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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCAGCGGCGACGCCTCGGGCGTTCCTACCCTGCCCCCTCTCCGGACCCCCACGCCGTCGGCGAAGCAGCCGGGCAAGAGCCCGATCCAGACCCCGCGAGgtcagttcagatcctgctcctcttctccctccccctccttccacagctagatctgcgcccctcaccccgctcgctcgaccacctccgatcgccacgcccg...

Basic information

species Zea mays
transcript GRMZM2G122135_T04
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|211104774|gb|FL158960.1|FL158960
EST:     CACGCCGTCGGCGAAGCAGCCGGGCAAGAGCCCGATCCAGACCCCGCGAG                         CAATCCTTGATATACCTGATGGCTATGATTGATGAGCCTCTGTACCCAATT
genomic: CACGCCGTCGGCGAAGCAGCCGGGCAAGAGCCCGATCCAGACCCCGCGAGgtcagttcag ... accaattcagCAATCCTTGATATACCTGATGGCTATGATTGATGAGCCTCTGTACCCAATT
EST: gi|211254031|gb|FL158980.1|FL158980
EST:     CACGCCGTCGGCGAAGCAGCCGGGCAAGAGCCCGATCCAGACCCCGCGAG                         CAATCCTTGATATACCTGATGGCTATGATTGATGAGCCTCTGTACCCAATT
genomic: CACGCCGTCGGCGAAGCAGCCGGGCAAGAGCCCGATCCAGACCCCGCGAGgtcagttcag ... accaattcagCAATCCTTGATATACCTGATGGCTATGATTGATGAGCCTCTGTACCCAATT
EST: gi|211104779|gb|FL158965.1|FL158965
EST:     CACGCCGTCGGCGAAGCAGCCGGGCAAGAGCCCGATCCAGACCCCGCGAG                         CAATCCTTGATATACCTGATGGCTATGATTGATGAGCCTCTGTACCCAATT
genomic: CACGCCGTCGGCGAAGCAGCCGGGCAAGAGCCCGATCCAGACCCCGCGAGgtcagttcag ... accaattcagCAATCCTTGATATACCTGATGGCTATGATTGATGAGCCTCTGTACCCAATT
EST: gi|149081317|gb|EE170431.2|EE170431
EST:     CACGCCGTCGGCGAAGCAGCCGGGCAAGAGCCCGATCCAGACCCCGCGAG                         CAATCCTTGATATACCTGATGGCTATGATTGATGAGCCTCTGTACCCAATT
genomic: CACGCCGTCGGCGAAGCAGCCGGGCAAGAGCCCGATCCAGACCCCGCGAGgtcagttcag ... accaattcagCAATCCTTGATATACCTGATGGCTATGATTGATGAGCCTCTGTACCCAATT
EST: gi|211254029|gb|FL158978.1|FL158978
EST:     CACGCCGTCGGCGAAGCAGCCGGGCAAGAGCCCGATCCAGACCCCGCGAG                         CAATCCTTGATATACCTGATGGCTATGATTGATGAGCCTCTGTACCCAATT
genomic: CACGCCGTCGGCGAAGCAGCCGGGCAAGAGCCCGATCCAGACCCCGCGAGgtcagttcag ... accaattcagCAATCCTTGATATACCTGATGGCTATGATTGATGAGCCTCTGTACCCAATT
EST: gi|87155925|gb|DY400714.1|DY400714
EST:     CACGCCGTCGGCGAAGCAGCCGGGCAAGAGCCCGATCCAGACCCCGCGAG                         CAATCCTTGATATACCTGATGGCTATGATTGATGAGCCTCTGTACCCAATT
genomic: CACGCCGTCGGCGAAGCAGCCGGGCAAGAGCCCGATCCAGACCCCGCGAGgtcagttcag ... accaattcagCAATCCTTGATATACCTGATGGCTATGATTGATGAGCCTCTGTACCCAATT
EST: gi|211254030|gb|FL158979.1|FL158979
EST:     CACGCCGTCGGCGAAGCAGCCGGGCAAGAGCCCGATCCAGACCCCGCGAG                         CAATCCTTGATATACCTGATGGCTATGA
genomic: CACGCCGTCGGCGAAGCAGCCGGGCAAGAGCCCGATCCAGACCCCGCGAGgtcagttcag ... accaattcagCAATCCTTGATATACCTGATGGCTATGA
EST: gi|211104780|gb|FL158966.1|FL158966
EST:     CACGCCGTCGGNGAAGCAGCCGGGCAAGAGCCCGATCCAGACCCCGCGAG                         CAATCCTTGATATACCTGATGGCTATGATTGATGAGCCTCTGTAACCAATT
genomic: CACGCCGTCGGCGAAGCAGCCGGGCAAGAGCCCGATCCAGACCCCGCGAGgtcagttcag ... accaattcagCAATCCTTGATATACCTGATGGCTATGATTGATGAGCCTCTGTACCCAATT
EST: gi|211104776|gb|FL158962.1|FL158962
EST:     CACGCCGTCGGCGAAGCAGCCGGGCAAGAGCCCGATCCAGACCCCGCGAG                         CAATCCTTGATATACCTGATGGCTATGATTGATGAGCCTCTGTACCCAATT
genomic: CACGCCGTCGGCGAAGCAGCCGGGCAAGAGCCCGATCCAGACCCCGCGAGgtcagttcag ... accaattcagCAATCCTTGATATACCTGATGGCTATGATTGATGAGCCTCTGTACCCAATT
EST: gi|211254024|gb|FL158973.1|FL158973
EST:     CACGCCGTCGGCGAAGCAGCCGGGCAAGAGCCCGATCCAGACCCCGCGAG                         CAATCCTTGATATACCTGATGGCTATGATTGATGAGCCTCTGTACCCAATT
genomic: CACGCCGTCGGCGAAGCAGCCGGGCAAGAGCCCGATCCAGACCCCGCGAGgtcagttcag ... accaattcagCAATCCTTGATATACCTGATGGCTATGATTGATGAGCCTCTGTACCCAATT
EST: gi|211254028|gb|FL158977.1|FL158977
EST:     CACGCCGTCGGCGAAGCAGCCGGGCAAGAGCCCGATCCAGACCCCGCGAG                         CAATCCTTGATATACCTGATGGCTATGATTGATGAGCCTCTGTAACCAATT
genomic: CACGCCGTCGGCGAAGCAGCCGGGCAAGAGCCCGATCCAGACCCCGCGAGgtcagttcag ... accaattcagCAATCCTTGATATACCTGATGGCTATGATTGATGAGCCTCTGTACCCAATT
EST: gi|31361797|gb|CD446154.1|CD446154
EST:     CACGCCGTCGGCGAAGCAGCCGGGCAAGAGCCCGATCCAGACCCCGCGAG                         CAATCCTTGATATACCTGATGGCTATGATTGATGAGCCTCTGTACCCAATT
genomic: CACGCCGTCGGCGAAGCAGCCGGGCAAGAGCCCGATCCAGACCCCGCGAGgtcagttcag ... accaattcagCAATCCTTGATATACCTGATGGCTATGATTGATGAGCCTCTGTACCCAATT
EST: gi|211254032|gb|FL158981.1|FL158981
EST:     CACGCCGTCGGCGAAGCAGCCGGGCAAGAGCCCGATCCAGACCCCGCGAG                         CAATCCTTGATATACCTGATGGCTATGATTGATGAGCCTCTGTACCCAATT
genomic: CACGCCGTCGGCGAAGCAGCCGGGCAAGAGCCCGATCCAGACCCCGCGAGgtcagttcag ... accaattcagCAATCCTTGATATACCTGATGGCTATGATTGATGAGCCTCTGTACCCAATT
EST: gi|211254025|gb|FL158974.1|FL158974
EST:     CACGCCGTCGGCGAAGCAGCCGGGCAAGAGCCCGATCCAAACCCCGCGAG                         CAATCCTTGATATACCTGATGGCTATGATTGATGAGCCTCTGTACCCAATT
genomic: CACGCCGTCGGCGAAGCAGCCGGGCAAGAGCCCGATCCAGACCCCGCGAGgtcagttcag ... accaattcagCAATCCTTGATATACCTGATGGCTATGATTGATGAGCCTCTGTACCCAATT
EST: gi|22472790|gb|BU037270.1|BU037270
EST:     CACGCCGTCGGCGAAGCAGCCGGGCAAGAGCCCGATCCAGACCCCGCGAG                         CAATCCTTGATATACCTGATGGCTATGATTGATGAGCCTCTGTACCCAATT
genomic: CACGCCGTCGGCGAAGCAGCCGGGCAAGAGCCCGATCCAGACCCCGCGAGgtcagttcag ... accaattcagCAATCCTTGATATACCTGATGGCTATGATTGATGAGCCTCTGTACCCAATT
EST: gi|211254021|gb|FL158970.1|FL158970
EST:     CACGCCGTCGGCGAAGCAGCCGGGCAAGAGCCCGATCCAGACCCCGCGAG                         CAATCCTTGATATACCTGATGGCTATGATTGATGAGCCTCTGTACCCAATT
genomic: CACGCCGTCGGCGAAGCAGCCGGGCAAGAGCCCGATCCAGACCCCGCGAGgtcagttcag ... accaattcagCAATCCTTGATATACCTGATGGCTATGATTGATGAGCCTCTGTACCCAATT
EST: gi|26457426|gb|CA829009.1|CA829009
EST:     CACGCCGTCGGCGAAGCAGCCGGGCAAGAGCCCGATCCAGACCCCGCGAG                         CAATCCTTGATATACCTGATGGCTATGATTGATGAGCCTCTGTACCCAATT
genomic: CACGCCGTCGGCGAAGCAGCCGGGCAAGAGCCCGATCCAGACCCCGCGAGgtcagttcag ... accaattcagCAATCCTTGATATACCTGATGGCTATGATTGATGAGCCTCTGTACCCAATT
EST: gi|67022275|gb|CO451024.1|CO451024
EST:     CACGCCGTCGGCGAAGCAGCCGGGCAAGAGCCCGATCCAGACCCCGCGAG                         CAATCCTTGATATACCTGATGGCTATGATTGATGAGCCTCTGTACCCAATT
genomic: CACGCCGTCGGCGAAGCAGCCGGGCAAGAGCCCGATCCAGACCCCGCGAGgtcagttcag ... accaattcagCAATCCTTGATATACCTGATGGCTATGATTGATGAGCCTCTGTACCCAATT
EST: gi|211419377|gb|FL436538.1|FL436538
EST:     CACGCCGTCGGCGAAGCAGCCGGGCAAGAGCCCGATCCAGACCCCGCGAG                         CAATCCTTGATATACCTGACGGCTATGAT
genomic: CACGCCGTCGGCGAAGCAGCCGGGCAAGAGCCCGATCCAGACCCCGCGAGgtcagttcag ... accaattcagCAATCCTTGATATACCTGATGGCTATGAT
EST: gi|211389439|gb|FL474314.1|FL474314
EST:     CACGCCGTCGGCGAAGCAGCCGGGCAAGAGCCCGATCCAGACCCCGCGAG                         CAATCCTTGATATACCTGATGGCTATGATT
genomic: CACGCCGTCGGCGAAGCAGCCGGGCAAGAGCCCGATCCAGACCCCGCGAGgtcagttcag ... accaattcagCAATCCTTGATATACCTGATGGCTATGATT

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), 48 (downstream exon)
Score: 46

CTCAGCGGCGACGCCTCGGGCGTTCCTACCCTGCCCCCTCTCCGGACCCCCACGCCGTCGGCGAAGCAGCCGGGCAAGAGCCCGATCCAGACCCCGCGAGgtcagttcag ... accaattcagCAATCCTTGATATACCTGATGGCTATGATTGATGAGCCTCTGTACCCAATTGCTGTACTGATTGATGAGCTTAAGAATGAGGACATCCAGTTGCGTCTAA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 51

CTCAGCGGCGACGCCTCGGGCGTTCCTACCCTGCCCCCTCTCCGGACCCCCACGCCGTCGGCGAAGCAGCCGGGCAAGAGCCCGATCCAGACCCCGCGAGgtcagttcag ... accaattcagCAATCCTTGATATACCTGATGGCTATGATTGATGAGCCTCTGTACCCAATTGCTGTACTGATTGATGAGCTTAAGAATGAGGACATCCAGTTGCGTCTAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 106

CTCAGCGGCGACGCCTCGGGCGTTCCTACCCTGCCCCCTCTCCGGACCCCCACGCCGTCGGCGAAGCAGCCGGGCAAGAGCCCGATCCAGACCCCGCGAGgtcagttcag ... accaattcagCAATCCTTGATATACCTGATGGCTATGATTGATGAGCCTCTGTACCCAATTGCTGTACTGATTGATGAGCTTAAGAATGAGGACATCCAGTTGCGTCTAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 57

CTCAGCGGCGACGCCTCGGGCGTTCCTACCCTGCCCCCTCTCCGGACCCCCACGCCGTCGGCGAAGCAGCCGGGCAAGAGCCCGATCCAGACCCCGCGAGgtcagttcag ... accaattcagCAATCCTTGATATACCTGATGGCTATGATTGATGAGCCTCTGTACCCAATTGCTGTACTGATTGATGAGCTTAAGAATGAGGACATCCAGTTGCGTCTAA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTCAGCGGCGACGCCTCGGGCGTTCCTACCCTGCCCCCTCTCCGGACCCCCACGCCGTCGGCGAAGCAGCCGGGCAAGAGCCCGATCCAGACCCCGCGAGgtcagttcagatcctgctcctcttctccctccccctccttccacagctagatctgcgcccctcaccccgctcgctcgaccacctccgatcgccacgcccg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA