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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGGACCCCAAAATCTCAGATCCTTCCTGCCCGCCCGCCCGTGCCCGTCGACGCGTCGTTCTTGCCGGCCGCGCCCCACCTCCGCCCTCTCCTCCTCCAGgtaggtgaatggtgattgctgcaaccgaccgtcttcgatggacggggattcttcggtggggttggattggtacgcggtgtggcggtcggattcggagact...

Basic information

species Zea mays
transcript GRMZM2G120918_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|60394949|gb|DN227818.1|DN227818
EST:     ACGCGTCGTTCTTGCCGGCCGCGCCCCACCTCCGCCCTCTCCTCCTCCAG                         GGGGATCGGATACGCCACAGGCTGCGCGATGGTGCTGTGGGTCTTCGGCTA
genomic: ACGCGTCGTTCTTGCCGGCCGCGCCCCACCTCCGCCCTCTCCTCCTCCAGgtaggtgaat ... gtttccgcagGGGGATCGGATACGCCACAGGCTGCGCGATGGTGCTGTGGGTCTTCGGCTA
EST: gi|211172665|gb|FL375062.1|FL375062
EST:     ACGCGTCGTTCTTGCCGGCCGCGCCCCACCTCCGCCCTCTCCTCCTCCAG                         GGGGATCGGATACGCCACAGGCTGCGCGATGGTGCTGTGGGTCTTCGGCTA
genomic: ACGCGTCGTTCTTGCCGGCCGCGCCCCACCTCCGCCCTCTCCTCCTCCAGgtaggtgaat ... gtttccgcagGGGGATCGGATACGCCACAGGCTGCGCGATGGTGCTGTGGGTCTTCGGCTA
EST: gi|211201995|gb|FL401734.1|FL401734
EST:     ACGCGTCGTTCTTGCCGGCCGCGCCCCACCTCCGCCCTCTCCTCCTCCAG                         GGGGATCGGATACGCCACAGGCTGCGCGATGGTGCTGTGGGTCTTCGGCTA
genomic: ACGCGTCGTTCTTGCCGGCCGCGCCCCACCTCCGCCCTCTCCTCCTCCAGgtaggtgaat ... gtttccgcagGGGGATCGGATACGCCACAGGCTGCGCGATGGTGCTGTGGGTCTTCGGCTA
EST: gi|211109289|gb|FL390878.1|FL390878
EST:     ACGCGTCGTTCTTGCCGGCCGCGCCCCACCTCCGCCCTCTCCTCCTCCAG                         GGGGATCGGATACGCCACAGGCTGCGCGATGGTGCTGTGGGTCTTCGGCTA
genomic: ACGCGTCGTTCTTGCCGGCCGCGCCCCACCTCCGCCCTCTCCTCCTCCAGgtaggtgaat ... gtttccgcagGGGGATCGGATACGCCACAGGCTGCGCGATGGTGCTGTGGGTCTTCGGCTA
EST: gi|149082091|gb|EE171269.2|EE171269
EST:     ACGCGTCGTTCTTGCCGGCCGCGCCCCACCTCCGCCCTCTCCTCCTCCAG                         GGGGATCGGATACGCCACAGGCTGCGCGATGGTGCTGTGGGTCTTCGGCTA
genomic: ACGCGTCGTTCTTGCCGGCCGCGCCCCACCTCCGCCCTCTCCTCCTCCAGgtaggtgaat ... gtttccgcagGGGGATCGGATACGCCACAGGCTGCGCGATGGTGCTGTGGGTCTTCGGCTA
EST: gi|211403195|gb|FL397526.1|FL397526
EST:     ACGCGTCGTTCTTGCCGGCCGCGCCCCACCTCCGCCCTCTCCTCCTCCAG                         GGGGATCGGATACGCCACAGGCTGCGCGATGGTGCTGTGGGTCTTCGGCTA
genomic: ACGCGTCGTTCTTGCCGGCCGCGCCCCACCTCCGCCCTCTCCTCCTCCAGgtaggtgaat ... gtttccgcagGGGGATCGGATACGCCACAGGCTGCGCGATGGTGCTGTGGGTCTTCGGCTA
EST: gi|211351030|gb|FL403671.1|FL403671
EST:     ACGCGTCGTTCTTGCCGGCCGCGCCCCACCTCCGCCCTCTCCTCCTCCAG                         GGGGATCGGATACGCCACAGGCTGCGCGATGGTGCTGTGGGTCTTCGGCTA
genomic: ACGCGTCGTTCTTGCCGGCCGCGCCCCACCTCCGCCCTCTCCTCCTCCAGgtaggtgaat ... gtttccgcagGGGGATCGGATACGCCACAGGCTGCGCGATGGTGCTGTGGGTCTTCGGCTA
EST: gi|211349226|gb|FL428900.1|FL428900
EST:     ACGCGTCGTTCTTGCCGGCCGNGCCCCACCTCCGCCCTCTCCTCCTCCAG                         GGGGATCGGATACGCCACAGGCTGCGCGATGGTGCTGTGGGTCTTCGGCTA
genomic: ACGCGTCGTTCTTGCCGGCCGCGCCCCACCTCCGCCCTCTCCTCCTCCAGgtaggtgaat ... gtttccgcagGGGGATCGGATACGCCACAGGCTGCGCGATGGTGCTGTGGGTCTTCGGCTA
EST: gi|211135556|gb|FL369510.1|FL369510
EST:     ACGCGTCGTTCTTGCCGGNCGCGCCCCACCTCCGCCCTCTCCTCCTCCAG                         GGGGATCGGATACGCC
genomic: ACGCGTCGTTCTTGCCGGCCGCGCCCCACCTCCGCCCTCTCCTCCTCCAGgtaggtgaat ... gtttccgcagGGGGATCGGATACGCC
EST: gi|211014195|gb|FL395355.1|FL395355
EST:     ACGCGTCGTTCTTGCCGGCCGCGCCCCACCTCCGCCCTCTCCTCCTCCAG                         GGGGATCGGATACGCCACAGGCTGCGCGATGGTGCTGTGGGTCTTCGGCTA
genomic: ACGCGTCGTTCTTGCCGGCCGCGCCCCACCTCCGCCCTCTCCTCCTCCAGgtaggtgaat ... gtttccgcagGGGGATCGGATACGCCACAGGCTGCGCGATGGTGCTGTGGGTCTTCGGCTA
EST: gi|211147747|gb|FL420929.1|FL420929
EST:     ACGCGTCGTTCTTGCCGGCCGCGCCCCACCTCCGCCCTCTCCTCCTCCAG                         GGGGATCGGATACGCCACAGGCTGCGCGATGGTGCTGTGGGTCTTCGGCTA
genomic: ACGCGTCGTTCTTGCCGGCCGCGCCCCACCTCCGCCCTCTCCTCCTCCAGgtaggtgaat ... gtttccgcagGGGGATCGGATACGCCACAGGCTGCGCGATGGTGCTGTGGGTCTTCGGCTA
EST: gi|211498977|gb|FL377917.1|FL377917
EST:     ACGCGTCGTTCTTGCCGGCCGCGCCCCACCTCCGCCCTCTCCTCCTCCAG                         GGGGATCGGATACGCCACAGGCTGCGCGATGGTGCTGTGGGTCTTCGGCTA
genomic: ACGCGTCGTTCTTGCCGGCCGCGCCCCACCTCCGCCCTCTCCTCCTCCAGgtaggtgaat ... gtttccgcagGGGGATCGGATACGCCACAGGCTGCGCGATGGTGCTGTGGGTCTTCGGCTA
EST: gi|20301255|gb|BQ164198.1|BQ164198
EST:     ACGCGTCGTTCTTGCCGGCCGCGCCCCACCTC-GCCCTCTCCTCCTCCAG                         GGGGATCGGATACGCCACAGGCTGCGCGA
genomic: ACGCGTCGTTCTTGCCGGCCGCGCCCCACCTCCGCCCTCTCCTCCTCCAGgtaggtgaat ... gtttccgcagGGGGATCGGATACGCCACAGGCTGCGCGA
EST: gi|211166318|gb|FL404279.1|FL404279
EST:     ACGCGTCGTTCTTGCCGGCCGCGCCCCACCTCCGCCCTCTCCTCCTCCAG                         GGGGATCGGATACGCCACAGGCTGCGCGATGGTGCTGNGGGTCTTCGGCTA
genomic: ACGCGTCGTTCTTGCCGGCCGCGCCCCACCTCCGCCCTCTCCTCCTCCAGgtaggtgaat ... gtttccgcagGGGGATCGGATACGCCACAGGCTGCGCGATGGTGCTGTGGGTCTTCGGCTA
EST: gi|60396968|gb|DN229787.1|DN229787
EST:     ACGCGTCGTTCTTGCCGGCCGCGCCCCACCTCCGCCCTCTCCTCCTCCAG                         GGGGATCGGATACGCCACAGGCTGCGCGATGGTGCTGTGGGTCTTCGGCTA
genomic: ACGCGTCGTTCTTGCCGGCCGCGCCCCACCTCCGCCCTCTCCTCCTCCAGgtaggtgaat ... gtttccgcagGGGGATCGGATACGCCACAGGCTGCGCGATGGTGCTGTGGGTCTTCGGCTA
EST: gi|211301082|gb|FL395605.1|FL395605
EST:     ACGCGTCGTTCTTGCCGGCCGCG-CCCACCTCCGCCCTCTCCTCCTCCAG                         GGGGATCGGATACGCCACAGGCTGCGCGATGGTGCTGTGGGTCTTCGGCTA
genomic: ACGCGTCGTTCTTGCCGGCCGCGCCCCACCTCCGCCCTCTCCTCCTCCAGgtaggtgaat ... gtttccgcagGGGGATCGGATACGCCACAGGCTGCGCGATGGTGCTGTGGGTCTTCGGCTA
EST: gi|211456945|gb|FL421189.1|FL421189
EST:     ACGCGTCGTTCTTGCCGGCCGCGCCCCACCTCCGCCCTCTCCTCCTCCAG                         GGGGATCGGATACGCCACAGGCTGCGCGATGGTGCTGTGGGTCTTCGGCTA
genomic: ACGCGTCGTTCTTGCCGGCCGCGCCCCACCTCCGCCCTCTCCTCCTCCAGgtaggtgaat ... gtttccgcagGGGGATCGGATACGCCACAGGCTGCGCGATGGTGCTGTGGGTCTTCGGCTA
EST: gi|211020406|gb|FL417355.1|FL417355
EST:     ACGCGTCGTTCTTGCCGGCCGCGCCCCACCTCCGCCCTCTCCTCCTCCAG                         GGGGATCGGATACGCCACAGGCTGCNCGATGGTGCTGTGGGNCTTCGGCTA
genomic: ACGCGTCGTTCTTGCCGGCCGCGCCCCACCTCCGCCCTCTCCTCCTCCAGgtaggtgaat ... gtttccgcagGGGGATCGGATACGCCACAGGCTGCGCGATGGTGCTGTGGGTCTTCGGCTA

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: 49 (upstream exon), 49 (downstream exon)
Score: 868

CAGGACCCCAAAATCTCAGATCCTTCCTGCCCGCCCGCCCGTGCCCGTCGACGCGTCGTTCTTGCCGGCCGCGCCCCACCTCCGCCCTCTCCTCCTCCAGgtaggtgaat ... gtttccgcagGGGGATCGGATACGCCACAGGCTGCGCGATGGTGCTGTGGGTCTTCGGCTACGGCTCCCTCATCTGGAACCCCGGCTTCGACTTCGACGACAAAATCCTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 811

CAGGACCCCAAAATCTCAGATCCTTCCTGCCCGCCCGCCCGTGCCCGTCGACGCGTCGTTCTTGCCGGCCGCGCCCCACCTCCGCCCTCTCCTCCTCCAGgtaggtgaat ... gtttccgcagGGGGATCGGATACGCCACAGGCTGCGCGATGGTGCTGTGGGTCTTCGGCTACGGCTCCCTCATCTGGAACCCCGGCTTCGACTTCGACGACAAAATCCTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 378

CAGGACCCCAAAATCTCAGATCCTTCCTGCCCGCCCGCCCGTGCCCGTCGACGCGTCGTTCTTGCCGGCCGCGCCCCACCTCCGCCCTCTCCTCCTCCAGgtaggtgaat ... gtttccgcagGGGGATCGGATACGCCACAGGCTGCGCGATGGTGCTGTGGGTCTTCGGCTACGGCTCCCTCATCTGGAACCCCGGCTTCGACTTCGACGACAAAATCCTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 468

CAGGACCCCAAAATCTCAGATCCTTCCTGCCCGCCCGCCCGTGCCCGTCGACGCGTCGTTCTTGCCGGCCGCGCCCCACCTCCGCCCTCTCCTCCTCCAGgtaggtgaat ... gtttccgcagGGGGATCGGATACGCCACAGGCTGCGCGATGGTGCTGTGGGTCTTCGGCTACGGCTCCCTCATCTGGAACCCCGGCTTCGACTTCGACGACAAAATCCTC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAGGACCCCAAAATCTCAGATCCTTCCTGCCCGCCCGCCCGTGCCCGTCGACGCGTCGTTCTTGCCGGCCGCGCCCCACCTCCGCCCTCTCCTCCTCCAGgtaggtgaatggtgattgctgcaaccgaccgtcttcgatggacggggattcttcggtggggttggattggtacgcggtgtggcggtcggattcggagact

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC