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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGGTACCGAATGTAGCTATGGCGAGAGGTGCCGCTATCCGCACAGCTACTGCATAAGCGATAGTATCGCGATGCTTACCTTGCTCAAGGGACACGAGCAGgtaaagtttaatctctgccaatttgcctgtctggcaaaaaaacatggaagtttttttctaaccgagctgcattggttgccttcag

Basic information

species Zea mays
transcript GRMZM2G037200_T01
intron # 1
splice site 5'
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|78114713|gb|DV533101.1|DV533101
EST:     GCATAAGCGATAGTATCGCGATGCTTACCTTGCTCAAGGGACACGAGCAG                         GGTGTCACGGGCATTGCACTGCCCGCTGGGTCAGACAAGCTTTATTCCGGG
genomic: GCATAAGCGATAGTATCGCGATGCTTACCTTGCTCAAGGGACACGAGCAGgtaaagttta ... ttgccttcagGGTGTCACGGGCATTGCACTGCCCGCTGGGTCAGACAAGCTTTATTCCGGG
EST: gi|71297929|gb|DR784934.1|DR784934
EST:     GCATAAGCGATAGTATCGCGATGCTTACCTTGCTCAAGGGACACGAGCAG                         GGTGTCACGGGCATTGCACTGCCCGCTGGGTCAGACAAGCTTTATTCCGGG
genomic: GCATAAGCGATAGTATCGCGATGCTTACCTTGCTCAAGGGACACGAGCAGgtaaagttta ... ttgccttcagGGTGTCACGGGCATTGCACTGCCCGCTGGGTCAGACAAGCTTTATTCCGGG
EST: gi|149095550|gb|EE181207.2|EE181207
EST:     GCATAAGCGATAGTATCGCGATGCTTACCTTGCTCAAGGGACACGAGCAG                         GGTGTCACGGGCATTGCACTGCCCGCTGGGTCAGACAAGCTTTATTCCGGG
genomic: GCATAAGCGATAGTATCGCGATGCTTACCTTGCTCAAGGGACACGAGCAGgtaaagttta ... ttgccttcagGGTGTCACGGGCATTGCACTGCCCGCTGGGTCAGACAAGCTTTATTCCGGG
EST: gi|93282169|gb|EB674433.1|EB674433
EST:     GCATAAGCGATAGTATCGCGATGCTTACCTTGCTCAAGGGACACGAGCAG                         GGTGTCACGGGCATTGCACTGCCCGCTGGGTCAGACAAGCTTTATTCCGGG
genomic: GCATAAGCGATAGTATCGCGATGCTTACCTTGCTCAAGGGACACGAGCAGgtaaagttta ... ttgccttcagGGTGTCACGGGCATTGCACTGCCCGCTGGGTCAGACAAGCTTTATTCCGGG
EST: gi|29576800|gb|CB616912.1|CB616912
EST:     GCATAAGCGATAGTATCGCGATGCTTACCTTGCTCAAGGGACACGAGCAG                         GGTGTCACGGGCATTGCACTGCCCGCTGGGTCAGACAAGCTTTATTCCGGG
genomic: GCATAAGCGATAGTATCGCGATGCTTACCTTGCTCAAGGGACACGAGCAGgtaaagttta ... ttgccttcagGGTGTCACGGGCATTGCACTGCCCGCTGGGTCAGACAAGCTTTATTCCGGG
EST: gi|31997696|gb|CD661719.1|CD661719
EST:     GCATAAGCGATAGTATCGCGATGCTTACCTTGCTCAAGGGACACGAGCAG                         GGTGTCACGGGCATTGCACTGCCCGCTGGGTCAGACAAGCTTTATTCCGGG
genomic: GCATAAGCGATAGTATCGCGATGCTTACCTTGCTCAAGGGACACGAGCAGgtaaagttta ... ttgccttcagGGTGTCACGGGCATTGCACTGCCCGCTGGGTCAGACAAGCTTTATTCCGGG
EST: gi|148948214|gb|EC893730.2|EC893730
EST:     GCATAAGCGATAGTATCGCGATGCTTACCTTGCTCAAGGGACACGAGCAG                         GGTGTCACGGGCATTGCACTGCCCGCTGGGTCAGACAAGCTTTATTCCGGG
genomic: GCATAAGCGATAGTATCGCGATGCTTACCTTGCTCAAGGGACACGAGCAGgtaaagttta ... ttgccttcagGGTGTCACGGGCATTGCACTGCCCGCTGGGTCAGACAAGCTTTATTCCGGG
EST: gi|149086361|gb|EE175902.2|EE175902
EST:     GCATAAGCGATAGTATCGCGATGCTTACCTTGCTCAAGGGACACGAGCAG                         GGTGTCACGGGCATTGCACTGCCCGCTGGGTCAGACAAGCTTTATTCCGGG
genomic: GCATAAGCGATAGTATCGCGATGCTTACCTTGCTCAAGGGACACGAGCAGgtaaagttta ... ttgccttcagGGTGTCACGGGCATTGCACTGCCCGCTGGGTCAGACAAGCTTTATTCCGGG
EST: gi|26559549|gb|CA831784.1|CA831784
EST:     GCATAAGCGATAGTATCGCGATGCTTACCTTGCTCAAGGGACACGAGCAG                         GGTGTCACGGGCATTGCACTGCCCGCTGGGTCAGACAAGCTTTATTCCGGG
genomic: GCATAAGCGATAGTATCGCGATGCTTACCTTGCTCAAGGGACACGAGCAGgtaaagttta ... ttgccttcagGGTGTCACGGGCATTGCACTGCCCGCTGGGTCAGACAAGCTTTATTCCGGG
EST: gi|71429257|gb|DR810307.1|DR810307
EST:     GCATAAGCGATAGTATCGCGATGCTTACCTTGCTCAAGGGACACGAGCAG                         GGTGTCACGGGCATTGCACTGCCCGCTGGGTCAGACAAGCTT
genomic: GCATAAGCGATAGTATCGCGATGCTTACCTTGCTCAAGGGACACGAGCAGgtaaagttta ... ttgccttcagGGTGTCACGGGCATTGCACTGCCCGCTGGGTCAGACAAGCTT
EST: gi|76935921|gb|DV174536.1|DV174536
EST:     GCATAAGCGATAGTATCGCGATGCTTACCTTGCTCAAGGGACACGAGCAG                         GGTGTCACGGGCATTGCACTGCCCGCTGGGTCAGACAAGCTTTATTCCGGG
genomic: GCATAAGCGATAGTATCGCGATGCTTACCTTGCTCAAGGGACACGAGCAGgtaaagttta ... ttgccttcagGGTGTCACGGGCATTGCACTGCCCGCTGGGTCAGACAAGCTTTATTCCGGG
EST: gi|88751063|gb|DY535204.1|DY535204
EST:     GCATAAGCGATAGTATCGCGATGCTTACCTTGCTCAAGGGACACGAGCAG                         GGTGTCACGGGCATTGCACTGCCCGCTGGGTCACACAAGCTTTATTCCGGG
genomic: GCATAAGCGATAGTATCGCGATGCTTACCTTGCTCAAGGGACACGAGCAGgtaaagttta ... ttgccttcagGGTGTCACGGGCATTGCACTGCCCGCTGGGTCAGACAAGCTTTATTCCGGG
EST: gi|22715752|gb|BU197942.1|BU197942
EST:     GCATAAGCGATAGTATCGCGATGCTTACCTTGCTCAAGGGACACGAGCAG                         GGTGTCACGGGCATTGCACTGCCCGCTGGGTCAGACAAGCTTTATTCCGGG
genomic: GCATAAGCGATAGTATCGCGATGCTTACCTTGCTCAAGGGACACGAGCAGgtaaagttta ... ttgccttcagGGTGTCACGGGCATTGCACTGCCCGCTGGGTCAGACAAGCTTTATTCCGGG
EST: gi|22819542|gb|BU499632.1|BU499632
EST:     GCATAAGCGATAGTATCGCGATGCTTACCTTGCTCAAGGGACACGAGCAG                         GGTGTCACGGGCATTGCACTGCCCGCTGGGTCAGACAAGCTTTATTCCGGG
genomic: GCATAAGCGATAGTATCGCGATGCTTACCTTGCTCAAGGGACACGAGCAGgtaaagttta ... ttgccttcagGGTGTCACGGGCATTGCACTGCCCGCTGGGTCAGACAAGCTTTATTCCGGG
EST: gi|78111040|gb|DV529437.1|DV529437
EST:     CATAAGCGATAGTATCGCGATGCTTACCTTGCTNCA-GGGACACGAGCAG                         GGTGTCACGGGCATTGCACTGCCCGCTGGGTCAGACAAGCTTTATTCCGGG
genomic: CATAAGCGATAGTATCGCGATGCTTACCTTGCT-CAAGGGACACGAGCAGgtaaagttta ... ttgccttcagGGTGTCACGGGCATTGCACTGCCCGCTGGGTCAGACAAGCTTTATTCCGGG
EST: gi|29576814|gb|CB616926.1|CB616926
EST:     GCATAAGCGATAGTATCGCGATGCTTACCTTGCTCAAGGGACACGAGCAG                         GGTGTCACGGGCATTGCACTGCCCGCTGGGTCAGACAAGCTTTATTCCGGG
genomic: GCATAAGCGATAGTATCGCGATGCTTACCTTGCTCAAGGGACACGAGCAGgtaaagttta ... ttgccttcagGGTGTCACGGGCATTGCACTGCCCGCTGGGTCAGACAAGCTTTATTCCGGG
EST: gi|149070982|gb|EE159387.2|EE159387
EST:     GCATAAGCGATAGTATCGCGATGCTTACCTTGCTCAAGGGACACGAGCAG                         GGTGTCACGGGCATTGCACTGCCCGCTGGGTCAGACAAGCTTTATTCCGGG
genomic: GCATAAGCGATAGTATCGCGATGCTTACCTTGCTCAAGGGACACGAGCAGgtaaagttta ... ttgccttcagGGTGTCACGGGCATTGCACTGCCCGCTGGGTCAGACAAGCTTTATTCCGGG
EST: gi|211300821|gb|FL154798.1|FL154798
EST:     GCATAAGCGATAGTATCGCGATGCTTACCTTGCTCAAGGGACACGAGCAG                         GGTGTCACGGGCATTGCACTGCCCGCTGGGTCAGACAAGCTTTATTCCGGG
genomic: GCATAAGCGATAGTATCGCGATGCTTACCTTGCTCAAGGGACACGAGCAGgtaaagttta ... ttgccttcagGGTGTCACGGGCATTGCACTGCCCGCTGGGTCAGACAAGCTTTATTCCGGG
EST: gi|91055829|gb|EB166247.1|EB166247
EST:     GCATAAGCGATAGTATCGCGATGCTTACCTTGCTCAAGGGACACGAGCAG                         GGTGTCACGGGCATTGCACTGCCCGCTGGGTCAGACAAGCTTTATTCCGGG
genomic: GCATAAGCGATAGTATCGCGATGCTTACCTTGCTCAAGGGACACGAGCAGgtaaagttta ... ttgccttcagGGTGTCACGGGCATTGCACTGCCCGCTGGGTCAGACAAGCTTTATTCCGGG
EST: gi|148937590|gb|EC881777.2|EC881777
EST:     GCATAAGCGATAGTATCGCGATGCTTACCTTGCTCAAGGGACACGAGCAG                         GGTGTCACGGGCATTGCACTGCCCGCTGGGTCAGACAAGCTTTATTCCGGG
genomic: GCATAAGCGATAGTATCGCGATGCTTACCTTGCTCAAGGGACACGAGCAGgtaaagttta ... ttgccttcagGGTGTCACGGGCATTGCACTGCCCGCTGGGTCAGACAAGCTTTATTCCGGG
EST: gi|91876611|gb|EB406568.1|EB406568
EST:     GCATAAGCGATAGTATCGCGATGCTTACCTTGCTCAAGGGACACGAGCAG                         GGTGTCACGGGCATTGCACTGCCCGCTGGGTCAGACAAGCTTTATTCCGGG
genomic: GCATAAGCGATAGTATCGCGATGCTTACCTTGCTCAAGGGACACGAGCAGgtaaagttta ... ttgccttcagGGTGTCACGGGCATTGCACTGCCCGCTGGGTCAGACAAGCTTTATTCCGGG
EST: gi|50334153|gb|CO529279.1|CO529279
EST:     CATAAGCGATAGTATCGCGATGCTTACCTTGCTNCA-GGGACACGAGCAG                         GGTGTCACGGGCATTGCACTGCCCGCTGGGTCAGACAAGCTTTAT
genomic: CATAAGCGATAGTATCGCGATGCTTACCTTGCT-CAAGGGACACGAGCAGgtaaagttta ... ttgccttcagGGTGTCACGGGCATTGCACTGCCCGCTGGGTCAGACAAGCTTTAT
EST: gi|87157418|gb|DY402207.1|DY402207
EST:     GCATAAGCGATAGTATCGCGATGCTTACCTTGCTCAAGGGACACGAGCAG                         GGTGTCACGGGCATTGCACTGCCCGCTGGGTCAGACAAGCTTTATTCCGGG
genomic: GCATAAGCGATAGTATCGCGATGCTTACCTTGCTCAAGGGACACGAGCAGgtaaagttta ... ttgccttcagGGTGTCACGGGCATTGCACTGCCCGCTGGGTCAGACAAGCTTTATTCCGGG

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 4 RNA-Seq libraries.


Block sizes: 43 (upstream exon), 48 (downstream exon)
Score: 40

CGGTACCGAATGTAGCTATGGCGAGAGGTGCCGCTATCCGCACAGCTACTGCATAAGCGATAGTATCGCGATGCTTACCTTGCTCAAGGGACACGAGCAGgtaaagttta ... ttgccttcagGGTGTCACGGGCATTGCACTGCCCGCTGGGTCAGACAAGCTTTATTCCGGGAGTAAGGATGGAACTGTTCGCATGTGGGATTGCCAAACTGGGCAG


Block sizes: 43 (upstream exon), 48 (downstream exon)
Score: 35

CGGTACCGAATGTAGCTATGGCGAGAGGTGCCGCTATCCGCACAGCTACTGCATAAGCGATAGTATCGCGATGCTTACCTTGCTCAAGGGACACGAGCAGgtaaagttta ... ttgccttcagGGTGTCACGGGCATTGCACTGCCCGCTGGGTCAGACAAGCTTTATTCCGGGAGTAAGGATGGAACTGTTCGCATGTGGGATTGCCAAACTGGGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 28

CGGTACCGAATGTAGCTATGGCGAGAGGTGCCGCTATCCGCACAGCTACTGCATAAGCGATAGTATCGCGATGCTTACCTTGCTCAAGGGACACGAGCAGgtaaagttta ... ttgccttcagGGTGTCACGGGCATTGCACTGCCCGCTGGGTCAGACAAGCTTTATTCCGGGAGTAAGGATGGAACTGTTCGCATGTGGGATTGCCAAACTGGGCAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 31

CGGTACCGAATGTAGCTATGGCGAGAGGTGCCGCTATCCGCACAGCTACTGCATAAGCGATAGTATCGCGATGCTTACCTTGCTCAAGGGACACGAGCAGgtaaagttta ... ttgccttcagGGTGTCACGGGCATTGCACTGCCCGCTGGGTCAGACAAGCTTTATTCCGGGAGTAAGGATGGAACTGTTCGCATGTGGGATTGCCAAACTGGGCAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGGTACCGAATGTAGCTATGGCGAGAGGTGCCGCTATCCGCACAGCTACTGCATAAGCGATAGTATCGCGATGCTTACCTTGCTCAAGGGACACGAGCAGgtaaagtttaatctctgccaatttgcctgtctggcaaaaaaacatggaagtttttttctaaccgagctgcattggttgccttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG