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 5'  3'   		2  
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atctgatccttgatggggtgagaccgcaagagggcactatgtgtttggatgttgacttcattcactaccctagtgcctaactacctgtgtccacttccagGATTCAGGATGGATCAGGAGGCGAAGGACTCTAGGCCCTCAAGGTCTCCCAGCGAGCCAAACCTCTTCCTGCAATGGGGTAGCCGTAAGAGGCTGCGATG

Basic information

species Zea mays
transcript GRMZM2G024395_T03
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G024395_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g59250.1 (Oryza sativa), 3'ss of exon 1
atctgatcc-ttgatggggtgagaccgcaagagggcactatgtgtttggatgttgacttcattcactaccctagtgcctaactacctgtgtccact--tccagGATTCAGGA------TGGATCAGGAGGCGAAGGACTCTAGGCCCTCAAGGTCTCCCAGCGAGCCAAACCTCTTCCTGCAATGGGGTAGCCGTAAGAGGCTGCGATG
 |  |||||     ||  || | |   | |          | | |   ||| ||  | ||| | | |    |  ||   || | || |  |   ||  | ||||| ||||||      ||||||  |||| ||||||||| ||||| || ||||||||| |||| ||||| || |||||||||||||| ||||| ||  | ||      
-ttggatccgcccctgtagttaaatatccattttttgggctatctactgat-ttcccgtcaatgattttgttgctgaa-aatttccagccttttctgcttcagGAATCAGGACATAGATGGATCCAGAGGTGAAGGACTCAAGGCCATCGAGGTCTCCCGGCGAACCAAATCTTTTCCTGCAATGGGGCAGCCGGAAACGACT------
















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|211189372|gb|FL038386.1|FL038386
EST:     GGTTTGCTGGAGTGCAGTGCACGGGGCGGTGGAGCAGCAAATCTGCAACT                         GATTCAGGATGGATCAGGAGGCGAAGGACTCTAGGCCCTCAAGGTCTCCCA
genomic: GGTTTGCTGGAGTGCAGTGCAC-GGGCGGTGGAGCAGCAAATCTGCAACTgtaagcaccg ... ccacttccagGATTCAGGATGGATCAGGAGGCGAAGGACTCTAGGCCCTCAAGGTCTCCCA
EST: gi|101390683|gb|EB817275.1|EB817275
EST:     AGGTTTGCTGGAGTGCAGTGCACGGGCGGTGGAGCAGCAAATCTGCAACT                         GATTCAGGATGGATCAGGAGGCGAAGGACTCTAGGCCCTCAAGGTCTCCCA
genomic: AGGTTTGCTGGAGTGCAGTGCACGGGCGGTGGAGCAGCAAATCTGCAACTgtaagcaccg ... ccacttccagGATTCAGGATGGATCAGGAGGCGAAGGACTCTAGGCCCTCAAGGTCTCCCA
EST: gi|78106870|gb|DV525288.1|DV525288
EST:     AGGTTTGCTGGAGTGCAGTGCACGGGCGGTGGAGCAGCAAATCTGCAACT                         GATTCAGGATGGATCAGGAGGCGAAGGACTCTAGGCCCTCAAGGTCTCCCA
genomic: AGGTTTGCTGGAGTGCAGTGCACGGGCGGTGGAGCAGCAAATCTGCAACTgtaagcaccg ... ccacttccagGATTCAGGATGGATCAGGAGGCGAAGGACTCTAGGCCCTCAAGGTCTCCCA
EST: gi|76286625|gb|DV026193.1|DV026193
EST:     AGGTTTGCTGGAGTGCAGTGCACGGGCGGTGGAGCAGCAAATCTGCAACT                         GATTCAGGATGGATCAGGAGGCGAAGGACTCTAGGCCCTCAAGGTCTCCCA
genomic: AGGTTTGCTGGAGTGCAGTGCACGGGCGGTGGAGCAGCAAATCTGCAACTgtaagcaccg ... ccacttccagGATTCAGGATGGATCAGGAGGCGAAGGACTCTAGGCCCTCAAGGTCTCCCA
EST: gi|211256988|gb|FL181068.1|FL181068
EST:     AGGTTTGCTGGAGTGCAGTGCACGGGCGGTGGAGCAGCAAATCTGCAACT                         GATTCAGGATGGATCAGGAGGCGAAGGACTCTAGGCCCTCAAGGTCTCCCA
genomic: AGGTTTGCTGGAGTGCAGTGCACGGGCGGTGGAGCAGCAAATCTGCAACTgtaagcaccg ... ccacttccagGATTCAGGATGGATCAGGAGGCGAAGGACTCTAGGCCCTCAAGGTCTCCCA
EST: gi|71440608|gb|DR821658.1|DR821658
EST:     AGGTTTGCTGGAGTGCAGTGCACGGGCGGTGGAGCAGCAAATCTGCAACT                         GATTCAGGATGGATCAGGAGGCGAAGGACTCTAGGCCCTCAAGGTCTCCCA
genomic: AGGTTTGCTGGAGTGCAGTGCACGGGCGGTGGAGCAGCAAATCTGCAACTgtaagcaccg ... ccacttccagGATTCAGGATGGATCAGGAGGCGAAGGACTCTAGGCCCTCAAGGTCTCCCA
EST: gi|93283412|gb|EB675676.1|EB675676
EST:     AGGTTTGCTGGAGTGCAGTGCACGGGCGGTGGAGCAGCAAATCTGCAACT                         GATTCAGGATGGATCAGGAGGCGAAGGACTCTAGGCCCTCAAGGTCTCCCA
genomic: AGGTTTGCTGGAGTGCAGTGCACGGGCGGTGGAGCAGCAAATCTGCAACTgtaagcaccg ... ccacttccagGATTCAGGATGGATCAGGAGGCGAAGGACTCTAGGCCCTCAAGGTCTCCCA
EST: gi|93284387|gb|EB676651.1|EB676651
EST:     AGGTTTGCTGGAGTGCAGTGCACGGGCGGTGGAGCAGCAAATCTGCAACT                         GATTCAGGATGGATCAGGAGGCGAAGGACTCTAGGCCCTCAAGGTCTCCCA
genomic: AGGTTTGCTGGAGTGCAGTGCACGGGCGGTGGAGCAGCAAATCTGCAACTgtaagcaccg ... ccacttccagGATTCAGGATGGATCAGGAGGCGAAGGACTCTAGGCCCTCAAGGTCTCCCA
EST: gi|76914671|gb|DV165630.1|DV165630
EST:     AGGTTTGCTGGAGTGCAGTGCACGGGCGGTGGAGCAGCAAATCTGCAACT                         GATTCAGGATGGATCAGGAGGCGAAGGACTCTAGGCCCTCAAGGTCTCCCA
genomic: AGGTTTGCTGGAGTGCAGTGCACGGGCGGTGGAGCAGCAAATCTGCAACTgtaagcaccg ... ccacttccagGATTCAGGATGGATCAGGAGGCGAAGGACTCTAGGCCCTCAAGGTCTCCCA
EST: gi|71435745|gb|DR816795.1|DR816795
EST:     AGGGTTGCTGGAGTGGAGTGGACGGGCGGTGGAGCAGCAAATCTGCAACT                         GATTCAGGATGGATCAGGAGGCGAAGGACTCTAGGCCCTCAAGGTCTCCCA
genomic: AGGTTTGCTGGAGTGCAGTGCACGGGCGGTGGAGCAGCAAATCTGCAACTgtaagcaccg ... ccacttccagGATTCAGGATGGATCAGGAGGCGAAGGACTCTAGGCCCTCAAGGTCTCCCA
EST: gi|89251344|gb|DY623130.1|DY623130
EST:     AGGTTTGCTGGAGTGCAGTGCACGGGCGGTGGAGCAGCAAATCTGCAACT                         GATTCAGGATGGATCAGGAGGCGAAGGACTCTAGGCCCTCAAGGTCTCCCA
genomic: AGGTTTGCTGGAGTGCAGTGCACGGGCGGTGGAGCAGCAAATCTGCAACTgtaagcaccg ... ccacttccagGATTCAGGATGGATCAGGAGGCGAAGGACTCTAGGCCCTCAAGGTCTCCCA
EST: gi|71775433|gb|DR973311.1|DR973311
EST:     AGGTTTGCTGGAGTGCAGTGCACGGGCGGTGGAGCAGCAAATCTGCAACT                         GATTCAGGATGGATCAGGAGGCGAAGGACTCTAGGCCCTCAAGGTCTCCCA
genomic: AGGTTTGCTGGAGTGCAGTGCACGGGCGGTGGAGCAGCAAATCTGCAACTgtaagcaccg ... ccacttccagGATTCAGGATGGATCAGGAGGCGAAGGACTCTAGGCCCTCAAGGTCTCCCA
EST: gi|101386838|gb|EB815436.1|EB815436
EST:     AGGTTTGCTGGAGTGCAGTGCACGGGCGGTGGAGCAGCAAATCTGCAACT                         GATTCAGGATGGATCAGGAGGCGAAGGACTCTAGGCCCTCAAGGTCTCCCA
genomic: AGGTTTGCTGGAGTGCAGTGCACGGGCGGTGGAGCAGCAAATCTGCAACTgtaagcaccg ... ccacttccagGATTCAGGATGGATCAGGAGGCGAAGGACTCTAGGCCCTCAAGGTCTCCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggatgttgacttcattcactaccctagtgcctaactacctgtgtccacttccagGATTCAGGATGGATCAGGAGGCGAAGGACTCTAGGCCCTCAAGGTCTCCCAGCGAGCCAAACCTCTTCCTGCAATGGGGTAGCCGTAAGAGGCTGCGATG
                             gcctaac  putative branch site (score: 2)
                                            tccacttcc  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atctgatccttgatggggtgagaccgcaagagggcactatgtgtttggatgttgacttcattcactaccctagtgcctaactacctgtgtccacttccagGATTCAGGATGGATCAGGAGGCGAAGGACTCTAGGCCCTCAAGGTCTCCCAGCGAGCCAAACCTCTTCCTGCAATGGGGTAGCCGTAAGAGGCTGCGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG