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Gene Dmel\knk

General Information
Symbol	Dmel\knk	Species	D. melanogaster
Name	knickkopf	Annotation symbol	CG6217
Feature type	protein_coding_gene	FlyBase ID	FBgn0001321
Gene Model Status	Current	Stock availability	8 publicly available
Genomic Location
Chromosome (arm)	3R	Recombination map	3-49.1
Cytogenetic map	85F13-85F13	Sequence location	3R:5,948,087..5,951,383 [-]
Genomic Maps Select View:Gene Models/EvidenceExpression/RegulationMegaViewGene Disruptions, Stocks and Reagents modENCODE GBrowse	Decorated FastA GenBankGFF Gene region Extended Gene region CDSIntronsExonsTranslationsTranscripts3' UTR5' UTR
Summary Information
Automatically generated summary See sections below for more information	The gene knickkopf is referred to in FlyBase by the symbol Dmel\knk (CG6217, FBgn0001321). It is a protein_coding_gene from Drosophila melanogaster. Its molecular function is unknown. There is experimental evidence that it is involved in the biological process: torso signaling pathway; terminal region determination; regulation of tube diameter, open tracheal system; chitin biosynthetic process; regulation of tube size, open tracheal system; regulation of tube architecture, open tracheal system; embryonic epithelial tube formation; open tracheal system development; chitin-based embryonic cuticle biosynthetic process; cuticle chitin biosynthetic process. 17 alleles are reported. The phenotypes of these alleles are annotated with: organ system; cuticle; embryonic/larval tracheal system; integumentary system; tracheal system; cephalopharyngeal skeleton; multicellular structure; portion of tissue; cuticular specialization; non-connected developing system. It has one annotated transcript and one annotated polypeptide. Protein features are: DM13 domain; DOMON domain. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of high expression to a trough of very low expression. Peak expression observed at stages throughout the pupal period. Summary of FlyAtlas Anatomical Expression Data: Expression at high levels in the following post-embryonic organs or tissues: larval trachea. Expression at moderate levels in the following post-embryonic organs or tissues: larval/adult hindgut, larval carcass. Comments on Affy2 ProbeSet: ProbeSet 1624121_at completely aligns to an exonic region of the only FlyBase-annotated transcript isoform of knk. Gene sequence location is 3R:5948087..5951383.
Phenotypic Description from the Red Book (Lindsley & Zimm 1992)
Gene/Allele symbols may differ from current usage	knk: knickkopf Homozygous lethal; head skeleton defective; denticle bands narrowed; embryo rarely inverted in egg case.
Recent Updates
Description	What does this section display? This section contains items that were added to this record for each release. It currently only tracks new links between this FlyBase report and other FlyBase data classes (e.g. genes, references, stocks) or controlled vocabulary terms (e.g. GO, anatomy terms). What does this section not display? This section does not currently display links that were removed or gene model changes.
Update Feed	Click the icon below to subscribe to this FlyBase record and receive updates automatically through your feed reader.
FB2011_10
FB2012_01	Sequence features BKN26472 HFA15993
All updates	Click here to see a list of all updates to this record from FB2010_08 and on.
Detailed Mapping Data
FlyBase Computed Cytological Location
Cytogenetic map Evidence for location 85F13-85F13   Limits computationally determined from genome sequence between P{EP}Fmr1EP3517&P{PZ}tws02414 and P{PZ}jumu06439&P{lacW}l(3)j8B6j8B6
Experimentally Determined Cytological Location
Cytogenetic map Notes References
Experimentally Determined Recombination Data
Location	3-49.1   3-49 (Tearle and Nusslein-Volhard, 1987)
Left of (cM)	P{PZ}tws01436 P{PZ}tws02414 (Ostrowski et al., 2002)
Right of (cM)
Notes
Gene Model & Products
Please see the GBrowse view of Dmel\knk for information on other features To submit a correction to a gene model please use the Contact FlyBase form
Comments on Gene Model
Transcript Data
Annotated Transcripts
Name FlyBase ID RefSeq ID Length (nt) Associated CDS (aa) knk-RA FBtr0082194  NM_141724   2671   689
Additional Transcript Data & Comments
Reported size (kB)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name FlyBase ID Predicted MW (kDa) Length (aa) Theoretical pI RefSeq ID GenBank protein knk-PA   FBpp0081672   77.7   689   5.89     NP_649981   AAF54497
Additional Polypeptide Data & Comments
Reported size (kDa)
Comments
External Data
Linkouts
Crossreferences	InterPro domains - A database of protein families, domains, and functional sites • DOMON domain (IPR005018) DM13 domain (IPR019545)
Sequences Consistent with the Gene Model
DDBJ / EMBL / GenBank	DNA sequence Protein sequence Name AE014297 AAF54497   AY071192 AAL48814   BI171491   BI216794   BI361691   BI580855   CK657828   CO302928   CO325492   CZ484400   CZ484401   CZ489896   GH794516   GH802674   GH832033   GH848360   GH851964   GH859014   GH868424   GH884698   GH893110   GH932562   GH938245
UniProtKB/Swiss-Prot
UniProtKB/TrEMBL	Q9VH23
Mapped Features
Mapped Features have been reorganized, please see this article for details. Additional mapped features and mutations can be found on GBrowse or related reports. Type Symbol & Location Additional Notes References
External Data
Linkouts
Crossreferences
Expression Data
Transcript Expression
in situ Stage Tissue/Position (including subcellular localization) Reference embryonic stage 13 -- 17   trachea   (Moussian et al., 2006) embryonic stage 15 -- 17   embryonic/larval pharynx   (Moussian et al., 2006) embryonic hindgut   (Moussian et al., 2006) embryonic epidermis   (Moussian et al., 2006)
Additional Descriptive Data
	knk transcript is observed in developing tracheae starting at embryonic stage 13, and in the pharynx,epidermis and hindgut starting at embryonic stage 15. (Moussian et al., 2006)
Marker for
Subcellular Localization
CV Term
Notes
Polypeptide Expression
immunolocalization Stage Tissue/Position (including subcellular localization) Reference embryonic stage 15 -- 17   epithelial cell of trachea   • apical part of cell (Moussian et al., 2006) embryonic stage 16 -- 17   epidermal cell   • apical part of cell (Moussian et al., 2006)
Additional Descriptive Data
	knk protein is anchored to the apical cell surface of cells in the developing tracheae and epidermis. knk protein is observed to localize to the apical and apical-lateral surface of epithelial cells in the developing trachea from embryonic stage 15, and at the apical surface of epidermal cells from embryonic stage 16. (Moussian et al., 2006)
Marker for
Subcellular Localization
CV Term
Notes
High-Throughput Expression Data
or
See Gelbart and Emmert, 2010.10.13 for analysis details and data files for all genes. modENCODE Temporal Expression Data for FBgn0001321    Styles Linear Logarithmic Heatmap    Scales max expr for FBgn0001321 Very low expression bin max Moderate expression bin max High expression bin max Extremely high expression bin max Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of high expression to a trough of very low expression. Peak expression observed at stages throughout the pupal period. [download data (TSV)] Guide to modENCODE expression level colors   No expression (0 - 0)   Extremely low expression (1 - 10)   Very low expression (11 - 100)   Low expression (101 - 400)   Moderate expression (401 - 1400)   Moderately high expression (1401 - 4000)   High expression (4001 - 10000)   Very high expression (10001 - 100000)   Extremely high expression (100001 - 2000000) Linear, scaled to maximum FBgn0001321 expression level Developmental Stage   Expression Level embryo 00-02hr    22 embryo 02-04hr    28 embryo 04-06hr    24 embryo 06-08hr    102 embryo 08-10hr    209 embryo 10-12hr    989 embryo 12-14hr    2268 embryo 14-16hr    3676 embryo 16-18hr    2058 embryo 18-20hr    877 embryo 20-22hr    268 embryo 22-24hr    417 larva L1    409 larva L2    1498 larva L3 12hr old    952 larva L3 puffstage 1-2    604 larva L3 puffstage 3-6    758 larva L3 puffstage 7-9    1586 white prepupae new    2300 white prepupae 12hr    8186 white prepupae 24hr    2582 pupae 2d postWPP    5575 pupae 3d postWPP    1567 pupae 4d postWPP    1495 adult male 01day    524 adult male 05day    188 adult male 30day    203 adult female 01day    312 adult female 05day    32 adult female 30day    31 Expression Level Scale  None   Extremely low   Very low   Low   Moderate   Moderately high   High  Linear, scaled to Very low expression Developmental Stage   Expression Level embryo 00-02hr    22 embryo 02-04hr    28 embryo 04-06hr    24 embryo 06-08hr  102 embryo 08-10hr  (209) embryo 10-12hr  (989) embryo 12-14hr  (2268) embryo 14-16hr  (3676) embryo 16-18hr  (2058) embryo 18-20hr  (877) embryo 20-22hr  (268) embryo 22-24hr  (417) larva L1  (409) larva L2  (1498) larva L3 12hr old  (952) larva L3 puffstage 1-2  (604) larva L3 puffstage 3-6  (758) larva L3 puffstage 7-9  (1586) white prepupae new  (2300) white prepupae 12hr  (8186) white prepupae 24hr  (2582) pupae 2d postWPP  (5575) pupae 3d postWPP  (1567) pupae 4d postWPP  (1495) adult male 01day  (524) adult male 05day  (188) adult male 30day  (203) adult female 01day  (312) adult female 05day    32 adult female 30day    31 Expression Level Scale  None   Extremely low   Very low   Low  Linear, scaled to Moderate expression Developmental Stage   Expression Level embryo 00-02hr    22 embryo 02-04hr    28 embryo 04-06hr    24 embryo 06-08hr    102 embryo 08-10hr    209 embryo 10-12hr    989 embryo 12-14hr  (2268) embryo 14-16hr  (3676) embryo 16-18hr  (2058) embryo 18-20hr    877 embryo 20-22hr    268 embryo 22-24hr    417 larva L1    409 larva L2  1498 larva L3 12hr old    952 larva L3 puffstage 1-2    604 larva L3 puffstage 3-6    758 larva L3 puffstage 7-9  (1586) white prepupae new  (2300) white prepupae 12hr  (8186) white prepupae 24hr  (2582) pupae 2d postWPP  (5575) pupae 3d postWPP  (1567) pupae 4d postWPP  1495 adult male 01day    524 adult male 05day    188 adult male 30day    203 adult female 01day    312 adult female 05day    32 adult female 30day    31 Expression Level Scale  None   Extremely low   Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Developmental Stage   Expression Level embryo 00-02hr    22 embryo 02-04hr    28 embryo 04-06hr    24 embryo 06-08hr    102 embryo 08-10hr    209 embryo 10-12hr    989 embryo 12-14hr    2268 embryo 14-16hr    3676 embryo 16-18hr    2058 embryo 18-20hr    877 embryo 20-22hr    268 embryo 22-24hr    417 larva L1    409 larva L2    1498 larva L3 12hr old    952 larva L3 puffstage 1-2    604 larva L3 puffstage 3-6    758 larva L3 puffstage 7-9    1586 white prepupae new    2300 white prepupae 12hr    8186 white prepupae 24hr    2582 pupae 2d postWPP    5575 pupae 3d postWPP    1567 pupae 4d postWPP    1495 adult male 01day    524 adult male 05day    188 adult male 30day    203 adult female 01day    312 adult female 05day    32 adult female 30day    31 Expression Level Scale  None   Extremely low   Very low   Low   Moderate   Moderately high   High   Very high  Linear, scaled to Extremely high expression Developmental Stage   Expression Level embryo 00-02hr    22 embryo 02-04hr    28 embryo 04-06hr    24 embryo 06-08hr    102 embryo 08-10hr    209 embryo 10-12hr    989 embryo 12-14hr    2268 embryo 14-16hr    3676 embryo 16-18hr    2058 embryo 18-20hr    877 embryo 20-22hr    268 embryo 22-24hr    417 larva L1    409 larva L2    1498 larva L3 12hr old    952 larva L3 puffstage 1-2    604 larva L3 puffstage 3-6    758 larva L3 puffstage 7-9    1586 white prepupae new    2300 white prepupae 12hr    8186 white prepupae 24hr    2582 pupae 2d postWPP    5575 pupae 3d postWPP    1567 pupae 4d postWPP    1495 adult male 01day    524 adult male 05day    188 adult male 30day    203 adult female 01day    312 adult female 05day    32 adult female 30day    31 Expression Level Scale  None   Extremely low   Very low   Low   Moderate   Moderately high   High   Very high   Extremely high  log, scaled to maximum FBgn0001321 expression level Developmental Stage   Expression Level embryo 00-02hr    22 embryo 02-04hr    28 embryo 04-06hr    24 embryo 06-08hr    102 embryo 08-10hr    209 embryo 10-12hr    989 embryo 12-14hr    2268 embryo 14-16hr    3676 embryo 16-18hr    2058 embryo 18-20hr    877 embryo 20-22hr    268 embryo 22-24hr    417 larva L1    409 larva L2    1498 larva L3 12hr old    952 larva L3 puffstage 1-2    604 larva L3 puffstage 3-6    758 larva L3 puffstage 7-9    1586 white prepupae new    2300 white prepupae 12hr    8186 white prepupae 24hr    2582 pupae 2d postWPP    5575 pupae 3d postWPP    1567 pupae 4d postWPP    1495 adult male 01day    524 adult male 05day    188 adult male 30day    203 adult female 01day    312 adult female 05day    32 adult female 30day    31 Expression Level Scale  None   Extremely low   Very low   Low   Moderate   Moderately high   High   Very high  log, scaled to Very low expression Developmental Stage   Expression Level embryo 00-02hr    22 embryo 02-04hr    28 embryo 04-06hr    24 embryo 06-08hr  102 embryo 08-10hr  (209) embryo 10-12hr  (989) embryo 12-14hr  (2268) embryo 14-16hr  (3676) embryo 16-18hr  (2058) embryo 18-20hr  (877) embryo 20-22hr  (268) embryo 22-24hr  (417) larva L1  (409) larva L2  (1498) larva L3 12hr old  (952) larva L3 puffstage 1-2  (604) larva L3 puffstage 3-6  (758) larva L3 puffstage 7-9  (1586) white prepupae new  (2300) white prepupae 12hr  (8186) white prepupae 24hr  (2582) pupae 2d postWPP  (5575) pupae 3d postWPP  (1567) pupae 4d postWPP  (1495) adult male 01day  (524) adult male 05day  (188) adult male 30day  (203) adult female 01day  (312) adult female 05day    32 adult female 30day    31 Expression Level Scale  None   Extremely low   Very low   Low  log, scaled to Moderate expression Developmental Stage   Expression Level embryo 00-02hr    22 embryo 02-04hr    28 embryo 04-06hr    24 embryo 06-08hr    102 embryo 08-10hr    209 embryo 10-12hr    989 embryo 12-14hr  2268 embryo 14-16hr  (3676) embryo 16-18hr  2058 embryo 18-20hr    877 embryo 20-22hr    268 embryo 22-24hr    417 larva L1    409 larva L2  1498 larva L3 12hr old    952 larva L3 puffstage 1-2    604 larva L3 puffstage 3-6    758 larva L3 puffstage 7-9  1586 white prepupae new  2300 white prepupae 12hr  (8186) white prepupae 24hr  (2582) pupae 2d postWPP  (5575) pupae 3d postWPP  1567 pupae 4d postWPP  1495 adult male 01day    524 adult male 05day    188 adult male 30day    203 adult female 01day    312 adult female 05day    32 adult female 30day    31 Expression Level Scale  None   Extremely low   Very low   Low   Moderate   Moderately high  log, scaled to High expression Developmental Stage   Expression Level embryo 00-02hr    22 embryo 02-04hr    28 embryo 04-06hr    24 embryo 06-08hr    102 embryo 08-10hr    209 embryo 10-12hr    989 embryo 12-14hr    2268 embryo 14-16hr    3676 embryo 16-18hr    2058 embryo 18-20hr    877 embryo 20-22hr    268 embryo 22-24hr    417 larva L1    409 larva L2    1498 larva L3 12hr old    952 larva L3 puffstage 1-2    604 larva L3 puffstage 3-6    758 larva L3 puffstage 7-9    1586 white prepupae new    2300 white prepupae 12hr    8186 white prepupae 24hr    2582 pupae 2d postWPP    5575 pupae 3d postWPP    1567 pupae 4d postWPP    1495 adult male 01day    524 adult male 05day    188 adult male 30day    203 adult female 01day    312 adult female 05day    32 adult female 30day    31 Expression Level Scale  None   Extremely low   Very low   Low   Moderate   Moderately high   High   Very high  log, scaled to Extremely high expression Developmental Stage   Expression Level embryo 00-02hr    22 embryo 02-04hr    28 embryo 04-06hr    24 embryo 06-08hr    102 embryo 08-10hr    209 embryo 10-12hr    989 embryo 12-14hr    2268 embryo 14-16hr    3676 embryo 16-18hr    2058 embryo 18-20hr    877 embryo 20-22hr    268 embryo 22-24hr    417 larva L1    409 larva L2    1498 larva L3 12hr old    952 larva L3 puffstage 1-2    604 larva L3 puffstage 3-6    758 larva L3 puffstage 7-9    1586 white prepupae new    2300 white prepupae 12hr    8186 white prepupae 24hr    2582 pupae 2d postWPP    5575 pupae 3d postWPP    1567 pupae 4d postWPP    1495 adult male 01day    524 adult male 05day    188 adult male 30day    203 adult female 01day    312 adult female 05day    32 adult female 30day    31 Expression Level Scale  None   Extremely low   Very low   Low   Moderate   Moderately high   High   Very high   Extremely high  Heatmap Developmental Stage   Expression Level embryo 00-02hr     embryo 02-04hr     embryo 04-06hr     embryo 06-08hr     embryo 08-10hr     embryo 10-12hr     embryo 12-14hr     embryo 14-16hr     embryo 16-18hr     embryo 18-20hr     embryo 20-22hr     embryo 22-24hr     larva L1     larva L2     larva L3 12hr old     larva L3 puffstage 1-2     larva L3 puffstage 3-6     larva L3 puffstage 7-9     white prepupae new     white prepupae 12hr     white prepupae 24hr     pupae 2d postWPP     pupae 3d postWPP     pupae 4d postWPP     adult male 01day     adult male 05day     adult male 30day     adult female 01day     adult female 05day     adult female 30day     FlyAtlas Anatomical Expression Data for FBgn0001321    Styles Linear Logarithmic Heatmap Back-to-back    Scales max expr for FBgn0001321 Moderate expression bin max High level expression bin max Very high expression bin max Summary of FlyAtlas Anatomical Expression Data: Expression at high levels in the following post-embryonic organs or tissues: larval trachea. Expression at moderate levels in the following post-embryonic organs or tissues: larval/adult hindgut, larval carcass. [download data (TSV)] Guide to FlyAtlas expression level colors   No expression (0 - 9.999)   Low expression (10 - 99.999)   Moderate expression (100 - 499.999)   High level expression (500 - 999.999)   Very high expression (1000 - 25000) Linear, scaled to maximum FBgn0001321 expression level Tissue   Expression Level Larval Central Nervous System    13.325 Larval Midgut no informative data Larval Hindgut    372.3 Larval Malpighian Tubules no informative data Larval Fat Body no informative data Larval Salivary Gland    17.5 Larval Trachea    545.875 Larval Carcass    347.25 Adult Head    35 Adult Eye    17.55 Adult Brain    5.6 Adult Thoracic-Abdominal Ganglion no informative data Adult Crop    60.4 Adult Midgut no informative data Adult Hindgut    186.6 Adult Malpighian Tubules no informative data Adult Fat Body no informative data Adult Salivary Gland no informative data Adult Heart    7.95 Adult VirginFemale Spermatheca no informative data Adult InseminatedFemale Spermatheca    26 Adult Ovary    6.4 Adult Testis    15.2 Adult Male Accessory Gland no informative data Adult Carcass no informative data Expression Level Scale  None   Low   Moderate   High  Linear, scaled to Moderate expression Tissue   Expression Level Larval Central Nervous System    13.325 Larval Midgut no informative data Larval Hindgut    372.3 Larval Malpighian Tubules no informative data Larval Fat Body no informative data Larval Salivary Gland    17.5 Larval Trachea  (545.875) Larval Carcass    347.25 Adult Head    35 Adult Eye    17.55 Adult Brain    5.6 Adult Thoracic-Abdominal Ganglion no informative data Adult Crop    60.4 Adult Midgut no informative data Adult Hindgut    186.6 Adult Malpighian Tubules no informative data Adult Fat Body no informative data Adult Salivary Gland no informative data Adult Heart    7.95 Adult VirginFemale Spermatheca no informative data Adult InseminatedFemale Spermatheca    26 Adult Ovary    6.4 Adult Testis    15.2 Adult Male Accessory Gland no informative data Adult Carcass no informative data Expression Level Scale  None   Low   Moderate   High  Linear, scaled to High level expression Tissue   Expression Level Larval Central Nervous System    13.325 Larval Midgut no informative data Larval Hindgut    372.3 Larval Malpighian Tubules no informative data Larval Fat Body no informative data Larval Salivary Gland    17.5 Larval Trachea    545.875 Larval Carcass    347.25 Adult Head    35 Adult Eye    17.55 Adult Brain    5.6 Adult Thoracic-Abdominal Ganglion no informative data Adult Crop    60.4 Adult Midgut no informative data Adult Hindgut    186.6 Adult Malpighian Tubules no informative data Adult Fat Body no informative data Adult Salivary Gland no informative data Adult Heart    7.95 Adult VirginFemale Spermatheca no informative data Adult InseminatedFemale Spermatheca    26 Adult Ovary    6.4 Adult Testis    15.2 Adult Male Accessory Gland no informative data Adult Carcass no informative data Expression Level Scale  None   Low   Moderate   High   Very high  Linear, scaled to Very high expression Tissue   Expression Level Larval Central Nervous System    13.325 Larval Midgut no informative data Larval Hindgut    372.3 Larval Malpighian Tubules no informative data Larval Fat Body no informative data Larval Salivary Gland    17.5 Larval Trachea    545.875 Larval Carcass    347.25 Adult Head    35 Adult Eye    17.55 Adult Brain    5.6 Adult Thoracic-Abdominal Ganglion no informative data Adult Crop    60.4 Adult Midgut no informative data Adult Hindgut    186.6 Adult Malpighian Tubules no informative data Adult Fat Body no informative data Adult Salivary Gland no informative data Adult Heart    7.95 Adult VirginFemale Spermatheca no informative data Adult InseminatedFemale Spermatheca    26 Adult Ovary    6.4 Adult Testis    15.2 Adult Male Accessory Gland no informative data Adult Carcass no informative data Expression Level Scale  None   Low   Moderate   High   Very high  log, scaled to maximum FBgn0001321 expression level Tissue   Expression Level Larval Central Nervous System    13.325 Larval Midgut no informative data Larval Hindgut    372.3 Larval Malpighian Tubules no informative data Larval Fat Body no informative data Larval Salivary Gland    17.5 Larval Trachea    545.875 Larval Carcass    347.25 Adult Head    35 Adult Eye    17.55 Adult Brain    5.6 Adult Thoracic-Abdominal Ganglion no informative data Adult Crop    60.4 Adult Midgut no informative data Adult Hindgut    186.6 Adult Malpighian Tubules no informative data Adult Fat Body no informative data Adult Salivary Gland no informative data Adult Heart    7.95 Adult VirginFemale Spermatheca no informative data Adult InseminatedFemale Spermatheca    26 Adult Ovary    6.4 Adult Testis    15.2 Adult Male Accessory Gland no informative data Adult Carcass no informative data Expression Level Scale  None   Low   Moderate   High   Very high  log, scaled to Moderate expression Tissue   Expression Level Larval Central Nervous System    13.325 Larval Midgut no informative data Larval Hindgut    372.3 Larval Malpighian Tubules no informative data Larval Fat Body no informative data Larval Salivary Gland    17.5 Larval Trachea  545.875 Larval Carcass    347.25 Adult Head    35 Adult Eye    17.55 Adult Brain    5.6 Adult Thoracic-Abdominal Ganglion no informative data Adult Crop    60.4 Adult Midgut no informative data Adult Hindgut    186.6 Adult Malpighian Tubules no informative data Adult Fat Body no informative data Adult Salivary Gland no informative data Adult Heart    7.95 Adult VirginFemale Spermatheca no informative data Adult InseminatedFemale Spermatheca    26 Adult Ovary    6.4 Adult Testis    15.2 Adult Male Accessory Gland no informative data Adult Carcass no informative data Expression Level Scale  None   Low   Moderate   High  log, scaled to High level expression Tissue   Expression Level Larval Central Nervous System    13.325 Larval Midgut no informative data Larval Hindgut    372.3 Larval Malpighian Tubules no informative data Larval Fat Body no informative data Larval Salivary Gland    17.5 Larval Trachea    545.875 Larval Carcass    347.25 Adult Head    35 Adult Eye    17.55 Adult Brain    5.6 Adult Thoracic-Abdominal Ganglion no informative data Adult Crop    60.4 Adult Midgut no informative data Adult Hindgut    186.6 Adult Malpighian Tubules no informative data Adult Fat Body no informative data Adult Salivary Gland no informative data Adult Heart    7.95 Adult VirginFemale Spermatheca no informative data Adult InseminatedFemale Spermatheca    26 Adult Ovary    6.4 Adult Testis    15.2 Adult Male Accessory Gland no informative data Adult Carcass no informative data Expression Level Scale  None   Low   Moderate   High   Very high  log, scaled to Very high expression Tissue   Expression Level Larval Central Nervous System    13.325 Larval Midgut no informative data Larval Hindgut    372.3 Larval Malpighian Tubules no informative data Larval Fat Body no informative data Larval Salivary Gland    17.5 Larval Trachea    545.875 Larval Carcass    347.25 Adult Head    35 Adult Eye    17.55 Adult Brain    5.6 Adult Thoracic-Abdominal Ganglion no informative data Adult Crop    60.4 Adult Midgut no informative data Adult Hindgut    186.6 Adult Malpighian Tubules no informative data Adult Fat Body no informative data Adult Salivary Gland no informative data Adult Heart    7.95 Adult VirginFemale Spermatheca no informative data Adult InseminatedFemale Spermatheca    26 Adult Ovary    6.4 Adult Testis    15.2 Adult Male Accessory Gland no informative data Adult Carcass no informative data Expression Level Scale  None   Low   Moderate   High   Very high  Heatmap Tissue   Expression Level Larval Central Nervous System     Larval Midgut no informative data Larval Hindgut     Larval Malpighian Tubules no informative data Larval Fat Body no informative data Larval Salivary Gland     Larval Trachea     Larval Carcass     Adult Head     Adult Eye     Adult Brain     Adult Thoracic-Abdominal Ganglion no informative data Adult Crop     Adult Midgut no informative data Adult Hindgut     Adult Malpighian Tubules no informative data Adult Fat Body no informative data Adult Salivary Gland no informative data Adult Heart     Adult VirginFemale Spermatheca no informative data Adult InseminatedFemale Spermatheca     Adult Ovary     Adult Testis     Adult Male Accessory Gland no informative data Adult Carcass no informative data FlyAtlas Organ/Tissue Expression, larval vs. adult Larval Expression Level Tissue Adult Expression Level   NA  Head    35   NA  Eye    17.55   NA  Brain    5.6   13.325  Central Nervous System    NA   NA  Thoracic-Abdominal Ganglion    no informative data   NA  Crop    60.4   no informative data  Midgut    no informative data   372.3  Hindgut    186.6   no informative data  Malpighian Tubules    no informative data   no informative data  Fat Body    no informative data   17.5  Salivary Gland    no informative data   NA  Heart    7.95   545.875  Trachea    NA   NA  VirginFemale Spermatheca    no informative data   NA  InseminatedFemale Spermatheca    26   NA  Ovary    6.4   NA  Testis    15.2   NA  Male Accessory Gland    no informative data   347.25  Carcass    no informative data modENCODE Temporal Expression Data (Graveley et al., 2011) FlyAtlas Anatomical Expression Data (Chintapalli et al., 2007)
Expression Clusters
	A cluster of genes with similar mRNA expression dynamics across development. (The modENCODE Consortium, 2010) mE2_34_mRNA_expression_cluster_25
External Data & Images
Linkouts	FLIGHT - Cell culture data for RNAi and other high-throughput technologies • FBgn0001321 FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array • CG6217-RA FlyExpress - Embryonic expression images (BDGP data) • Show all FlyExpress processed images for knk Stages(s) 11-12
Alleles & Phenotypes
Summary of Allele Phenotypes
Lethality Allele lethal knkunspecified lethal | embryonic stage | recessive knk1 knkunspecified lethal | pupal stage, with Scer\GAL4pnr-MD237 knkGD4952 Other Phenotypes Allele visible | somatic clone knkunspecified Phenotype manifest in Allele cephalopharyngeal skeleton knk1 knk2 knk4 knkunspecified denticle belt knk1 knk2 knk4 knkunspecified embryonic/first instar larval cuticle knk1 embryonic/larval cuticle knk1 knk2 embryonic/larval dorsal trunk knkex59 embryonic/larval dorsal trunk | embryonic stage 15 knk1 knk2 embryonic/larval dorsal trunk | embryonic stage 16 knk1 knk2 embryonic/larval tracheal system knkex59 knkunspecified embryonic/larval transverse connective knkex59 epicuticle knk1 larval head knk1 knk2 presumptive embryonic/larval tracheal system knk1 knk2 procuticle knk1 tracheal system knkunspecified vertical bridge knk1 wing hair | somatic clone knkunspecified
Classical Alleles ( 12 )
For All Classical Alleles Show
Allele of knk Class Mutagen Stocks Known lesion knk1 amorphic allele - genetic evidence ethyl methanesulfonate 2 Yes knkf01902 piggyBac transposase 2 -- knkf07119 piggyBac transposase 1 -- knk2 amorphic allele - genetic evidence ethyl methanesulfonate 0 Yes knk4 amorphic allele - genetic evidence ethyl methanesulfonate 0 Yes knk3-7H ethyl methanesulfonate 0 Yes knk3 ethyl methanesulfonate 0 -- knk50-12 ethyl methanesulfonate 0 Yes knk56-2 ethyl methanesulfonate 0 Yes knk5 ethyl methanesulfonate 0 -- knkex59 loss of function allele 0 -- knkunspecified 0 --
Alleles Carried on Transgenic Constructs ( 5 )
For All Alleles Carried on Transgenic Constructs Show
Allele of knk Class Mutagen Stocks Known lesion knkGD4952 in vitro construct - RNAi in vitro construct - regulatory fusion 2 Yes knkKK106472 in vitro construct - RNAi in vitro construct - regulatory fusion 1 Yes knkScer\UAS.cDa in vitro construct - regulatory fusion 0 Yes knkScer\UAS.cMa in vitro construct - regulatory fusion 0 Yes knkT:Avic\GFP in vitro construct - coding region fusion 0 Yes
Aneuploid Aberrations
Disrupted in	Df(3R)BSC526 (Christensen et al., 2008.6.11) Df(3R)BSC621 (Cook et al., 2008.9.29) Df(3R)by10 (Tearle and Nusslein-Volhard, 1987) Df(3R)by62 (Beitel and Krasnow, 2000, Harbecke and Lengyel, 1995) Df(3R)Exel6265 (Ryder, 2004.4.26) Df(3R)FA11 (Jurgens et al., 1984) Ts(YLt;3Lt)G42+Ts(YSt;3Rt)R36 (Jurgens et al., 1984)
Not disrupted in	Df(3R)by10 (Ostrowski et al., 2002)
Transgenic Constructs & Insertions
Transgenic Constructs
	Type of construct Name Expression data UAS construct P{GD4952} NA P{KK106472} NA P{UAS-knk.M} NA characterization construct P{knk-GFP.D} NA
Insertions
	Type of insertions Name Expression data miscellaneous insertions PBac{WH}knkf01902 NA PBac{WH}knkf07119 NA insertion of enhancer trap P{luc-sniffer}tws90-14 No
Gene Ontology: Function, Process & Cellular Component ( 10 unique terms )
Terms Based on Experimental Evidence ( 10 terms )
Molecular Function ( 0 terms)
Biological Process
CV term Evidence References
chitin-based embryonic cuticle biosynthetic process inferred from mutant phenotype (Ostrowski et al., 2002) chitin biosynthetic process inferred from mutant phenotype (Moussian et al., 2006) cuticle chitin biosynthetic process inferred from mutant phenotype (Devine et al., 2005) embryonic epithelial tube formation inferred from mutant phenotype (Devine et al., 2005) open tracheal system development inferred from mutant phenotype (Beitel and Krasnow, 2000, Moussian et al., 2006) regulation of tube architecture, open tracheal system inferred from mutant phenotype (Moussian et al., 2006) regulation of tube diameter, open tracheal system inferred from mutant phenotype (Moussian et al., 2006) regulation of tube size, open tracheal system inferred from mutant phenotype (Beitel and Krasnow, 2000) terminal region determination inferred from genetic interaction with tor (Strecker et al., 1991) torso signaling pathway inferred from genetic interaction with tor (Strecker et al., 1991)
Cellular Component ( 0 terms)
Terms Based on Predictions or Assertions ( 0 terms )
Sequence Ontology: Class of Gene
	nuclear_gene   protein_coding_gene
Interactions & Pathways
Summary of Physical Interactions
Protein-protein
Interacting group Assay References
Summary of Genetic Interactions
Interacts with	Please look at the allele data for full details of the genetic interactions knk allele Gene References knk1 shg (Ostrowski et al., 2002)
External Data
Linkouts	DPiM - DPiM, Drosophila Protein interaction Map • FBgn0001321 DroID - A comprehensive database of gene and protein interactions. • FBgn0001321
Orthologs
Genome-wide drosophilid orthologs	Dana\GF18136 Dere\GG17300 Dgri\GH13421 Dmoj\GI22389 Dper\GL23675 Dpse\GA26697 Dsec\GM26184 Dsim\GD20733 Dvir\GJ24421 Dwil\GK11432 Dyak\GE24703
Curated drosophilid orthologs	Dpse\GA19448
Linkouts	InParanoid A subset of ortholog calls from InParanoid. • AAEL014044-PA Aedes aegypti (mosquito) AGAP004500-PA Anopheles gambiae (mosquito) XP_394084.3 Apis mellifera (honey bee) XP_001950825.1 Acyrthosiphon pisum (pea aphid) CN07875 Caenorhabditis brenneri (small nematode) CBP03575 Caenorhabditis briggsae (nematode) CE26751 Caenorhabditis elegans (worm) JA11600 Caenorhabditis japonica (nematode) CPIJ012991 Culex pipens (mosquito) RP33816 Caenorhabditis remanei (nematode) 305711 Daphnia pulex (daphnia) ISCW003417-PA Ixodes scapularis (deer tick) XP_001606352.1 Nasonia vitripennis (wasp) PHUM003783-PA Pediculus humanus (human body louse) XP_001808745.1 Tribolium castaneum (red flour beetle) OrthoDB (Arthropod subset) The hierarchical catalog of eukaryotic orthologs. • NV13036 LH21118 ISCW003417 FBgn0241808 FBgn0213443 FBgn0211501 FBgn0192199 FBgn0181039 FBgn0250099 FBgn0261669 JGI_V11_305711 FBgn0161265 FBgn0145117 FBgn0120897 FBgn0109527 FBgn0095154 CPIJ012991 BGIBMGA010774 ACYPI004851 GB30045 GB30044 GB13189 AGAP012575 AGAP004500 AAEL014044 PB25912 PHUM461040 GLEAN_10653
Stocks & Reagents
Stocks Listed in FlyBase ( 8 )
Bloomington	18487 w1118; PBac{WH}knkf01902/TM6B, Tb1 3097 ru1 h1 th1 st1 knk1 cu1 sr1 es ca1/TM3, Sb1 Ser1
Harvard	- PBac{WH}knkf01902 - PBac{WH}knkf07119
Kyoto	106838 ru1 h1 th1 st1 knk1 cu1 sr1 es ca1/TM3, Sb1 Ser1
VDRC	v106302 P{KK106472}VIE-260B v44564 w1118; P{GD4952}v44564 v44565 w1118; P{GD4952}v44565/CyO
Genomic Clones ( 1 )
	BACR39F04 Please Note FlyBase no longer curates genomic clone accessions so this list may not be complete
cDNA Clones ( 19 )
	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 GBrowse for alignment of the cDNAs and ESTs to the gene model.
cDNA Clones, Fully Sequenced
BDGP DGC clones	RE24065
Other clones	DPiM_RE24065
cDNA Clones, End Sequenced (ESTs)
BDGP DGC clones	LP24431 RE13280 RE46022 RE75093
Other clones	EK185204 EK196639 RP003013701 RP003126482 RP003241887 RP003406411 RP003488397 RP003494834 RP003555056 RP003577838 RP003618285 RP003646085 RP003660406
RNAi & Array Information
Linkouts	DRSC - Results from RNAi screens. • FBgn0001321 GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents • 47137 247218
Antibody Information
	polyclonal (Moussian et al., 2006)
Other Information
Discoverer
Etymology
Identification
Relationship to Other Genes
Source for database identity of
Source for database merge of	Source for merge of: knk CG6217 (Ostrowski et al., 2002) Source for merge of: knk gnar (Devine et al., 2005)
Additional comments	One allele is temperature-sensitive.
