Gene Dmel\bcd
| General Information | ||||
|---|---|---|---|---|
| Symbol | Dmel\bcd | Species | D. melanogaster | |
| Name | bicoid | Annotation symbol | CG1034 | |
| Feature type | protein_coding_gene | FlyBase ID | FBgn0000166 | |
| Created / Updated | 2003-12-01/2008-06-23 | |||
| Genomic Location | ||||
| Chromosome (arm) | 3R | Recombination map | 3-48 | |
| Cytogenetic map | 84A5-84A5 | Sequence location | 3R:2,581,564..2,585,199 [-] | |
| Map ( GBrowse ) |
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Summary Information
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Automatically generated summary
See sections below for more information | The gene bicoid is referred to in FlyBase by the symbol bcd (CG1034, FBgn0000166). It has the cytological map location 84A5. Its sequence location is 3R:2581564..2585199. Its molecular function is described as: specific RNA polymerase II transcription factor activity; morphogen activity; protein binding; translation regulator activity; sequence-specific DNA binding; transcription factor activity. It is involved in the biological processes: anterior region determination; segment polarity determination; determination of anterior/posterior axis, embryo; regulation of transcription, DNA-dependent; maternal determination of anterior/posterior axis, embryo; regulation of transcription from RNA polymerase II promoter; anterior/posterior axis specification; negative regulation of translation; oogenesis; regulation of translation. 413 alleles are reported. The phenotypes of these alleles are annotated with 61 unique terms, many of which group under: embryonic abdomen; embryonic segment; organ system; abdominal ventral denticle belt; cephalopharyngeal skeleton; thoracic segment; larval abdominal segment; embryonic tagma; spiracle; embryonic head. It has 5 annotated transcripts and 5 annotated polypeptides. | |||
| External Summaries | ||||
Phenotypic Description from the Red Book (Lindsley & Zimm 1992)
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| Gene/Allele symbols may differ from current usage | bcd: bicoid
Maternal-effect lethal mutations showing defective
head and thorax development. Females homozygous for strong
alleles produce embryos in which head and thorax are replaced
by duplicated telson, including anal plates, tuft, spiracles,
and filzkorper; however, no pole cells formed at the anterior
end. Deletions and fusions of anterior abdominal segments and
occasionally anterior abdominal segments in reversed polarity
are also observed. Strong alleles amorphic based on phenotypic similarities of embryos produced by homozygous and hemizygous females. Weak alleles result in pattern defects in
heads of embryos; lack only labral derivatives (median tooth,
dorsal bridge); intermediate weak genotypes produce reduced
head but retain normal thoracic development; intermediate
strong produce further reduction of head, deletion of second
and third and reduction of first thoracic dentical belts;
thoracic segments fused. Partial rescue of embryonic phenotype effected by injection of cytoplasm (5% of volume) from
the anterior ends of unfertilized wild-type eggs into the
anterior pole of newly fertilized eggs of bcd mothers; injection into ectopic sites stimulates differentiation of anterior
structures at site of injection; efficiency proportional to
number of bcd+ alleles carried by cytoplasm donor. Phenocopies result from leakage of 5% of egg volume from anterior
perforation of normal embryos. The distance of the head fold
at gastrulation is proportional to the number of bcd+ alleles
in the maternal genotype. bcd mRNA appears as a flattened
disc plastered to the anterior extremity of early embryos; by
the time of pole cell migration it has become localized to the
clear cytoplasm at the periphery, forming a cap over the anterior end of the egg and is distributed in a steeply decreasing
gradient such that 90% of the RNA is in the anterior 18% of
egg length; by nuclear cycle 14 the RNA begins to disappear
and becomes undetectable by midway through cellularization.
bcd protein on the other hand forms a shallower gradient in
which 57% of protein is in the anterior 18% of egg length, and
the gradient doesn't reach baseline until the posterior 30% of
egg length; the gradient forms from two to four hours after
oviposition in both fertilized and unfertilized eggs, and
except during mitosis is concentrated in nuclei; diffusion
postulated to account for the establishment of the protein
gradient following translation from anteriorly anchored RNA.
Protein levels decrease during cellularization, although some
nuclear staining persists until the end of germ-band elongation. bcd transcript first detectable in the ovaries of bcd
females; forms a ring around the anterior margin of the
developing oocyte in stages 5 and 6; in stages 9 and 10
nurse-cell accumulation observed to be localized toward the
periphery of the cyst; by stage 12 the nurse cells have emptied their contents into the oocyte and the bcd transcript
appears as an anterior cap (St. Johnston, Driever, Berleth,
Richstein, and Nusslein-Volhard, 1989, Development
Supplement: 13-19). No evidence of translation of bcd protein during oogenesis. Formation of the bcd gradient is regulated by three maternally active genes exu, sww, and stau; exu
appears necessary for nurse cell accumulation; sww is required
for anterior localization of bcd mRNA in the oocyte; and stau
appears to be involved in RNA localization in the embryo. A
defect in any of these functions results in little or no gradient of bcd activity. bcd in turn appears to control the
activity of anterior gene activity; specifically the anterior
pattern of hb expression is not observed and is replaced by a
mirror-image posterior hb stripe in bcd- embryos (Tautz, 1988,
Nature 332: 281-84; Schroder, Tautz, Seifertz, and Jackle,
1988, EMBO J. 7: 2881-87).
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Detailed Mapping Data
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| FlyBase Computed Cytological Location | ||||
Cytogenetic map Evidence for location 84A5-84A5
Limits computationally determined from genome sequence between P{PZ}pb04498 and P{lacW}l(3)L2100L2100
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| Experimentally Determined Cytological Location | ||||
Cytogenetic map Notes References 84A1-84A1 (determined by in situ hybridisation)
84A-84A (determined by in situ hybridisation)
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| Experimentally Determined Recombination Data | ||||
| Location | ||||
| Left of (cM) | ||||
| Right of (cM) | ||||
| Notes | ||||
| Molecular Map Data | ||||
Gene Order (in direction of increasing cytology)
References In direction of increasing cytology: bcd- anon-84Aa+ Gene Order (overall orientation not stated) References | ||||
Gene Model & Products
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Please see the
GBrowse view of
Dmel\bcd
for information on other features
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| Comments on Gene Model | ||||
Transcript Data
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| Annotated Transcripts | ||||
Name FlyBase ID RefSeq ID Length (nt) Associated CDS (aa) | ||||
| Additional Transcript Data & Comments | ||||
| Reported size (kB) | 2.4 (unknown) 2.6, 1.6 (northern blot, sequence analsyis) | |||
| Comments | ||||
| External Data | ||||
| Crossreferences | ||||
Polypeptide Data
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| Annotated Polypeptides | ||||
Name FlyBase ID
Predicted MW (kD)
Length (aa)
Theoretical pI
RefSeq ID
GenBank protein
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| Additional Polypeptide Data & Comments | ||||
| Reported size (kD) | 494 (aa) | |||
| Comments | The author compared the sequences of several Drosophila melanogater genes and one human gene with consensus RNA Recognition Motifs (RRM) to bcd protein sequence and identified a putative RRM. bcd protein is translated from in vitro transcribed bcd mRNA in wheat germ extract and rabit reticulocyte lysate and is expressed in Drosophila Scheider cells to yeild a 58 kD protein. Exchange of the bcd 5\\'\\' UTR for Xenopus beta-globin 5\\'\\' UTR yeilds higher protein levels in these translation systems. One of several products generated by alternative splicing. bcd protein regulates the expression of cad through translational repression by binding to the cad 3\\'\\'UTR at specific "bicoid binding regions" (BBR). Expression pattern analysis, UV crosslink assays and Schnieder cell co-transfection assays all conclude that the homeodomain of bcd protein is necessary and suffiecient for binding to the BBR of cad transcripts. bcd protein will supress translation of "BBR-containing"mRNAs. Antibodies recognize a doublet of proteins of 55kD and 57kD. The appearance of two bands is thought to be due to posttranslational modification because the 5aa difference between the two bcd proteins is not enough to account for the 2-3kD size difference. Both the cad protein
gradient and the hb transcript expression pattern are dependant upon the
homeodomain and the PEST domain of bcd protein. Deletions and mutations of
PEST sequences in the bcd coding region resulted in an inability to repress
cad expression in the anterior region of the embryo. Similar deltions result
is a loss of hb expression between 20 and 50% egg length in the anterior
expression domain. Thus, the deletional analysis of bcd protein domains
shows that the domain that is required for translational represssion of cad
is also required for transcriptional activation of hb. The bcd protein was expressed and purified from embryos, Drosophila Schneider cells, and E. coli. The bcd protein produced by embryos and Schneider cells was 58kD, while the protein from E. coli was 53kD,indicating that the protein produced in Drosophila was highly phosphorylated. Indeed, when bcd protein isolated from Drosophila embryos or cells was incubated with phosphatase prior to elecrtophoresis, the protein was resolved at 53kD. Both the cad protein gradient and the hb transcript expression pattern are dependant upon the homeodomain and the PEST domain of bcd protein. Deletions and mutations of PEST sequences in the bcd coding region resulted in an inability to repress cad expression in the anterior region of the embryo. Similar deltions result is a loss of hb expression between 20 and 50% egg length in the anterior expression domain. Thus, the deletional analysis of bcd protein domains shows that the domain that is required for translational represssion of cad is also required for transcriptional activation of hb. bcd protein is
expressed in yeast under the control of βestradiol in order to control the
amount of bcd protein produced. Cooperative binding to bcd response regions
on various lacZ reporter constructs was studied with transcription assays, in
vitro gel shift assays and foot print analysis. The bcd responsive region of
kni was used both in vitro and in vivo to ascertain the strength of bcd
binding sites. CAT assays with bcd protein expressed in Schneider cells show that bcd activates a promoter containing three copies of a bcd consensus sequence. Through studies both in vivo and in vitro it has been shown that the activation of transcription due to bcd is dependant upon the phosphorylation state of bcd protein. Phosphorylated bcd will not activate transcription, and the phosphorylation of bcd is dependant upon tor and phl. The expression pattern of genes downstream of bcd were analysed after egg ligation at various egg lengths. It was observed that the bcd protein gradient, as well as the cad protein gradient were blocked by egg ligation, and thus, the expression of downstream gap genes were altered. The authors suggest that alteration of the bcd protein gradient, alters the hb expression profile and in turn, through regulation by hb, Kr and kni expression domains are altered, consequently altering the domains of pair-rule gene expression. | |||
| External Data | ||||
| Linkouts | PANTHER
- Protein classification by function, families, and pathways
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| Crossreferences | InterPro
domains - A database of protein families, domains, and functional sites
• TRANSFAC
- Eukaryotic transcription factors, their genomic binding sites, and DNA-binding profiles
•
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Sequences Consistent with the Gene Model
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| DDBJ
/
EMBL / GenBank | DNA sequence Protein sequence Name | |||
| UniProtKB/Swiss-Prot | ||||
| UniProtKB/TrEMBL | ||||
| Maps to | ||||
| Does NOT map to | ||||
| Identified with | ||||
Mapped Features & Mutations
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Please see
GBrowse
or insertion reports for information on insertions of transgenic
constructs and features not listed here
Type Symbol & Location Additional Notes References complex substitution bcd[6] 3R:2,583,759..2,583,927 comment=A deletion of 169 bases and insertion of the bases TA. The net result is that bcd amino acids 156-494 are replaced by 55 out-of-frame amino acids. evidence=experimental deletion bcd[PRD-] 3R:2,584,835..2,584,993 comment=A deletion which removes the first 53 amino acids including the PRD domain. Exact boundaries including the location of the 5' end of the deletion unspecified in FBrf0049337. evidence=experimental deletion bcd[7] 3R:2,583,127..2,584,272 comment=Approximate location of bcd[7] deletion. bcd[7] is a small deletion of approximately 260bp. The 3' end of deletion was determined by SI nuclease mapping. The size of the deletion was determined by genomic southern analysis of HindIII digests. evidence=experimental linked_to=HindIII-HindIII_rfrag deletion bcd[11] 3R:2,583,989..2,584,021 comment=In-frame deletion of amino acids 125-135. evidence=experimental point mutation bcd[9] 3R:2,584,016..2,584,016 evidence=experimental na_change=C2584016T pr_change=L122F|bcd-PD,L51F|bcd-PE,L46F|bcd-PF,L127F|bcd -PG reported_na_change=C2393T reported_pr_change=L127F point mutation bcd[8] 3R:2,584,003..2,584,003 evidence=experimental na_change=C2584003T pr_change=S126L|bcd-PD,S55L|bcd-PE,S50L|bcd-PF,S131L|bcd -PG reported_na_change=C2406T reported_pr_change=S131L point mutation bcd[12] 3R:2,583,923..2,583,923 evidence=experimental na_change=C2583923T pr_change=Q153|bcd-PD,Q82|bcd-PE,Q77|bcd-PF,Q158|bcd -PG reported_na_change=C2486T reported_pr_change=Q158@ point mutation bcd[1] 3R:2,583,845..2,583,845 evidence=experimental na_change=C2583845T pr_change=Q179|bcd-PD,Q108|bcd-PE,Q103|bcd-PF,Q184|b cd-PG reported_na_change=C2564T reported_pr_change=Q184@ point mutation bcd[5] 3R:2,583,611..2,583,611 evidence=experimental na_change=C2583611T pr_change=Q257|bcd-PD,Q186|bcd-PE,Q181|bcd-PF,Q262|b cd-PG reported_na_change=C2798T reported_pr_change=Q262@ point mutation bcd[10] 3R:2,583,605..2,583,605 evidence=experimental na_change=C2583605T pr_change=Q259|bcd-PD,Q188|bcd-PE,Q183|bcd-PF,Q264|b cd-PG reported_na_change=C2804T reported_pr_change=Q264@ point mutation bcd[2] 3R:2,582,525..2,582,525 evidence=experimental na_change=T2582525A pr_change=L108H|bcd-PA,L448H|bcd-PD,L377H|bcd-PE,L372H|b cd-PF,L453H|bcd-PG reported_na_change=T3885A reported_pr_change=L453H protein binding site bcd-protein_bind-5 3R:2,585,015..2,585,027 bound_moiety=Sry-deltaXP comment=sdbsB evidence=experimental protein binding site bcd-protein_bind-6 3R:2,584,994..2,585,006 bound_moiety=Sry-deltaXP comment=sdbsA evidence=experimental protein binding site bcd-protein_bind-22 3R:2,581,738..2,582,217 protein binding site bcd-protein_bind-1 3R:2,581,894..2,581,946 protein binding site bcd-protein_bind-2 3R:2,581,894..2,581,946 regulatory region bcd-reg_element-1 3R:2,582,338..2,582,346 comment=nonamer RNA localization signal evidence=experimental regulatory region bcd-reg_element-2 3R:2,581,894..2,581,946 rescue fragment bcd[+t8.7] 3R:2,580,586..2,589,326 comment=Position of restriction fragment on reference sequence inferred by FlyBase curator evidence=experimental linked_to=EcoRI-EcoRI_rfrag | ||||
External Data
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| Linkouts | DEDB
- Drosophila exon database: splicing graphs
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| Crossreferences | ||||
Expression Data
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| FlyBase-Curated Data | ||||
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Transcript and Protein data | Please see the FlyBase Gene Expression Report for details of gene expression from the literature. | |||
Summary of Transcript Expression
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Stage Tissue/Position
Reference
oogenesis stage,adult stage | stage S5-S7
oocyte | anterior
oogenesis stage,adult stage
nurse cell
oogenesis stage,adult stage
nurse cell
embryonic stage | stage 4
embryonic stage | stage 4
embryonic stage | stage 1-2
oogenesis stage,adult stage
oocyte | anterior
oogenesis stage
ovary
oogenesis stage,adult stage
nurse cell
embryonic stage | stage 1-2
oogenesis stage | stage S10
ovary
embryonic stage
oogenesis stage,adult stage
oocyte | anterior
embryonic stage | 0-3.25 hr
whole organism
embryonic stage | early
embryonic stage | stage 3-4
embryonic stage
oogenesis stage | stage S10B
ovary ( | ||||
