Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGCAGCGCAGCTTATCCCCAGGTTCTTCCGGAGCTTCCCTGCACTCGGCACGCGCGCCATGTCAGCCATGTTCGATCTCGTCGATATGGAGGAGCTCGCGgtatatgcctgtatctctctagattcccctgcccgttggcagagcggtatgtttgggcattattctgtgtaactacctgttgagagcaaacccactagca...

Basic information

species Zea mays
transcript GRMZM2G059039_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G059039_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os02g20930.1 (Oryza sativa), 5'ss of exon 2
CGCAGCGCAGCTTATCCCCAGGTTCTTCCGGAGCTTCCCTGCACTCGGCACGCGCGCCATGTCAGCCATGTTCGATCTCGTCGATATGGAGGAGCTCGCGgtatatgcctgtatctctctagattcccctgcccgttggcagagcggtatgtttgggcattattctgtgtaactacctgttgagagcaaacccactagca----
||| |||||||| |||||| | ||||||||||||||||| ||||||| | |||||||||||   ||||||||||| |||||||| |||||||| ||||||||||   |       | || ||| |||       | ||   | |   || |     |  |   | |    || |||     |||  ||    || ||       
CGCGGCGCAGCTCATCCCCCGCTTCTTCCGGAGCTTCCCGGCACTCGCCCCGCGCGCCATGGAGGCCATGTTCGACCTCGTCGACATGGAGGAACTCGCGgtatgcactctcccttttcgagaatccagataatgctgctcgtg---tacgacctagtttagctttacagaattacagaacgagt-cacttgcattatttgcta
















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|211179438|gb|FL364366.1|FL364366
EST:     CGCGCGCCATGTCAGCCATGTTCGATCTCGTCGATATGGAGGAGCTCGCG                         ATCAGAATACAAGCTATTCGTGGCTTTCCACTTCTTGGCAAAGATACTGAA
genomic: CGCGCGCCATGTCAGCCATGTTCGATCTCGTCGATATGGAGGAGCTCGCGgtatatgcct ... gttcctacagATCAGAATACAAGCTATTCGTGGCTTTCCACTTCTTGGCAAAGATACTGAA
EST: gi|211344380|gb|FL313708.1|FL313708
EST:     CGCGCGCCATGTCAGCCATGTTCGATCTCGTCGATATGGAGGAGCTCGCG                         NTCAGAATACAAGCTATTCGTGGCTTTCCACTTCTTGGCAAAGATACTGAA
genomic: CGCGCGCCATGTCAGCCATGTTCGATCTCGTCGATATGGAGGAGCTCGCGgtatatgcct ... gttcctacagATCAGAATACAAGCTATTCGTGGCTTTCCACTTCTTGGCAAAGATACTGAA
EST: gi|148969036|gb|EE019749.2|EE019749
EST:     CGCGCGCCATGTCAGCCATGTTCGATCTCGTCGATATGGAGGAGCTCGCG                         ATCAGAATACAAGCTATTCGTGGCTTTCCACTTCTTGGCAAAGATACTGAA
genomic: CGCGCGCCATGTCAGCCATGTTCGATCTCGTCGATATGGAGGAGCTCGCGgtatatgcct ... gttcctacagATCAGAATACAAGCTATTCGTGGCTTTCCACTTCTTGGCAAAGATACTGAA
EST: gi|211444762|gb|FL341640.1|FL341640
EST:     CGCGCGCCATGTCAGCCATGTTCGATCTCGTCGATATGGAGGAGCTCGCG                         ATCAGAATACAAGCTATTCGTGGCTTTCCACTTCTTGGCAAAGATACTGAA
genomic: CGCGCGCCATGTCAGCCATGTTCGATCTCGTCGATATGGAGGAGCTCGCGgtatatgcct ... gttcctacagATCAGAATACAAGCTATTCGTGGCTTTCCACTTCTTGGCAAAGATACTGAA
EST: gi|71766575|gb|DR964512.1|DR964512
EST:     CGCGCGCCATGTCAGCCATGTTCGATCTCGTCGATATGGAGGAGCTCGCG                         ATCAGAATACAAGCTATTCGTGGCTTTCCACTTCTTGGCAAAGATACTGAA
genomic: CGCGCGCCATGTCAGCCATGTTCGATCTCGTCGATATGGAGGAGCTCGCGgtatatgcct ... gttcctacagATCAGAATACAAGCTATTCGTGGCTTTCCACTTCTTGGCAAAGATACTGAA
EST: gi|211281795|gb|FL349528.1|FL349528
EST:     CGCGCGCCATGTCAGCCATGTTCGATCTCGTCGATATGGAGGAGCTCGCG                         ATCAGAATACAAGCTATTCGTGGCTTTCCACTTCTTGGCAAAGATACTGAA
genomic: CGCGCGCCATGTCAGCCATGTTCGATCTCGTCGATATGGAGGAGCTCGCGgtatatgcct ... gttcctacagATCAGAATACAAGCTATTCGTGGCTTTCCACTTCTTGGCAAAGATACTGAA
EST: gi|211012398|gb|FL319259.1|FL319259
EST:     CGCGCGCCATGTCAGCCATGTTCGATCTCGTCGATATGGAGGAGCTCGCG                         ATCAGAATACAAGCTATTCGTGGCTTTCCACTTCTTGGCAAAGATACTGAA
genomic: CGCGCGCCATGTCAGCCATGTTCGATCTCGTCGATATGGAGGAGCTCGCGgtatatgcct ... gttcctacagATCAGAATACAAGCTATTCGTGGCTTTCCACTTCTTGGCAAAGATACTGAA
EST: gi|211407222|gb|FL345640.1|FL345640
EST:     CGCGCGCCATGTCAGCCATGTTCGATCTCGTCGATATGGAGGAGCTCGCG                         ATCAGAATACAAGCTATTCGTGGCTTTCCACTTCTTGGCAAAGATACTGAA
genomic: CGCGCGCCATGTCAGCCATGTTCGATCTCGTCGATATGGAGGAGCTCGCGgtatatgcct ... gttcctacagATCAGAATACAAGCTATTCGTGGCTTTCCACTTCTTGGCAAAGATACTGAA
EST: gi|211433492|gb|FL365020.1|FL365020
EST:     CGCGCGCCATGTCAGCCATGTTCGATCTCGTCGATATGGAGGAGCTCGCG                         ATCAGAATACAAGCTATTCGTGGCTTTCCACTTCTTGGCAAAGATACTGAA
genomic: CGCGCGCCATGTCAGCCATGTTCGATCTCGTCGATATGGAGGAGCTCGCGgtatatgcct ... gttcctacagATCAGAATACAAGCTATTCGTGGCTTTCCACTTCTTGGCAAAGATACTGAA
EST: gi|148943964|gb|EC889044.2|EC889044
EST:     CGCGCGCCATGTCAGCCATGTTCGATCTCGTCGATATGGAGGAGCTCGCG                         ATCAGAATACAAGCTATTCGTGGCTTTCCACTTCTTGGCAAAGATACTGAA
genomic: CGCGCGCCATGTCAGCCATGTTCGATCTCGTCGATATGGAGGAGCTCGCGgtatatgcct ... gttcctacagATCAGAATACAAGCTATTCGTGGCTTTCCACTTCTTGGCAAAGATACTGAA
EST: gi|211185388|gb|FL309812.1|FL309812
EST:     CGCGCGCCATGTCAGCCATGTTCGATCTCGTCGATATGGAGGAGCTCGCG                         ATCAGAATACAAGCTATTCGTGGCTTTCCACTTCTTGGCAAAGATACTGAA
genomic: CGCGCGCCATGTCAGCCATGTTCGATCTCGTCGATATGGAGGAGCTCGCGgtatatgcct ... gttcctacagATCAGAATACAAGCTATTCGTGGCTTTCCACTTCTTGGCAAAGATACTGAA
EST: gi|211314239|gb|FL336753.1|FL336753
EST:     CGCGCGCCATGTCAGCCATGTTCGATCTCGTCTATATGGAGGAGCTCGCG                         ATCAGAATACAAGCTATTCGTGGCTTTCCACTTCTTGGCAAAGATACTGAA
genomic: CGCGCGCCATGTCAGCCATGTTCGATCTCGTCGATATGGAGGAGCTCGCGgtatatgcct ... gttcctacagATCAGAATACAAGCTATTCGTGGCTTTCCACTTCTTGGCAAAGATACTGAA
EST: gi|76014976|gb|DT942146.1|DT942146
EST:     CGCGCGCCATGTCAGCCATGTTCGATCTCGTCGATATGGAGGAGCTCGCG                         ATCAGAATACAAGCTATTCGTGGCTTTCCACTTCTTGGCAAAGATACTGAA
genomic: CGCGCGCCATGTCAGCCATGTTCGATCTCGTCGATATGGAGGAGCTCGCGgtatatgcct ... gttcctacagATCAGAATACAAGCTATTCGTGGCTTTCCACTTCTTGGCAAAGATACTGAA
EST: gi|211158733|gb|FL327703.1|FL327703
EST:     CGCGCGCCATGTCAGCCATGTTCGATCTCGTCGATATGGAGGAGCTCGCG                         ATCAGAATACAAGCTATTCGTGGCTTTCCACTTCTTGGCAAAGATACTGAA
genomic: CGCGCGCCATGTCAGCCATGTTCGATCTCGTCGATATGGAGGAGCTCGCGgtatatgcct ... gttcctacagATCAGAATACAAGCTATTCGTGGCTTTCCACTTCTTGGCAAAGATACTGAA
EST: gi|211170432|gb|FL336616.1|FL336616
EST:     CGCGCGCCATGTCAGCCATGTTCGATCTCGTCGATATGGAGGAGCTCGCG                         ATCAGAATACAAGCTATTCGTGGCTTTCCACTTCTTGGCAAAGATACTGAA
genomic: CGCGCGCCATGTCAGCCATGTTCGATCTCGTCGATATGGAGGAGCTCGCGgtatatgcct ... gttcctacagATCAGAATACAAGCTATTCGTGGCTTTCCACTTCTTGGCAAAGATACTGAA
EST: gi|32164953|gb|CD670271.1|CD670271
EST:     CGCGCGCCATGTCAGCCATGTTCGATCTCGTCGATATGGAGGAGCTCGCG                         ATCAGAATACAAGCTATTCGTGGCTTTCCACTTCTTGGCAAAGATACTGAA
genomic: CGCGCGCCATGTCAGCCATGTTCGATCTCGTCGATATGGAGGAGCTCGCGgtatatgcct ... gttcctacagATCAGAATACAAGCTATTCGTGGCTTTCCACTTCTTGGCAAAGATACTGAA
EST: gi|211306674|gb|FL363564.1|FL363564
EST:     CGCGCGCCATGTCAGCCATGTTCGATCTCGTCGATATGGAGGAGCTCGCG                         ATCAGAATACAAGCTATTCGTGGCTTTCCACTTCTTGGCAAAGATACTGAA
genomic: CGCGCGCCATGTCAGCCATGTTCGATCTCGTCGATATGGAGGAGCTCGCGgtatatgcct ... gttcctacagATCAGAATACAAGCTATTCGTGGCTTTCCACTTCTTGGCAAAGATACTGAA
EST: gi|211375331|gb|FL327051.1|FL327051
EST:     CGCGCGCCATGTCAGCCATGTTCGATCTCGTCGATATGGAGGAGCTCGCG                         ATCAGAATACAAGCTATTCGTGGCTTTCCACTTCTTGGCAAAGATACTGAA
genomic: CGCGCGCCATGTCAGCCATGTTCGATCTCGTCGATATGGAGGAGCTCGCGgtatatgcct ... gttcctacagATCAGAATACAAGCTATTCGTGGCTTTCCACTTCTTGGCAAAGATACTGAA
EST: gi|108824166|gb|EC278174.1|EC278174
EST:     CGCGCGCCATGTCAGCCATGTTCGATCTCGTCGATATGGAGGAGCTCGCG                         ATCAGAATACAAGCTATTCGTGGCTTTCCACTTCTTGGCAAAGATACTGAA
genomic: CGCGCGCCATGTCAGCCATGTTCGATCTCGTCGATATGGAGGAGCTCGCGgtatatgcct ... gttcctacagATCAGAATACAAGCTATTCGTGGCTTTCCACTTCTTGGCAAAGATACTGAA
EST: gi|31356580|gb|CD440937.1|CD440937
EST:     CGCGCGCCATGTCAGCCATGTTCGATCTCGTCGATATGGAGGAGCTCGCG                         ATCAGAATACAATCTATTCGTGGCTTTCCACTTCTTGGCAAAGATACTGAA
genomic: CGCGCGCCATGTCAGCCATGTTCGATCTCGTCGATATGGAGGAGCTCGCGgtatatgcct ... gttcctacagATCAGAATACAAGCTATTCGTGGCTTTCCACTTCTTGGCAAAGATACTGAA
EST: gi|211041006|gb|FL343143.1|FL343143
EST:     CGCGCGCCATGTCAGCCATGTTCGATCTCGTCGATATGGAGGAGCTCGCG                         ATCAGAANACAAGCTATTCGNGGNTTTCCACTTCTTGGCAAAGATACTGAA
genomic: CGCGCGCCATGTCAGCCATGTTCGATCTCGTCGATATGGAGGAGCTCGCGgtatatgcct ... gttcctacagATCAGAATACAAGCTATTCGTGGCTTTCCACTTCTTGGCAAAGATACTGAA
EST: gi|211050490|gb|FL366022.1|FL366022
EST:     CGCGCGCCATGTCAGCCATGTTCGATCTCGTCGATATGGAGGAGCTCGCG                         ATCAGAATACAAGCTATTCGTGGCTTTCCACTTCTTGGCAAAGATACTGAA
genomic: CGCGCGCCATGTCAGCCATGTTCGATCTCGTCGATATGGAGGAGCTCGCGgtatatgcct ... gttcctacagATCAGAATACAAGCTATTCGTGGCTTTCCACTTCTTGGCAAAGATACTGAA
EST: gi|211103808|gb|FL341011.1|FL341011
EST:     CGCGCGCCATGTCAGCCATGTTCGATCTCGTCGATATGGAGGAGCTCGCG                         ATCAGAATACAAGCTATTCGNGGCTTTCCACTTCTTGGCAAAGATACTGAA
genomic: CGCGCGCCATGTCAGCCATGTTCGATCTCGTCGATATGGAGGAGCTCGCGgtatatgcct ... gttcctacagATCAGAATACAAGCTATTCGTGGCTTTCCACTTCTTGGCAAAGATACTGAA
EST: gi|211055963|gb|FL348933.1|FL348933
EST:     CGCGCGCCATGTCAGCCATGTTCGATCTCGTCGATATGGAGGAGCTCGCG                         ATCAGAATACAAGCTATTCGTGGCTTTCCACTTCTTGGCAAAGATACTGAA
genomic: CGCGCGCCATGTCAGCCATGTTCGATCTCGTCGATATGGAGGAGCTCGCGgtatatgcct ... gttcctacagATCAGAATACAAGCTATTCGTGGCTTTCCACTTCTTGGCAAAGATACTGAA
EST: gi|89761569|gb|DY689527.1|DY689527
EST:     CGCGCGCCATGTCAGCCATGTTCGATCTCGTCGATATGGAGGAGCTCGCG                         ATCAGAATACAAGCTATTCGTGGCTTTCCACTTCTTGGCAAAGATACTGAA
genomic: CGCGCGCCATGTCAGCCATGTTCGATCTCGTCGATATGGAGGAGCTCGCGgtatatgcct ... gttcctacagATCAGAATACAAGCTATTCGTGGCTTTCCACTTCTTGGCAAAGATACTGAA
EST: gi|149105666|gb|EE291222.2|EE291222
EST:     CGCGCGCCATGTCAGCCATGTTCGATCTCGTCGATATGGAGGAGCTCGCG                         ATCAGAATACAAGCTATTCGTGGCTTTCCACTTCTTGGCAAAGATACTGAA
genomic: CGCGCGCCATGTCAGCCATGTTCGATCTCGTCGATATGGAGGAGCTCGCGgtatatgcct ... gttcctacagATCAGAATACAAGCTATTCGTGGCTTTCCACTTCTTGGCAAAGATACTGAA
EST: gi|50326790|gb|CO521916.1|CO521916
EST:     CGCGCGCCATGTCAGCCATGTTCGATCTCGTCGATATGGAGGAGCTCGCG                         ATCAGAATACAAGCTATTCGTGGCTTTCCACTTCTTGGCAAAGATACTGAA
genomic: CGCGCGCCATGTCAGCCATGTTCGATCTCGTCGATATGGAGGAGCTCGCGgtatatgcct ... gttcctacagATCAGAATACAAGCTATTCGTGGCTTTCCACTTCTTGGCAAAGATACTGAA
EST: gi|211416754|gb|FL321419.1|FL321419
EST:     CGCGCGCCATGTCAGCCATGTTCGATCTCGTCGATATGGAGGAGCTCGCG                         ATCAGAATACAAGCTATTCGTGGCTTTCCACTTCTTGGCAAAGATACTGAA
genomic: CGCGCGCCATGTCAGCCATGTTCGATCTCGTCGATATGGAGGAGCTCGCGgtatatgcct ... gttcctacagATCAGAATACAAGCTATTCGTGGCTTTCCACTTCTTGGCAAAGATACTGAA
EST: gi|211145125|gb|FL324993.1|FL324993
EST:     CGCGCGCCATGTCAGCCATGTTCGATCTCGTCGATATGGAGGAGCTCGCG                         ATCAGAATACAAGCTATTCGTGGCTTTCCACTTCTTGGCAAAGATACTGAA
genomic: CGCGCGCCATGTCAGCCATGTTCGATCTCGTCGATATGGAGGAGCTCGCGgtatatgcct ... gttcctacagATCAGAATACAAGCTATTCGTGGCTTTCCACTTCTTGGCAAAGATACTGAA

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: 286

CGCAGCGCAGCTTATCCCCAGGTTCTTCCGGAGCTTCCCTGCACTCGGCACGCGCGCCATGTCAGCCATGTTCGATCTCGTCGATATGGAGGAGCTCGCGgtatatgcct ... gttcctacagATCAGAATACAAGCTATTCGTGGCTTTCCACTTCTTGGCAAAGATACTGAATTTGTGTCAAAAATTGCAGATGTTTTGGGTCAGCTCCTTACAAGCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 113

CGCAGCGCAGCTTATCCCCAGGTTCTTCCGGAGCTTCCCTGCACTCGGCACGCGCGCCATGTCAGCCATGTTCGATCTCGTCGATATGGAGGAGCTCGCGgtatatgcct ... gttcctacagATCAGAATACAAGCTATTCGTGGCTTTCCACTTCTTGGCAAAGATACTGAATTTGTGTCAAAAATTGCAGATGTTTTGGGTCAGCTCCTTACAAGCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 130

CGCAGCGCAGCTTATCCCCAGGTTCTTCCGGAGCTTCCCTGCACTCGGCACGCGCGCCATGTCAGCCATGTTCGATCTCGTCGATATGGAGGAGCTCGCGgtatatgcct ... gttcctacagATCAGAATACAAGCTATTCGTGGCTTTCCACTTCTTGGCAAAGATACTGAATTTGTGTCAAAAATTGCAGATGTTTTGGGTCAGCTCCTTACAAGCG


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

CGCAGCGCAGCTTATCCCCAGGTTCTTCCGGAGCTTCCCTGCACTCGGCACGCGCGCCATGTCAGCCATGTTCGATCTCGTCGATATGGAGGAGCTCGCGgtatatgcct ... gttcctacagATCAGAATACAAGCTATTCGTGGCTTTCCACTTCTTGGCAAAGATACTGAATTTGTGTCAAAAATTGCAGATGTTTTGGGTCAGCTCCTTACAAGCG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGCAGCGCAGCTTATCCCCAGGTTCTTCCGGAGCTTCCCTGCACTCGGCACGCGCGCCATGTCAGCCATGTTCGATCTCGTCGATATGGAGGAGCTCGCGgtatatgcctgtatctctctagattcccctgcccgttggcagagcggtatgtttgggcattattctgtgtaactacctgttgagagcaaacccactagca

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cccctgc