Other Comments
	knk is an apical GPI-linked protein that acts at the plasma membrane. knk is required for chitin filament assembly in the tracheal lumen and cuticle. (Moussian et al., 2006) Mutation in knk alters tracheal tube size in embryos without affecting other aspects of tracheal development including primary branch budding and outgrowth or branch fusion. (Beitel and Krasnow, 2000) Zygotically active locus involved in the terminal developmental program in the embryo. (Strecker et al., 1991) knk mutants display a defective head skeleton, narrow denticle bands and the embryo is rarely inverted in the egg case. (Jurgens et al., 1984)
External Crossreferences & Linkouts
Sequence Crossreferences
	RefSeq (Transcripts) • NM_141724 RefSeq (Proteins) • NP_649981 DDBJ / EMBL / GenBank • AAF54497 AAL48814 AY071192 BI216794 CZ484400 CZ484401 CZ489896 Entrez Gene - A searchable database of RefSeq genes. • 47137 UniProtKB/TrEMBL • Q9VH23
Other Crossreferences
	InterPro domains - A database of protein families, domains, and functional sites • DOMON domain (IPR005018) DM13 domain (IPR019545)
Linkouts
	DPiM - DPiM, Drosophila Protein interaction Map • FBgn0001321 DroID - A comprehensive database of gene and protein interactions. • FBgn0001321 DRSC - Results from RNAi screens. • FBgn0001321 FLIGHT - Cell culture data for RNAi and other high-throughput technologies • FBgn0001321 FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array • CG6217-RA FlyMine - Integrated genomics database for Drosophila, Anopheles, and C.elegans • FBgn0001321 GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents • 47137 247218 InParanoid A subset of ortholog calls from InParanoid. • AAEL014044-PA Aedes aegypti (mosquito) AGAP004500-PA Anopheles gambiae (mosquito) XP_394084.3 Apis mellifera (honey bee) XP_001950825.1 Acyrthosiphon pisum (pea aphid) CN07875 Caenorhabditis brenneri (small nematode) CBP03575 Caenorhabditis briggsae (nematode) CE26751 Caenorhabditis elegans (worm) JA11600 Caenorhabditis japonica (nematode) CPIJ012991 Culex pipens (mosquito) RP33816 Caenorhabditis remanei (nematode) 305711 Daphnia pulex (daphnia) ISCW003417-PA Ixodes scapularis (deer tick) XP_001606352.1 Nasonia vitripennis (wasp) PHUM003783-PA Pediculus humanus (human body louse) XP_001808745.1 Tribolium castaneum (red flour beetle) modMine - Data generated by the modENCODE project. • FBgn0001321 OrthoDB (Arthropod subset) The hierarchical catalog of eukaryotic orthologs. • NV13036 LH21118 ISCW003417 FBgn0241808 FBgn0213443 FBgn0211501 FBgn0192199 FBgn0181039 FBgn0250099 FBgn0261669 JGI_V11_305711 FBgn0161265 FBgn0145117 FBgn0120897 FBgn0109527 FBgn0095154 CPIJ012991 BGIBMGA010774 ACYPI004851 GB30045 GB30044 GB13189 AGAP012575 AGAP004500 AAEL014044 PB25912 PHUM461040 GLEAN_10653
Synonyms & Secondary IDs ( 9 )
Reported As
Symbol Synonym	CG6217 (Aravind, 2001, Stempfl et al., 2002, Keleman et al., 2009.8.5) gnar (Beitel and Krasnow, 2000, ) Gnarled (Swanson and Beitel, 2006) knk (Moussian et al., 2006, Christensen et al., 2008.6.11, Cook et al., 2008.9.29, Behr et al., 2007, Gangishetti et al., 2009, Shaik et al., 2011) Knk (Swanson and Beitel, 2006, Norum et al., 2010, Nilton et al., 2010) l(3)85Eg
Name Synonym	gnarled (Beitel and Krasnow, 2000) knickkopf (Jurgens et al., 1984, Behr et al., 2007) Knickkopf (Norum et al., 2010, Nilton et al., 2010, Shaik et al., 2011)
Secondary FlyBase IDs
	FBgn0037790 FBgn0042639
References ( 35 )
Generate a list of	All references relating to this gene ( 35 )
List References by type	Research paper  ( 17 ) Supplementary material  ( 2 ) Review  ( 2 ) Personal communication to FlyBase  ( 7 ) Abstract  ( 1 ) Stock list  ( 1 ) Computer file  ( 3 ) Book  ( 1 )
Recent research papers ( 4 )
	Ghabrial et al., 2011, PLoS Genet. 7(7): e1002087 A systematic screen for tube morphogenesis and branching genes in the Drosophila tracheal system. [FBrf0214368] Shaik et al., 2011, Glycobiology 21(6): 743--756 The Alg5 ortholog Wollknäuel is essential for correct epidermal differentiation during Drosophila late embryogenesis. [FBrf0214472] Nilton et al., 2010, Development 137(14): 2427--2437 Crooked, coiled and crimpled are three Ly6-like proteins required for proper localization of septate junction components. [FBrf0211147] Norum et al., 2010, PLoS ONE 5(5): e10802 Trafficking through COPII stabilises cell polarity and drives secretion during Drosophila epidermal differentiation. [FBrf0210959] Show all research papers ...
Recent reviews (0)
	All reviews listed in FlyBase were published before 2010 Show reviews ...