Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctacattagctaattttgccatggctatagtactgcatactgtagaccattcccatggatgatttcttgagccttggtctgacatatctgataccaatagGTACGCTCATCTGCTGTCTTTGTGCCAGAACATCCTGGGAGGCCTGGGGAAAAATTTATGTTCACTTACTCAATTCGCATGTCAGTTCCAGAGGCATGCA

Basic information

species Zea mays
transcript GRMZM2G173354_T02
intron # 2
splice site 3'
intron type U2

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|211534671|gb|FL445689.1|FL445689
EST:     ATCCAGAAGCACCTCCATCATGCAGTTCAGCTGTTACAAATGGCATTAAG                         GTACGCTCATCTGCTGTCTTTGTGCCAGAACATCCTGGGAGGCCTGGGGAA
genomic: ATCCAGAAGCACCTCCATCATGCAGTTCAGCTGTTACAAATGGCATTAAGgtggtaattc ... ataccaatagGTACGCTCATCTGCTGTCTTTGTGCCAGAACATCCTGGGAGGCCTGGGGAA
EST: gi|148986479|gb|EE030223.2|EE030223
EST:     ATCCAGAAGCACCTCCATCATGCAGTTCAGCTGTTACAAATGGCATTAAG                         GTACGCTCATCTGCTGTCTTTGTGCCAGAACATCCTGGGAGGCCTGGGGAA
genomic: ATCCAGAAGCACCTCCATCATGCAGTTCAGCTGTTACAAATGGCATTAAGgtggtaattc ... ataccaatagGTACGCTCATCTGCTGTCTTTGTGCCAGAACATCCTGGGAGGCCTGGGGAA
EST: gi|94475660|gb|EB704618.1|EB704618
EST:     ATCCAGAAGCACCTCCATCATGCAGTTCAGCTGTTACAAATGGCATTAAG                         GTACGCTCATCTGCTGTCTTTGTGCCAGAACATCCTGGGAGGCCTGGGGAA
genomic: ATCCAGAAGCACCTCCATCATGCAGTTCAGCTGTTACAAATGGCATTAAGgtggtaattc ... ataccaatagGTACGCTCATCTGCTGTCTTTGTGCCAGAACATCCTGGGAGGCCTGGGGAA
EST: gi|101390441|gb|EB817155.1|EB817155
EST:     ATCCAGAAGCACCTCCATCATGCAGTTCAGCTGTTACAAATGGCATTAAG                         GTACGCTCATCTGCTGTCTTTGTGCCAGAACATCCTGGGAGGCCTGGGGAA
genomic: ATCCAGAAGCACCTCCATCATGCAGTTCAGCTGTTACAAATGGCATTAAGgtggtaattc ... ataccaatagGTACGCTCATCTGCTGTCTTTGTGCCAGAACATCCTGGGAGGCCTGGGGAA
EST: gi|30306849|gb|CD001522.1|CD001522
EST:     ATCCAGAAGCACCTCCATCATGCAGTTCAGCTGTTACAAATGGCATTAAG                         GTACGCTCATCTGCTGTCTTTGTGCCAGAACATCCTGGGAGGCCTGGGGAA
genomic: ATCCAGAAGCACCTCCATCATGCAGTTCAGCTGTTACAAATGGCATTAAGgtggtaattc ... ataccaatagGTACGCTCATCTGCTGTCTTTGTGCCAGAACATCCTGGGAGGCCTGGGGAA
EST: gi|71762381|gb|DR960318.1|DR960318
EST:     ATCCAGAAGCACCTCCATCATGCAGTTCAGCTGTTACAAATGGCATTAAG                         GTACGCTCATCTGCTGTCTTTGTGCCAGAACATCCTGGGAGGCCTGGGGAA
genomic: ATCCAGAAGCACCTCCATCATGCAGTTCAGCTGTTACAAATGGCATTAAGgtggtaattc ... ataccaatagGTACGCTCATCTGCTGTCTTTGTGCCAGAACATCCTGGGAGGCCTGGGGAA
EST: gi|78090335|gb|DV518709.1|DV518709
EST:     ATCCAGAAGCACCTCCATCATGCAGTTCAGCTGTTACAAATGGCATTAAG                         GTACGCTCATCTGCTGTCTTTGTGCCAGAACATCCTGGGAGGCCTGGGGAA
genomic: ATCCAGAAGCACCTCCATCATGCAGTTCAGCTGTTACAAATGGCATTAAGgtggtaattc ... ataccaatagGTACGCTCATCTGCTGTCTTTGTGCCAGAACATCCTGGGAGGCCTGGGGAA
EST: gi|86467750|gb|DY234120.1|DY234120
EST:     ATCCAGAAGCACCTCCATCATGCAGTTCAGCTGTTACAAATGGCATTAAG                         GTACGCTCATCTGCTGTCTTTGTGCCAGAACATCCTGGGAGGCCTGGGGAA
genomic: ATCCAGAAGCACCTCCATCATGCAGTTCAGCTGTTACAAATGGCATTAAGgtggtaattc ... ataccaatagGTACGCTCATCTGCTGTCTTTGTGCCAGAACATCCTGGGAGGCCTGGGGAA
EST: gi|78078858|gb|DV507270.1|DV507270
EST:     ATCCAGAAGCACCTCCATCATGCAGTTCAGCTGTTACAAATGGCATTAAG                         GTACGCTCATCTGCTGTCTTTGTGCCAGAACATCCTGGGAGGCCTGGGGAA
genomic: ATCCAGAAGCACCTCCATCATGCAGTTCAGCTGTTACAAATGGCATTAAGgtggtaattc ... ataccaatagGTACGCTCATCTGCTGTCTTTGTGCCAGAACATCCTGGGAGGCCTGGGGAA
EST: gi|211097822|gb|FL296746.1|FL296746
EST:     ATCCAGAAGCACCTCCATCATGCAGTTCAGCTGTTACAAATGGCATTAAG                         GTACGCTCATCTGCTGTCTTTGTGCCAGAACATCCTGGGAGGCCTGGGGAA
genomic: ATCCAGAAGCACCTCCATCATGCAGTTCAGCTGTTACAAATGGCATTAAGgtggtaattc ... ataccaatagGTACGCTCATCTGCTGTCTTTGTGCCAGAACATCCTGGGAGGCCTGGGGAA
EST: gi|26557637|gb|CA829872.1|CA829872
EST:     ATCCAGAAGCACCTCCATCATGCAGTTCAGCTGTTACAAATGGCATTAAG                         GTACGCTCATCTGCTGTCTTTGTGCCAGAACATCCTGGGAGGCCTGGGGAA
genomic: ATCCAGAAGCACCTCCATCATGCAGTTCAGCTGTTACAAATGGCATTAAGgtggtaattc ... ataccaatagGTACGCTCATCTGCTGTCTTTGTGCCAGAACATCCTGGGAGGCCTGGGGAA
EST: gi|76010764|gb|DT937934.1|DT937934
EST:     ATCCAGAAGCACCTCCATCATGCAGTTCAGCTGTTACAAATGGCATTAAG                         GTACGCTCATCTGCTGTCTTTGTGCCAGAACATCCTGGGAGGCCTGGGGAA
genomic: ATCCAGAAGCACCTCCATCATGCAGTTCAGCTGTTACAAATGGCATTAAGgtggtaattc ... ataccaatagGTACGCTCATCTGCTGTCTTTGTGCCAGAACATCCTGGGAGGCCTGGGGAA
EST: gi|60340433|gb|DN207406.1|DN207406
EST:     ATCCAGAAGCACCTCCATCATGCAGTTCAGCTGTTACAAATGGCATTAAG                         GTACGCTCATCTGCTGTCTTTGTGCCAGAACATCCTGGGAGGCCTGGGGAA
genomic: ATCCAGAAGCACCTCCATCATGCAGTTCAGCTGTTACAAATGGCATTAAGgtggtaattc ... ataccaatagGTACGCTCATCTGCTGTCTTTGTGCCAGAACATCCTGGGAGGCCTGGGGAA
EST: gi|71427864|gb|DR808914.1|DR808914
EST:     ATCCAGAAGCACCTCCATCATGCAGTTCAGCTGTTACAAATGGCATTAAG                         GTACGCTCATCTGCTGTCTTTGTGCCAGAACATCCTGGGAGGCCTGGGGAA
genomic: ATCCAGAAGCACCTCCATCATGCAGTTCAGCTGTTACAAATGGCATTAAGgtggtaattc ... ataccaatagGTACGCTCATCTGCTGTCTTTGTGCCAGAACATCCTGGGAGGCCTGGGGAA
EST: gi|211097821|gb|FL296745.1|FL296745
EST:     TCAGCTGTTACAAATGGCATTAAG                         GTACGCTCATCTGCTGTCTTTGTGCCAGAACATCCTGGGAGGCCTGGGGAA
genomic: TCAGCTGTTACAAATGGCATTAAGgtggtaattc ... ataccaatagGTACGCTCATCTGCTGTCTTTGTGCCAGAACATCCTGGGAGGCCTGGGGAA
EST: gi|76911327|gb|DV164233.1|DV164233
EST:     ATCCAGAAGCACCTCCATCATGCAGTTCAGCTGTTACAAATGGCATTAAG                         GTACGCTCATCTGCTGTCTTTGTGCCAGAACATCCTGGGAGGCCTGGGGAA
genomic: ATCCAGAAGCACCTCCATCATGCAGTTCAGCTGTTACAAATGGCATTAAGgtggtaattc ... ataccaatagGTACGCTCATCTGCTGTCTTTGTGCCAGAACATCCTGGGAGGCCTGGGGAA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 236

TGGCATGATCAAGACCCGTATGCTGATGGCATCGAGATATATCAGCTTATATCCAGAAGCACCTCCATCATGCAGTTCAGCTGTTACAAATGGCATTAAGgtggtaattc ... ataccaatagGTACGCTCATCTGCTGTCTTTGTGCCAGAACATCCTGGGAGGCCTGGGGAAAAATTTATGTTCACTTACTCAATTCGCATGTCAGTTCCAGAGGCATGCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 182

TGGCATGATCAAGACCCGTATGCTGATGGCATCGAGATATATCAGCTTATATCCAGAAGCACCTCCATCATGCAGTTCAGCTGTTACAAATGGCATTAAGgtggtaattc ... ataccaatagGTACGCTCATCTGCTGTCTTTGTGCCAGAACATCCTGGGAGGCCTGGGGAAAAATTTATGTTCACTTACTCAATTCGCATGTCAGTTCCAGAGGCATGCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 133

TGGCATGATCAAGACCCGTATGCTGATGGCATCGAGATATATCAGCTTATATCCAGAAGCACCTCCATCATGCAGTTCAGCTGTTACAAATGGCATTAAGgtggtaattc ... ataccaatagGTACGCTCATCTGCTGTCTTTGTGCCAGAACATCCTGGGAGGCCTGGGGAAAAATTTATGTTCACTTACTCAATTCGCATGTCAGTTCCAGAGGCATGCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 292

TGGCATGATCAAGACCCGTATGCTGATGGCATCGAGATATATCAGCTTATATCCAGAAGCACCTCCATCATGCAGTTCAGCTGTTACAAATGGCATTAAGgtggtaattc ... ataccaatagGTACGCTCATCTGCTGTCTTTGTGCCAGAACATCCTGGGAGGCCTGGGGAAAAATTTATGTTCACTTACTCAATTCGCATGTCAGTTCCAGAGGCATGCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

accattcccatggatgatttcttgagccttggtctgacatatctgataccaatagGTACGCTCATCTGCTGTCTTTGTGCCAGAACATCCTGGGAGGCCTGGGGAAAAATTTATGTTCACTTACTCAATTCGCATGTCAGTTCCAGAGGCATGCA
             atgattt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctacattagctaattttgccatggctatagtactgcatactgtagaccattcccatggatgatttcttgagccttggtctgacatatctgataccaatagGTACGCTCATCTGCTGTCTTTGTGCCAGAACATCCTGGGAGGCCTGGGGAAAAATTTATGTTCACTTACTCAATTCGCATGTCAGTTCCAGAGGCATGCA

- - - - - - - - -gccatgg
- - - - - - - - - - - - - - - - -tgcatac
- - - - - - - - - - - - - - - - - - - - - - - - - - - atggatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tttcttg