A Database of Drosophila Genes & Genomes

FB2008_07, released August 8, 2008
 

Gene Dmel\kni

General Information
SymbolDmel\kniSpeciesD. melanogaster
NameknirpsAnnotation symbolCG4717
Feature typeprotein_coding_geneFlyBase IDFBgn0001320
Created / Updated2003-12-01/2003-12-01
Genomic Location
Chromosome (arm)3LRecombination map
Cytogenetic map77E3-77E3Sequence location3L:20,685,430..20,688,463 [-]
Map ( GBrowse ) detailed view
hide Summary Information
Automatically generated summary

See sections below for more information
The gene knirps is referred to in FlyBase by the symbol kni (CG4717, FBgn0001320). It has the cytological map location 77E3. Its sequence location is 3L:20685430..20688463. Its molecular function is described as: ligand-dependent nuclear receptor activity; transcription factor activity; specific transcriptional repressor activity; zinc ion binding; sequence-specific DNA binding. It is involved in the biological processes described with 13 unique terms, many of which group under: anatomical structure development; open tracheal system development; regulation of metabolic process; regulation of biological process; transcription, DNA-dependent; organ development; system development; embryonic pattern specification; trunk segmentation; cell cycle; anterior/posterior axis specification. 97 alleles are reported. The phenotypes of these alleles are annotated with 32 unique terms, many of which group under: embryonic abdomen; anatomical structure; embryonic segment; adult segment; thoracic segment; embryonic tagma; organ system; embryonic/larval tracheal system; adult mesothoracic segment; abdominal segment 7. It has one annotated transcript and one annotated polypeptide.

External Summaries
hide Phenotypic Description from the Red Book (Lindsley & Zimm 1992)
Gene/Allele symbols may differ from current usage
kni: knirps
Zygotic gap gene whose mutants are homozygous lethal; their denticle belts in segments one through seven are fused into a single field (Nusslein-Volhard and Wieschaus, 1980), but the head, thorax, eighth abdominal segment, and tail region appear normal. Embryos homozygous for a strong kni mutant show a wide band of ftz staining instead of the normal number of ftz stripes (Carroll and Scott, 1986).
ri: radius incompletus
thumb
ri: radius incompletus
From Edith M. Wallace, unpublished.
Vein L2 interrupted. Wings slightly warped and blunt. Acts during contraction period in D. simulans, inhibiting fusion of small spaces into a vein (Waddington, 1940, J. Genet. 41: 75-139). RK1.
hide Detailed Mapping Data
FlyBase Computed Cytological Location
Cytogenetic map
Evidence for location
77E3-77E3  
Limits computationally determined from genome sequence between P{EP}trblEP3519 and P{EP}fngEP3082&P{lacW}skdL7062  
Experimentally Determined Cytological Location
Cytogenetic map
Notes
References
77E1-77E2
(determined by in situ hybridisation)  
77E1-77E2
(determined by in situ hybridisation)  
Experimentally Determined Recombination Data
Location
3-47.1
Left of (cM)
Right of (cM)
Notes
Molecular Map Data
Gene Order (in direction of increasing cytology)
References
Gene Order (overall orientation not stated)
References
hide Gene Model & Products
Please see the GBrowse view of Dmel\kni for information on other features
detailed view FBtr0078283 FBpp0077941 FBti0042963 FBti0036997
Comments on Gene Model
hide Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Associated CDS (aa)
FBtr0078283
  2085
  429
Additional Transcript Data & Comments
Reported size (kB)
2.5, 2.2 (northern blot)
Comments
A 2 kb cDNA was sequenced. It is not known which transcript it corresponds to.
External Data
Crossreferences
hide Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kD)
Length (aa)
Theoretical pI
RefSeq ID
GenBank protein
kni-PA  
FBpp0077941  
45.6  
429  
8.35  
Additional Polypeptide Data & Comments
Reported size (kD)
429 (aa); 45.6 (kD predicted)
Comments
External Data
Linkouts
PANTHER - Protein classification by function, families, and pathways
Crossreferences
InterPro domains - A database of protein families, domains, and functional sites
TRANSFAC - Eukaryotic transcription factors, their genomic binding sites, and DNA-binding profiles
  • R02619
  • R02620
  • R04959
  • R04960
  • R04961
  • R04962
  • T00445
hide Sequences Consistent with the Gene Model
DDBJ /
EMBL /
GenBank
DNA sequence
Protein sequence
Name
 
UniProtKB/Swiss-Prot
UniProtKB/TrEMBL
    Maps to
    Does NOT map to
    Identified with
    hide Mapped Features & Mutations
    Please see GBrowse or insertion reports for information on insertions of transgenic constructs and features not listed here
    Type
    Symbol & Location
    Additional Notes
    References
    aberration junction
    Tp(3;2)kni-FC82.bk2
    3L:20,690,666..20,692,381
    comment=The proximal breakpoint on 3L maps ~2.5kb upstream of the kni transcription unit. The deletion removes the kni and knrl transcription units. Overlaps the Tp(3;2)kni-FC82 deletion by less than 1kb.
    linked_to=EcoRI-EcoRI_rfrag
    aberration junction
    Df(3L)kni[ri-XT2].bk1
    3L:20,690,666..20,692,381
    comment=Distal breakpoint of a ~50kb deletion with breaks ~2.5kb upstream of the kni transcription unit and 45-50kb further upstream. Overlaps the Df(3L)kni[ri-XT2] deletion by less than 1kb.
    linked_to=EcoRI-EcoRI_rfrag
    point mutation
    comment=Single base pair change in the putative regulatory region for wing vein L2 expression. Regulatory region with point muation when placed in reporter construct, fails to drive expression in wing vein L2. (Note that the reported base change is on the opposite strand and in relation to the EcoRI-XhoI fragment.)
    evidence=experimental
    na_change=G20641117T
    reported_na_change=C596A
    point mutation
    evidence=experimental
    na_change=C20628120T
    pr_change=T21I|kni-PA
    reported_na_change=C2640T
    reported_pr_change=T21I
    point mutation
    evidence=experimental
    na_change=G20627875A
    pr_change=R31H|kni-PA
    reported_na_change=G2884A
    reported_pr_change=R31H
    point mutation
    evidence=experimental
    na_change=T20627825A
    pr_change=C48S|kni-PA
    reported_na_change=T2934A
    reported_pr_change=C48S
    point mutation
    evidence=experimental
    na_change=T20627825A
    pr_change=C48S|kni-PA
    reported_na_change=T2934A
    reported_pr_change=C48S
    point mutation
    evidence=experimental
    na_change=G20627782A
    pr_change=R62H|kni-PA
    reported_na_change=G2977A
    reported_pr_change=R62H
    point mutation
    evidence=experimental
    na_change=G20627758A
    pr_change=G70D|kni-PA
    reported_na_change=G3001A
    reported_pr_change=G70D
    point mutation
    evidence=experimental
    na_change=C20627534T
    pr_change=Q145@|kni-PA
    reported_na_change=C3225T
    reported_pr_change=?145@
    point mutation
    evidence=experimental
    na_change=C20627413A
    pr_change=S185@|kni-PA
    reported_na_change=C3347A
    reported_pr_change=?185@
    protein binding site
    kni-protein_bind-1
    3L:20,700,420..20,700,428
    bound_moiety=sd-XP
    comment=A mutation in this site along with two other Sd-binding sites in a kni wing reporter construct leads to complete loss of wing disc expression.
    evidence=experimental
    bound_moiety=Sd-XP
    protein binding site
    kni-protein_bind-2
    3L:20,700,350..20,700,358
    bound_moiety=sd-XP
    bound_moiety=Sd-XP
    comment=A mutation in this site along with two other Sd-binding sites in a kni wing reporter construct leads to complete loss of wing disc expression.(binding site reported on opposite strand with respect to kni gene transcription)
    evidence=experimental
    protein binding site
    kni-protein_bind-3
    3L:20,700,303..20,700,311
    bound_moiety=Sd-XP
    bound_moiety=sd-XP
    comment=(binding site reported on opposite strand with respect to kni gene transcription)
    evidence=experimental
    protein binding site
    kni-protein_bind-4
    3L:20,700,243..20,700,251
    bound_moiety=Sd-XP
    bound_moiety=sd-XP
    evidence=experimental
    protein binding site
    kni-protein_bind-5
    3L:20,700,051..20,700,068
    bound_moiety=sd-XP
    comment=Tandem Sd-binding site. A mutation in this site along with two other Sd-binding sites in a kni wing reporter construct leads to complete loss of wing disc expression. (binding site reported on opposite strand with respect to kni gene transcription)
    evidence=experimental
    bound_moiety=Sd-XP
    protein binding site
    kni-protein_bind-6
    3L:20,690,647..20,690,657
    bound_moiety=cad-XP
    comment=cad binding site 1
    evidence=experimental
    protein binding site
    kni-protein_bind-7
    3L:20,690,610..20,690,622
    bound_moiety=cad-XP
    comment=cad binding site 2. The binding site has two extra T residues in the reference sequence relative to the reported sequence.
