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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCCTCACCGCCGGCCTCTGCTCCTCTTCCGCCGCCGCAGGATCTCGTATCGCCGGAGACCATGTACCGCGCCGCCGGGAGCCACCTCCGCTCCCTCAAGgttccgccctcctattctcccctgccttccccttccccgttgcatgcacgtctcgatccactcgggtatgattgcacttaggttagatccgaacgggtcg...

Basic information

species Zea mays
transcript GRMZM2G005036_T01
intron # 1
splice site 5'
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|211371009|gb|FL375201.1|FL375201
EST:     CGCCGGAGACCATGTACCGCGCCGCCGGGAGCCACCTCCGCTCCCTCAAG                         CATCATGGTGCTTCTAGGCTTGCCAGTACAAGTGTTGCGAAGCAGTCCTCA
genomic: CGCCGGAGACCATGTACCGCGCCGCCGGGAGCCACCTCCGCTCCCTCAAGgttccgccct ... tcattttcagCATCATGGTGCTTCTAGGCTTGCCAGTACAAGTGTTGCGAAGCAGTCCTCA
EST: gi|211360499|gb|FL383507.1|FL383507
EST:     CGCCGGAGACCATGTACCGCGCCGCCGGGAGCCACCTCCGCTCCCTCAAG                         CATCATGGTGCTTCTAGGCTTGCCAGTACAAGTGTTGCG-A-CRGTTCCTC
genomic: CGCCGGAGACCATGTACCGCGCCGCCGGGAGCCACCTCCGCTCCCTCAAGgttccgccct ... tcattttcagCATCATGGTGCTTCTAGGCTTGCCAGTACAAGTGTTGCGAAGCAG-TCCTC
EST: gi|149042117|gb|EE047095.2|EE047095
EST:     CGCCGGAGACCATGTACCGCGCCGCCGGGAGCCACCTCCGCTCCCTCAAG                         CATCATGGTGCTTCTAGGCTTGCCAGTACAAGTGTTGCGAAGCAGTCCTCA
genomic: CGCCGGAGACCATGTACCGCGCCGCCGGGAGCCACCTCCGCTCCCTCAAGgttccgccct ... tcattttcagCATCATGGTGCTTCTAGGCTTGCCAGTACAAGTGTTGCGAAGCAGTCCTCA
EST: gi|71764445|gb|DR962382.1|DR962382
EST:     CGCCGGAGACCATGTACCGCGCCGCCGGGAGCCACCTCCGCTCCCTCAAG                         CATCATGGTGCTTCTAGGCTTGCCAGTACAAGTGTTGCGAAGCAGTCCTCA
genomic: CGCCGGAGACCATGTACCGCGCCGCCGGGAGCCACCTCCGCTCCCTCAAGgttccgccct ... tcattttcagCATCATGGTGCTTCTAGGCTTGCCAGTACAAGTGTTGCGAAGCAGTCCTCA
EST: gi|211403744|gb|FL425459.1|FL425459
EST:     CGCCGGAGACCATGTACCGCGCCGCCGGGAGCCACCTCCGCTCCCTCAAG                         CATCATGGNTGCTTCTAGGCTTGCCAGTACAAGTGTTGCGAAGCAGTCCTC
genomic: CGCCGGAGACCATGTACCGCGCCGCCGGGAGCCACCTCCGCTCCCTCAAGgttccgccct ... tcattttcagCATCATGG-TGCTTCTAGGCTTGCCAGTACAAGTGTTGCGAAGCAGTCCTC
EST: gi|211474431|gb|FL414208.1|FL414208
EST:     CGCCGGAGACCATGTACCGCGCCGCCGGGAGCCACCTCCGCTCCCTCAAG                         CATCATGGTGCTTCTAGGCTTGCCAGTACAAGTGTTGCGAAGCAGTCCTCA
genomic: CGCCGGAGACCATGTACCGCGCCGCCGGGAGCCACCTCCGCTCCCTCAAGgttccgccct ... tcattttcagCATCATGGTGCTTCTAGGCTTGCCAGTACAAGTGTTGCGAAGCAGTCCTCA
EST: gi|88755467|gb|DY539608.1|DY539608
EST:     CGCCGGAGACCATGTACCGCGCCGCCGGGAGCCACCTCCGCTCCCTCAAG                         CATCATGGTGCTTCTAGGCTTGCCAGTACAAGTGTTGCGAAGCAGTCCTCA
genomic: CGCCGGAGACCATGTACCGCGCCGCCGGGAGCCACCTCCGCTCCCTCAAGgttccgccct ... tcattttcagCATCATGGTGCTTCTAGGCTTGCCAGTACAAGTGTTGCGAAGCAGTCCTCA
EST: gi|76935641|gb|DV174409.1|DV174409
EST:     CGCCGGAGACCATGTACCGCGCCGCCGGGAGCCACCTCCGCTCCCTCAAG                         CATCATGGTGCTTCTAGGCTTGCCAGTACAAGTGTTGCGAAGCAGTCCTCA
genomic: CGCCGGAGACCATGTACCGCGCCGCCGGGAGCCACCTCCGCTCCCTCAAGgttccgccct ... tcattttcagCATCATGGTGCTTCTAGGCTTGCCAGTACAAGTGTTGCGAAGCAGTCCTCA
EST: gi|211328211|gb|FL409833.1|FL409833
EST:     CGCCGGAGACCATGTACCGCGCCGCCGGGAGCCACCTCCGCTCCCTCAAG                         CATCATGGTGCTTCTAGGCTTGCCAGTACAAGTGTTGCGAAGCAGTCCTCA
genomic: CGCCGGAGACCATGTACCGCGCCGCCGGGAGCCACCTCCGCTCCCTCAAGgttccgccct ... tcattttcagCATCATGGTGCTTCTAGGCTTGCCAGTACAAGTGTTGCGAAGCAGTCCTCA
EST: gi|211340942|gb|FL378185.1|FL378185
EST:     CGCCGGAGACCATGTACCGCGCCGCCGGGAGCCACCTCCGCTCCCTCAAG                         CATCATGGTGCTTCTAGGCTTGCCAGTACAAGTGTTGCGAAGCAGTCCTCA
genomic: CGCCGGAGACCATGTACCGCGCCGCCGGGAGCCACCTCCGCTCCCTCAAGgttccgccct ... tcattttcagCATCATGGTGCTTCTAGGCTTGCCAGTACAAGTGTTGCGAAGCAGTCCTCA
EST: gi|211273249|gb|FL384317.1|FL384317
EST:     CGCCGGAGACCATGTACCGCGCCGCCGGGAGCCACCTCCGCTCCCTCAAG                         CATCATGGTGCTTCTAGGCTTGCCAGTACAAGTGTTGCGAAGCAGTCCTCA
genomic: CGCCGGAGACCATGTACCGCGCCGCCGGGAGCCACCTCCGCTCCCTCAAGgttccgccct ... tcattttcagCATCATGGTGCTTCTAGGCTTGCCAGTACAAGTGTTGCGAAGCAGTCCTCA
EST: gi|31354401|gb|CD438758.1|CD438758
EST:     CGCCGGAGACCATGTACCTTTAAGCCGGGAGCCACCTCCGCTCCCTCAAG                         CATCATGGTGCTTCTAGGCTTGCCAGTACAAGTGTTGCTAAGCAGTCCTCA
genomic: CGCCGGAGACCATGTACCGCGCCGCCGGGAGCCACCTCCGCTCCCTCAAGgttccgccct ... tcattttcagCATCATGGTGCTTCTAGGCTTGCCAGTACAAGTGTTGCGAAGCAGTCCTCA
EST: gi|211283949|gb|FL372048.1|FL372048
EST:     GGAGACCATGTACCGCGCCGCCGGGAGCCACCTCCGCTCCCTCAAG                         CATCATGGTGCTTCTAGGCTTGCCAGTACAAGTGTTGCG-A-VSGTCCTCA
genomic: GGAGACCATGTACCGCGCCGCCGGGAGCCACCTCCGCTCCCTCAAGgttccgccct ... tcattttcagCATCATGGTGCTTCTAGGCTTGCCAGTACAAGTGTTGCGAAGCAGTCCTCA
EST: gi|211149279|gb|FL424930.1|FL424930
EST:     CGCCGGAGACCATGTACCGCGCCGCCGGGAGCCACCTCCGCTCCCTCAAG                         CATCATGGTGCTTCTAGGCTTGCCAGTACAAGTGTTGCGAAGCAGTCCTCA
genomic: CGCCGGAGACCATGTACCGCGCCGCCGGGAGCCACCTCCGCTCCCTCAAGgttccgccct ... tcattttcagCATCATGGTGCTTCTAGGCTTGCCAGTACAAGTGTTGCGAAGCAGTCCTCA
EST: gi|211411533|gb|FL428561.1|FL428561
EST:     CGCCGGAGACCATGTACCGCGCCGCCGGGAGCCACCTCCGCTCCCTCAAG                         CATCATGGTGCTTCTAGGCTTGCCAGTACAAGTGTTGCGAAGCAGTCCTCA
genomic: CGCCGGAGACCATGTACCGCGCCGCCGGGAGCCACCTCCGCTCCCTCAAGgttccgccct ... tcattttcagCATCATGGTGCTTCTAGGCTTGCCAGTACAAGTGTTGCGAAGCAGTCCTCA
EST: gi|76912595|gb|DV164810.1|DV164810
EST:     CGCCGGAGACCATGTACCGCGCCGCCGGGAGCCACCTCCGCTCCCTCAAG                         CATCATGGTGCTTCTAGGCTTGCCAGTACAAGTGTTGCGAAGCAGTCCTCA
genomic: CGCCGGAGACCATGTACCGCGCCGCCGGGAGCCACCTCCGCTCCCTCAAGgttccgccct ... tcattttcagCATCATGGTGCTTCTAGGCTTGCCAGTACAAGTGTTGCGAAGCAGTCCTCA
EST: gi|78092878|gb|DV521252.1|DV521252
EST:     CGCCGGAGACCATGTACCGCGCCGCCGGGAGCCACCTCCGCTCCCTCAAG                         CATCATGGTGCTTCTAGGCTTGCCAGTACAAGTGTTGCGAAGCAGTCCTCA
genomic: CGCCGGAGACCATGTACCGCGCCGCCGGGAGCCACCTCCGCTCCCTCAAGgttccgccct ... tcattttcagCATCATGGTGCTTCTAGGCTTGCCAGTACAAGTGTTGCGAAGCAGTCCTCA
EST: gi|211451674|gb|FL376119.1|FL376119
EST:     CGCCGGAGACCATGTACCGCGCCGCCGGGAGCCACCTCCGCTCCCTCAAG                         CATCATGGTGCTTCTAGGCTTGCCAGTACAAGTGTTGCGAAGCAGTCCTCA
genomic: CGCCGGAGACCATGTACCGCGCCGCCGGGAGCCACCTCCGCTCCCTCAAGgttccgccct ... tcattttcagCATCATGGTGCTTCTAGGCTTGCCAGTACAAGTGTTGCGAAGCAGTCCTCA
EST: gi|148965824|gb|EE016713.2|EE016713
EST:     CGCCGGAGACCATGTACCGCGCCGCCGGGAGCCACCTCCGCTCCCTCAAG                         CATCATGGTGCTTCTAGGCTTGCCAGTACAAGTGTTGCGAAGCAGTCCTCA
genomic: CGCCGGAGACCATGTACCGCGCCGCCGGGAGCCACCTCCGCTCCCTCAAGgttccgccct ... tcattttcagCATCATGGTGCTTCTAGGCTTGCCAGTACAAGTGTTGCGAAGCAGTCCTCA
EST: gi|148944905|gb|EC890064.2|EC890064
EST:     CGCCGGAGACCATGTACCGCGCCGCCGGGAGCCACCTCCGCTCCCTCAAG                         CATCATGGTGCTTCTAGGCTTGCCAGTACAAGTGTTGCGAAGCAGTCCTCA
genomic: CGCCGGAGACCATGTACCGCGCCGCCGGGAGCCACCTCCGCTCCCTCAAGgttccgccct ... tcattttcagCATCATGGTGCTTCTAGGCTTGCCAGTACAAGTGTTGCGAAGCAGTCCTCA
EST: gi|89247626|gb|DY619412.1|DY619412
EST:     CGCCGGAGACCATGTACCGCGCCGCCGGGAGCCACCTCCGCTCCCTCAAG                         CATCATGGTGCTTCTAGGCTTGCCAGTACAAGTGTTGCGAAGCAGTCCTCA
genomic: CGCCGGAGACCATGTACCGCGCCGCCGGGAGCCACCTCCGCTCCCTCAAGgttccgccct ... tcattttcagCATCATGGTGCTTCTAGGCTTGCCAGTACAAGTGTTGCGAAGCAGTCCTCA
EST: gi|211381649|gb|FL369275.1|FL369275
EST:     CGCCGGAGACCATGTACCGCGCCGCCGGGAGCCACCTCCGCTCCCTCAAG                         CATCATGGTGCTTCTAGGCTTGCCAGTACAAGTGTTGCGAAGCAGTCCTCA
genomic: CGCCGGAGACCATGTACCGCGCCGCCGGGAGCCACCTCCGCTCCCTCAAGgttccgccct ... tcattttcagCATCATGGTGCTTCTAGGCTTGCCAGTACAAGTGTTGCGAAGCAGTCCTCA
EST: gi|38687651|gb|CK144682.1|CK144682
EST:     CGCCGGAGACCATGTACCGCGCCGCCGGGAGCCACCTCCGCTCCCTCAAG                         CATCATGGTGCTTCTAGGCTTGCCAGTACAAGTGTTGCGAAGCAGTCCTCA
genomic: CGCCGGAGACCATGTACCGCGCCGCCGGGAGCCACCTCCGCTCCCTCAAGgttccgccct ... tcattttcagCATCATGGTGCTTCTAGGCTTGCCAGTACAAGTGTTGCGAAGCAGTCCTCA
EST: gi|5555303|gb|AI881254.1|AI881254
EST:     CCGCGCCGCCGGGGAGCCACCTCCGCTCCCTCAAG                         CATCATGGTGCTTCTAGGCTTGCCAGTACAAGTGTTGCGAAGCAGTCCTCA
genomic: CCGCGCCGCC-GGGAGCCACCTCCGCTCCCTCAAGgttccgccct ... tcattttcagCATCATGGTGCTTCTAGGCTTGCCAGTACAAGTGTTGCGAAGCAGTCCTCA
EST: gi|211300764|gb|FL380982.1|FL380982
EST:     CGCCGGAGACCATGTACCGCGCCGCCGGGAGCCACCTCCGCTCCCTCAAG                         CATCATGGTGCTTCTAGGCTTGCCAGTACAAGTGTTGCGAAGCAGTCCTCA
genomic: CGCCGGAGACCATGTACCGCGCCGCCGGGAGCCACCTCCGCTCCCTCAAGgttccgccct ... tcattttcagCATCATGGTGCTTCTAGGCTTGCCAGTACAAGTGTTGCGAAGCAGTCCTCA
EST: gi|37421502|gb|CF648451.1|CF648451
EST:     CGCCGGAGACCATGTACCGCGCCGCCGGGAGCCACCTCCGCTCCCTCAAG                         CATCATGGTGCTTCTAGGCTTGCCAGTACAAGTGTTGCGAAGCAGTCCTCA
genomic: CGCCGGAGACCATGTACCGCGCCGCCGGGAGCCACCTCCGCTCCCTCAAGgttccgccct ... tcattttcagCATCATGGTGCTTCTAGGCTTGCCAGTACAAGTGTTGCGAAGCAGTCCTCA
EST: gi|78106581|gb|DV524999.1|DV524999
EST:     CGCCGGAGACCATGTACCGCGCCGCCGGGAGCCACCTCCGCTCCCTCAAG                         CATCATGGTGCTTCTAGGCTTGCCAGTACAAGTGTTGCGAAGCAGTCCTCA
genomic: CGCCGGAGACCATGTACCGCGCCGCCGGGAGCCACCTCCGCTCCCTCAAGgttccgccct ... tcattttcagCATCATGGTGCTTCTAGGCTTGCCAGTACAAGTGTTGCGAAGCAGTCCTCA
EST: gi|149081535|gb|EE170671.2|EE170671
EST:     CGCCGGAGACCATGTACCGCGCCGCCGGGAGCCACCTCCGCTCCCTCAAG                         CATCATGGTGCTTCTAGGCTTGCCAGTACAAGTGTTGCGAAGCAGTCCTCA
genomic: CGCCGGAGACCATGTACCGCGCCGCCGGGAGCCACCTCCGCTCCCTCAAGgttccgccct ... tcattttcagCATCATGGTGCTTCTAGGCTTGCCAGTACAAGTGTTGCGAAGCAGTCCTCA
EST: gi|211164240|gb|FL370536.1|FL370536
EST:     CGCCGGAGACCATGTACCGCGCCGCCGGGAGCCACCTCCGCTCCCTCAAG                         CATCATGGTGCTTCTAGGCTTGCCAGTACAAGTGTTGCGAAGCAGTCCTCA
genomic: CGCCGGAGACCATGTACCGCGCCGCCGGGAGCCACCTCCGCTCCCTCAAGgttccgccct ... tcattttcagCATCATGGTGCTTCTAGGCTTGCCAGTACAAGTGTTGCGAAGCAGTCCTCA
EST: gi|31349354|gb|CD433711.1|CD433711
EST:     CGCCGGAGACCATGTACCGCGCCGCCGGGAGCCACCTCCGCTCCCTCAAG                         CATCATGGTGCTTCTATGCTTGCCAGTACAAGTGTTGCGAAGCAGTCCTCA
genomic: CGCCGGAGACCATGTACCGCGCCGCCGGGAGCCACCTCCGCTCCCTCAAGgttccgccct ... tcattttcagCATCATGGTGCTTCTAGGCTTGCCAGTACAAGTGTTGCGAAGCAGTCCTCA
EST: gi|211159959|gb|FL410900.1|FL410900
EST:     CGCCGGAGACCATGTACCGCGCCGCCGGGAGCCACCTCCGCTCCCTCAAG                         CATCATGGTGCTTCTAGGCTTGCCAGTACAAGTGTTGCGAAGCAGTCCTCA
genomic: CGCCGGAGACCATGTACCGCGCCGCCGGGAGCCACCTCCGCTCCCTCAAGgttccgccct ... tcattttcagCATCATGGTGCTTCTAGGCTTGCCAGTACAAGTGTTGCGAAGCAGTCCTCA
EST: gi|211428589|gb|FL379172.1|FL379172
EST:     CGCCGGAGACCATGTACCGCGCCGCCGGGAGCCACCTCCGCTCCCTCAAG                         CATCATGGTGCTTCTAGGCTTGCCAGTACAAGTGTTGCGAAGCAGTCCTCA
genomic: CGCCGGAGACCATGTACCGCGCCGCCGGGAGCCACCTCCGCTCCCTCAAGgttccgccct ... tcattttcagCATCATGGTGCTTCTAGGCTTGCCAGTACAAGTGTTGCGAAGCAGTCCTCA

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), 47 (downstream exon)
Score: 179

TCCCTCACCGCCGGCCTCTGCTCCTCTTCCGCCGCCGCAGGATCTCGTATCGCCGGAGACCATGTACCGCGCCGCCGGGAGCCACCTCCGCTCCCTCAAGgttccgccct ... tcattttcagCATCATGGTGCTTCTAGGCTTGCCAGTACAAGTGTTGCGAAGCAGTCCTCAGGTGGTCTGTTCAGCTGGCTTCTTGGTGGAAAATCAAGCGAACTCCCTC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 166

TCCCTCACCGCCGGCCTCTGCTCCTCTTCCGCCGCCGCAGGATCTCGTATCGCCGGAGACCATGTACCGCGCCGCCGGGAGCCACCTCCGCTCCCTCAAGgttccgccct ... tcattttcagCATCATGGTGCTTCTAGGCTTGCCAGTACAAGTGTTGCGAAGCAGTCCTCAGGTGGTCTGTTCAGCTGGCTTCTTGGTGGAAAATCAAGCGAACTCCCTC


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 255

TCCCTCACCGCCGGCCTCTGCTCCTCTTCCGCCGCCGCAGGATCTCGTATCGCCGGAGACCATGTACCGCGCCGCCGGGAGCCACCTCCGCTCCCTCAAGgttccgccct ... tcattttcagCATCATGGTGCTTCTAGGCTTGCCAGTACAAGTGTTGCGAAGCAGTCCTCAGGTGGTCTGTTCAGCTGGCTTCTTGGTGGAAAATCAAGCGAACTCCCTC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 175

TCCCTCACCGCCGGCCTCTGCTCCTCTTCCGCCGCCGCAGGATCTCGTATCGCCGGAGACCATGTACCGCGCCGCCGGGAGCCACCTCCGCTCCCTCAAGgttccgccct ... tcattttcagCATCATGGTGCTTCTAGGCTTGCCAGTACAAGTGTTGCGAAGCAGTCCTCAGGTGGTCTGTTCAGCTGGCTTCTTGGTGGAAAATCAAGCGAACTCCCTC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCCCTCACCGCCGGCCTCTGCTCCTCTTCCGCCGCCGCAGGATCTCGTATCGCCGGAGACCATGTACCGCGCCGCCGGGAGCCACCTCCGCTCCCTCAAGgttccgccctcctattctcccctgccttccccttccccgttgcatgcacgtctcgatccactcgggtatgattgcacttaggttagatccgaacgggtcg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cccctgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccccttcc