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Gene Dmel\vnd

General Information
Symbol	Dmel\vnd	Species	D. melanogaster
Name	ventral nervous system defective	Annotation symbol	CG6172
Feature type	protein_coding_gene	FlyBase ID	FBgn0003986
Created / Updated	2003-12-01/2008-02-01
Genomic Location
Chromosome (arm)	X	Recombination map	1-0.0
Cytogenetic map	1B10-1B10	Sequence location	X:476,732..491,855 [+]
Map ( 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 ventral nervous system defective is referred to in FlyBase by the symbol vnd (CG6172, FBgn0003986). It has the cytological map location 1B10. Its sequence location is X:476732..491855. Its molecular function is described as: transcription factor activity; transcription regulator activity; sequence-specific DNA binding. It is involved in the biological processes: neuroblast development; glial cell development; neuroblast fate determination; regulation of transcription, DNA-dependent; ventral cord development; dorsal/ventral pattern formation; brain development; ectoderm development; central nervous system development; pattern specification process. 74 alleles are reported. The phenotypes of these alleles are annotated with 35 unique terms, many of which group under: embryonic nervous system; nervous system; primordium; organ system; ventral nerve cord primordium; embryonic neuron; portion of tissue; embryonic glial cell; embryonic procephalic segment; muscle founder cell; neuroblast NB3-2; commissure; antennal segment. It has 2 annotated transcripts and 2 annotated polypeptides.
External Summaries
Phenotypic Description from the Red Book (Lindsley & Zimm 1992)
Gene/Allele symbols may differ from current usage	NK2 (M. Nirenberg) NK2 is a homeobox gene whose expression starts at the blastoderm stage during cell membrane formation (2.5-3.25-hour embryos) in the region that gives rise to the ventral nervous system. NK2 transcripts detected in the ventral nervous system at later stages of embryonic development. NK2 transcripts also found in the midgut starting at 12 hours of embryonic development and thereafter during embryonic development. NK2 mRNA also found in larvae and pupae but the abundance of the mRNA is lower than that of embryos. NK2 mRNA is expressed in the central nervous system of the adult. vnd: ventral nervous system defective Late embryonic lethal. Ventral nervous system disorganized and not condensed. Mutants have fewer cells in the CNS; pattern of neuronal connections damaged (Jimenez and Campos-Ortega, 1987).
Detailed Mapping Data
FlyBase Computed Cytological Location
Cytogenetic map Evidence for location 1B10-1B10   Limits computationally determined from genome sequence between P{EP}svrEP356&P{EP}argEP452 and P{EP}DreddEP1412&P{EP}Suv4-20EP1216a
Experimentally Determined Cytological Location
Cytogenetic map Notes References 1C1-1C5 (determined by in situ hybridisation)   (Kim and Nirenberg, 1989)
Experimentally Determined Recombination Data
Location	1-0.0
Left of (cM)
Right of (cM)
Notes
Molecular Map Data
Gene Order (in direction of increasing cytology) References In direction of increasing cytology: Appl? vnd+ l(1)1Bg? (Jimenez et al., 1995) Gene Order (overall orientation not stated) References
Gene Model & Products
Please see the GBrowse view of Dmel\vnd for information on other features
Comments on Gene Model
Transcript Data
Annotated Transcripts
Name FlyBase ID RefSeq ID Length (nt) Associated CDS (aa) vnd-RA FBtr0070110  NM_057438   3036   723 vnd-RB FBtr0110929  NM_001042788   2505   577
Additional Transcript Data & Comments
Reported size (kB)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name FlyBase ID Predicted MW (kD) Length (aa) Theoretical pI RefSeq ID GenBank protein vnd-PA   FBpp0070105   76.4   723   7.45     NP_476786   AAF45521 vnd-PB   FBpp0110229   61.4   577   6.97     NP_001036253   ABI30961
Additional Polypeptide Data & Comments
Reported size (kD)	722 (aa) (Jimenez et al., 1995)
Comments
External Data
Linkouts	PANTHER - Protein classification by function, families, and pathways • FBgn0003986
Crossreferences	InterPro domains - A database of protein families, domains, and functional sites • Homeobox (IPR001356) Homeodomain-like (IPR009057) Homeodomain-related (IPR012287) PDB - Protein Data Bank. An information portal to biological macromolecular structures • 1NK2 1NK3 1QRY 1VND
Sequences Consistent with the Gene Model
DDBJ / EMBL / GenBank	DNA sequence Protein sequence Name AE003418 AAF45521   CO277472   CO279964   CO303208   CO304448   CO316398   CO343167   EC202771   EC209170   EC233729   EC237610   EC238482   EC252390   M27290 AAA28617   S78691 AAB34960   X87141 CAA60619
UniProtKB/Swiss-Prot	P22808
UniProtKB/TrEMBL
Maps to	11F6 118B3 (FlyBase, 1992-)
Does NOT map to
Identified with	D1031 (BDGP Project Members, 1994-1999)
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 Df(1)yT7-376.bk2 X:464,876..476,621 comment=aberration breakpoint localized to a restriction fragment; position of restriction fragment on reference sequence inferred by FlyBase curator evidence=experimental linked_to=EcoRI-EcoRI_rfrag (Jimenez et al., 1995) aberration junction Df(1)yT8-409.bk2 X:482,864..490,102 comment=aberration breakpoint localized to a restriction fragment; position of restriction fragment on reference sequence inferred by FlyBase curator evidence=experimental linked_to=EcoRI-EcoRI_rfrag (Rosen et al., 1989) aberration junction Df(1)yT8-184.bk2 X:482,864..490,102 comment=aberration breakpoint localized to a restriction fragment; position of restriction fragment on reference sequence inferred by FlyBase curator evidence=experimental linked_to=EcoRI-EcoRI_rfrag (Rosen et al., 1989) aberration junction Df(1)yT8-385.bk2 X:482,864..490,102 comment=aberration breakpoint localized to a restriction fragment; position of restriction fragment on reference sequence inferred by FlyBase curator evidence=experimental linked_to=EcoRI-EcoRI_rfrag (Rosen et al., 1989) aberration junction T(1;Y)y[+]m[46].bk X:494,256..499,297 evidence=experimental linked_to=EcoRI-EcoRI_rfrag comment=aberration breakpoint localized to a restriction fragment; position of restriction fragment on reference sequence inferred by FlyBase curator (Jimenez et al., 1995) point mutation vnd[29] X:490,907..490,907 evidence=experimental pr_change=A433T|vnd-PB,A579T|vnd-PA reported_na_change=G2073A reported_pr_change=A578T na_change=G490907A (Jimenez et al., 1995) uncharacterized change in nucleotide sequence vnd[19] X:482,864..490,102 comment=position of restriction fragment on reference sequence inferred by FlyBase curator; two breakpoints are mapped within this restriction fragment evidence=experimental linked_to=EcoRI-EcoRI_rfrag (Jimenez et al., 1995) uncharacterized change in nucleotide sequence vnd[30] X:490,097..494,261 evidence=experimental linked_to=EcoRI-EcoRI_rfrag comment=mutation localized to a restriction fragment; position of restriction fragment on reference sequence inferred by FlyBase curator (Jimenez et al., 1995)
External Data
Linkouts	DEDB - Drosophila exon database: splicing graphs • 101
Crossreferences
Expression Data
FlyBase-Curated Data
Transcript and Protein data	Please see the FlyBase Gene Expression Report for details of gene expression from the literature.
Summary of Transcript Expression
Stage Tissue/Position Reference  embryonic stage | stage 11  neuroblast NB1-2 (Chu et al., 1998)  embryonic stage | stage 11  neuroblast NB2-1 (Chu et al., 1998)  embryonic stage | stage 8-11  neurectoderm | restricted (Chu et al., 1998)  embryonic stage | stage 11  neuroblast NB4-1 (Chu et al., 1998)  embryonic stage | stage >=10  central nervous system | restricted (Jimenez et al., 1995)  embryonic stage | stage >=13  posterior embryonic/larval midgut (Jimenez et al., 1995)  embryonic stage | stage 7-8  neurectoderm (Jimenez et al., 1995)  embryonic stage | stage 8-11  neuroblast | subset (Chu et al., 1998)  embryonic stage | stage 11  neuroblast NB2-2 (Chu et al., 1998)  embryonic stage | stage 11  neuroblast NB1-1 (Chu et al., 1998)  embryonic stage | stage >=13  anterior embryonic/larval midgut (Jimenez et al., 1995)  embryonic stage | stage 11  neuroblast NB6-2 (Chu et al., 1998)  embryonic stage | stage 11  neuroblast NB5-2 (Chu et al., 1998)  embryonic stage | stage 11  neuroblast NB3-1 (Chu et al., 1998)  embryonic stage | stage 11  neuroblast NB6-1 (Chu et al., 1998)  embryonic stage | stage 7,8  ventral midline (Jimenez et al., 1995)  embryonic stage | stage 11  neuroblast MP2 (Chu et al., 1998)  embryonic stage | stage 11  neuroblast NB5-1 (Chu et al., 1998)  embryonic stage | stage 11  neuroblast NB7-2 (Chu et al., 1998)  embryonic stage | stage 11  neuroblast NB7-1 (Chu et al., 1998)
Marker for
Subcellular Localization
CV Term
Summary of Polypeptide Expression
Stage Tissue/Position Reference  embryonic stage | stage 11  pCC neuron (McDonald et al., 1998)  embryonic stage | stage 11  U neuron (McDonald et al., 1998)  embryonic stage | stage 11  embryonic neuron | subset (McDonald et al., 1998)  embryonic stage | stage 8-9  neuroblast | subset (McDonald et al., 1998)  embryonic stage | stage 9-11  procephalic neuroblast | subset & ventral (Urbach and Technau, 2003)  embryonic stage | stage 9-11  protocerebral neuroblast | subset (Urbach and Technau, 2003)  embryonic stage | stage 9-11  tritocerebral neuroblast | subset (Urbach and Technau, 2003)  embryonic stage | stage 8  ventral midline (McDonald et al., 1998)  embryonic stage | stage 9-11  neurectoderm & embryonic antennal segment | ventral & restricted (Urbach and Technau, 2003)  embryonic stage | stage 9-11  deuterocerebral neuroblast | subset (Urbach and Technau, 2003)  embryonic stage | stage 8-9  neurectoderm | restricted (McDonald et al., 1998)  embryonic stage | stage 9-11  neurectoderm & embryonic intercalary segment | ventral & restricted (Urbach and Technau, 2003)  embryonic stage | stage 9-11  neurectoderm & embryonic acron | ventral & restricted (Urbach and Technau, 2003)  embryonic stage | cellular blastoderm   (McDonald et al., 1998)
Marker for
	pCC neuron
Subcellular Localization
CV Term
External Data & Images
Linkouts	FLIGHT - Cell culture data for RNAi and other high-throughput technologies • FBgn0003986 FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array • FBgn0003986 GEO (NCBI) - Gene expression data: microarray and other high-throughput technologies • FBgn0003986
Alleles & Phenotypes
Summary of Allele Phenotypes
Lethality Allele lethal | recessive vnd25 vnd27 lethal | partially | recessive vnd4 lethal | embryonic stage vnd19 vnd1 vndhs.PM lethal | embryonic stage | recessive vnd1 vnd24 vnd27 vnd28 vnd2 vnd3 vnd5 vnd6 lethal | embryonic stage, with Scer\GAL4Kr.PM vndScer\UAS.cMa lethal | embryonic stage, with Scer\GAL4sca-109-68 vndScer\UAS.cMa lethal, with Scer\GAL4Kr.PM vndScer\UAS.cKa vndY54M.Scer\UAS vndΔNK-2box.Scer\UAS vndΔacidic.Scer\UAS vndΔtinman.Scer\UAS Other Phenotypes Allele cell death increase | embryonic stage vnd6 neuroanatomy defective vnd1 vnd5 vndD38 vndS1 neuroanatomy defective | embryonic stage vnd6 neuroanatomy defective | embryonic stage, with Scer\GAL4sca-537.4 vndScer\UAS.cCa Phenotype manifest in Allele central nervous system vnd1 vndS1 ventral nervous system vnd5 neuroblast NB7-1 vnd6 neuroblast MP2 vnd6 neuroblast NB2-2 vnd6 neuroblast NB3-2 vnd6 neuroblast NB5-2 vnd6 neuroblast NB5-3 vnd6 fascicle vnd6 vndhs.PM commissure vnd6 vndhs.PM ventral nerve cord vnd6 vndhs.PM motor neuron vnd6 embryonic neuroblast | ventral vnd6 RP2 neuron vnd6 vndD38 RP2sib neuron vnd6 muscle founder cell vnd6 ventral oblique muscle vnd6 abdominal ventral longitudinal muscle 4 vnd6 embryonic tritocerebrum vnd6 embryonic deutocerebrum vnd6 embryonic glial cell vnd6 ventral tritocerebral neuroblast vnd6 embryonic foregut vnd6 Pcv6 neuroblast & stage 9 embryo vnd6 Pcv3 neuroblast & stage 9 embryo vnd6 Pcv1 neuroblast & stage 9 embryo vnd6 Pcv7 neuroblast & stage 9 embryo vnd6 Ppv2 neuroblast & stage 9 embryo vnd6 Dv2 neuroblast & stage 9 embryo vnd6 Dv3 neuroblast & stage 9 embryo vnd6 Dv6 neuroblast & stage 9 embryo vnd6 Dd1 neuroblast & stage 9 embryo vnd6 Pcv6 neuroblast & stage 11 embryo vnd6 Pcv8 neuroblast & stage 11 embryo vnd6 Pcv5 neuroblast & stage 11 embryo vnd6 Pcv2 neuroblast & stage 11 embryo vnd6 Pcv3 neuroblast & stage 11 embryo vnd6 Pcv7 neuroblast & stage 11 embryo vnd6 Pcv4 neuroblast & stage 11 embryo vnd6 Pcv1 neuroblast & stage 11 embryo vnd6 Pav1 neuroblast & stage 11 embryo vnd6 Pad1 neuroblast & stage 11 embryo vnd6 Ppv1 neuroblast & stage 11 embryo vnd6 Ppv2 neuroblast & stage 11 embryo vnd6 Ppv3 neuroblast & stage 11 embryo vnd6 Dv5 neuroblast & stage 11 embryo vnd6 Dv1 neuroblast & stage 11 embryo vnd6 Dv3 neuroblast & stage 11 embryo vnd6 Dv6 neuroblast & stage 11 embryo vnd6 Dv7 neuroblast & stage 11 embryo vnd6 Dv2 neuroblast & stage 11 embryo vnd6 Dv4 neuroblast & stage 11 embryo vnd6 Dv8 neuroblast & stage 11 embryo vnd6 Tv2 neuroblast & stage 11 embryo vnd6 Tv3 neuroblast & stage 11 embryo vnd6 Tv4 neuroblast & stage 11 embryo vnd6 Tv5 neuroblast & stage 11 embryo vnd6 Td1 neuroblast & stage 11 embryo vnd6 Td2 neuroblast & stage 11 embryo vnd6 Td3 neuroblast & stage 11 embryo vnd6 Dd1 neuroblast & stage 11 embryo vnd6 Dd2 neuroblast & stage 11 embryo vnd6 Tv1 neuroblast & stage 11 embryo vnd6 embryonic deutocerebrum & stage 11 embryo vnd6 embryonic protocerebrum & stage 11 embryo vnd6 embryonic glial cell | supernumerary & embryonic deutocerebrum & stage 12 embryo vnd6 embryonic glial cell | supernumerary & embryonic tritocerebrum & stage 12 embryo vnd6 neuroblast NB6-1 vndD38 neuroblast NB4-1 vndD38 medial ventral neurectoderm vndD38 dMP2 neuron vndD38 vMP2 neuron vndD38 aCC neuron vndD38 vndhs.PM pCC neuron vndD38 vndhs.PM neuroblast vndS1 muscle founder cell | ectopic, with Scer\GAL469B vndScer\UAS.cCa neuroblast of ventral nerve cord primordium | ectopic, with Scer\GAL469B vndScer\UAS.cCa aCC neuron, with Scer\GAL4sca-537.4 vndScer\UAS.cCa pCC neuron, with Scer\GAL4sca-537.4 vndScer\UAS.cCa RP2 neuron, with Scer\GAL4sca-537.4 vndScer\UAS.cCa embryonic glial cell & embryonic deutocerebrum & stage 12 embryo, with Scer\GAL4sca-537.4 vndScer\UAS.cCa embryonic glial cell & embryonic tritocerebrum & stage 12 embryo, with Scer\GAL4sca-537.4 vndScer\UAS.cCa embryonic glial cell & embryonic protocerebrum & stage 12 embryo, with Scer\GAL4sca-537.4 vndScer\UAS.cCa U neuron, with Scer\GAL4Kr.PM vndScer\UAS.cCa aCC neuron, with Scer\GAL4Kr.PM vndScer\UAS.cCa pCC neuron, with Scer\GAL4Kr.PM vndScer\UAS.cCa RP2 neuron, with Scer\GAL4Kr.PM vndScer\UAS.cCa fascicle, with Scer\GAL4sca-109-68 vndScer\UAS.cMa ventral nerve cord, with Scer\GAL4sca-109-68 vndScer\UAS.cMa commissure, with Scer\GAL4sca-109-68 vndScer\UAS.cMa CNS glial cell, with Scer\GAL4sca-109-68 vndScer\UAS.cMa fascicle, with Scer\GAL4Kr.PM vndScer\UAS.cMa ventral nerve cord, with Scer\GAL4Kr.PM vndScer\UAS.cMa commissure, with Scer\GAL4Kr.PM vndScer\UAS.cMa CNS glial cell, with Scer\GAL4Kr.PM vndScer\UAS.cMa embryonic central nervous system, with Scer\GAL4elav.PLu vndScer\UAS.cMa U neuron vndhs.PM
Classical Alleles ( 33 )
For All Classical Alleles Show
Allele of vnd Class Mutagen Stocks Known lesion vnd101 0 -- vnd10 ethyl methanesulfonate 0 -- vnd11 ethyl methanesulfonate 0 -- vnd12 ethyl methanesulfonate 0 -- vnd13 ethyl methanesulfonate 0 -- vnd14 ethyl methanesulfonate 0 -- vnd15 methyl methanesulfonate 0 -- vnd16 methyl methanesulfonate 0 -- vnd17 triethylenemelamine 0 -- vnd18 X ray 0 -- vnd19 X ray 0 Yes vnd1 ethyl methanesulfonate 0 -- vnd20 X ray 0 -- vnd21 X ray 0 -- vnd22 X ray 0 -- vnd23 X ray 0 -- vnd24 ethyl methanesulfonate 0 -- vnd25 ethyl methanesulfonate 0 -- vnd26 ethyl methanesulfonate 0 -- vnd27 spontaneous 0 -- vnd28 ethyl nitrosourea 0 -- vnd29 ethyl nitrosourea 0 Yes vnd2 ethyl methanesulfonate 0 -- vnd30 hypomorph 0 Yes vnd3 ethyl methanesulfonate 0 -- vnd4 hypomorph ethyl methanesulfonate 0 -- vnd5 ethyl methanesulfonate 0 -- vnd6 loss of function ethyl methanesulfonate 0 -- vnd7 ethyl methanesulfonate 0 -- vnd8 ethyl methanesulfonate 0 -- vnd9 ethyl methanesulfonate 0 -- vndD38 P-element activity 0 Yes vndS1 loss of function 0 --
Alleles Carried on Transgenic Constructs ( 41 )
For All Alleles Carried on Transgenic Constructs Show
Allele of vnd Class Mutagen Stocks Known lesion vndGD4406 in vitro construct | RNAi in vitro construct | regulatory fusion 1 Yes vndHD.MNPV(Op)\IE-2.T:Ivir\HA1 in vitro construct | deletion 0 Yes vndILL163AAA.MNPV(Op)\IE-2.T:Ivir\HA1 in vitro construct | site directed mutagenesis 0 Yes vndMNPV(Op)\IE-2.T:Ivir\HA1 in vitro construct | regulatory fusion in vitro construct | coding region fusion 0 Yes vndN3Δ294-544ΔC-term.MNPV(Op)\IE-2.T:Ivir\HA1 in vitro construct | deletion 0 Yes vndN3Δ394-505.MNPV(Op)\IE-2.T:Ivir\HA1 in vitro construct | deletion 0 Yes vndN3Δ505-534.MNPV(Op)\IE-2.T:Ivir\HA1 in vitro construct | deletion 0 Yes vndN3Δ619-723.MNPV(Op)\IE-2.T:Ivir\HA1 in vitro construct | deletion 0 Yes vndN595A.MNPV(Op)\IE-2.T:Ivir\HA1 in vitro construct | site directed mutagenesis 0 Yes vndRD-Hom.MNPV(Op)\IE-2.T:Ivir\HA1 in vitro construct | deletion 0 Yes vndScer\UAS.cCa in vitro construct | regulatory fusion 0 Yes vndScer\UAS.cKa in vitro construct | regulatory fusion 0 Yes vndScer\UAS.cMa in vitro construct | regulatory fusion 0 Yes vndW155A.MNPV(Op)\IE-2.T:Ivir\HA1 in vitro construct | site directed mutagenesis 0 Yes vndW158A.F155A.MNPV(Op)\IE-2.T:Ivir\HA1 in vitro construct | site directed mutagenesis 0 Yes vndW158A.MNPV(Op)\IE-2.T:Ivir\HA1 in vitro construct | site directed mutagenesis 0 Yes vndW166A.MNPV(Op)\IE-2.T:Ivir\HA1 in vitro construct | site directed mutagenesis 0 Yes vndY54M.Scer\UAS in vitro construct | site directed mutagenesis 0 Yes vndhs.PM in vitro construct | regulatory fusion 0 Yes vndΔ1-194.MNPV(Op)\IE-2.T:Ivir\HA1 in vitro construct | deletion 0 Yes vndΔ1-208.MNPV(Op)\IE-2.T:Ivir\HA1 in vitro construct | deletion 0 Yes vndΔ1-277.MNPV(Op)\IE-2.T:Ivir\HA1 in vitro construct | deletion 0 Yes vndΔ1-307.MNPV(Op)\IE-2.T:Ivir\HA1 in vitro construct | deletion 0 Yes vndΔ1-344.MNPV(Op)\IE-2.T:Ivir\HA1 in vitro construct | deletion 0 Yes vndΔ1-392.MNPV(Op)\IE-2.T:Ivir\HA1 in vitro construct | deletion 0 Yes vndΔ1-97.MNPV(Op)\IE-2.T:Ivir\HA1 in vitro construct | deletion 0 Yes vndΔ167-277.MNPV(Op)\IE-2.T:Ivir\HA1 in vitro construct | deletion 0 Yes vndΔ194-277.MNPV(Op