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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGGTTACCGAAATTATGTTTGATCTGAGAGCTAGTGGCCAAAGTTCTTCGGAGTCCGAAGCCGGCTGGTTTGATCTTTTCAGCAAGCGTTACTGGAAAGgtattttttcgttgacagtctcggaattggctaatttggttccctaacaattgcatgatgaaatattatctgattattctcttcttataccattgtattg...

Basic information

species Zea mays
transcript GRMZM2G153704_T01
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G153704_T01 (Zea mays), 5'ss of exon 13
lower sequence: LOC_Os01g04190.4 (Oryza sativa), 5'ss of exon 9
ATGGTTACCGAAATTATGTTTGATCTGAGAGCTAGTGGCCAAAGTTCTTCGGAGTCCGAAGCCGGCTGGTTTGATCTTTTCAGCAAGCGTTACTGGAAAGgtattttttcgttgacagtctcggaattggctaatttggttccctaacaattgcatgatgaaatattatctgattattctcttcttataccattgtattg---------------------------------------------------------------------------
|  ||| | ||| |||||| ||| || | ||||    ||||| ||||||| ||| | || || |||||||| |||||||||||||| || || |||||||||| ||||   ||  | || || ||  || ||| |||| ||||  ||  ||||||| ||||||| ||  |||||| || | | ||   ||  |||| |||                                                                           
AAAGTTGCTGAAGTTATGTATGACCTAAAAGCTGCCAGCCAAGGTTCTTCTGAGCCAGATGCTGGCTGGTTGGATCTTTTCAGCAAACGCTATTGGAAAGgtagttttgttttctctgtttcagatctgactattttgattcctcaa--attgcatcatgaaatcttccctgattgttatttcct---actcttgtgttgctaaaataaaaacccaacatttaaccaaaacatcagtttggtgatttgttgctgacatattttttcataccgcag

upper sequence: GRMZM2G153704_T01 (Zea mays), 5'ss of exon 13
lower sequence: AT5G16150.1 (Arabidopsis thaliana), 5'ss of exon 9
ATGGTTACCGAAATTATGTTTGATCTGAGAGCTAGTGGCCAAAGTTCTTCGGAGTCCGAAGCCGGCTGGTTTGATCTTTTCAGCAAGCGTTACTGGAAAGgtattttttcgttgacagtctcggaattggctaatttggttcc----ctaaca-attgcatgatgaaatattatctgattattctcttcttataccattgtattg-------------
|  ||    ||| |  |    ||  |   |||   ||||||| ||||||| ||| | || || || ||||||||||| |||||||  || ||||||||||||||        |    |       ||||  || ||||         || ||  ||| | |    |  |  |||| ||||  ||  ||   |||   |  | |               
AGAGTGGTTGAACTAGTTCGCGACTTATCAGCCTCTGGCCAAGGTTCTTCTGAGCCGGAGGCAGGATGGTTTGATCTATTCAGCAGCCGCTACTGGAAAGgtatagcaagacttggtggagatacattgtttagtttgtaataaaagctgacggattcctttcaaaggtcatatcggattgatcaatttacatagtttcttgtctgttcttgttgtag
















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|60400456|gb|DN233263.1|DN233263
EST:     GGAGTCCGAAGCCGGCTGGTTTGATCTTTTCAGCAAGCGTTACTGGAAAG                         TTGTGAGTGTGGGGGCAGCACTGTTTTTGTTCCAGCAGCTTGCTGGTATAA
genomic: GGAGTCCGAAGCCGGCTGGTTTGATCTTTTCAGCAAGCGTTACTGGAAAGgtattttttc ... tcatttgcagTTGTGAGTGTGGGGGCAGCACTGTTTTTGTTCCAGCAGCTTGCTGGTATAA
EST: gi|32832104|gb|CD971782.1|CD971782
EST:     GGAGTCCGAAGCCGGCTGGTTTGATCTTTTCAGCAAGCGTTACTGGAAAG                         TTGTGAGTGTGGGGGCAGCACTTGTTTT-GTTCCAGCAGCTTGCTGGTATA
genomic: GGAGTCCGAAGCCGGCTGGTTTGATCTTTTCAGCAAGCGTTACTGGAAAGgtattttttc ... tcatttgcagTTGTGAGTGTGGGGGCAGCACT-GTTTTTGTTCCAGCAGCTTGCTGGTATA
EST: gi|101389575|gb|EB816720.1|EB816720
EST:     GGAGTCCGAAGCCGGCTGGTTTGATCTTTTCAGCAAGCGTTACTGGAAAG                         TTGTGAGTGTGGGGGCAGCACTGTTTTTGTTCCAGCAGCTTGCTGGTATAA
genomic: GGAGTCCGAAGCCGGCTGGTTTGATCTTTTCAGCAAGCGTTACTGGAAAGgtattttttc ... tcatttgcagTTGTGAGTGTGGGGGCAGCACTGTTTTTGTTCCAGCAGCTTGCTGGTATAA
EST: gi|61119088|gb|DN560049.1|DN560049
EST:     GGAGTCCGAAGCCGGCTGGTTTGATCTTTTCAGCAAGCGTTACTGGAAAG                         TTGTGAGTGTGGGGGCAGCACTGTTTTTGTTCCAGCAGCTTGCTGGTATAA
genomic: GGAGTCCGAAGCCGGCTGGTTTGATCTTTTCAGCAAGCGTTACTGGAAAGgtattttttc ... tcatttgcagTTGTGAGTGTGGGGGCAGCACTGTTTTTGTTCCAGCAGCTTGCTGGTATAA
EST: gi|67035008|gb|CO463541.1|CO463541
EST:     GGAGTCCGAAGCCGGCTGGTTTGATCTTTTCAGCAAGCGTTACTGGAAAG                         TTGTGAGTGTGGGGGCAGCACTGTTTTTGTTCCAGCAGCTTGCTGGTATAA
genomic: GGAGTCCGAAGCCGGCTGGTTTGATCTTTTCAGCAAGCGTTACTGGAAAGgtattttttc ... tcatttgcagTTGTGAGTGTGGGGGCAGCACTGTTTTTGTTCCAGCAGCTTGCTGGTATAA
EST: gi|60339583|gb|DN206556.1|DN206556
EST:     GGAGTCCGAAGCCGGCTGGTTTGATCTTTTCAGCAAGCGTTACTGGAAAG                         TTGTGAGTGTGGGGGCAGCACTGTTTTTGTTCCAGCAGCTTGCTGGTATAA
genomic: GGAGTCCGAAGCCGGCTGGTTTGATCTTTTCAGCAAGCGTTACTGGAAAGgtattttttc ... tcatttgcagTTGTGAGTGTGGGGGCAGCACTGTTTTTGTTCCAGCAGCTTGCTGGTATAA
EST: gi|67037358|gb|CO464198.1|CO464198
EST:     GGAGTCCGAAGCCGGCTGGTTTGATCTTTTCAGCAAGCGTTACTGGAAAG                         TTGTGAGTGTGGGGGCAGCACTGTTTTTGTTCCAGCAGCTTGCTGGTATAA
genomic: GGAGTCCGAAGCCGGCTGGTTTGATCTTTTCAGCAAGCGTTACTGGAAAGgtattttttc ... tcatttgcagTTGTGAGTGTGGGGGCAGCACTGTTTTTGTTCCAGCAGCTTGCTGGTATAA
EST: gi|32933856|gb|CF038668.1|CF038668
EST:     GGAGTCCGAAGCCGGCTGGTTTGATCTTTTCAGCAAGCGTTACTGGAAAG                         TTGTGAGTGTGGGGGCAGCACTGTTTTTGTTCCAGCAGCTTGCTGGTATAA
genomic: GGAGTCCGAAGCCGGCTGGTTTGATCTTTTCAGCAAGCGTTACTGGAAAGgtattttttc ... tcatttgcagTTGTGAGTGTGGGGGCAGCACTGTTTTTGTTCCAGCAGCTTGCTGGTATAA
EST: gi|67011667|gb|CO440416.1|CO440416
EST:     TCCGAA-CCGGCTGGTTTGATCTTTTCAGCAAGCGTTACTGGAAAG                         TTGTGAGTGTGGGGGCAGCACTGTTTTTGTTCCAGCAGCTTGCTGGTATAA
genomic: TCCGAAGCCGGCTGGTTTGATCTTTTCAGCAAGCGTTACTGGAAAGgtattttttc ... tcatttgcagTTGTGAGTGTGGGGGCAGCACTGTTTTTGTTCCAGCAGCTTGCTGGTATAA
EST: gi|7844519|gb|AW787741.1|AW787741
EST:     GGAGTCCGAAGCCGGCTGGTTTGATCTTTTCAGCAAGCGTTACTGGAAAG                         TTGTGAGTGTGGGGGCAGCACTGTTTTTGTTCCAGCAGCTTGCTGGTATAA
genomic: GGAGTCCGAAGCCGGCTGGTTTGATCTTTTCAGCAAGCGTTACTGGAAAGgtattttttc ... tcatttgcagTTGTGAGTGTGGGGGCAGCACTGTTTTTGTTCCAGCAGCTTGCTGGTATAA
EST: gi|78179345|gb|DV549718.1|DV549718
EST:     GGAGTCCGAAGCCGGCTGGTTTGATCTTTTCAGCAAGCGTTACTGGAAAG                         TTGTGAGTGTGGGGGCAGCACTGTTTTTGTTCCAGCAGCTTGCTGGTATAA
genomic: GGAGTCCGAAGCCGGCTGGTTTGATCTTTTCAGCAAGCGTTACTGGAAAGgtattttttc ... tcatttgcagTTGTGAGTGTGGGGGCAGCACTGTTTTTGTTCCAGCAGCTTGCTGGTATAA
EST: gi|60358931|gb|DN225904.1|DN225904
EST:     GGAGTCCGAAGCCGGCTGGTTTGATCTTTTCAGCAAGCGTTACTGGAAAG                         TTGTGAGTGTGGGGGCAGCACTGTTTTTGTTCCAGCAGCTTGCTGGTATAA
genomic: GGAGTCCGAAGCCGGCTGGTTTGATCTTTTCAGCAAGCGTTACTGGAAAGgtattttttc ... tcatttgcagTTGTGAGTGTGGGGGCAGCACTGTTTTTGTTCCAGCAGCTTGCTGGTATAA
EST: gi|7844129|gb|AW787332.1|AW787332
EST:     GGAGTCCGAAGCCGGCTGGTTTGATCTTTTCAGCAAGCGTTACTGGAAAG                         TTGTGAGTGTGGGGGCAGCACTGTTTTTGTTCCAGCAGCTTGCTGGTATAA
genomic: GGAGTCCGAAGCCGGCTGGTTTGATCTTTTCAGCAAGCGTTACTGGAAAGgtattttttc ... tcatttgcagTTGTGAGTGTGGGGGCAGCACTGTTTTTGTTCCAGCAGCTTGCTGGTATAA
EST: gi|32847646|gb|CD987327.1|CD987327
EST:     GGAGTCCGAAGCCGGCTGGTTTGATCTTTTCAGCAAGCGTTACTGGAAAG                         TTGTGAGTGTGGGGGCAGCACTGTTTT-GTTCCAGCAGCTTGCTGGTATAA
genomic: GGAGTCCGAAGCCGGCTGGTTTGATCTTTTCAGCAAGCGTTACTGGAAAGgtattttttc ... tcatttgcagTTGTGAGTGTGGGGGCAGCACTGTTTTTGTTCCAGCAGCTTGCTGGTATAA
EST: gi|32835079|gb|CD974757.1|CD974757
EST:     GGAGTCCGAAGCCGGCTGGTTTGATCTTTTCAGCAAGCGTTACTGGAAAG                         TTGTGAGTGTGGGGGCAGCACTGTTTTTGTTCCAGCAGCTTGCTGGTATAA
genomic: GGAGTCCGAAGCCGGCTGGTTTGATCTTTTCAGCAAGCGTTACTGGAAAGgtattttttc ... tcatttgcagTTGTGAGTGTGGGGGCAGCACTGTTTTTGTTCCAGCAGCTTGCTGGTATAA
EST: gi|22545719|gb|BU098078.1|BU098078
EST:     GGAGTCCGAAGCCGGCTGGTTTGATCTTTTCAGCAAGCGTTACTGGAAAG                         TTGTGAGTGTGGGGGCAGCACTGTTTTTGTTCCAGCAGCTTGCTGGTATAA
genomic: GGAGTCCGAAGCCGGCTGGTTTGATCTTTTCAGCAAGCGTTACTGGAAAGgtattttttc ... tcatttgcagTTGTGAGTGTGGGGGCAGCACTGTTTTTGTTCCAGCAGCTTGCTGGTATAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGGTTACCGAAATTATGTTTGATCTGAGAGCTAGTGGCCAAAGTTCTTCGGAGTCCGAAGCCGGCTGGTTTGATCTTTTCAGCAAGCGTTACTGGAAAGgtattttttcgttgacagtctcggaattggctaatttggttccctaacaattgcatgatgaaatattatctgattattctcttcttataccattgtattg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG