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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tccatatcatctccgtttaatttcattccagattctaagcaatccctgaagcaacacgcggggtatcttctagtaatcacatatgtatatgtctgcgcagGTACTTGGAGTTGGCAATGGAGACAATCACATGAGAATCATCCAG

Basic information

species Zea mays
transcript GRMZM2G108849_T01
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|211436682|gb|FL284630.1|FL284630
EST:     GCGAACTGCTGCTTGCKCTCCTCCTCGTCTCTGCTGCTGCCGCCCCTCAG                         GTACTTGGAGTTGGCAATGGAGACAATCACATGAGAATCATCCAG
genomic: GCGAACTGCTGCTTGCGCTCCTCCTCGTCTCTGCTGCTGCCGCCCCTCAGgtccgcatcc ... gtctgcgcagGTACTTGGAGTTGGCAATGGAGACAATCACATGAGAATCATCCAG
EST: gi|13177948|gb|BG349206.1|BG349206
EST:     GCGAACTGCTGCTTGCGCTCCTCCTCGTCTCTGCTGCTGCCGCCCCTCAG                         GTACTTGGAGTTGGCAATGGAGACAATCACATGAGAATCATCCAG
genomic: GCGAACTGCTGCTTGCGCTCCTCCTCGTCTCTGCTGCTGCCGCCCCTCAGgtccgcatcc ... gtctgcgcagGTACTTGGAGTTGGCAATGGAGACAATCACATGAGAATCATCCAG
EST: gi|211436681|gb|FL284629.1|FL284629
EST:     GCGAACTGCTGCTTGCKCTCCTCCTCGTCTCTGCTGCTGCCGCCCCTCAG                         GTACTTGGAGTTGGCAATGGAGACAATCACATGAGAATCATCCAG
genomic: GCGAACTGCTGCTTGCGCTCCTCCTCGTCTCTGCTGCTGCCGCCCCTCAGgtccgcatcc ... gtctgcgcagGTACTTGGAGTTGGCAATGGAGACAATCACATGAGAATCATCCAG
EST: gi|211491807|gb|FL092422.1|FL092422
EST:     GCGCACTGCTGCTTGCDCTCCTCCTCGTCTCTGCTGCTGCCGCCCCTCAG                         GTACTTGGAGTTGGCAATGGAGACAATCACATGAGAATCATCCAG
genomic: GCGAACTGCTGCTTGCGCTCCTCCTCGTCTCTGCTGCTGCCGCCCCTCAGgtccgcatcc ... gtctgcgcagGTACTTGGAGTTGGCAATGGAGACAATCACATGAGAATCATCCAG
EST: gi|211439281|gb|FL284648.1|FL284648
EST:     GCGAACTGCTGCTTGCKCTCCTCCTCGTCTCTGCTGCTGCCGCCCCTCAG                         GTACTTGGAGTTGGCAATGGAGACAATCACATGAGAATCATCCAG
genomic: GCGAACTGCTGCTTGCGCTCCTCCTCGTCTCTGCTGCTGCCGCCCCTCAGgtccgcatcc ... gtctgcgcagGTACTTGGAGTTGGCAATGGAGACAATCACATGAGAATCATCCAG
EST: gi|211439276|gb|FL284643.1|FL284643
EST:     GCGAACTGCTGCTTGCGCTCCTCCTCGTCTCTGCTGCTGCCGCCCCTCAG                         GTACTTGGAGTTGTCAATGGAGACAATCACATGAGAATCATCCAG
genomic: GCGAACTGCTGCTTGCGCTCCTCCTCGTCTCTGCTGCTGCCGCCCCTCAGgtccgcatcc ... gtctgcgcagGTACTTGGAGTTGGCAATGGAGACAATCACATGAGAATCATCCAG
EST: gi|211436678|gb|FL284626.1|FL284626
EST:     GCGAACTGCTGCTTGCKCTCCTCCTCGTCTCTGCTGCTGCCGCCCCTCAG                         GTACTTGGAGTTGGCAATGGAGACAATCACATGAGAATCATCCAG
genomic: GCGAACTGCTGCTTGCGCTCCTCCTCGTCTCTGCTGCTGCCGCCCCTCAGgtccgcatcc ... gtctgcgcagGTACTTGGAGTTGGCAATGGAGACAATCACATGAGAATCATCCAG
EST: gi|211439282|gb|FL284649.1|FL284649
EST:     GCGAACTGCTGCTTGCGCTCCTCCTCGTCTCTGCTGCTGCCGCCCCTCAG                         GTACTTGGAGTTGGCAATGGAGAC
genomic: GCGAACTGCTGCTTGCGCTCCTCCTCGTCTCTGCTGCTGCCGCCCCTCAGgtccgcatcc ... gtctgcgcagGTACTTGGAGTTGGCAATGGAGAC
EST: gi|211439272|gb|FL284639.1|FL284639
EST:     GCGAACTGCTGCTTGCGCTCCTCCTCGTCTCTGCTGCTGCCGCCCCTCAG                         GTACTTGGAGTTGGCAATGGAGACAATCACATGAGAATCATCCAG
genomic: GCGAACTGCTGCTTGCGCTCCTCCTCGTCTCTGCTGCTGCCGCCCCTCAGgtccgcatcc ... gtctgcgcagGTACTTGGAGTTGGCAATGGAGACAATCACATGAGAATCATCCAG
EST: gi|211488922|gb|FL092407.1|FL092407
EST:     GCGCACTGCTGCTTGCNCTCCTCCTCGTCTCTGCTGCTGCCGCCCCTCAG                         GTACTTGGAGTTGGCAATGGAGACAATCACATGAGAATCATCCAG
genomic: GCGAACTGCTGCTTGCGCTCCTCCTCGTCTCTGCTGCTGCCGCCCCTCAGgtccgcatcc ... gtctgcgcagGTACTTGGAGTTGGCAATGGAGACAATCACATGAGAATCATCCAG
EST: gi|211436674|gb|FL284622.1|FL284622
EST:     GCGAACTGCTGCTTGCGCTCCTCCTCGTCTCTGCTGCTGCCGCCCCTCAG                         GTACTTGGAGTTGGCAATGGAGACAATCACATGAGAATCATCCAG
genomic: GCGAACTGCTGCTTGCGCTCCTCCTCGTCTCTGCTGCTGCCGCCCCTCAGgtccgcatcc ... gtctgcgcagGTACTTGGAGTTGGCAATGGAGACAATCACATGAGAATCATCCAG
EST: gi|211439275|gb|FL284642.1|FL284642
EST:     GCGAACTGCTGCTTGCKCTCCTCCTCGTCTCTGCTGCTGCCGCCCCTCAG                         GTACTTGGAGTTGGCAATGGAGACAATCACATGAGAATCATCCAG
genomic: GCGAACTGCTGCTTGCGCTCCTCCTCGTCTCTGCTGCTGCCGCCCCTCAGgtccgcatcc ... gtctgcgcagGTACTTGGAGTTGGCAATGGAGACAATCACATGAGAATCATCCAG
EST: gi|211439277|gb|FL284644.1|FL284644
EST:     GCGAACTGCTGCTTGCKCTCCTCCTCGTCTCTGCTGCTGCCGCCCCTCAG                         GTACTTGGAGTTGGCAATGGAGACAATCACATGAGAATCATCCAG
genomic: GCGAACTGCTGCTTGCGCTCCTCCTCGTCTCTGCTGCTGCCGCCCCTCAGgtccgcatcc ... gtctgcgcagGTACTTGGAGTTGGCAATGGAGACAATCACATGAGAATCATCCAG
EST: gi|211436686|gb|FL284634.1|FL284634
EST:     GCGAACTGCTGCTTGCKCTCCTCCTCGTCTCTGCTGCTGCCGCCCCTCAG                         GTACTTGGAGTTGGCAATGGAGACAATCACATGAGAATCATCCAG
genomic: GCGAACTGCTGCTTGCGCTCCTCCTCGTCTCTGCTGCTGCCGCCCCTCAGgtccgcatcc ... gtctgcgcagGTACTTGGAGTTGGCAATGGAGACAATCACATGAGAATCATCCAG
EST: gi|211491808|gb|FL092423.1|FL092423
EST:     GCGCACTGCTGCTTGCGCTCCTCCTCGTCTCTGCTGCTGCCGCCCCTCAG                         GTACTTGGAGTT-GCAATGGAGACAATCACATGAGAATCATCCAG
genomic: GCGAACTGCTGCTTGCGCTCCTCCTCGTCTCTGCTGCTGCCGCCCCTCAGgtccgcatcc ... gtctgcgcagGTACTTGGAGTTGGCAATGGAGACAATCACATGAGAATCATCCAG
EST: gi|211439269|gb|FL284636.1|FL284636
EST:     GCGAACTGCTGCTTGCNCTCCTCCTCGTCTCTGCTGCTGCCGCCCCTCAG                         GTACTTGGGAGTTGGCAATGGAGACAATCACATGAGAATCATCCAG
genomic: GCGAACTGCTGCTTGCGCTCCTCCTCGTCTCTGCTGCTGCCGCCCCTCAGgtccgcatcc ... gtctgcgcagGTACTT-GGAGTTGGCAATGGAGACAATCACATGAGAATCATCCAG
EST: gi|211436679|gb|FL284627.1|FL284627
EST:     GCGAACTGCTGCTTGCNMTCCTCCTCGTCTCTACTGCTGCCGCCCCTCAG                         GTACTTGGAGTTGGCAATGGAGACAATCACATGAGAATCATCCAG
genomic: GCGAACTGCTGCTTGCGCTCCTCCTCGTCTCTGCTGCTGCCGCCCCTCAGgtccgcatcc ... gtctgcgcagGTACTTGGAGTTGGCAATGGAGACAATCACATGAGAATCATCCAG

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), 45 (downstream exon)
Score: 366

GGGGAGGGGGAGGACCAAGCGAAAGGGGGAACTAGAGCAAGATGGGCGGCGAACTGCTGCTTGCGCTCCTCCTCGTCTCTGCTGCTGCCGCCCCTCAGgtccgcatcc ... gtctgcgcagGTACTTGGAGTTGGCAATGGAGACAATCACATGAGAATCATCCAG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 849

GGGGAGGGGGAGGACCAAGCGAAAGGGGGAACTAGAGCAAGATGGGCGGCGAACTGCTGCTTGCGCTCCTCCTCGTCTCTGCTGCTGCCGCCCCTCAGgtccgcatcc ... gtctgcgcagGTACTTGGAGTTGGCAATGGAGACAATCACATGAGAATCATCCAG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 737

GGGGAGGGGGAGGACCAAGCGAAAGGGGGAACTAGAGCAAGATGGGCGGCGAACTGCTGCTTGCGCTCCTCCTCGTCTCTGCTGCTGCCGCCCCTCAGgtccgcatcc ... gtctgcgcagGTACTTGGAGTTGGCAATGGAGACAATCACATGAGAATCATCCAG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 571

GGGGAGGGGGAGGACCAAGCGAAAGGGGGAACTAGAGCAAGATGGGCGGCGAACTGCTGCTTGCGCTCCTCCTCGTCTCTGCTGCTGCCGCCCCTCAGgtccgcatcc ... gtctgcgcagGTACTTGGAGTTGGCAATGGAGACAATCACATGAGAATCATCCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgaagcaacacgcggggtatcttctagtaatcacatatgtatatgtctgcgcagGTACTTGGAGTTGGCAATGGAGACAATCACATGAGAATCATCCAG
                                   atatgtatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tccatatcatctccgtttaatttcattccagattctaagcaatccctgaagcaacacgcggggtatcttctagtaatcacatatgtatatgtctgcgcagGTACTTGGAGTTGGCAATGGAGACAATCACATGAGAATCATCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA