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

...attttaagtaacactctgtgactataataagaatagagcaggatggcttcttgggattgctacatatgcaacacagtgatatttctgctggatcttgtagGTGTGCTTGATGAGAACGGGAAGTTCCTGCTAGCAGCGAAAAGGAGCCGCAGGATGGCGCACACGGAGTATGCAATTTTTATGGACTCGAGGAATTTCTC

Basic information

species Zea mays
transcript GRMZM2G108228_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G108228_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os04g59130.1 (Oryza sativa), 3'ss of exon 3
attttaagtaacactctgtgacta-taataagaatagagcaggatggcttcttgggattgctacatatgcaacacagtgata-tttctgctggatcttgtagGTGTGCTTGATGAGAACGGGAAGTTCCTGCTAGCAGCGAAAAGGAGCCGCAGGATGGCGCACACGGAGTATGCAATTTTTATGGACTCGAGGAATTTCTC
|||      | || | |  ||  | |  | | ||||   | |  | |  | |||         | ||   |   || | | | |||    || ||||||||| ||||||||||||||  || |||||||| ||| |||| |||||||||||  | | | | ||||| || ||    |||| ||||||||| |  ||| ||||
attacctacagcattttcagataactcgttacaatact-ctgagtagtatattgaagagaaagc-tagaaattgcactaacaattttaattgcatcttgtagCTGTGCTTGATGAGACTGGAAAGTTCCTACTATCAGCTAAAAGGAGCCGGCGAACGACACACACTGACTACATCATTTCTATGGACTCCAAAAATATCTC
















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|71318795|gb|DR796159.1|DR796159
EST:     AAGGGACAAATCAAAGCTAACGTACCGGCTCTACTTGTCCCTTAGCTCTG                         GTGTGCTTGATGAGAACGGGAAGTTCCTGCTAGCAGCGAAAAGGAGCCGCA
genomic: AAGGGACAAATCAAAGCTAACGTACCGGCTCTACTTGTCCCTTAGCTCTGgtaagtgtca ... gatcttgtagGTGTGCTTGATGAGAACGGGAAGTTCCTGCTAGCAGCGAAAAGGAGCCGCA
EST: gi|71445229|gb|DR826279.1|DR826279
EST:     AAGGGACAAATCAAAGCTAACGTACCGGCTCTACTTGTCCCTTAGCTCTG                         GTGTGCTTGATGAGAACGGGAAGTTCCTGCTAGCAGCGAAAAGGAGCCGCA
genomic: AAGGGACAAATCAAAGCTAACGTACCGGCTCTACTTGTCCCTTAGCTCTGgtaagtgtca ... gatcttgtagGTGTGCTTGATGAGAACGGGAAGTTCCTGCTAGCAGCGAAAAGGAGCCGCA
EST: gi|91049386|gb|EB159804.1|EB159804
EST:     AAGGGACAAATCAAAGCTAACGTACCGGCTCTACTTGTCCCTTAGCTCTG                         GTGTGCTTGATGAGAACGGGAAGTTCCTGCTAGCAGCGAANAGGAGCCGCA
genomic: AAGGGACAAATCAAAGCTAACGTACCGGCTCTACTTGTCCCTTAGCTCTGgtaagtgtca ... gatcttgtagGTGTGCTTGATGAGAACGGGAAGTTCCTGCTAGCAGCGAAAAGGAGCCGCA
EST: gi|50332914|gb|CO528040.1|CO528040
EST:     AAGGGACAAATCAAAGCTAACGTACCGGCTCTACTTGTCCCTTAGCTCTG                         GTGTGCTTGATGAGAACGGGAAGTTCCTGCTAGCAGCGAAAAGGAGCCGCA
genomic: AAGGGACAAATCAAAGCTAACGTACCGGCTCTACTTGTCCCTTAGCTCTGgtaagtgtca ... gatcttgtagGTGTGCTTGATGAGAACGGGAAGTTCCTGCTAGCAGCGAAAAGGAGCCGCA
EST: gi|71765600|gb|DR963537.1|DR963537
EST:     AAGGGACAAATCAAAGCTAACGTATTGGCTCTACTTGTCCCTTAGCTCTG                         GTGTGCTTGATGAGAACGGGAAGTTCCTGCTAGCAGCGAAAAGGAGCCGCA
genomic: AAGGGACAAATCAAAGCTAACGTACCGGCTCTACTTGTCCCTTAGCTCTGgtaagtgtca ... gatcttgtagGTGTGCTTGATGAGAACGGGAAGTTCCTGCTAGCAGCGAAAAGGAGCCGCA
EST: gi|76288559|gb|DV028127.1|DV028127
EST:     AAGGGACAAATCAAAGCTAACGTACCGGCTCTACTTGTCCCTTAGCTCTG                         GTGTGCTTGATGAGAACGGGAAGTTCCTGCTAGCAGCGAAAAGGAGCCGCA
genomic: AAGGGACAAATCAAAGCTAACGTACCGGCTCTACTTGTCCCTTAGCTCTGgtaagtgtca ... gatcttgtagGTGTGCTTGATGAGAACGGGAAGTTCCTGCTAGCAGCGAAAAGGAGCCGCA
EST: gi|32942208|gb|CF047027.1|CF047027
EST:     ACCGGCTCTACTTGTCCCTTAGCTCTG                         GTGTGCTTGATGAGAACGGGAAGTTCCTGCTAGCAGCGAAAAGGAGCCGCA
genomic: ACCGGCTCTACTTGTCCCTTAGCTCTGgtaagtgtca ... gatcttgtagGTGTGCTTGATGAGAACGGGAAGTTCCTGCTAGCAGCGAAAAGGAGCCGCA
EST: gi|148970343|gb|EE021209.2|EE021209
EST:     AAGGGACAAATCAAAGCTAACGTACCGGCTCTACTTGTCCCTTAGCTCTG                         GTGTGCTTGATGAGAACGGGA
genomic: AAGGGACAAATCAAAGCTAACGTACCGGCTCTACTTGTCCCTTAGCTCTGgtaagtgtca ... gatcttgtagGTGTGCTTGATGAGAACGGGA
EST: gi|31359011|gb|CD443368.1|CD443368
EST:     AAGGGACAAATCAAAGCTAACGTACCGGCTCTACTTGTCCCTTAGCTCTG                         GTGTGCTTGATGAGAACGGGAAGTTCCTGCTAGCAGCGAAAAGGAGCCGCA
genomic: AAGGGACAAATCAAAGCTAACGTACCGGCTCTACTTGTCCCTTAGCTCTGgtaagtgtca ... gatcttgtagGTGTGCTTGATGAGAACGGGAAGTTCCTGCTAGCAGCGAAAAGGAGCCGCA
EST: gi|148960184|gb|EE153436.2|EE153436
EST:     AAGGGACAAATCAAAGCTAACGTACCGGCTCTACTTGTCCCTTAGCTCTG                         GTGTGCTTGATGAGAACGGGAAAGT-CCTGCTAGCAGCGAAAAGG
genomic: AAGGGACAAATCAAAGCTAACGTACCGGCTCTACTTGTCCCTTAGCTCTGgtaagtgtca ... gatcttgtagGTGTGCTTGATGAGAACGGGAA-GTTCCTGCTAGCAGCGAAAAGG
EST: gi|76021266|gb|DT948436.1|DT948436
EST:     AAGGGACAAATCAAAGCTAACGTACCGGCTCTACTTGTCCCTTAGCTCTG                         GTGTGCTTGATGAGAACGGGAAGTTCCTGCTAGCAGCGAAAAGGAGCCGCA
genomic: AAGGGACAAATCAAAGCTAACGTACCGGCTCTACTTGTCCCTTAGCTCTGgtaagtgtca ... gatcttgtagGTGTGCTTGATGAGAACGGGAAGTTCCTGCTAGCAGCGAAAAGGAGCCGCA
EST: gi|78111619|gb|DV530016.1|DV530016
EST:     AAGGGACAAATCAAAGCTAACGTACCGGCTCTACTTGTCCCTTAGCTCTG                         GTGTGCTTGATGAGAACGGGAAGTTCCTGCTAGCAGCGAAAAGGAGCCGCA
genomic: AAGGGACAAATCAAAGCTAACGTACCGGCTCTACTTGTCCCTTAGCTCTGgtaagtgtca ... gatcttgtagGTGTGCTTGATGAGAACGGGAAGTTCCTGCTAGCAGCGAAAAGGAGCCGCA
EST: gi|149090300|gb|EE179604.2|EE179604
EST:     AAGGGACAAATCAAAGCTAACGTACCGGCTCTACTTGTCCCTTAGCTCTG                         GTGTGCTTGATGAGAACGGGAAGTTCCTGCTAGCAGCGAAAAGGAGCCGCA
genomic: AAGGGACAAATCAAAGCTAACGTACCGGCTCTACTTGTCCCTTAGCTCTGgtaagtgtca ... gatcttgtagGTGTGCTTGATGAGAACGGGAAGTTCCTGCTAGCAGCGAAAAGGAGCCGCA
EST: gi|71442832|gb|DR823882.1|DR823882
EST:     AAGGGACAAATCAAAGCTAACGTACCGGCTCTACTTGTCCCTTAGCTCTG                         GTGTGCTTGATGAGAACGGGAAGTTCCTGCTAGCAGCGAAAAGGAGCCGCA
genomic: AAGGGACAAATCAAAGCTAACGTACCGGCTCTACTTGTCCCTTAGCTCTGgtaagtgtca ... gatcttgtagGTGTGCTTGATGAGAACGGGAAGTTCCTGCTAGCAGCGAAAAGGAGCCGCA
EST: gi|71766358|gb|DR964295.1|DR964295
EST:     AAGGGACAAATCAAAGCTAACGTACCGGCTCTACTTGTCCCTTAGCTCTG                         GTGTGCTTGATGAGAACGGGAAGTTCCTGCTAGCAGCGAAAAGGAGCCGCA
genomic: AAGGGACAAATCAAAGCTAACGTACCGGCTCTACTTGTCCCTTAGCTCTGgtaagtgtca ... gatcttgtagGTGTGCTTGATGAGAACGGGAAGTTCCTGCTAGCAGCGAAAAGGAGCCGCA
EST: gi|93283817|gb|EB676081.1|EB676081
EST:     AAGGGACAAATCAAAGCTAACGTACCGGCTCTACTTGTCCCTTAGCTCTG                         GTGTGCTTGATGAGAACGGGAAGTTCCTGCTAGCAGCGAANAGGAGCCGCA
genomic: AAGGGACAAATCAAAGCTAACGTACCGGCTCTACTTGTCCCTTAGCTCTGgtaagtgtca ... gatcttgtagGTGTGCTTGATGAGAACGGGAAGTTCCTGCTAGCAGCGAAAAGGAGCCGCA
EST: gi|148941245|gb|EC886139.2|EC886139
EST:     AAGGGACAAATCAAAGCTAACGTACCGGCTCTACTTGTCCCTTAGCTCTG                         GTGTGCTTGATGAGAACGGGAAGTTCCTGCTAGCAGCGAAAAGGAGCCGCA
genomic: AAGGGACAAATCAAAGCTAACGTACCGGCTCTACTTGTCCCTTAGCTCTGgtaagtgtca ... gatcttgtagGTGTGCTTGATGAGAACGGGAAGTTCCTGCTAGCAGCGAAAAGGAGCCGCA
EST: gi|148940679|gb|EC885493.2|EC885493
EST:     AAGGGACAAATCAAAGCTAACGTACCGGCTCTACTTGTCCCTTAGCTCTG                         GTGTGCTTGATGAGAACGGGAAGTTCCTGCTAGCAGCGAAAAGGAGCCGCA
genomic: AAGGGACAAATCAAAGCTAACGTACCGGCTCTACTTGTCCCTTAGCTCTGgtaagtgtca ... gatcttgtagGTGTGCTTGATGAGAACGGGAAGTTCCTGCTAGCAGCGAAAAGGAGCCGCA
EST: gi|50327951|gb|CO523077.1|CO523077
EST:     AAGGGACAAATCAAAGCTAACGTACCGGCTCTACTTGTCCCTTAGCTCTG                         GTGTGCTTGATGAGAACGGGAAGTTCCTGCTAGCAGCGAAAAGGAGCCGCA
genomic: AAGGGACAAATCAAAGCTAACGTACCGGCTCTACTTGTCCCTTAGCTCTGgtaagtgtca ... gatcttgtagGTGTGCTTGATGAGAACGGGAAGTTCCTGCTAGCAGCGAAAAGGAGCCGCA
EST: gi|211428128|gb|FL358025.1|FL358025
EST:     AAGGGACAAATCAAAGCTAACGTACCGGCTCTACTTGTCCCTTAGCTCTG                         GTGTGCTTGATGAGAACGGGAAGTTCCTGCTAGCAGCGAAAAGGAGCCGCA
genomic: AAGGGACAAATCAAAGCTAACGTACCGGCTCTACTTGTCCCTTAGCTCTGgtaagtgtca ... gatcttgtagGTGTGCTTGATGAGAACGGGAAGTTCCTGCTAGCAGCGAAAAGGAGCCGCA
EST: gi|32843854|gb|CD983535.1|CD983535
EST:     TACCGGCTCTACTTGTCCCTTAGCTCTG                         GTGTGCTTGATGAGAACGGGAAGTTCCTGCTAGCAGCGAAAAGGAGCCGCA
genomic: TACCGGCTCTACTTGTCCCTTAGCTCTGgtaagtgtca ... gatcttgtagGTGTGCTTGATGAGAACGGGAAGTTCCTGCTAGCAGCGAAAAGGAGCCGCA
EST: gi|148959531|gb|EE010853.2|EE010853
EST:     AAGGGACAAATCAAAGCTAACGTACCGGCTCTACTTGTCCCTTAGCTCTG                         GTGTGCTTGATGAGAACGGGGAAGTTCCTGCTAGCAGCGAAAA
genomic: AAGGGACAAATCAAAGCTAACGTACCGGCTCTACTTGTCCCTTAGCTCTGgtaagtgtca ... gatcttgtagGTGTGCTTGATGAGAACGGG-AAGTTCCTGCTAGCAGCGAAAA
EST: gi|78111743|gb|DV530140.1|DV530140
EST:     AAGGGACAAATCAAAGCTAACGTACCGGCTCTACTTGTCCCTTAGCTCTG                         GTGTGCTTGATGAGAACGGGAAGTTCCTGCTAGCAGCGAAAAGGAGCCGCA
genomic: AAGGGACAAATCAAAGCTAACGTACCGGCTCTACTTGTCCCTTAGCTCTGgtaagtgtca ... gatcttgtagGTGTGCTTGATGAGAACGGGAAGTTCCTGCTAGCAGCGAAAAGGAGCCGCA
EST: gi|50332231|gb|CO527357.1|CO527357
EST:     AAGGGACAAATCAAAGCTAACGTACCGGCTCTACTTGTCCCTTAGCTCTG                         GTGTGCTTGATGAGAACGGGAAGTTCCTGCTAGCAGCGAAAAGGAGCCGCA
genomic: AAGGGACAAATCAAAGCTAACGTACCGGCTCTACTTGTCCCTTAGCTCTGgtaagtgtca ... gatcttgtagGTGTGCTTGATGAGAACGGGAAGTTCCTGCTAGCAGCGAAAAGGAGCCGCA
EST: gi|91049274|gb|EB159692.1|EB159692
EST:     AAGGGACAAATCAAAGCTAACGTACCGGCTCTACTTGTCCCTTAGCTCTG                         GTGTGCTTGATGAGAACGGGAAGTTCCTGCTAGCAGCGAAAAGGAGCCGCA
genomic: AAGGGACAAATCAAAGCTAACGTACCGGCTCTACTTGTCCCTTAGCTCTGgtaagtgtca ... gatcttgtagGTGTGCTTGATGAGAACGGGAAGTTCCTGCTAGCAGCGAAAAGGAGCCGCA
EST: gi|78113977|gb|DV532366.1|DV532366
EST:     AAGGGACAAATCAAAGCTAACGTACCGGCTCTACTTGTCCCTTAGCTCTG                         GTGTGCTTGATGAGAACGGGAAGTTCCTGCTAGCAGCGAAAAGGAGCCGCA
genomic: AAGGGACAAATCAAAGCTAACGTACCGGCTCTACTTGTCCCTTAGCTCTGgtaagtgtca ... gatcttgtagGTGTGCTTGATGAGAACGGGAAGTTCCTGCTAGCAGCGAAAAGGAGCCGCA
EST: gi|101387605|gb|EB815817.1|EB815817
EST:     AAGGGACAAATCAAAGCTAACGTACCGGCTCTACTTGTCCCTTAGCTCTG                         GTGTGCTTGATGAGAACGGGGAGTTCCTGCTAGCAGCGAAAAGGAGCCCGC
genomic: AAGGGACAAATCAAAGCTAACGTACCGGCTCTACTTGTCCCTTAGCTCTGgtaagtgtca ... gatcttgtagGTGTGCTTGATGAGAACGGGAAGTTCCTGCTAGCAGCGAAAAGGAGCC-GC
EST: gi|71312297|gb|DR792672.1|DR792672
EST:     AAGGGACAAATCAAAGCTAACGTACCGGCTCTACTTGTCCCTTAGCTCTG                         GTGTGCTTGATGAGAACGGGAAGTTCCTGCTAGCAGCGAAAAGGAGCCGCA
genomic: AAGGGACAAATCAAAGCTAACGTACCGGCTCTACTTGTCCCTTAGCTCTGgtaagtgtca ... gatcttgtagGTGTGCTTGATGAGAACGGGAAGTTCCTGCTAGCAGCGAAAAGGAGCCGCA
EST: gi|78079710|gb|DV508122.1|DV508122
EST:     AAGGGACAAATCAAAGCTAACGTACCGGCTCTACTTGTCCCTTAGCTCTG                         GTGTGCTTGATGAGAACGGGAAGTTCCTGCTAGCAGCGAAAAGGAGCCGCA
genomic: AAGGGACAAATCAAAGCTAACGTACCGGCTCTACTTGTCCCTTAGCTCTGgtaagtgtca ... gatcttgtagGTGTGCTTGATGAGAACGGGAAGTTCCTGCTAGCAGCGAAAAGGAGCCGCA
EST: gi|149009205|gb|EE041318.2|EE041318
EST:     AAGGGACAAATCAAAGCTAACGTACCGGCTCTACTTGTCCCTTAGCTCTG                         GTGTGCTTGATGAGAACGGGAAGTTCCTGCTAGCAGCGAAAAGGAGCCGCA
genomic: AAGGGACAAATCAAAGCTAACGTACCGGCTCTACTTGTCCCTTAGCTCTGgtaagtgtca ... gatcttgtagGTGTGCTTGATGAGAACGGGAAGTTCCTGCTAGCAGCGAAAAGGAGCCGCA
EST: gi|91050137|gb|EB160555.1|EB160555
EST:     AAGGGACAAATCAAAGCTAACGTACCGGCTCTACTTGTCCCTTAGCTCTG                         GTGTGCTTGATGAGAACGGGAAGTTCCTGCTAGCAGCGAANAGGAGCCGCA
genomic: AAGGGACAAATCAAAGCTAACGTACCGGCTCTACTTGTCCCTTAGCTCTGgtaagtgtca ... gatcttgtagGTGTGCTTGATGAGAACGGGAAGTTCCTGCTAGCAGCGAAAAGGAGCCGCA
EST: gi|149082440|gb|EE171627.2|EE171627
EST:     AAGGGACAAATCAAAGCTAACGTACCGGCTCTACTTGTCCCTTAGCTCTG                         GTGTGCTTGATGAGAACGGGAAGTTCCTGCTAGCAGCGAAAAGGAGCCGCA
genomic: AAGGGACAAATCAAAGCTAACGTACCGGCTCTACTTGTCCCTTAGCTCTGgtaagtgtca ... gatcttgtagGTGTGCTTGATGAGAACGGGAAGTTCCTGCTAGCAGCGAAAAGGAGCCGCA
EST: gi|91871229|gb|EB401309.1|EB401309
EST:     AAGGGACAAATCAAAGCTAACGTACCGGCTCTACTTGTCCCTTAGCTCTG                         GTGTGCTTGATGAGAACGGGAAGTTCCTGCTAGCAGCGAAAAGGAGCCGCA
genomic: AAGGGACAAATCAAAGCTAACGTACCGGCTCTACTTGTCCCTTAGCTCTGgtaagtgtca ... gatcttgtagGTGTGCTTGATGAGAACGGGAAGTTCCTGCTAGCAGCGAAAAGGAGCCGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcttcttgggattgctacatatgcaacacagtgatatttctgctggatcttgtagGTGTGCTTGATGAGAACGGGAAGTTCCTGCTAGCAGCGAAAAGGAGCCGCAGGATGGCGCACACGGAGTATGCAATTTTTATGGACTCGAGGAATTTCTC
                               tgatattt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attttaagtaacactctgtgactataataagaatagagcaggatggcttcttgggattgctacatatgcaacacagtgatatttctgctggatcttgtagGTGTGCTTGATGAGAACGGGAAGTTCCTGCTAGCAGCGAAAAGGAGCCGCAGGATGGCGCACACGGAGTATGCAATTTTTATGGACTCGAGGAATTTCTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG