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

ATCACCGCTGGTCGGCTATGTGCATCGCGGCATGGGCGTGGCACTGCCACCCGACGCACCGCCTGCTTCTGCTGTTCAATCGCGACGAGTATCACTCCAGgtgcgcgcccctcccctcgccgtccatctccacatccccatctctctctctctctaaatctctaagccggtacacccgcgaatcggtccag

Basic information

species Zea mays
transcript GRMZM2G003057_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|211484497|gb|FL376552.1|FL376552
EST:     CCGACGCACCGCCTGCTTCTGCTGTTCAATCGCGACGAGTATCACTCCAG                         GCCGACGCAGCCGGCGCAGTGGTGGGCGGCGGGGGAGGAAGCCAAGGAAAT
genomic: CCGACGCACCGCCTGCTTCTGCTGTTCAATCGCGACGAGTATCACTCCAGgtgcgcgccc ... atcggtccagGCCGACGCAGCCGGCGCAGTGGTGGGCGGCGGGGGAGGAAGCCAAGGAAAT
EST: gi|211394987|gb|FL376971.1|FL376971
EST:     CCGACGCACCGCCTGCTTCTGCTGTTCAATCGCGACGAGTATCACTCCAG                         GCCGACGCAGCCGGCGCAGTGGTGGGCGGCGGGGGAGGAAGCCAAGGAAAT
genomic: CCGACGCACCGCCTGCTTCTGCTGTTCAATCGCGACGAGTATCACTCCAGgtgcgcgccc ... atcggtccagGCCGACGCAGCCGGCGCAGTGGTGGGCGGCGGGGGAGGAAGCCAAGGAAAT
EST: gi|211509432|gb|FL413813.1|FL413813
EST:     CCGACGCACCGCCTGCTTCTGCTGTTCAATCGCGACGAGTATCACTCCAG                         GCCGACGCAGCCGGCGCAGTGGTGGGCGGCGGGGGAGGAAGCCAAGGAAAT
genomic: CCGACGCACCGCCTGCTTCTGCTGTTCAATCGCGACGAGTATCACTCCAGgtgcgcgccc ... atcggtccagGCCGACGCAGCCGGCGCAGTGGTGGGCGGCGGGGGAGGAAGCCAAGGAAAT
EST: gi|211074490|gb|FL413464.1|FL413464
EST:     CCGACGCACCGCCTGCTKCTGCTGTTCAATCGCGACGAGTATCACACCAG                         GCCGACGCAGCCGGCGCAGTGGTGGGCGGCGGGKGAGGAAGCCAAGGAAAT
genomic: CCGACGCACCGCCTGCTTCTGCTGTTCAATCGCGACGAGTATCACTCCAGgtgcgcgccc ... atcggtccagGCCGACGCAGCCGGCGCAGTGGTGGGCGGCGGGGGAGGAAGCCAAGGAAAT
EST: gi|211242704|gb|FL378106.1|FL378106
EST:     CCGACGCACCGCCTGCTTCTGCTGTTCAATCGCGACGAGTATCACTCCAG                         GCCGACGCAGCCGGCGCAGTGGTGGGCGGCGGGGGAGGAAGCCAAGGAAAT
genomic: CCGACGCACCGCCTGCTTCTGCTGTTCAATCGCGACGAGTATCACTCCAGgtgcgcgccc ... atcggtccagGCCGACGCAGCCGGCGCAGTGGTGGGCGGCGGGGGAGGAAGCCAAGGAAAT
EST: gi|211309013|gb|FL381285.1|FL381285
EST:     CCGACGCACCGCCTGCTTCTGCTGTTCAATCGCGACGAGTATCACTCCAG                         GCCGACGCAGCCGGCGCAGTGGTGGGCGGCGGGGGAGGAAGCCAAGGAAAT
genomic: CCGACGCACCGCCTGCTTCTGCTGTTCAATCGCGACGAGTATCACTCCAGgtgcgcgccc ... atcggtccagGCCGACGCAGCCGGCGCAGTGGTGGGCGGCGGGGGAGGAAGCCAAGGAAAT
EST: gi|211256544|gb|FL390497.1|FL390497
EST:     CCGACGCACCGCCTGCTTCTGCTGTTCAATCGCGACGAGTATCACTCCAG                         GCCGACGCAGCCGGCGCAGTGGTGGGCGGCGGGGGAGGAAGCCAAGGAAAT
genomic: CCGACGCACCGCCTGCTTCTGCTGTTCAATCGCGACGAGTATCACTCCAGgtgcgcgccc ... atcggtccagGCCGACGCAGCCGGCGCAGTGGTGGGCGGCGGGGGAGGAAGCCAAGGAAAT
EST: gi|211150343|gb|FL403094.1|FL403094
EST:     CCGACGCACCGCCTGCTTCTGCTGTTCAATCGCGACGAGTATCACTCCAG                         GCCGACGCAGCCGGCGCAGTGGTGGGCGGCGGGGGAGGAAGCCAAGGAAAT
genomic: CCGACGCACCGCCTGCTTCTGCTGTTCAATCGCGACGAGTATCACTCCAGgtgcgcgccc ... atcggtccagGCCGACGCAGCCGGCGCAGTGGTGGGCGGCGGGGGAGGAAGCCAAGGAAAT
EST: gi|211115170|gb|FL372345.1|FL372345
EST:     CGNACGCACCGCCTGCTTCTGCTGTTCAATCGCGACGAGTATCACTCCAG                         GCCGACGCAGCCGGCGCAGTGGTGGGCGGCGGGGGAGGAAGCCAAGGAAAT
genomic: CG-ACGCACCGCCTGCTTCTGCTGTTCAATCGCGACGAGTATCACTCCAGgtgcgcgccc ... atcggtccagGCCGACGCAGCCGGCGCAGTGGTGGGCGGCGGGGGAGGAAGCCAAGGAAAT
EST: gi|149100496|gb|EE186576.2|EE186576
EST:     CCGACGCACCGCCTGCTTCTGCTGTTCAATCGCGACGAGTATCACTCCAG                         GCCGACGCAGCCGGCGCAGTGGTGGGCGGCGGGGGAGGAAGCCAAGGAAAT
genomic: CCGACGCACCGCCTGCTTCTGCTGTTCAATCGCGACGAGTATCACTCCAGgtgcgcgccc ... atcggtccagGCCGACGCAGCCGGCGCAGTGGTGGGCGGCGGGGGAGGAAGCCAAGGAAAT
EST: gi|211127336|gb|FL391795.1|FL391795
EST:     CGACGCACCGCCTGCTTCTGCTGTTCAATCGCGACGAGTATCACTCGCAG                         GCCGACGCAGCCGGCGCAGTGGTGGGCGGCGGGGGAGGAAGCCAAGGAAA
genomic: CGACGCACCGCCTGCTTCTGCTGTTCAATCGCGACGAGTATCACTC-CAGgtgcgcgccc ... atcggtccagGCCGACGCAGCCGGCGCAGTGGTGGGCGGCGGGGGAGGAAGCCAAGGAAA
EST: gi|211421544|gb|FL418414.1|FL418414
EST:     CCGACGCACCGCCTGCTTCTGCTGTTCAATCGCGACGAGTATCACTCCAG                         GCCGACGCAGCCGGCGCAGTGGTGGGCGGCGGGGGAGGAAGCCAAGGAAAT
genomic: CCGACGCACCGCCTGCTTCTGCTGTTCAATCGCGACGAGTATCACTCCAGgtgcgcgccc ... atcggtccagGCCGACGCAGCCGGCGCAGTGGTGGGCGGCGGGGGAGGAAGCCAAGGAAAT

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: 53

ATCACCGCTGGTCGGCTATGTGCATCGCGGCATGGGCGTGGCACTGCCACCCGACGCACCGCCTGCTTCTGCTGTTCAATCGCGACGAGTATCACTCCAGgtgcgcgccc ... atcggtccagGCCGACGCAGCCGGCGCAGTGGTGGGCGGCGGGGGAGGAAGCCAAGGAAATCCTTGGAGGCAGGGACGAGCTCGGCGGGGGAACGTGGATGGGGTGCACG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 111

ATCACCGCTGGTCGGCTATGTGCATCGCGGCATGGGCGTGGCACTGCCACCCGACGCACCGCCTGCTTCTGCTGTTCAATCGCGACGAGTATCACTCCAGgtgcgcgccc ... atcggtccagGCCGACGCAGCCGGCGCAGTGGTGGGCGGCGGGGGAGGAAGCCAAGGAAATCCTTGGAGGCAGGGACGAGCTCGGCGGGGGAACGTGGATGGGGTGCACG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 80

ATCACCGCTGGTCGGCTATGTGCATCGCGGCATGGGCGTGGCACTGCCACCCGACGCACCGCCTGCTTCTGCTGTTCAATCGCGACGAGTATCACTCCAGgtgcgcgccc ... atcggtccagGCCGACGCAGCCGGCGCAGTGGTGGGCGGCGGGGGAGGAAGCCAAGGAAATCCTTGGAGGCAGGGACGAGCTCGGCGGGGGAACGTGGATGGGGTGCACG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 100

ATCACCGCTGGTCGGCTATGTGCATCGCGGCATGGGCGTGGCACTGCCACCCGACGCACCGCCTGCTTCTGCTGTTCAATCGCGACGAGTATCACTCCAGgtgcgcgccc ... atcggtccagGCCGACGCAGCCGGCGCAGTGGTGGGCGGCGGGGGAGGAAGCCAAGGAAATCCTTGGAGGCAGGGACGAGCTCGGCGGGGGAACGTGGATGGGGTGCACG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCACCGCTGGTCGGCTATGTGCATCGCGGCATGGGCGTGGCACTGCCACCCGACGCACCGCCTGCTTCTGCTGTTCAATCGCGACGAGTATCACTCCAGgtgcgcgcccctcccctcgccgtccatctccacatccccatctctctctctctctaaatctctaagccggtacacccgcgaatcggtccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT