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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacacatacaaaccgtaatgatatatcaatacacttggtaaatttcaaattatacaacttatttcataaaaaaatgaacttactttgagggaggattataaaaaaaaactgaaagaatcgtactcttgttctgggcagCACAAGGATCAAAATGGACCAAGTATTTGGACACGAGCCGTTTTGGTGGGAGGAAATGCTTCGATACCTCTGGTCTGCACTGGACTGAACATGATGAATC

Basic information

species Zea mays
transcript GRMZM2G107985_T02
intron # 5
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|60399481|gb|DN232293.1|DN232293
EST:     GCAGATCAAGCAAGGATCAAATCCCCACTGTGCAACTACTACTGCTGAAG                         CACAAGGATCAAAATGGACCAAGTATTTGGACACGAGCCGTTTTGGTGGGA
genomic: GCAGATCAAGCAAGGATCAAATCCCCACTGTGCAACTACTACTGCTGAAGgtaacacata ... ttctgggcagCACAAGGATCAAAATGGACCAAGTATTTGGACACGAGCCGTTTTGGTGGGA
EST: gi|78024477|gb|DV492864.1|DV492864
EST:     GCAGATCAAGCAAGGATCAAGTCCCCACTGTGCAACTACTACTGCTGAAG                         CACAAGGATCAAAATGGACCAAGTATTTGGACACGAGCCGTTTTGGTGGGA
genomic: GCAGATCAAGCAAGGATCAAATCCCCACTGTGCAACTACTACTGCTGAAGgtaacacata ... ttctgggcagCACAAGGATCAAAATGGACCAAGTATTTGGACACGAGCCGTTTTGGTGGGA
EST: gi|76912082|gb|DV164566.1|DV164566
EST:     GCAGATCAAGCAAGGATCAAATCCCCACTGTGCAACTACTACTGCTGAAG                         CACAAGGATCAAAATGGACCAAGTATTTGGACACGAGCCGTTTTGGTGGGA
genomic: GCAGATCAAGCAAGGATCAAATCCCCACTGTGCAACTACTACTGCTGAAGgtaacacata ... ttctgggcagCACAAGGATCAAAATGGACCAAGTATTTGGACACGAGCCGTTTTGGTGGGA
EST: gi|78120583|gb|DV538967.1|DV538967
EST:     GCAGATCAAGCAAGGATCAAATCCCCACTGTGCAACTACTACTGCTGAAG                         CACAAGGATCAAAATGGACCAAGTATTTGGACACGAGCCGTTTTGGTGGGA
genomic: GCAGATCAAGCAAGGATCAAATCCCCACTGTGCAACTACTACTGCTGAAGgtaacacata ... ttctgggcagCACAAGGATCAAAATGGACCAAGTATTTGGACACGAGCCGTTTTGGTGGGA
EST: gi|88751488|gb|DY535629.1|DY535629
EST:     GCAGATCAAGCAAGGATCAAATCCCCACTGTGCAACTACTACTGCTGAAG                         CACAAGGATCAAAATGGACCAAGTATTTGGACTCGAGCCGTTTTGGTGGGG
genomic: GCAGATCAAGCAAGGATCAAATCCCCACTGTGCAACTACTACTGCTGAAGgtaacacata ... ttctgggcagCACAAGGATCAAAATGGACCAAGTATTTGGACACGAGCCGTTTTGGTGGGA
EST: gi|78074278|gb|DV502712.1|DV502712
EST:     GCAGATCAAGCAAGGATCAAATCCCCACTGTGCAACTACTACTGCTGAAG                         CACAAGGATCAAAATGGACCAAGTATTTGGACACGAGCCGTTTTGGTGGGA
genomic: GCAGATCAAGCAAGGATCAAATCCCCACTGTGCAACTACTACTGCTGAAGgtaacacata ... ttctgggcagCACAAGGATCAAAATGGACCAAGTATTTGGACACGAGCCGTTTTGGTGGGA
EST: gi|71759770|gb|DR957707.1|DR957707
EST:     GCAGATCAAGCAAGGATCAAATCCCCACTGTGCAACTACTACTGCTGAAG                         CACAAGGATCAAAATGGACCAAGTATTTGGACACGAGCCGTTTTGGTGGGA
genomic: GCAGATCAAGCAAGGATCAAATCCCCACTGTGCAACTACTACTGCTGAAGgtaacacata ... ttctgggcagCACAAGGATCAAAATGGACCAAGTATTTGGACACGAGCCGTTTTGGTGGGA
EST: gi|74234638|gb|DT642552.1|DT642552
EST:     GCAGATCAAGCAAGGATCAAATCCCCACTGTGCAACTACTACTGCTGAAG                         CACAAGGATCAAAATGGACCAAGTATTTGGACACGAGCCGTTTTGGTGGGA
genomic: GCAGATCAAGCAAGGATCAAATCCCCACTGTGCAACTACTACTGCTGAAGgtaacacata ... ttctgggcagCACAAGGATCAAAATGGACCAAGTATTTGGACACGAGCCGTTTTGGTGGGA
EST: gi|24768229|gb|CA403358.1|CA403358
EST:     GCAGATCAAGCAAGGATCAAATCCCCACTGTGCAACTACTACTGCTGAAG                         CACAAGGATCAAAATGGACCAAGTATTTGGACACGAGCCGTTTTGGTGGGA
genomic: GCAGATCAAGCAAGGATCAAATCCCCACTGTGCAACTACTACTGCTGAAGgtaacacata ... ttctgggcagCACAAGGATCAAAATGGACCAAGTATTTGGACACGAGCCGTTTTGGTGGGA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 3 RNA-Seq libraries.


Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 4

GGAAAGAGAACCAAGCTGTCAACACATCCCACTTTATGTAATAAGAGGCAGCAGATCAAGCAAGGATCAAATCCCCACTGTGCAACTACTACTGCTGAAGgtaacacata ... ttctgggcagCACAAGGATCAAAATGGACCAAGTATTTGGACACGAGCCGTTTTGGTGGGAGGAAATGCTTCGATACCTCTGGTCTGCACTGGACTGAACATGATGAATC


Block sizes: 47 (upstream exon), 30 (downstream exon)
Score: 3

GGAAAGAGAACCAAGCTGTCAACACATCCCACTTTATGTAATAAGAGGCAGCAGATCAAGCAAGGATCAAATCCCCACTGTGCAACTACTACTGCTGAAGgtaacacata ... ttctgggcagCACAAGGATCAAAATGGACCAAGTATTTGGACACGAGCCGTTTTGGTGGGAGGAAATGCTTCGATACCTCTGGTCTGCACTGGACTGAACATGATGAATC


Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 10

GGAAAGAGAACCAAGCTGTCAACACATCCCACTTTATGTAATAAGAGGCAGCAGATCAAGCAAGGATCAAATCCCCACTGTGCAACTACTACTGCTGAAGgtaacacata ... ttctgggcagCACAAGGATCAAAATGGACCAAGTATTTGGACACGAGCCGTTTTGGTGGGAGGAAATGCTTCGATACCTCTGGTCTGCACTGGACTGAACATGATGAATC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgagggaggattataaaaaaaaactgaaagaatcgtactcttgttctgggcagCACAAGGATCAAAATGGACCAAGTATTTGGACACGAGCCGTTTTGGTGGGAGGAAATGCTTCGATACCTCTGGTCTGCACTGGACTGAACATGATGAATC
                                       ctcttgttct  CT-rich tract
           attataaaaaaaaact  TA-rich tract