kni knirps [Drosophila melanogaster (fruit fly)] - Gene

Summary

Official Symbol: kniprovided by FlyBase
Official Full Name: knirpsprovided by FlyBase
Primary source: FLYBASE:FBgn0001320
Locus tag: Dmel_CG4717
See related: AllianceGenome:FB:FBgn0001320
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: CG4717; Dm-kni; Dmel\CG4717; kn; Kn; Kni; KNI; KNIRPS; knr; NR0A1; ri
Summary: Enables DNA-binding transcription factor binding activity and DNA-binding transcription repressor activity, RNA polymerase II-specific. Involved in negative regulation of DNA-templated transcription and regulation of mitotic nuclear division. Predicted to be located in chromatin. Predicted to be active in nucleus. Is expressed in several structures, including endoderm anlage; gut section; head epidermis primordium; mesoderm; and primary tracheal branch. [provided by Alliance of Genome Resources, Dec 2024]
Orthologs: all
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Genomic context

Location:: 77E3-77E3; 3-47 cM

Exon count:: 4

Annotation release	Status	Assembly	Chr	Location
Release 6.54	current	Release 6 plus ISO1 MT (GCF_000001215.4)	3L	NT_037436.4 (20692330..20695378, complement)
Release 5.57	previous assembly	Release 5 (GCF_000001215.2)	3L	NT_037436.3 (20685430..20688478, complement)

Chromosome 3L - NT_037436.4 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Exploring a Drosophila Transcription Factor Interaction Network to Identify Cis-Regulatory Modules.
Title: Exploring a Drosophila Transcription Factor Interaction Network to Identify Cis-Regulatory Modules.
Phenotypic analysis of these 'in locus' mutations based on both expression of Kni protein and adult wing phenotypes, reveals novel unexpected features of L2-cis-regulatory module function including evidence for a chromosome pairing-dependent process that promotes transcription.
Title: CRISPR/Cas9 and active genetics-based trans-species replacement of the endogenous Drosophila kni-L2 CRM reveals unexpected complexity.
In this study, ChIP/chip datasets are analyzed using the corresponding PWMs for the well-studied TFs; CAUDAL, HUNCHBACK, KNIRPS and KRUPPEL, to determine the distribution of predicted binding sites. All four TFs are critical regulators of gene expression along the anterio-posterior axis in early Drosophila development
Title: Spatial distribution of predicted transcription factor binding sites in Drosophila ChIP peaks.
Vvl and Kni directly regulate ecdysone biosynthesis by transcriptional control of biosynthetic gene expression and indirectly by affecting prothoracicotropic hormone and TOR/S6 Kinase signaling.
Title: Transcriptional control of steroid biosynthesis genes in the Drosophila prothoracic gland by ventral veins lacking and knirps.
analysis of combinatorial activation and concentration-dependent repression of the Drosophila even skipped stripe 3+7 enhancer; Zld is required for activation; Kni and Hb are dedicated repressors that function by direct DNA binding
Title: Combinatorial activation and concentration-dependent repression of the Drosophila even skipped stripe 3+7 enhancer.
Knirps causes local changes of histone density and acetylation, and the inhibition of activator recruitment, without affecting the recruitment of basal transcriptional machinery.
Title: Long- and short-range transcriptional repressors induce distinct chromatin states on repressed genes.
Functional similarity of Knirps CtBP-dependent and C-terminal Binding Protein-independent transcriptional repressor activities.
Title: Functional similarity of Knirps CtBP-dependent and CtBP-independent transcriptional repressor activities.
DNA-binding Gal4-CtBP fusion proteins also require NAD binding for activity, indicating that NAD plays a role in repression at a step subsequent to CtBP recruitment to the promoter
Title: CtBP contributes quantitatively to Knirps repression activity in an NAD binding-dependent manner.
findings indicate that Rpd3 contributes to Knirps repression activity in vivo
Title: Functional interaction between the Drosophila knirps short range transcriptional repressor and RPD3 histone deacetylase.
identifed a 1.4 kb cis-acting enhancer element from the kni locus that faithfully directs gene expression in the second longitudinal wing vein (L2) primordium
Title: Activation of the knirps locus links patterning to morphogenesis of the second wing vein in Drosophila.

Submit: New GeneRIF Correction See all GeneRIFs (13)

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 transcription factor activity	IDA Inferred from Direct Assay more info	PubMed
enables DNA-binding transcription factor activity	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription factor binding	IPI Inferred from Physical Interaction more info	PubMed
enables DNA-binding transcription repressor activity, RNA polymerase II-specific	IDA Inferred from Direct Assay more info	PubMed
enables estrogen response element binding	IBA Inferred from Biological aspect of Ancestor more info
enables nuclear receptor activity	IBA Inferred from Biological aspect of Ancestor more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables sequence-specific DNA binding	IEA Inferred from Electronic Annotation more info
enables zinc ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in epithelial cell migration, open tracheal system	TAS Traceable Author Statement more info	PubMed
involved_in negative regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in regulation of DNA-templated transcription	IGI Inferred from Genetic Interaction more info	PubMed
involved_in regulation of DNA-templated transcription	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of mitotic nuclear division	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 trunk segmentation	TAS Traceable Author Statement more info	PubMed
involved_in zygotic determination of anterior/posterior axis, embryo	TAS Traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
located_in chromatin	IBA Inferred from Biological aspect of Ancestor more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: knirps

Names: CG4717-PA; CG4717-PB; kni-PA; kni-PB; radius incompletus

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_037436.4 Reference assembly

Range

20692330..20695378 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_079463.3 → NP_524187.1 knirps, isoform A [Drosophila melanogaster]

See identical proteins and their annotated locations for NP_524187.1

Status: REVIEWED

UniProtKB/Swiss-Prot

P10734, Q540X6, Q9VPC6

Related

FBpp0077941

Conserved Domains (1) summary

cl02596
Location:3 → 87

NR_DBD_like; DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers
NM_001300201.1 → NP_001287130.1 knirps, isoform B [Drosophila melanogaster]

See identical proteins and their annotated locations for NP_001287130.1

Status: REVIEWED

UniProtKB/TrEMBL

X2JGX8

Conserved Domains (1) summary

cl02596
Location:8 → 92

NR_DBD_like; DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers