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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtcgccgttcgttcgacatgcatgcgcgcgaccttcgttcggtgtccttgtcgtcgtccatccctgacgcgctccggcgctgcgtctagtagtctggtctggttcggcggccacggccttctgggtcgttgctggtgctgattaaattgtttatccggccgctgttcagATGGGATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAACTG

Basic information

species Zea mays
transcript GRMZM2G116185_T03
intron # 1
splice site 3'
intron type U2

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|78086977|gb|DV515370.1|DV515370
EST:     GTGTACGCCGTCTTCTGGCGGATCCTCCCCAGAAACTACCCGCCCCCAAA                         ATGGGATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAA
genomic: GTGTACGCCGTCTTCTGGCGGATCCTCCCCAGAAACTACCCGCCCCCAAAgtgagtcgcc ... cgctgttcagATGGGATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAA
EST: gi|71441212|gb|DR822262.1|DR822262
EST:     GTGTACGCCGTCTTCTGGCGGATCCTCCCCAGAAACTACCCGCCCCCAAA                         ATGGGATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAA
genomic: GTGTACGCCGTCTTCTGGCGGATCCTCCCCAGAAACTACCCGCCCCCAAAgtgagtcgcc ... cgctgttcagATGGGATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAA
EST: gi|78092358|gb|DV520732.1|DV520732
EST:     GTGTACGCCGTCTTCTGGCGGATCCTCCCCAGAAACTACCCGCCCCCAAA                         ATGGGATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAA
genomic: GTGTACGCCGTCTTCTGGCGGATCCTCCCCAGAAACTACCCGCCCCCAAAgtgagtcgcc ... cgctgttcagATGGGATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAA
EST: gi|71299046|gb|DR785511.1|DR785511
EST:     GTGTACGCCGTCTTCTGGCGGATCCTCCCCAGAAACTACCCGCCCCCAAA                         ATGGGATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAA
genomic: GTGTACGCCGTCTTCTGGCGGATCCTCCCCAGAAACTACCCGCCCCCAAAgtgagtcgcc ... cgctgttcagATGGGATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAA
EST: gi|91055983|gb|EB166401.1|EB166401
EST:     GTGTACGCCGTCTTCTGGCGGATCCTCCCCAGAAACTACCCGCCCCCAAA                         ATGGGATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAA
genomic: GTGTACGCCGTCTTCTGGCGGATCCTCCCCAGAAACTACCCGCCCCCAAAgtgagtcgcc ... cgctgttcagATGGGATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAA
EST: gi|101385166|gb|EB814629.1|EB814629
EST:     GTGTACGCCGTCTTCTGGCGGATCCTCCCCAGAAACTACCCGCCCCCAAA                         ATGGGATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAA
genomic: GTGTACGCCGTCTTCTGGCGGATCCTCCCCAGAAACTACCCGCCCCCAAAgtgagtcgcc ... cgctgttcagATGGGATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAA
EST: gi|76291869|gb|DV031437.1|DV031437
EST:     GTGTACGCCGTCTTCTGGCGGATCCTCCCCAGAAACTACCCGCCCCCAAA                         ATGGGATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAA
genomic: GTGTACGCCGTCTTCTGGCGGATCCTCCCCAGAAACTACCCGCCCCCAAAgtgagtcgcc ... cgctgttcagATGGGATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAA
EST: gi|71316518|gb|DR794933.1|DR794933
EST:     GTGTACGCCGTCTTCTGGCGGATCCTCCCCAGAAACTACCCGCCCCCAAA                         ATGGGATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAA
genomic: GTGTACGCCGTCTTCTGGCGGATCCTCCCCAGAAACTACCCGCCCCCAAAgtgagtcgcc ... cgctgttcagATGGGATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAA
EST: gi|20803186|gb|BQ294236.1|BQ294236
EST:     GTGTACGCCGTCTTCTGGCGGATCCTCCCCAGAAACTACCCGCCCCCAAA                         ATGGGATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAA
genomic: GTGTACGCCGTCTTCTGGCGGATCCTCCCCAGAAACTACCCGCCCCCAAAgtgagtcgcc ... cgctgttcagATGGGATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAA
EST: gi|148953903|gb|EC899284.2|EC899284
EST:     GTGTACGCCGTCTTCTGGCGGATCCTCCCCAGAAACTACCCGCCCCCAAA                         ATGGGATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAA
genomic: GTGTACGCCGTCTTCTGGCGGATCCTCCCCAGAAACTACCCGCCCCCAAAgtgagtcgcc ... cgctgttcagATGGGATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAA
EST: gi|76934748|gb|DV174011.1|DV174011
EST:     GTGTACGCCGTCTTCTGGCGGATCCTCCCCAGAAACTACCCGCCCCCAAA                         ATGGGATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAA
genomic: GTGTACGCCGTCTTCTGGCGGATCCTCCCCAGAAACTACCCGCCCCCAAAgtgagtcgcc ... cgctgttcagATGGGATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAA
EST: gi|50336434|gb|CO531560.1|CO531560
EST:     GTGTACGCCGTCTTCTGGCGGATCCTCCCCAGAAACTACCCGCCCCCAAA                         ATGGGATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAA
genomic: GTGTACGCCGTCTTCTGGCGGATCCTCCCCAGAAACTACCCGCCCCCAAAgtgagtcgcc ... cgctgttcagATGGGATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAA
EST: gi|91048202|gb|EB158620.1|EB158620
EST:     GTGTACGCCGTCTTCTGGCGGATCCTCCCCAGAAACTACCCGCCCCCCAA                         ATGGGATCTCCAGGGCGGCATATACAACCGGACAAGAGGGACCAGGAGGAA
genomic: GTGTACGCCGTCTTCTGGCGGATCCTCCCCAGAAACTACCCGCCCCCAAAgtgagtcgcc ... cgctgttcagATGGGATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAA
EST: gi|40335358|gb|CK369428.1|CK369428
EST:     GTGTACGCCGTCTTCTGGCGGATCCTCCCCAGAAACTACCCGCCCCCCAA                         ATGGGATCTCCAGGGCGGCATATACGACCGGACAAGA
genomic: GTGTACGCCGTCTTCTGGCGGATCCTCCCCAGAAACTACCCGCCCCCAAAgtgagtcgcc ... cgctgttcagATGGGATCTCCAGGGCGGCATATACGACCGGACAAGA
EST: gi|91049965|gb|EB160383.1|EB160383
EST:     GTGTACGCCGTCTTCTGGCGGATCCTCCCCAGAAACTACCCGCCCCCAAA                         ATGGGATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAA
genomic: GTGTACGCCGTCTTCTGGCGGATCCTCCCCAGAAACTACCCGCCCCCAAAgtgagtcgcc ... cgctgttcagATGGGATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAA
EST: gi|86472078|gb|DY238448.1|DY238448
EST:     GTGTACGCCGTCTTCTGGCGGATCCTCCCCAGAAACTACCCGCCCCCAAA                         GTGGGATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAA
genomic: GTGTACGCCGTCTTCTGGCGGATCCTCCCCAGAAACTACCCGCCCCCAAAgtgagtcgcc ... cgctgttcagATGGGATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAA
EST: gi|71442162|gb|DR823212.1|DR823212
EST:     GTGTACGCCGTCTTCTGGCGGATCCTCCCCAGAAACTACCCGCCCCCAAA                         ATGGGATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAA
genomic: GTGTACGCCGTCTTCTGGCGGATCCTCCCCAGAAACTACCCGCCCCCAAAgtgagtcgcc ... cgctgttcagATGGGATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAA
EST: gi|26456486|gb|CA828069.1|CA828069
EST:     GTGTACGCCGTCTTCTGGCGGATCCTCCCCAGAAACTACCCGCCCCCAAA                         ATGGGATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAA
genomic: GTGTACGCCGTCTTCTGGCGGATCCTCCCCAGAAACTACCCGCCCCCAAAgtgagtcgcc ... cgctgttcagATGGGATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAA
EST: gi|78084497|gb|DV512890.1|DV512890
EST:     GTGTACGCCGTCTTCTGGCGGATCCTCCCCAGAAACTACCCGCCCCCAAA                         ATGGGATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAA
genomic: GTGTACGCCGTCTTCTGGCGGATCCTCCCCAGAAACTACCCGCCCCCAAAgtgagtcgcc ... cgctgttcagATGGGATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAA
EST: gi|93012864|gb|EB638384.1|EB638384
EST:     GTGTACGCCGTCTTCTGGTGGATCCTCCCCAGAAACTACCCGCCCCCAAA                         ATGGGATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAA
genomic: GTGTACGCCGTCTTCTGGCGGATCCTCCCCAGAAACTACCCGCCCCCAAAgtgagtcgcc ... cgctgttcagATGGGATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAA
EST: gi|149109966|gb|EE293776.2|EE293776
EST:     GTGTACGCCGTCTTCTGGCGGATCCTCCCCAGAAACTACCCGCCCCCAAA                         ATGGGATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAA
genomic: GTGTACGCCGTCTTCTGGCGGATCCTCCCCAGAAACTACCCGCCCCCAAAgtgagtcgcc ... cgctgttcagATGGGATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAA
EST: gi|101393159|gb|EB818510.1|EB818510
EST:     GTGTACGCCGTCTTCTGGCGGATCCTCCCCAGAAACTACCCGCCCCCAAA                         ATGGGATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAA
genomic: GTGTACGCCGTCTTCTGGCGGATCCTCCCCAGAAACTACCCGCCCCCAAAgtgagtcgcc ... cgctgttcagATGGGATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAA
EST: gi|50330625|gb|CO525751.1|CO525751
EST:     GTGTACGCCGTCTTCTGGCGGATCCTCCCCAGAAACTACCCGCCCCCAAA                         ATGGGATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAA
genomic: GTGTACGCCGTCTTCTGGCGGATCCTCCCCAGAAACTACCCGCCCCCAAAgtgagtcgcc ... cgctgttcagATGGGATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAA
EST: gi|76014748|gb|DT941918.1|DT941918
EST:     GTGTACGCCGTCTTCTGGCGGATCCTCCCCAGAAACTACCCGCCCCCAAA                         ATGGGATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAA
genomic: GTGTACGCCGTCTTCTGGCGGATCCTCCCCAGAAACTACCCGCCCCCAAAgtgagtcgcc ... cgctgttcagATGGGATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAA
EST: gi|101395608|gb|EB819733.1|EB819733
EST:     GTGTACGCCGTCTTCTGGCGGATCCTCCCCAGAAACTACCCGCCCCCAAA                         ATGGGATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAA
genomic: GTGTACGCCGTCTTCTGGCGGATCCTCCCCAGAAACTACCCGCCCCCAAAgtgagtcgcc ... cgctgttcagATGGGATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAA
EST: gi|78112591|gb|DV530985.1|DV530985
EST:     GTGTACGCCGTCTTCTGGCGGATCCTCCCCAGAAACTACCCGCCCCCAAA                         ATGGGATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAA
genomic: GTGTACGCCGTCTTCTGGCGGATCCTCCCCAGAAACTACCCGCCCCCAAAgtgagtcgcc ... cgctgttcagATGGGATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggccttctgggtcgttgctggtgctgattaaattgtttatccggccgctgttcagATGGGATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAACTG
                     tgctgat  putative branch site (score: 3)
                        tgattaaattgtttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtcgccgttcgttcgacatgcatgcgcgcgaccttcgttcggtgtccttgtcgtcgtccatccctgacgcgctccggcgctgcgtctagtagtctggtctggttcggcggccacggccttctgggtcgttgctggtgctgattaaattgtttatccggccgctgttcagATGGGATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAACTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA