic, helix-loop-helix (HLH)-containing transcription factors. COE family proteins are all transcription factors and play an important role in variety of developmental processes. Mouse EBF is involved ...

pfam16423
Location:517 → 560

COE1_HLH; Transcription factor COE1 helix-loop-helix domain
NM_137146.3 → NP_610990.2 knot, isoform D [Drosophila melanogaster]

See identical proteins and their annotated locations for NP_610990.2

Status: REVIEWED

UniProtKB/TrEMBL

A1Z9V2

Conserved Domains (3) summary

cd11606
Location:52 → 263

COE_DBD; Colier/Olf/Early B-cell factor (EBF) DNA Binding Domain

cd01175
Location:299 → 383

IPT_COE; IPT domain of the COE family (Col/Olf-1/EBF) of non-basic, helix-loop-helix (HLH)-containing transcription factors. COE family proteins are all transcription factors and play an important role in variety of developmental processes. Mouse EBF is involved ...

pfam16423
Location:384 → 427

COE1_HLH; Transcription factor COE1 helix-loop-helix domain
NM_080074.4 → NP_524813.2 knot, isoform A [Drosophila melanogaster]

See identical proteins and their annotated locations for NP_524813.2

Status: REVIEWED

UniProtKB/TrEMBL

V5LWW0

Related

FBpp0086595

Conserved Domains (3) summary

cd11606
Location:52 → 263

COE_DBD; Colier/Olf/Early B-cell factor (EBF) DNA Binding Domain

cd01175
Location:299 → 383

IPT_COE; IPT domain of the COE family (Col/Olf-1/EBF) of non-basic, helix-loop-helix (HLH)-containing transcription factors. COE family proteins are all transcription factors and play an important role in variety of developmental processes. Mouse EBF is involved ...

pfam16423
Location:385 → 428

COE1_HLH; Transcription factor COE1 helix-loop-helix domain
NM_166070.3 → NP_725419.2 knot, isoform B [Drosophila melanogaster]

See identical proteins and their annotated locations for NP_725419.2

Status: REVIEWED

UniProtKB/Swiss-Prot

P56721, Q8MS49, Q9V758

UniProtKB/TrEMBL

E2QCN0

Conserved Domains (3) summary

cd11606
Location:52 → 263

COE_DBD; Colier/Olf/Early B-cell factor (EBF) DNA Binding Domain

cd01175
Location:299 → 383

IPT_COE; IPT domain of the COE family (Col/Olf-1/EBF) of non-basic, helix-loop-helix (HLH)-containing transcription factors. COE family proteins are all transcription factors and play an important role in variety of developmental processes. Mouse EBF is involved ...

pfam16423
Location:385 → 428

COE1_HLH; Transcription factor COE1 helix-loop-helix domain
NM_001274051.1 → NP_001260980.1 knot, isoform E [Drosophila melanogaster]

See identical proteins and their annotated locations for NP_001260980.1

Status: REVIEWED

UniProtKB/TrEMBL

A0A0B4KFQ1

Conserved Domains (3) summary

cd11606
Location:55 → 251

COE_DBD; Colier/Olf/Early B-cell factor (EBF) DNA Binding Domain

cd01175
Location:266 → 350

IPT_COE; IPT domain of the COE family (Col/Olf-1/EBF) of non-basic, helix-loop-helix (HLH)-containing transcription factors. COE family proteins are all transcription factors and play an important role in variety of developmental processes. Mouse EBF is involved ...

pfam16423
Location:351 → 394

COE1_HLH; Transcription factor COE1 helix-loop-helix domain