    evidence=experimental
    protein binding site
    kni-protein_bind-8
    3L:20,690,583..20,690,593
    bound_moiety=cad-XP
    comment=cad binding site 3
    evidence=experimental
    protein binding site
    kni-protein_bind-9
    3L:20,690,557..20,690,567
    bound_moiety=cad-XP
    comment=cad binding site 4
    evidence=experimental
    protein binding site
    kni-protein_bind-10
    3L:20,690,527..20,690,537
    bound_moiety=cad-XP
    comment=cad binding site 5
    evidence=experimental
    protein binding site
    kni-protein_bind-11
    3L:20,690,504..20,690,513
    bound_moiety=bcd-XP
    comment=bcd binding site 1
    evidence=experimental
    protein binding site
    kni-protein_bind-12
    3L:20,690,494..20,690,503
    bound_moiety=bcd-XP
    comment=bcd binding site 2
    evidence=experimental
    protein binding site
    kni-protein_bind-13
    3L:20,690,492..20,690,502
    bound_moiety=cad-XP
    comment=cad binding site 6
    evidence=experimental
    protein binding site
    kni-protein_bind-14
    3L:20,690,483..20,690,492
    bound_moiety=bcd-XP
    comment=bcd binding site 3
    evidence=experimental
    protein binding site
    kni-protein_bind-15
    3L:20,690,468..20,690,482
    bound_moiety=bcd-XP
    comment=bcd binding site 4
    evidence=experimental
    protein binding site
    kni-protein_bind-16
    3L:20,690,462..20,690,471
    bound_moiety=bcd-XP
    comment=bcd binding site 5
    evidence=experimental
    protein binding site
    kni-protein_bind-17
    3L:20,690,452..20,690,461
    bound_moiety=bcd-XP
    comment=bcd binding site 6
    evidence=experimental
    protein binding site
    kni-protein_bind-18
    3L:20,690,400..20,690,407
    bound_moiety=hb-XP
    comment=hb binding site 1
    evidence=experimental
    protein binding site
    kni-protein_bind-19
    3L:20,690,359..20,690,366
    bound_moiety=hb-XP
    comment=hb binding site 2
    evidence=experimental
    protein binding site
    kni-protein_bind-20
    3L:20,690,221..20,690,228
    bound_moiety=hb-XP
    comment=hb binding site 3
    evidence=experimental
    protein binding site
    kni-protein_bind-21
    3L:20,690,190..20,690,197
    bound_moiety=hb-XP
    comment=hb binding site 4
    evidence=experimental
    protein binding site
    kni-protein_bind-22
    3L:20,690,054..20,690,061
    bound_moiety=hb-XP
    comment=hb binding site 5
    evidence=experimental
    protein binding site
    kni-protein_bind-23
    3L:20,690,032..20,690,039
    bound_moiety=hb-XP
    comment=hb binding site 6 (weak site)
    evidence=experimental
    protein binding site
    kni-protein_bind-24
    3L:20,689,985..20,689,993
    bound_moiety=tll-XP
    comment=tll binding site 1
    evidence=experimental
    protein binding site
    kni-protein_bind-25
    3L:20,689,961..20,689,969
    bound_moiety=tll-XP
    comment=tll binding site 2 (last base differs from that reported in FBrf0057643).
    evidence=experimental
    protein binding site
    kni-protein_bind-26
    3L:20,689,859..20,689,867
    bound_moiety=tll-XP
    comment=tll binding site 3
    evidence=experimental
    protein binding site
    kni-protein_bind-27
    3L:20,689,798..20,689,808
    bound_moiety=Kr-XP
    comment=Kr binding site K1
    evidence=experimental
    protein binding site
    kni-protein_bind-28
    3L:20,689,768..20,689,778
    bound_moiety=Kr-XP
    comment=Kr binding site K2
    evidence=experimental
    protein binding site
    kni-protein_bind-29
    3L:20,689,643..20,689,651
    bound_moiety=tll-XP
    comment=tll binding site 4
    evidence=experimental
    protein binding site
    kni-protein_bind-30
    3L:20,689,688..20,689,713
    bound_moiety=tll-XP
    evidence=experimental
    protein binding site
    kni-protein_bind-31
    3L:20,690,695..20,690,707
    bound_moiety=hb-XP
    evidence=experimental
    protein binding site
    kni-protein_bind-32
    3L:20,689,735..20,689,750
    bound_moiety=tll-XP
    evidence=experimental
    protein binding site
    kni-protein_bind-33
    3L:20,689,700..20,689,725
    bound_moiety=hb-XP
    evidence=experimental
    protein binding site
    kni-protein_bind-34
    3L:20,690,704..20,690,712
    bound_moiety=cad-XP
    evidence=experimental
    protein binding site
    kni-protein_bind-35
    3L:20,689,701..20,689,724
    bound_moiety=Kr-XP
    evidence=experimental
    protein binding site
    kni-protein_bind-36
    3L:20,690,525..20,690,540
    bound_moiety=hb-XP
    evidence=experimental
    protein binding site
    kni-protein_bind-37
    3L:20,690,503..20,690,509
    bound_moiety=His2B-XP
    evidence=experimental
    protein binding site
    kni-protein_bind-38
    3L:20,690,492..20,690,499
    bound_moiety=His2B-XP
    evidence=experimental
    protein binding site
    kni-protein_bind-39
    3L:20,690,484..20,690,489
    bound_moiety=His2B-XP
    evidence=experimental
    protein binding site
    kni-protein_bind-40
    3L:20,690,473..20,690,480
    bound_moiety=His2B-XP
    evidence=experimental
    protein binding site
    kni-protein_bind-41
    3L:20,690,462..20,690,468
    bound_moiety=His2B-XP
    evidence=experimental
    protein binding site
    kni-protein_bind-42
    3L:20,690,058..20,690,072
    bound_moiety=gt-XP
    evidence=experimental
    protein binding site
    kni-protein_bind-43
    3L:20,690,035..20,690,046
    bound_moiety=gt-XP
    evidence=experimental
    protein binding site
    kni-protein_bind-44
    3L:20,689,796..20,689,814
    bound_moiety=Kr-XP
    evidence=experimental
    protein binding site
    kni-protein_bind-45
    3L:20,689,776..20,689,792
    evidence=experimental
    bound_moiety=tll-XP
    protein binding site
    kni-protein_bind-46
    3L:20,689,764..20,689,783
    bound_moiety=Kr-XP
    evidence=experimental
    protein binding site
    kni-protein_bind-47
    3L:20,689,632..20,689,649
    bound_moiety=Kr-XP
    evidence=experimental
    protein binding site
    kni-protein_bind-48
    3L:20,689,636..20,689,649
    bound_moiety=hb-XP
    evidence=experimental
    protein binding site
    kni-protein_bind-49
    3L:20,689,640..20,689,656
    bound_moiety=tll-XP
    evidence=experimental
    protein binding site
    kni-protein_bind-50
    3L:20,689,819..20,689,839
    bound_moiety=Kr-XP
    evidence=experimental
    protein binding site
    kni-protein_bind-51
    3L:20,689,743..20,689,766
    bound_moiety=hb-XP
    evidence=experimental
    regulatory region
    kni-reg_element-1
    3L:20,699,781..20,701,141
    comment=Region sufficient to direct the correct spatial pattern of kni expression in the wing vein L2 primordium in wing imaginal discs.
    linked_to=XhoI-EcoRI_rfrag
    regulatory region
    kni-reg_element-2
    3L:20,688,236..20,693,017
    comment=Region sufficient to direct the correct spatial pattern of kni expression in the anterior and posterior domains in the blastoderm embryo.
    evidence=experimental
    linked_to=BamHI-NruI_rfrag
    regulatory region
    kni-reg_element-3
    3L:20,689,640..20,690,516
    comment=Fragment directs kni wild-type-like abdominal expression pattern in blastoderm embryos.
    linked_to=KpnI-DraI_rfrag
    regulatory region
    kni-reg_element-4
    3L:20,690,014..20,690,464
    comment=Fragment required for setting the anterior boundary of kni expression in the abdomen in blastoderm embryos.
    evidence=experimental
    linked_to=PstI-EcoRI_rfrag
    regulatory region
    kni-reg_element-5
    3L:20,689,640..20,690,019
    comment=Fragment required for setting the posterior boundary of kni expression in the abdomen in blastoderm embryos.
    linked_to=EcoRI-DraI_rfrag
    rescue fragment
    comment=Fragment rescues the kni mutant abdominal segment pattern and weakly rescues the head defects.
    evidence=experimental
    linked_to=SalI-HindIII_rfrag
    sequence variant
    comment=252bp deletion in the putative regulatory region for wing vein L2 expression.
    evidence=experimental
    sequence variant
    comment=252bp deletion in the putative regulatory region for wing vein L2 expression. kni[ri-92f] may be a re-isolate of the kni[ri-1] allele.
    evidence=experimental
    sequence variant
    comment=252bp deletion in the putative regulatory region for wing vein L2 expression. kni[riM] may be a re-isolate of the kni[ri-1] allele.
    evidence=experimental
    sequence variant
    comment=The approximately 2kb kni[8] deletion lies within the EcoRI-BamHI fragment.
    evidence=experimental
    linked_to=EcoRI-BamHI_rfrag
    sequence variant
    comment=Deletion of 245bp leads to a frameshift, producing a protein with the N-terminal 232 amino acids of kni followed by an additional 105 amino acids.
    evidence=experimental
    hide External Data
    Linkouts
    DEDB - Drosophila exon database: splicing graphs
    Crossreferences
    hide Expression Data
    FlyBase-Curated Data
    Transcript and
    Protein data
    Please see the FlyBase Gene Expression Report for details of gene expression from the literature.
    hide Summary of Transcript Expression
    Stage
    Tissue/Position
    Reference
     embryonic stage | cellular blastoderm
     embryonic stage | stage 4
     embryonic stage | stage 4
     embryonic stage
     embryonic stage | early
     larval stage | third instar
     wing vein L2 | precursor
     embryonic stage | stage 4
     embryonic stage | stage 4
     embryonic stage | blastoderm
    Marker for
      Subcellular Localization
      CV Term
      hide Summary of Polypeptide Expression
      Stage
      Tissue/Position
      Reference
      Marker for
        Subcellular Localization
        CV Term
        hide External Data & Images
        Linkouts
        FLIGHT - Cell culture data for RNAi and other high-throughput technologies
        FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
        GEO (NCBI) - Gene expression data: microarray and other high-throughput technologies
        hide Alleles & Phenotypes
        hide Summary of Allele Phenotypes
        Lethality
        Allele
        Other Phenotypes
        Allele
        Sterility
        Allele
        Phenotype manifest in
        Allele
        adherens junction & embryonic dorsal trunk, with Scer\GAL4btl.PS
        adult thorax & macrochaeta, with Scer\GAL4Bx-MS1096
        embryonic/first instar larval cuticle & abdominal segment 1
        embryonic/first instar larval cuticle & abdominal segment 2
        embryonic/first instar larval cuticle & abdominal segment 3
        embryonic/first instar larval cuticle & abdominal segment 4
        embryonic/first instar larval cuticle & abdominal segment 5
        embryonic/first instar larval cuticle & abdominal segment 6
        embryonic/first instar larval cuticle & abdominal segment 7
        hide Classical Alleles ( 35 )
        For All Classical Alleles Show

        Allele of kniClassMutagenStocksKnown lesion
        kni10amorph, loss of function3 --
        kni11loss of function0 --
        kni120 --
        kni11 --
        kni2loss of function0 --
        kni30 Yes
        kni40 --
        kni5loss of function1 --
        kni5H
          0 --
          kni6loss of function3 Yes
          kni7loss of function0