SELECTION [X]
Zoom in
Recenter on this region
Dump selection as FASTA
Submit selection to UCSC BLAT
Submit selection to NCBI BLAST

Maize B73 RefGen_v2: 3.009 kbp from Chr1:128,236..131,244

The region shown in the Genome Browser window below lies at approximately (Unknown) cM on the ISU Integrated IBM 2009 genetic map for chromosome ?. This region (from to bp) represents cM.

Close X
Markers used to generate the map reported in Liu et al. 2009 were used to estimate cM per bp. The full map is also available at MaizeGDB. For this calculation, markers were ignored in regions where RefGen_v2 and the genetic map were not collinear. The full dataset used for this calculation is available here. Markers removed from the original Liu et al. dataset are available as a list here

Map positions reported are the centimorgan coordinate for the left side of the genome browser window shown below.

Regions at chromosome tips are reported as 0 cM. Regions smaller than 1 cM are reported as <1 cM. If the reported region is <1 cM, zoom out or check the "Segments of known genetic distance" track for more precise estimates.

Browser Select Tracks Snapshots Community Tracks Custom Tracks Preferences

Search

Landmark or Region : Examples : Chr1:34,400..230,000, Chr2:2,000,000..4,000,000, Chr3:194343000..194350000, UNMAPPED:34,400..530,000, Centromere1, GRMZM2G100969, GRMZM5G859979, GRMZM5G816453, MAGIv4.0_76504, AC177838.2, GRMZM2G104572_T01, GRMZM2G089944, Chr1:2993000..3044000, mu-illumina_11900, Mt:59000..86000, Cp:90000..130000, MIR2118e, K4L2.
Data Source	Scroll/Zoom: Flip

Overview

Region

Details

MAGI [from the Schnable Lab]

B73 RefGen_v2 Gene Models: Filtered Gene Set (green) and Working Gene Set (yellow) [from MaizeSequence.org]

Bins

Clear highlighting

<< Back to Browser Show Favorites Only

Clear All Favorites

Tracks

Community Tracks

[Add]

outGFF10.gff

uploaded by an anonymous user
public

No description

Source files:

outGFF10.gff Fri Apr 19 13:31:57 2013 980033 bytes
Configuration Fri Apr 19 13:36:44 2013 973 bytes

[Add]

Canonical TATA box motifs

uploaded by Carson Andorf <carson.andorf@gmail.com>
public

This track was created by finding the canonical TATA box motif (TATAWA) within the first 300 bases upstream from the transcriptional start site (TSS) of a gene model in the filtered gene set (Carson Andorf-MaizeGDB).

Source files:

http_ftp.maizegdb.org_FTP_Private_gff_tata.gff Fri Jul 20 11:57:33 2012 3401340 bytes
Configuration Fri Jul 20 11:59:41 2012 959 bytes

anti-CENH3 ChIP [from Jiang/Presting] [?]	FPC Contig [?]	Nucleosome Occupancy Likelihood (FSU HsA375.ZmB73rg2) [from Bass & Dennis, FSU] [?]
B73 RefGen_v2 [from MGSC and AGI] [?] [ showing 2/2 subtracks ]	Gaps in the B73 RefGen_v2 [from MGSC and AGI] [?]	Reconstructed Chromosomes from the Maize Tetraploidy [from J. Schnable and M. Freeling] [?]
Bins [?]	GSS_PlantGDB [?]
Centromere [from Jiang/Presting] [?]	Knobs [?]

HapMap1 [from Panzea] [?]	ISU SNPs mapped on 291 IBM RILs [Liu et al. 2010, Genetics] [?]	Palomero Toluqueño contigs [CINVESTAV-Langebio] [?]
HapMap2 [from Panzea] [?]	Mo17 SNPs and Indels [from JGI] [?]

5' Methylcytosine Methylation in B73 and Mo17 [?] [ showing 2/2 subtracks ]	ESTs [from PlantGDB] [?]	Microarray Probes at PLEXdb [aligned by PlantGDB] [?]
Affymetrix Maize100WT Probe Sets [from the Wise group/PLEXdb] [?]	Genome-wide Atlas Expression Across Tissues by Probe [PLEXdb/MaizeGDB Collaboration] [?]	Microarray-based Genome-wide Expression Atlas [NimbleGen from the Kaeppler Group, PLEXdb/MaizeGDB Collaboration] [?]
Affymetrix Maize100WT Probes [from the Wise group/PLEXdb] [?]	Genome-wide Atlas Maximum Mean Normalized Expression by Probe [PLEXdb/MaizeGDB Collaboration] [?]	miRNA [from mirBASE] [?]
Affymetrix Maize100WT Source Sequence [from the Wise group/PLEXdb; assembly B73 RefGen_v1 and MaizeSequence.org annotations 4.53a] [?]	Genome-wide Expression Atlas Coefficient of Variation by Probe [PLEXdb/MaizeGDB Collaboration] [?]	PlantGDB Unique Transcripts (PUTs) [?]
Agilent Microarray Annotation and Expression [?] [ showing 4/4 subtracks ]	IBM SAM eQTL Data [from the Muehlbauer lab - SAM Group] [?]	Shoot Apical Meristem at Six Stages [from the Scanlon lab - SAM Group] [?]
cDNA [from PlantGDB] [?]	KNOTTED1 Binding Regions [?] [ showing 2/2 subtracks ]

B73 RefGen_v2 Gene Models: Filtered Gene Set (green) and Working Gene Set (yellow) [from MaizeSequence.org] [?]	Community Annotations via DAS [ZmGDB] [?]	Sorghum-B73 Syntenic Genes [?] [ showing 2/2 subtracks ]
B73 RefGen_v2 Gene Models: Quality (ZmGDB_v175 Gene Models) [?]	MAGI [from the Schnable Lab] [?]	Split Genes [?]
Chloroplast genes (strain Inrakorn) [?]	Mitochondrial genes (strain NB) [?]

Ac/Ds [Brutnell and Vollbrecht, via PlantGDB] [?]	Heritable Mu Insertions [from the Mu-Illumina Group] [?]
Ac/Ds [from the Dooner Lab] [?]	UniformMu (Release 4.6) [from the UniformMu Group] [?]

Maize B73 RefGen_v2: 3.009 kbp from Chr1:128,236..131,244

Snapshots

Snapshot Name

Snapshot Timestamp [GMT]

Community Tracks

outGFF10.gff

Canonical TATA box motifs

Custom Tracks

Show grid	Image Width 450 640 800 1024	Highlight feature(s) (feature1 feature2...) Clear highlighting
Cache tracks		Highlight regions (region1:start..end region2:start..end) Clear highlighting
Show tooltips		Region Size (bp)