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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAGTACAAGCAGGGGAAGATGTCAGACGCGCTGATCAACGGCCTCGCCGGCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACCgtacgtggctcgacgcctcgctgccgacctttagccctggatttctgggtcgctgatatttggaggtttccctcggtgcag

Basic information

species Zea mays
transcript GRMZM2G540403_T02
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G540403_T02 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os03g15860.1 (Oryza sativa), 5'ss of exon 1
AGAGTACAAGCAGGGGAAGATGTCAGACGCGCTGATCAACGGCCTCGCCGGCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACCgtacgtggctcgacgcctcgctgcc--gacctttagccc-------tggatttctgggtcgct-gatatttggaggtttccc--tcggtgcag--
 |    | ||   | | ||||||| |||||||||||||||||| ||||||||||||||||||||||||||||||||||||| |||||||||||||| |||||||| | | |  | ||||  | |   ||    |||          |  ||| || ||| | |  |||   |  |||||     | |||||    
GGGTGGCGAGGCTGCGGAGATGTCGGACGCGCTGATCAACGGCGTCGCCGGCGCCGGCGGCGGGATCATCGCCCAGCTCCTCACCTACCCGCTCCAAACCgtacgcgccacctctcctccatccttggattgctagattgtttgggtcaattgcttggttgtttaataacggagggtttgggggtgggtgcgcag
















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|37418570|gb|CF646954.1|CF646954
EST:     GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACC                         GTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
genomic: GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACCgtacgtggct ... ctcggtgcagGTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
EST: gi|149109204|gb|EE190074.2|EE190074
EST:     GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACC                         GTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
genomic: GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACCgtacgtggct ... ctcggtgcagGTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
EST: gi|78112113|gb|DV530509.1|DV530509
EST:     GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACC                         GTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
genomic: GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACCgtacgtggct ... ctcggtgcagGTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
EST: gi|149071944|gb|EE160331.2|EE160331
EST:     GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACC                         GTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
genomic: GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACCgtacgtggct ... ctcggtgcagGTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
EST: gi|78120502|gb|DV538886.1|DV538886
EST:     GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACC                         GTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
genomic: GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACCgtacgtggct ... ctcggtgcagGTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
EST: gi|211496381|gb|FL046952.1|FL046952
EST:     GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACC                         GTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
genomic: GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACCgtacgtggct ... ctcggtgcagGTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
EST: gi|211496383|gb|FL046954.1|FL046954
EST:     GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACC                         GTGAACGCGCGGCAACA
genomic: GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACCgtacgtggct ... ctcggtgcagGTGAACGCGCGGCAACA
EST: gi|88756340|gb|DY540481.1|DY540481
EST:     GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACC                         GTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
genomic: GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACCgtacgtggct ... ctcggtgcagGTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
EST: gi|148952677|gb|EC898511.2|EC898511
EST:     GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACC                         GTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
genomic: GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACCgtacgtggct ... ctcggtgcagGTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
EST: gi|91877627|gb|EB407584.1|EB407584
EST:     GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACC                         GTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
genomic: GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACCgtacgtggct ... ctcggtgcagGTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
EST: gi|211175056|gb|FL087597.1|FL087597
EST:     GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACC                         GTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
genomic: GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACCgtacgtggct ... ctcggtgcagGTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
EST: gi|8367157|gb|BE050102.1|BE050102
EST:     GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACC                         GTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
genomic: GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACCgtacgtggct ... ctcggtgcagGTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
EST: gi|211173388|gb|FL087593.1|FL087593
EST:     GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACC                         GTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
genomic: GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACCgtacgtggct ... ctcggtgcagGTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
EST: gi|71766550|gb|DR964487.1|DR964487
EST:     GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACC                         GTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
genomic: GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACCgtacgtggct ... ctcggtgcagGTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
EST: gi|148964459|gb|EC905815.2|EC905815
EST:     GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACC                         GTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
genomic: GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACCgtacgtggct ... ctcggtgcagGTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
EST: gi|76936044|gb|DV174582.1|DV174582
EST:     GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACC                         GTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
genomic: GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACCgtacgtggct ... ctcggtgcagGTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
EST: gi|148957275|gb|EC903307.2|EC903307
EST:     GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACC                         GTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
genomic: GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACCgtacgtggct ... ctcggtgcagGTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
EST: gi|211173387|gb|FL087592.1|FL087592
EST:     GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACC                         GTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
genomic: GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACCgtacgtggct ... ctcggtgcagGTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
EST: gi|149027549|gb|EE046558.2|EE046558
EST:     GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACC                         GTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
genomic: GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACCgtacgtggct ... ctcggtgcagGTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
EST: gi|211175053|gb|FL087594.1|FL087594
EST:     GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACC                         GTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
genomic: GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACCgtacgtggct ... ctcggtgcagGTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
EST: gi|211496382|gb|FL046953.1|FL046953
EST:     GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACC                         GTGAAMGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAA
genomic: GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACCgtacgtggct ... ctcggtgcagGTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAA
EST: gi|149013466|gb|EE042980.2|EE042980
EST:     GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACC                         GTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
genomic: GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACCgtacgtggct ... ctcggtgcagGTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
EST: gi|71422924|gb|DR805897.1|DR805897
EST:     GATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACC                         GTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
genomic: GATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACCgtacgtggct ... ctcggtgcagGTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
EST: gi|71448089|gb|DR829139.1|DR829139
EST:     GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACC                         GTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
genomic: GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACCgtacgtggct ... ctcggtgcagGTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
EST: gi|78121537|gb|DV539921.1|DV539921
EST:     GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACC                         GTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
genomic: GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACCgtacgtggct ... ctcggtgcagGTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
EST: gi|91051844|gb|EB162262.1|EB162262
EST:     GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACC                         GTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
genomic: GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACCgtacgtggct ... ctcggtgcagGTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
EST: gi|211175055|gb|FL087596.1|FL087596
EST:     GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACC                         GTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
genomic: GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACCgtacgtggct ... ctcggtgcagGTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAGTACAAGCAGGGGAAGATGTCAGACGCGCTGATCAACGGCCTCGCCGGCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACCgtacgtggctcgacgcctcgctgccgacctttagccctggatttctgggtcgctgatatttggaggtttccctcggtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC