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

File
Help

no error

no details

Maize B73 RefGen_v2: 195.6 kbp from Chr1:34,400..230,000

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

Warning Test2

Overview

Region

Details

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

Bins

Clear highlighting

<< Back to Browser Show Active Tracks Only Show Favorites Only

Clear All Favorites

Tracks

Assembly/Genome Features

All on All off

anti-CENH3 ChIP [from Jiang/Presting] [?]	Core Bin Markers [?]	Knobs [?]
B73 RefGen_v2 [from MGSC and AGI] [?] [ showing 2/2 subtracks ]	FPC Contig [?]	Nucleosome Occupancy Likelihood (FSU HsA375.ZmB73rg2) [from Bass & Dennis, FSU] [?]
Bins [?]	Gaps in the B73 RefGen_v2 [from MGSC and AGI] [?]	Pan Genome Sequence Anchors [From Lu et. al.(2015)] [?]
Centromere [from Jiang/Presting] [?]	GSS_PlantGDB [?]	Reconstructed Chromosomes from the Maize Tetraploidy [from J. Schnable and M. Freeling] [?]

Diversity

All on All off

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 (XIN 2013) [from JGI] [?]
Illumina MaizeSNP50 BeadChip [from Ganal et al 2011 and Bauer et al 2013] [?]	Mo17 SNPs and Indels [from JGI] [?]

Expression — proteins

All on All off

Fluorescent protein tags [from JCVI] [?]

Proteomics Atlas of B73 Seed Development [Maize Proteomics Project, UCSD]

All on All off

Non-modified peptides identified in B73 seed development [Maize Proteomics Project, UCSD] [?]

Phosphorylated Peptides identified in B73 seed development [Maize Proteomics Project, UCSD] [?]

Expression and Transcripts

All on All off

5' Methylcytosine Methylation in B73 and Mo17 [?] [ showing 2/2 subtracks ]	ESTs [from PlantGDB] [?]	Microarray-based Genome-wide Expression Atlas [NimbleGen from the Kaeppler Group, PLEXdb/MaizeGDB Collaboration] [?]
Affymetrix Maize100WT Probe Sets [from the Wise group/PLEXdb] [?]	Genome-wide Atlas Expression Across Tissues by Probe [PLEXdb/MaizeGDB Collaboration] [?]	miRNA [from mirBASE] [?]
Affymetrix Maize100WT Probes [from the Wise group/PLEXdb] [?]	Genome-wide Atlas Maximum Mean Normalized Expression by Probe [PLEXdb/MaizeGDB Collaboration] [?]	PlantGDB Unique Transcripts (PUTs) [?]
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] [?]	RNA-Seq based Expression Atlas in B73 [?]
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 ]

G4 Tracks

All on All off

All Maize G4v2 Motifs [?]	Patches [?] [ showing 2/2 subtracks ]
Genomic Feature Grouping [?] [ showing 2/2 subtracks ]	Published Gene-Related Grouping [?] [ showing 4/4 subtracks ]

Gene Models

All on All off

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) [?]

Genetic Map

All on All off

Genetically Mapped Illumina MaizeSNP50 [from Ganal et al 2011 and Bauer et al 2013] [?]

ISU Integrated IBM2009 Markers [from the Schnable Lab] [?]

Segments of Known Genetic Distance [?]

Insertions

All on All off

Ac/Ds [Brutnell and Vollbrecht, via acdstagging.org] [?]

Ac/Ds/GFP-Ds [from the Dooner Lab] [?]

UniformMu (Release 8.0) [from the UniformMu Group] [?]

Repetitive Elements

All on All off

MIPS Repeats [via MaizeSequence.org] [?]

Sirevirus LTR retrotransposon [from the Bioinformatics Analysis Team] [?] [ showing 9/9 subtracks ]

Snapshots

Snapshot Name

Snapshot Timestamp [GMT]

Community Tracks

Filter: Showing 0 files.

There are no available unused public available tracks. Select "Custom Tracks" to see ones you've already added to your session.

Custom Tracks

[Help with uploading custom tracks]

There are no tracks yet.

Add custom tracks : [From text] [From a URL] [From a file]

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)