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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCCGCCTAAGAGGCAAAATAGACTCGAATGGTGTTGTTGCCGCATACTTGGAAGAGAGGTTGAACATGGGTGTCAACTTCCTTCTATCTGCTGAGgtaagcatcagttccagggaacattgtttcttttccccattgcactctttgaatgagcaagaggtaaggcctttgtaatttatcaacgttgcaatttcacgttgcag

Basic information

species Zea mays
transcript GRMZM2G174696_T02
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G174696_T02 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os03g20750.1 (Oryza sativa), 5'ss of exon 10
TGCCGCCTAAGAGGCAAAATAGACTCGAATGGTGTTGTTGCCGCATACTTGGAAGAGAGGTTGAACATGGGTGTCAACTTCCTTCTATCTGCTGAGgtaagcatcagttccagggaacattgtttcttttccccattgcactctttgaatgagcaagaggtaaggcctttgtaatttatcaacgttgcaatttcacgttgcag
||||| ||||| || ||| | ||||| |||||||||||||| ||||| ||||||||||| ||||||||||| || || || ||||| ||||| ||||||    |  ||   |  |  ||  | |    | | | |||     |  || ||    |     |  |  | |   | |  ||||   | |||| ||     |    
TGCCGACTAAGGGGAAAATTTGACTCAAATGGTGTTGTTGCTGCATATTTGGAAGAGAGATTGAACATGGGAGTTAATTTTCTTCTTTCTGCAGAGgtattagtt-gtattacagttcag-gctaacctgctctattcttaccactgtatttatactccctctgatcataaaagt--atcatattcgcaactttgaacta---
















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|113638448|gb|DW801794.1|DW801794
EST:     ATGGGTGTCAACTTCCTTCTATCTGCTGAG                         ATTGACCATTGTAAGAAGAACTACAAGTTTGGTTTTGGAATGACCGTAGGA
genomic: ATGGGTGTCAACTTCCTTCTATCTGCTGAGgtaagcatca ... cacgttgcagATTGACCATTGTAAGAAGAACTACAAGTTTGGTTTTGGAATGACCGTAGGA
EST: gi|32919687|gb|CF024499.1|CF024499
EST:     ACTTGGAAGAGAGGTTGAACATGGGTGTCAACTTCCTTCTATCTGCTGAG                         ATTGGCCATTGTAAGAAGAACTACAAGTTTGGTTTTGGAATGACCGTAGGA
genomic: ACTTGGAAGAGAGGTTGAACATGGGTGTCAACTTCCTTCTATCTGCTGAGgtaagcatca ... cacgttgcagATTGACCATTGTAAGAAGAACTACAAGTTTGGTTTTGGAATGACCGTAGGA
EST: gi|37398312|gb|CF636468.1|CF636468
EST:     ACTTGGAAGAGAGGTTGAACATGGGTGTCAACTTCCTTCTATCTGTTGAG                         ATTGACCATTGTAAGAAGAACTACAAGTTTGGTTTTGGAATGACCGTAGGA
genomic: ACTTGGAAGAGAGGTTGAACATGGGTGTCAACTTCCTTCTATCTGCTGAGgtaagcatca ... cacgttgcagATTGACCATTGTAAGAAGAACTACAAGTTTGGTTTTGGAATGACCGTAGGA
EST: gi|211276272|gb|FL458556.1|FL458556
EST:     ACTTGGAAGAGAGGTTGAACATGGGTGTCAACTTCCTTCTATCTGCTGAG                         ATTGACCATTGTAAGAAGAACTACAAGTTTGGTTTTGGAATGACCGTAGGA
genomic: ACTTGGAAGAGAGGTTGAACATGGGTGTCAACTTCCTTCTATCTGCTGAGgtaagcatca ... cacgttgcagATTGACCATTGTAAGAAGAACTACAAGTTTGGTTTTGGAATGACCGTAGGA
EST: gi|166531878|gb|EG258452.1|EG258452
EST:     GGTTGAACGTGGGTGTCAACTTCCTTCTATCTGCTGAG                         ATTGACCATTGTAAGAAGAACTACAAGTTTGGTTTTGGAATGACCGTAGGA
genomic: GGTTGAACATGGGTGTCAACTTCCTTCTATCTGCTGAGgtaagcatca ... cacgttgcagATTGACCATTGTAAGAAGAACTACAAGTTTGGTTTTGGAATGACCGTAGGA
EST: gi|6095402|gb|AW120069.1|AW120069
EST:     ACTTGGAAGAGAGGTTGAACATGGGTGTCAACTTCCTTCTATCTGCTGAG                         ATTGACCATTGTAAGAAGAACTACAAGTTTGGTTTTGGAATGACCGTAGGA
genomic: ACTTGGAAGAGAGGTTGAACATGGGTGTCAACTTCCTTCTATCTGCTGAGgtaagcatca ... cacgttgcagATTGACCATTGTAAGAAGAACTACAAGTTTGGTTTTGGAATGACCGTAGGA
EST: gi|6095403|gb|AW120070.1|AW120070
EST:     ACTTGGAAGAGAGGTTGAACATGGGTGTCAACTTCCTTCTATCTGCTGAG                         ATTGACCATTGTAAGAAGAACTACAAGTTTGGTTTTGGAATGACCGTAGGA
genomic: ACTTGGAAGAGAGGTTGAACATGGGTGTCAACTTCCTTCTATCTGCTGAGgtaagcatca ... cacgttgcagATTGACCATTGTAAGAAGAACTACAAGTTTGGTTTTGGAATGACCGTAGGA
EST: gi|211352868|gb|FL030242.1|FL030242
EST:     ACTTGGAAGAGAGGTTGAACATGGGTGTCAACTTCCTTCTATCTGCTGAG                         ATTGACCATTGTAAGAAGAACTACAAGTTTGGTTTTTGGAATGACCGTAGG
genomic: ACTTGGAAGAGAGGTTGAACATGGGTGTCAACTTCCTTCTATCTGCTGAGgtaagcatca ... cacgttgcagATTGACCATTGTAAGAAGAACTACAAGTTTGGTTTT-GGAATGACCGTAGG
EST: gi|71428446|gb|DR809496.1|DR809496
EST:     ACTTGGAAGAGAGGTTGAACATGGGTGTCAACTTCCTTCTATCTGCTGAG                         ATTGACCATTGTAAGAAGAACTACAAGTTTGGTTTTGGAATGACCGTAGGA
genomic: ACTTGGAAGAGAGGTTGAACATGGGTGTCAACTTCCTTCTATCTGCTGAGgtaagcatca ... cacgttgcagATTGACCATTGTAAGAAGAACTACAAGTTTGGTTTTGGAATGACCGTAGGA
EST: gi|32911927|gb|CF016739.1|CF016739
EST:     ACTTGGAAGAGAGGTTGAACATGGGTGTCAACTTCCTTCTATCTGCTGAG                         ATTGACCATTGTAAGAAGAACTACAAGTTTGGTTTTGGAATGACCGTAGGA
genomic: ACTTGGAAGAGAGGTTGAACATGGGTGTCAACTTCCTTCTATCTGCTGAGgtaagcatca ... cacgttgcagATTGACCATTGTAAGAAGAACTACAAGTTTGGTTTTGGAATGACCGTAGGA
EST: gi|60338504|gb|DN205477.1|DN205477
EST:     ACTTGGAAGAGAGGTTGAACATGGGTGTCAACTTCTTTCTATCTGCTGAG                         ATTGACCATTGTAAGAAGAACTACAAGTTTGGTTTTGGAATGACCGTAGGA
genomic: ACTTGGAAGAGAGGTTGAACATGGGTGTCAACTTCCTTCTATCTGCTGAGgtaagcatca ... cacgttgcagATTGACCATTGTAAGAAGAACTACAAGTTTGGTTTTGGAATGACCGTAGGA
EST: gi|5607738|gb|AI901405.1|AI901405
EST:     ACTTGGAAGAGAGGTTGAACATGGGTGTCAACTTCCTTCTATCTGCTGAG                         ATTGACCATTGTAAGAAGAACTACAAGTTTGGT
genomic: ACTTGGAAGAGAGGTTGAACATGGGTGTCAACTTCCTTCTATCTGCTGAGgtaagcatca ... cacgttgcagATTGACCATTGTAAGAAGAACTACAAGTTTGGT
EST: gi|6095404|gb|AW120071.1|AW120071
EST:     ACTTGGAAGAGAGGTTGAACATGGGTGTCAACTTCCTTCTATCTGCTGAG                         ATTGACCATTGTAAGAAGAACTACAAGTTTGGTTTTGGAATGACCGTAGGA
genomic: ACTTGGAAGAGAGGTTGAACATGGGTGTCAACTTCCTTCTATCTGCTGAGgtaagcatca ... cacgttgcagATTGACCATTGTAAGAAGAACTACAAGTTTGGTTTTGGAATGACCGTAGGA
EST: gi|60355450|gb|DN222423.1|DN222423
EST:     ACTTGGAAGAGAGGTTGAACATGGGTGTCAACTTCCTTCTATCTGCTGAG                         ATTGACCATTGTAAGAAGAACTACAAGTTTGGTTTTGGAATGACCGTAGGA
genomic: ACTTGGAAGAGAGGTTGAACATGGGTGTCAACTTCCTTCTATCTGCTGAGgtaagcatca ... cacgttgcagATTGACCATTGTAAGAAGAACTACAAGTTTGGTTTTGGAATGACCGTAGGA
EST: gi|83279399|gb|DV943407.1|DV943407
EST:     ACTTGGAAGAGAGGTTGAACATGGGTGTCAACTTCCTTCTATCTGCTGAG                         ATTGACCATTGTAAGAAGAACTACAAGTTTGGTTTTGGAATGACCGTAGGA
genomic: ACTTGGAAGAGAGGTTGAACATGGGTGTCAACTTCCTTCTATCTGCTGAGgtaagcatca ... cacgttgcagATTGACCATTGTAAGAAGAACTACAAGTTTGGTTTTGGAATGACCGTAGGA
EST: gi|32919688|gb|CF024500.1|CF024500
EST:     ACTTGGAAGAGAGGTTGAACATGGGTGTCAACTTCCTTCTATCTGCTGAG                         ATTGGCCATTGTAAGAAGAACTACAAGTTTGGTTTTGGAATGACCGTAGGA
genomic: ACTTGGAAGAGAGGTTGAACATGGGTGTCAACTTCCTTCTATCTGCTGAGgtaagcatca ... cacgttgcagATTGACCATTGTAAGAAGAACTACAAGTTTGGTTTTGGAATGACCGTAGGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCCGCCTAAGAGGCAAAATAGACTCGAATGGTGTTGTTGCCGCATACTTGGAAGAGAGGTTGAACATGGGTGTCAACTTCCTTCTATCTGCTGAGgtaagcatcagttccagggaacattgtttcttttccccattgcactctttgaatgagcaagaggtaaggcctttgtaatttatcaacgttgcaatttcacgttgcag

- - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG