Difference between revisions of "FlyBase:Maps"

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FlyBase offers a downloadable [http://flybase.org/w/images/a/a2/DmelMapTable.xlsx '''spreadsheet'''] that lists the genomic coordinates, cytological (polytene band) position and genetic map position for all annotated D. melanogaster genes. Information for each chromosome arm is available on a separate tab of the spreadsheet. For both cytological and genetic map positions, we report both experimentally determined values reported in the literature as well as FlyBase computational estimates. For genetic map positions, we also provide an alternative computational estimate based on the mapping of millions of SNPs from thousands or recombination events [http://flybase.org/reports/FBrf0219727 '''Comeron et. al., 2012'''].
 
FlyBase offers a downloadable [http://flybase.org/w/images/a/a2/DmelMapTable.xlsx '''spreadsheet'''] that lists the genomic coordinates, cytological (polytene band) position and genetic map position for all annotated D. melanogaster genes. Information for each chromosome arm is available on a separate tab of the spreadsheet. For both cytological and genetic map positions, we report both experimentally determined values reported in the literature as well as FlyBase computational estimates. For genetic map positions, we also provide an alternative computational estimate based on the mapping of millions of SNPs from thousands or recombination events [http://flybase.org/reports/FBrf0219727 '''Comeron et. al., 2012'''].
  
−
= D. melanogaster Chromosome Images =
+
= D. melanogaster Chromosome Maps =
  
 
In progress - files will be available shortly.
 
In progress - files will be available shortly.
  
 +
Table 1. The original illustrations of D. melanogaster polytene chromosomes by Bridges and Slizynski.
 
{| class="wikitable sortable"
 
{| class="wikitable sortable"
 
|-
 
|-
−
! Species !! Chromosome !! Muller Element !! illustration !! micrograph !! annotation !! References !! File !! Comments
+
! Species !! Chromosome !! Muller Element !! References !! File
 
|-
 
|-
−
| style="white-space: nowrap;" | D. melanogaster || X || A || yes || no || no || [http://flybase.org/reports/FBrf0004055 '''Bridges 1938'''], [http://flybase.org/reports/FBrf0003150 '''Bridges 1935'''] || [[:File:Dmel_X_Bridges.png]] || Original illustrations.
+
| style="white-space: nowrap;" | D. melanogaster || X || A || [http://flybase.org/reports/FBrf0004055 '''Bridges 1938'''], [http://flybase.org/reports/FBrf0003150 '''Bridges 1935'''] || [[File:Dmel_X_Bridges.png]]
 
|-
 
|-
−
| D. melanogaster || 2L || B || yes || no || no || [http://flybase.org/reports/FBrf0005766 '''Bridges 1942'''], [http://flybase.org/reports/FBrf0003150 '''Bridges 1935'''] || [[:File:Dmel_2L_Bridges.png]] || Original illustrations.
+
| D. melanogaster || 2L || B || [http://flybase.org/reports/FBrf0005766 '''Bridges 1942'''], [http://flybase.org/reports/FBrf0003150 '''Bridges 1935'''] || [[File:Dmel_2L_Bridges.png]]
 
|-
 
|-
−
| D. melanogaster || 2R || C || yes || no || no || [http://flybase.org/reports/FBrf0004320 '''Bridges and Bridges 1939'''], [http://flybase.org/reports/FBrf0003150 '''Bridges 1935'''] || [[:File:Dmel_2R_Bridges.png]] || Original illustrations.
+
| D. melanogaster || 2R || C || [http://flybase.org/reports/FBrf0004320 '''Bridges and Bridges 1939'''], [http://flybase.org/reports/FBrf0003150 '''Bridges 1935'''] || [[File:Dmel_2R_Bridges.png]]
 
|-
 
|-
−
| D. melanogaster || 3L || D || yes || no || no || [http://flybase.org/reports/FBrf0005488 '''Bridges 1941'''], [http://flybase.org/reports/FBrf0003150 '''Bridges 1935'''] || [[:File:Dmel_3L_Bridges.png]] || Original illustrations.
+
| D. melanogaster || 3L || D || [http://flybase.org/reports/FBrf0005488 '''Bridges 1941'''], [http://flybase.org/reports/FBrf0003150 '''Bridges 1935'''] || [[File:Dmel_3L_Bridges.png]]
 
|-
 
|-
−
| D. melanogaster || 3R || E || yes || no || no || [http://flybase.org/reports/FBrf0005486 '''Bridges 1941'''], [http://flybase.org/reports/FBrf0003150 '''Bridges 1935'''] || [[:File:Dmel_3R_Bridges.png]] || Original illustrations.
+
| D. melanogaster || 3R || E || [http://flybase.org/reports/FBrf0005486 '''Bridges 1941'''], [http://flybase.org/reports/FBrf0003150 '''Bridges 1935'''] || [[File:Dmel_3R_Bridges.png]]
 
|-
 
|-
−
| D. melanogaster || 4 || F || yes || no || no || [http://flybase.org/reports/FBrf0006183 '''Slizynski 1944'''] || [[:File:Dmel_4_Slizynski.png]] || Original illustrations.
+
| D. melanogaster || 4 || F || [http://flybase.org/reports/FBrf0006183 '''Slizynski 1944'''] || [[File:Dmel_4_Slizynski.png]]
 +
|}
 +
 
 +
 
 +
Table 2. The original electron micrographs of D. melanogaster polytene chromosomes by Lefevre. High magnification electron micrographs of individual D. melanogaster polytene chromosome bands are available from [http://www.helsinki.fi/~saura/EM/index.html '''Saura, Saura and Sorsa'''], University of Helsinki. These electron micrographs offer an alternative reference for checking polytene band references.
 +
{| class="wikitable sortable"
 +
|-
 +
! Species !! Chromosome !! Muller Element !! References !! File
 +
|-
 +
| D. melanogaster || X || A || [http://flybase.org/reports/FBrf0028326.html '''Lefevre 1976'''] || [[File:Dmel_X_Lefevre.png]]
 
|-
 
|-
−
| D. melanogaster || X || A || yes || yes || no || [http://flybase.org/reports/FBrf0028326.html '''Lefevre 1976'''] || [[:File:Dmel_X_Lefevre.png]] || Original electron micrographs.
+
| D. melanogaster || 2L || B || [http://flybase.org/reports/FBrf0028326.html '''Lefevre 1976'''] || [[File:Dmel_2L_Lefevre.png]]
 
|-
 
|-
−
| D. melanogaster || 2L || B || yes || yes || no || [http://flybase.org/reports/FBrf0028326.html '''Lefevre 1976'''] || [[:File:Dmel_2L_Lefevre.png]] || Original electron micrographs.
+
| D. melanogaster || 2R || C || [http://flybase.org/reports/FBrf0028326.html '''Lefevre 1976'''] || [[File:Dmel_2R_Lefevre.png]]
 
|-
 
|-
−
| D. melanogaster || 2R || C || yes || yes || no || [http://flybase.org/reports/FBrf0028326.html '''Lefevre 1976'''] || [[:File:Dmel_2R_Lefevre.png]] || Original electron micrographs.
+
| D. melanogaster || 3L || D || [http://flybase.org/reports/FBrf0028326.html '''Lefevre 1976'''] || [[File:Dmel_3L_Lefevre.png]]
 
|-
 
|-
−
| D. melanogaster || 3L || D || yes || yes || no || [http://flybase.org/reports/FBrf0028326.html '''Lefevre 1976'''] || [[:File:Dmel_3L_Lefevre.png]] || Original electron micrographs.
+
| D. melanogaster || 3R || E || [http://flybase.org/reports/FBrf0028326.html '''Lefevre 1976'''] || [[File:Dmel_3R_Lefevre.png]]
 
|-
 
|-
−
| D. melanogaster || 3R || E || yes || yes || no || [http://flybase.org/reports/FBrf0028326.html '''Lefevre 1976'''] || [[:File:Dmel_3R_Lefevre.png]] || Original electron micrographs.
+
| D. melanogaster || 4 || F || [http://flybase.org/reports/FBrf0028326.html '''Lefevre 1976'''] || [[File:Dmel_4_Lefevre.png]]
 +
|}
 +
 
 +
 
 +
Table 3. Annotated D. melanogaster chromosome maps that combine illustrations and electron micrographs with annotation of the genomic, genetic and cytological positions indicated for select genes. Note that for the Y chromosome, the micrograph shown is of a prometaphase mitotic chromosome. Note also that large genome assembly gaps are not depicted in GBrowse, and so Y chromosome genes look closer together than they really are.
 +
{| class="wikitable sortable"
 
|-
 
|-
−
| D. melanogaster || 4 || F || yes || yes || no || [http://flybase.org/reports/FBrf0028326.html '''Lefevre 1976'''] || [[:File:Dmel_4_Lefevre.png]] || Original electron micrographs.
+
! Species !! Chromosome !! Muller Element !! References !! File
 
|-
 
|-
−
| D. melanogaster || X || A || yes || yes || yes || . || [[:File:Dmel_X.png]] || Genomic, genetic and cytological positions indicated for select genes.
+
| D. melanogaster || X || A || . || [[File:Dmel_X.png]]
 
|-
 
|-
−
| D. melanogaster || 2L || B || yes || yes || yes || . || [[:File:Dmel_2L.png]] || Genomic, genetic and cytological positions indicated for select genes.
+
| D. melanogaster || 2L || B || . || [[File:Dmel_2L.png]]
 
|-
 
|-
−
| D. melanogaster || 2R || C || yes || yes || yes || . || [[:File:Dmel_2R.png]] || Genomic, genetic and cytological positions indicated for select genes.
+
| D. melanogaster || 2R || C || . || [[File:Dmel_2R.png]]
 
|-
 
|-
−
| D. melanogaster || 3L || D || yes || yes || yes || . || [[:File:Dmel_3L.png]] || Genomic, genetic and cytological positions indicated for select genes.
+
| D. melanogaster || 3L || D || . || [[File:Dmel_3L.png]]
 
|-
 
|-
−
| D. melanogaster || 3R || E || yes || yes || yes || . || [[:File:Dmel_3R.png]] || Genomic, genetic and cytological positions indicated for select genes.
+
| D. melanogaster || 3R || E || . || [[File:Dmel_3R.png]]
 
|-
 
|-
−
| D. melanogaster || 4 || F || yes || yes || yes || . || [[:File:Dmel_4.png]] || Genomic, genetic and cytological positions indicated for select genes.
+
| D. melanogaster || 4 || F || . || [[File:Dmel_4.png]]
 
|-
 
|-
−
| D. melanogaster || Y || . || yes || yes || yes || [http://flybase.org/reports/FBrf0036525.html '''Kennison 1981'''], [http://flybase.org/reports/FBrf0037663.html '''Hazelrigg et. al., 1982'''], [http://flybase.org/reports/FBrf0039037.html '''Gatti and Pimpinelli 1983'''] || [[:File:Dmel_Y.jpg]] || Sequence from big assembly gaps is not represented in the GBrowse view.
+
| D. melanogaster || Y || . || [http://flybase.org/reports/FBrf0036525.html '''Kennison 1981'''], [http://flybase.org/reports/FBrf0037663.html '''Hazelrigg et. al., 1982'''], [http://flybase.org/reports/FBrf0039037.html '''Gatti and Pimpinelli 1983'''] || [[File:Dmel_Y.jpg]]
 
|}
 
|}

Revision as of 17:56, 18 September 2015

Genetic, Cytological and Genomic Map Coordinates for D. melanogaster Genes

FlyBase offers a downloadable spreadsheet that lists the genomic coordinates, cytological (polytene band) position and genetic map position for all annotated D. melanogaster genes. Information for each chromosome arm is available on a separate tab of the spreadsheet. For both cytological and genetic map positions, we report both experimentally determined values reported in the literature as well as FlyBase computational estimates. For genetic map positions, we also provide an alternative computational estimate based on the mapping of millions of SNPs from thousands or recombination events Comeron et. al., 2012.

D. melanogaster Chromosome Maps

In progress - files will be available shortly.

Table 1. The original illustrations of D. melanogaster polytene chromosomes by Bridges and Slizynski.

Species Chromosome Muller Element References File
D. melanogaster X A Bridges 1938, Bridges 1935 File:Dmel X Bridges.png
D. melanogaster 2L B Bridges 1942, Bridges 1935 File:Dmel 2L Bridges.png
D. melanogaster 2R C Bridges and Bridges 1939, Bridges 1935 File:Dmel 2R Bridges.png
D. melanogaster 3L D Bridges 1941, Bridges 1935 File:Dmel 3L Bridges.png
D. melanogaster 3R E Bridges 1941, Bridges 1935 File:Dmel 3R Bridges.png
D. melanogaster 4 F Slizynski 1944 File:Dmel 4 Slizynski.png


Table 2. The original electron micrographs of D. melanogaster polytene chromosomes by Lefevre. High magnification electron micrographs of individual D. melanogaster polytene chromosome bands are available from Saura, Saura and Sorsa, University of Helsinki. These electron micrographs offer an alternative reference for checking polytene band references.

Species Chromosome Muller Element References File
D. melanogaster X A Lefevre 1976 File:Dmel X Lefevre.png
D. melanogaster 2L B Lefevre 1976 File:Dmel 2L Lefevre.png
D. melanogaster 2R C Lefevre 1976 File:Dmel 2R Lefevre.png
D. melanogaster 3L D Lefevre 1976 File:Dmel 3L Lefevre.png
D. melanogaster 3R E Lefevre 1976 File:Dmel 3R Lefevre.png
D. melanogaster 4 F Lefevre 1976 File:Dmel 4 Lefevre.png


Table 3. Annotated D. melanogaster chromosome maps that combine illustrations and electron micrographs with annotation of the genomic, genetic and cytological positions indicated for select genes. Note that for the Y chromosome, the micrograph shown is of a prometaphase mitotic chromosome. Note also that large genome assembly gaps are not depicted in GBrowse, and so Y chromosome genes look closer together than they really are.

Species Chromosome Muller Element References File
D. melanogaster X A . File:Dmel X.png
D. melanogaster 2L B . File:Dmel 2L.png
D. melanogaster 2R C . File:Dmel 2R.png
D. melanogaster 3L D . File:Dmel 3L.png
D. melanogaster 3R E . File:Dmel 3R.png
D. melanogaster 4 F . Dmel 4.png
D. melanogaster Y . Kennison 1981, Hazelrigg et. al., 1982, Gatti and Pimpinelli 1983 Dmel Y.jpg
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