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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCTGGTGGTCTCTTTCAGATTCAAAATATGCTGGGACAGCTATGTTTATAAAGAAAAAGTTTGAGCCTAAGAAGGTGTCTTTCAACTTGGATAGAACATgtatgtttggagatgatttcatattatcctagctctgtacacaattttctattttctatgctaatgtagcagcaattctgttttgcatattatagtttta...

Basic information

species Zea mays
transcript GRMZM2G170291_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G170291_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os12g18200.1 (Oryza sativa), 5'ss of exon 3
GTCTGGTGGTCTCTTTCAGATTCAAAATATGCTGGGACAGCTATGTTTATAAAGAAAAAGTTTGAGCCTAAGAAGGTGTCTTTCAACTTGGATAGAACATgtatgtttggag--------atgatttcatattatcctagctctgtacacaattttctattttctatgc-taatgtagcagcaattctgttttgcatattatagtttta
|||||||||||||||||||| || |||||||| || ||||||||| |||||||||| |||||||| || ||||| ||||| ||||||||||||||||||||||||||  |||        |||| |||||||| ||||   |   ||  |||| | |  || ||  ||  |  |||||   | ||    |||    |  | |       
GTCTGGTGGTCTCTTTCAGACTCCAAATATGCAGGCACAGCTATGATTATAAAGAAGAAGTTTGAACCAAAGAAAGTGTCATTCAACTTGGATAGAACATgtatgttcagagttgcatgcatgacttcatattttcct---ttcataggcaatctcccgttatcggtgtgttttgtagtgtccatgtgctttgctctggtgtg------

upper sequence: GRMZM2G170291_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA04G36610.1 (Glycine max), 5'ss of exon 3
GTCTGGTGGTCTCTTTCAGATTCAAAATATGCTGGGACAGCTATGTTTATAAAGAAAAAGTTTGAGCCTAAGAAGGTGTCTTTCAACTTGGATAGAACATgtatgtttggagatgatttcatattatcctagctctgtacacaattttctattttctatgctaatgtagcagcaattctgttttgcatattatagtttta
|| |||||||||||| |||||||||| ||||| ||||||||  |  |  | || |||   ||  |||| || |  ||   ||||||  | |||| |  | ||||              |  |  |||  |   | ||     ||   | | ||||  ||    || ||     |  | | | ||    |||  | | | |
GTTTGGTGGTCTCTTGCAGATTCAAAGTATGCAGGGACAGCACTACTGGTGAAAAAATGCTTCAAGCCAAAAAGTGTTGTTTTCAATCTTGATAAATTAGgtatccagctttgcagacttttcctattgtgtttatggcattaaacatttcttttgcatatatatatatatatatatatatattcagcattcaaatgtca
















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|78105400|gb|DV523818.1|DV523818
EST:     AAAGAAAAAGTTTGAGCCTAAGAAGGTGTCTTTCAACTTGGATAGAACAT                         CTTCTAAGCATGAAGCCGATGGGCGTGTTATAATTGCGGAATTTGAATCAT
genomic: AAAGAAAAAGTTTGAGCCTAAGAAGGTGTCTTTCAACTTGGATAGAACATgtatgtttgg ... cacttttcagCTTCTAAGCATGAAGCCGATGGGCGTGTTATAATTGCGGAATTTGAATCAT
EST: gi|71770443|gb|DR968380.1|DR968380
EST:     AAAGAAAAAGTTTGAGCCTAAGAAGGTGTCTTTCAACTTGGATAGAACAT                         CTTCTAAGCATGAAGCCGATGGGCGTGTTATAATTGCGGAATTTGAATCAT
genomic: AAAGAAAAAGTTTGAGCCTAAGAAGGTGTCTTTCAACTTGGATAGAACATgtatgtttgg ... cacttttcagCTTCTAAGCATGAAGCCGATGGGCGTGTTATAATTGCGGAATTTGAATCAT
EST: gi|211194081|gb|FL030608.1|FL030608
EST:     AAAGAAAAAGTTTGAGCCTAAGAAGGTGTCTTTCAACTTGGATAGAACAT                         CTTCTAAGCATGAAGCCGATGGGCGTGTTATAA
genomic: AAAGAAAAAGTTTGAGCCTAAGAAGGTGTCTTTCAACTTGGATAGAACATgtatgtttgg ... cacttttcagCTTCTAAGCATGAAGCCGATGGGCGTGTTATAA
EST: gi|94475567|gb|EB704525.1|EB704525
EST:     AAAGAAGAAGTTTGAGCCTAAGAAGGTGTCCTTCAACTGGGATAGAACAT                         CTTCTACGCATGAAGCCGATGGGCGGTGT-ATAATTGCGGATTTTGAATCA
genomic: AAAGAAAAAGTTTGAGCCTAAGAAGGTGTCTTTCAACTTGGATAGAACATgtatgtttgg ... cacttttcagCTTCTAAGCATGAAGCCGATGGGCG-TGTTATAATTGCGGAATTTGAATCA
EST: gi|71431551|gb|DR812601.1|DR812601
EST:     AAAGAAAAAGTTTGAGCCTAAGAAGGTGTCTTTCAACTTGGATAGAACAT                         CTTCTAAGCATGAAGCCGATGGGCGTGTTATAATTGCGGAATTTGAATCAT
genomic: AAAGAAAAAGTTTGAGCCTAAGAAGGTGTCTTTCAACTTGGATAGAACATgtatgtttgg ... cacttttcagCTTCTAAGCATGAAGCCGATGGGCGTGTTATAATTGCGGAATTTGAATCAT
EST: gi|149095617|gb|EE168978.2|EE168978
EST:     AAAGAAAAAGTTTGAGCCTAAGAAGGTGTCTTTCAACTTGGATAGAACAT                         CTTCTAAGCATGAAGCCGATGGGCGTGTTATAATTGCGGAATTTGAATCAT
genomic: AAAGAAAAAGTTTGAGCCTAAGAAGGTGTCTTTCAACTTGGATAGAACATgtatgtttgg ... cacttttcagCTTCTAAGCATGAAGCCGATGGGCGTGTTATAATTGCGGAATTTGAATCAT
EST: gi|76018500|gb|DT945670.1|DT945670
EST:     AAAGAAAAAGTTTGAGCCTAAGAAGGTGTCTTTCAACTTGGATAGAACAT                         CTTCTAAGCATGAAGCCGATGGGCGTGTTATAATTGCGGAATTTGAATCAT
genomic: AAAGAAAAAGTTTGAGCCTAAGAAGGTGTCTTTCAACTTGGATAGAACATgtatgtttgg ... cacttttcagCTTCTAAGCATGAAGCCGATGGGCGTGTTATAATTGCGGAATTTGAATCAT
EST: gi|40287182|gb|CK327574.1|CK327574
EST:     AAAGAAAAAGTTTGAGCCTAAGAAGGTGTCTTTCAACTTGGATAGAACAT                         CTTCTAAGCATGAAGCCGATAGGCGTGTTATAATTGCGGAATTTGAATCAT
genomic: AAAGAAAAAGTTTGAGCCTAAGAAGGTGTCTTTCAACTTGGATAGAACATgtatgtttgg ... cacttttcagCTTCTAAGCATGAAGCCGATGGGCGTGTTATAATTGCGGAATTTGAATCAT
EST: gi|71771442|gb|DR969379.1|DR969379
EST:     AAAGAAAAAGTTTGAGCCTAAGAAGGTGTCTTTCAACTTGGATAGAACAT                         CTTCTAAGCATGAAGCCGATGGGCGTGTTATAATTGCGGAATTTGAATCAT
genomic: AAAGAAAAAGTTTGAGCCTAAGAAGGTGTCTTTCAACTTGGATAGAACATgtatgtttgg ... cacttttcagCTTCTAAGCATGAAGCCGATGGGCGTGTTATAATTGCGGAATTTGAATCAT
EST: gi|211194080|gb|FL030607.1|FL030607
EST:     AAGAAAANGTTTGAGCCTAAGAAGGTGTCTTTNCA-CTTGGATAGAACAT                         CTTCTAAGCATGAAGCCGATGGGCGTGTTATAATTGCGGAATT-GAATCAT
genomic: AAGAAAAAGTTTGAGCCTAAGAAGGTGTCTTT-CAACTTGGATAGAACATgtatgtttgg ... cacttttcagCTTCTAAGCATGAAGCCGATGGGCGTGTTATAATTGCGGAATTTGAATCAT
EST: gi|91872355|gb|EB402312.1|EB402312
EST:     AAAGAAAAAGTTTGAGCCTAAGAAGGTGTCTTTCAACTTGGATAGAACAT                         CTTCTAAGCATGAAGCCGATGGGCGTGTTATAATTGCGGAATTTGAATCAT
genomic: AAAGAAAAAGTTTGAGCCTAAGAAGGTGTCTTTCAACTTGGATAGAACATgtatgtttgg ... cacttttcagCTTCTAAGCATGAAGCCGATGGGCGTGTTATAATTGCGGAATTTGAATCAT
EST: gi|78074005|gb|DV502439.1|DV502439
EST:     AAAGAAAAAGTTTGAGCCTAAGAAGGTGTCTTTCAACTTGGATAGAACAT                         CTTCTAAGCATGAAGCCGATGGGCGTGTTATAATTGCGGAATTTGAATCAT
genomic: AAAGAAAAAGTTTGAGCCTAAGAAGGTGTCTTTCAACTTGGATAGAACATgtatgtttgg ... cacttttcagCTTCTAAGCATGAAGCCGATGGGCGTGTTATAATTGCGGAATTTGAATCAT
EST: gi|84980468|gb|DW530817.1|DW530817
EST:     AAAGAAAAAGTTTGAGCCTAAGAAGGTGTCTTTCAACTTGGATAGAACAT                         CTTCTAAGCATGAAGCCGATGGGCGTGTTATAATTGCGGAATTTGAATCAT
genomic: AAAGAAAAAGTTTGAGCCTAAGAAGGTGTCTTTCAACTTGGATAGAACATgtatgtttgg ... cacttttcagCTTCTAAGCATGAAGCCGATGGGCGTGTTATAATTGCGGAATTTGAATCAT
EST: gi|76016191|gb|DT943361.1|DT943361
EST:     AAAGAAAAAGTTTGAGCCTAAGAAGGTGTCTTTCAACTTGGATAGAACAT                         CTTCTAAGCATGAAGCCGATGGGCGTGTTATAATTGCGGAATTTGAATCAT
genomic: AAAGAAAAAGTTTGAGCCTAAGAAGGTGTCTTTCAACTTGGATAGAACATgtatgtttgg ... cacttttcagCTTCTAAGCATGAAGCCGATGGGCGTGTTATAATTGCGGAATTTGAATCAT
EST: gi|76021196|gb|DT948366.1|DT948366
EST:     AAAGAAAAAGTTTGAGCCTAAGAAGGTGTCTTTCAACTTGGATAGAACAT                         CTTCTAAGCATGAAGCCGATGGGCGTGTTATAATTGCGGAATTTGAATCAT
genomic: AAAGAAAAAGTTTGAGCCTAAGAAGGTGTCTTTCAACTTGGATAGAACATgtatgtttgg ... cacttttcagCTTCTAAGCATGAAGCCGATGGGCGTGTTATAATTGCGGAATTTGAATCAT
EST: gi|50330655|gb|CO525781.1|CO525781
EST:     AAAGAAAAAGTTTGAGCCTAAGAAGGTGTCTTTCAACTTGGATAGAACAT                         CTTCTAAGCATGAAGCCGATGGGCGTGTTATAATTGCGGAATTTGAATCAT
genomic: AAAGAAAAAGTTTGAGCCTAAGAAGGTGTCTTTCAACTTGGATAGAACATgtatgtttgg ... cacttttcagCTTCTAAGCATGAAGCCGATGGGCGTGTTATAATTGCGGAATTTGAATCAT
EST: gi|74236588|gb|DT644502.1|DT644502
EST:     AAAGAAAAAGTTTGAGCCTAAGAAGGTGTCTTTCAACTTGGATAGAACAT                         CTTCTAAGCATGAAGCCGATGGGCGTGTTATAATTGCGGAATTTGAATCAT
genomic: AAAGAAAAAGTTTGAGCCTAAGAAGGTGTCTTTCAACTTGGATAGAACATgtatgtttgg ... cacttttcagCTTCTAAGCATGAAGCCGATGGGCGTGTTATAATTGCGGAATTTGAATCAT
EST: gi|50332550|gb|CO527676.1|CO527676
EST:     AAAGAAAAAGTTTGAGCCTAAGAAGGTGTCTTTCAACTTGGATAGAACAT                         CTTCTAAGCATGAAGCCGATGGGCGTGTTATAATTGCGGAATTTGAATCAT
genomic: AAAGAAAAAGTTTGAGCCTAAGAAGGTGTCTTTCAACTTGGATAGAACATgtatgtttgg ... cacttttcagCTTCTAAGCATGAAGCCGATGGGCGTGTTATAATTGCGGAATTTGAATCAT
EST: gi|50325227|gb|CO520353.1|CO520353
EST:     AAAGAAAAAGTTTGAGCCTAAGAAGGTGTCTTTCAACTTGGATAGAACAT                         CTTCTAAGCATGAAGCCGATGGGCGTGTTATAATTGCGGAATTTGAATCAT
genomic: AAAGAAAAAGTTTGAGCCTAAGAAGGTGTCTTTCAACTTGGATAGAACATgtatgtttgg ... cacttttcagCTTCTAAGCATGAAGCCGATGGGCGTGTTATAATTGCGGAATTTGAATCAT
EST: gi|76010861|gb|DT938031.1|DT938031
EST:     AAAGAAAAAGTTTGAGCCTAAGAAGGTGTCTTTCAACTTGGATAGAACAT                         CTTCTAAGCATGAAGCCGATGGGCGTGTTATAATTGCGGAATTTGAATCAT
genomic: AAAGAAAAAGTTTGAGCCTAAGAAGGTGTCTTTCAACTTGGATAGAACATgtatgtttgg ... cacttttcagCTTCTAAGCATGAAGCCGATGGGCGTGTTATAATTGCGGAATTTGAATCAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCTGGTGGTCTCTTTCAGATTCAAAATATGCTGGGACAGCTATGTTTATAAAGAAAAAGTTTGAGCCTAAGAAGGTGTCTTTCAACTTGGATAGAACATgtatgtttggagatgatttcatattatcctagctctgtacacaattttctattttctatgctaatgtagcagcaattctgttttgcatattatagtttta

- - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG