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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTTGAGCAGGCAAAGAAGTTGTTCAATAAGCTATCAACTGACCCTACAACAACAAACATGTTGGTCGCTAAGCAACCAGCCTCTTTCACGGGTTCTGAGgtgggttctgcaatttttcactctatacttagttgtgctatttttcatgaacccacattatttcaccattgtatgctctcttggtag

Basic information

species Zea mays
transcript GRMZM2G091563_T01
intron # 3
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|60337054|gb|DN204027.1|DN204027
EST:     CAACAAACATGTTGGTCGCTAAGCAACCAGCCTCTTTCACGGGTTCTGAG                         GTTCGAATCATTGACGATGACATGCCCCTTGCTCAATTTGCTGTTGCTTTC
genomic: CAACAAACATGTTGGTCGCTAAGCAACCAGCCTCTTTCACGGGTTCTGAGgtgggttctg ... ctcttggtagGTTCGAATCATTGACGATGACATGCCCCTTGCTCAATTTGCTGTTGCTTTC
EST: gi|32920213|gb|CF025025.1|CF025025
EST:     CAACAAACATGTTGGTCGCTAAGCAACCAGCCTCTTTCACGGGTTCTGAG                         GTTCGAATCATTGACGATGACATGCCCCTTGCTCAATTTGCTGTTGCTTTC
genomic: CAACAAACATGTTGGTCGCTAAGCAACCAGCCTCTTTCACGGGTTCTGAGgtgggttctg ... ctcttggtagGTTCGAATCATTGACGATGACATGCCCCTTGCTCAATTTGCTGTTGCTTTC
EST: gi|32921737|gb|CF026549.1|CF026549
EST:     CAACAAACATGTTGGTCGCTAAGCAACCAGCCTCTTTCACGGGTTCTGAG                         GTTCGAATCATTGACGATGACATGCCCCTTGCTCAATTTGCTGTTGCTTTC
genomic: CAACAAACATGTTGGTCGCTAAGCAACCAGCCTCTTTCACGGGTTCTGAGgtgggttctg ... ctcttggtagGTTCGAATCATTGACGATGACATGCCCCTTGCTCAATTTGCTGTTGCTTTC
EST: gi|32920952|gb|CF025764.1|CF025764
EST:     CAACAAACATGTTGGTCGCTAAGCAGCCAGCCTCTTTCACGGGTTCTGAG                         GTTCGAATCATTGACGATGACATGCCCCTTGCTCAATTTGCTGTTGCTTTC
genomic: CAACAAACATGTTGGTCGCTAAGCAACCAGCCTCTTTCACGGGTTCTGAGgtgggttctg ... ctcttggtagGTTCGAATCATTGACGATGACATGCCCCTTGCTCAATTTGCTGTTGCTTTC
EST: gi|32826457|gb|CD966135.1|CD966135
EST:     CAACAAACATGTTGGTCGCTAAGCAACCAGCCTCTTTCACGGGTTCTGAG                         GTTCGAATCATTGACGATGACATGCCCCTTGCTCAATTTGCTGTTGCTTTC
genomic: CAACAAACATGTTGGTCGCTAAGCAACCAGCCTCTTTCACGGGTTCTGAGgtgggttctg ... ctcttggtagGTTCGAATCATTGACGATGACATGCCCCTTGCTCAATTTGCTGTTGCTTTC
EST: gi|32922064|gb|CF026876.1|CF026876
EST:     CAACAAACATGTTGGTCGCTAAGCAACCAGCCTCTTTCACGGGTTCTGAG                         GTTCGAATCATTGACGATGACATGCCCCTTGCTCAATTTGCTGTTGCTTTC
genomic: CAACAAACATGTTGGTCGCTAAGCAACCAGCCTCTTTCACGGGTTCTGAGgtgggttctg ... ctcttggtagGTTCGAATCATTGACGATGACATGCCCCTTGCTCAATTTGCTGTTGCTTTC
EST: gi|60355748|gb|DN222721.1|DN222721
EST:     CAACAAACATGTTGGTCGCTAAGCAACCAGCCTCTTTCACGGGTTCTGAG                         GTTCGAATCATTGACGATGACATGCCCCTTGCTCAATTTGCTGTTGCTTTC
genomic: CAACAAACATGTTGGTCGCTAAGCAACCAGCCTCTTTCACGGGTTCTGAGgtgggttctg ... ctcttggtagGTTCGAATCATTGACGATGACATGCCCCTTGCTCAATTTGCTGTTGCTTTC
EST: gi|32920826|gb|CF025638.1|CF025638
EST:     CAACAAACATGTTGGTCGCTAAGCAGCCAGCCTCTTTCACGGGTTCTGAG                         GTTCGAATCATTGACGATGACATGCCCCTTGCTCAATTTGCTGTTGCTTTC
genomic: CAACAAACATGTTGGTCGCTAAGCAACCAGCCTCTTTCACGGGTTCTGAGgtgggttctg ... ctcttggtagGTTCGAATCATTGACGATGACATGCCCCTTGCTCAATTTGCTGTTGCTTTC
EST: gi|32922080|gb|CF026892.1|CF026892
EST:     CAACAAACATGTTGGTCGCTAAGCAACCAGCCTCTTTCACGGGTTCTGAG                         GTTCGAATCATTGACGATGACATGCCCCTTGCTCAATTTGCTGTTGCTTTC
genomic: CAACAAACATGTTGGTCGCTAAGCAACCAGCCTCTTTCACGGGTTCTGAGgtgggttctg ... ctcttggtagGTTCGAATCATTGACGATGACATGCCCCTTGCTCAATTTGCTGTTGCTTTC
EST: gi|5895629|gb|AW036875.1|AW036875
EST:     CAACAAACATGTTGGTCGCTAAGCAACCAGCCTCTTTCACGGGTTCTGAG                         GTTCGAATCATTGACGATGACATGCCCCTTGCTCAATTTGCTGTTGCTTTC
genomic: CAACAAACATGTTGGTCGCTAAGCAACCAGCCTCTTTCACGGGTTCTGAGgtgggttctg ... ctcttggtagGTTCGAATCATTGACGATGACATGCCCCTTGCTCAATTTGCTGTTGCTTTC

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: 202

TGTTGAGCAGGCAAAGAAGTTGTTCAATAAGCTATCAACTGACCCTACAACAACAAACATGTTGGTCGCTAAGCAACCAGCCTCTTTCACGGGTTCTGAGgtgggttctg ... ctcttggtagGTTCGAATCATTGACGATGACATGCCCCTTGCTCAATTTGCTGTTGCTTTCAATGGAGCATCATGGGTAGATCCTGATTCTGTTGCACTGATGGTTATGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 282

TGTTGAGCAGGCAAAGAAGTTGTTCAATAAGCTATCAACTGACCCTACAACAACAAACATGTTGGTCGCTAAGCAACCAGCCTCTTTCACGGGTTCTGAGgtgggttctg ... ctcttggtagGTTCGAATCATTGACGATGACATGCCCCTTGCTCAATTTGCTGTTGCTTTCAATGGAGCATCATGGGTAGATCCTGATTCTGTTGCACTGATGGTTATGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 256

TGTTGAGCAGGCAAAGAAGTTGTTCAATAAGCTATCAACTGACCCTACAACAACAAACATGTTGGTCGCTAAGCAACCAGCCTCTTTCACGGGTTCTGAGgtgggttctg ... ctcttggtagGTTCGAATCATTGACGATGACATGCCCCTTGCTCAATTTGCTGTTGCTTTCAATGGAGCATCATGGGTAGATCCTGATTCTGTTGCACTGATGGTTATGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 351

TGTTGAGCAGGCAAAGAAGTTGTTCAATAAGCTATCAACTGACCCTACAACAACAAACATGTTGGTCGCTAAGCAACCAGCCTCTTTCACGGGTTCTGAGgtgggttctg ... ctcttggtagGTTCGAATCATTGACGATGACATGCCCCTTGCTCAATTTGCTGTTGCTTTCAATGGAGCATCATGGGTAGATCCTGATTCTGTTGCACTGATGGTTATGC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTTGAGCAGGCAAAGAAGTTGTTCAATAAGCTATCAACTGACCCTACAACAACAAACATGTTGGTCGCTAAGCAACCAGCCTCTTTCACGGGTTCTGAGgtgggttctgcaatttttcactctatacttagttgtgctatttttcatgaacccacattatttcaccattgtatgctctcttggtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA