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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCTTCTCCTCGTCCGCCCCAGTCTAATCCGATTCAAACCGCCCGTTCCCCGTGTCCGTGCCAAGCAAGCCGAGCCCAACCCCCAAGAGCCAGCTGCTCGgtgagtgccgcgccccgtcgcctcctcacgcttcgttgcttgcaatcaacgcgatcgtctggtctcgtcttgttccagtgtgtcatttctctctgacgggtgagatttggtttggatctggtcggaccag

Basic information

species Zea mays
transcript GRMZM2G165357_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|148939205|gb|EC883670.2|EC883670
EST:     CGTGTCCGTGCCAAGCAAGCCGAGCCCAACCCCCAAGAGCCAGCTGCTCG                         GTGCTCCACGCGATGGCGCAGAAGGAGACTAATGGCAGCAACGGCGATCAC
genomic: CGTGTCCGTGCCAAGCAAGCCGAGCCCAACCCCCAAGAGCCAGCTGCTCGgtgagtgccg ... gtcggaccagGTGCTCCACGCGATGGCGCAGAAGGAGACTAATGGCAGCAACGGCGATCAC
EST: gi|211377009|gb|FL406724.1|FL406724
EST:     CGTGTCCGTGCCAAGCAAGCCGAGCCCAACCCCCAAGAGCCAGCTGCTCG                         GTGCTCCACGCGATGGCGCAGAAGGAGACTAATGGCAGCAACGGCGATCAC
genomic: CGTGTCCGTGCCAAGCAAGCCGAGCCCAACCCCCAAGAGCCAGCTGCTCGgtgagtgccg ... gtcggaccagGTGCTCCACGCGATGGCGCAGAAGGAGACTAATGGCAGCAACGGCGATCAC
EST: gi|149065532|gb|EE286652.2|EE286652
EST:     CGTGTCCGTGCCAAGCAAGCCGAGCCCAACCCCCAAGAGCCAGCTGCTCG                         GTGCTCCACGCGATGGCGCAGAAGGAGACTAATGGCAGCAACGGCGATCAC
genomic: CGTGTCCGTGCCAAGCAAGCCGAGCCCAACCCCCAAGAGCCAGCTGCTCGgtgagtgccg ... gtcggaccagGTGCTCCACGCGATGGCGCAGAAGGAGACTAATGGCAGCAACGGCGATCAC
EST: gi|211139565|gb|FL400395.1|FL400395
EST:     CGTGTCCGTGCCAAGCAAGCCGAGCCCAACCCCCAAGAGCCAGCTGCTCG                         GTGCTCCACGCGATGGCGCAGAAGGAGACTAATGGCAGCAACGGCGATCAC
genomic: CGTGTCCGTGCCAAGCAAGCCGAGCCCAACCCCCAAGAGCCAGCTGCTCGgtgagtgccg ... gtcggaccagGTGCTCCACGCGATGGCGCAGAAGGAGACTAATGGCAGCAACGGCGATCAC
EST: gi|211364308|gb|FL429333.1|FL429333
EST:     CGTGTCCGTGCCAAGCAAGCCGAGCCCAA-CCCCAAGAGCCAGCTGCTCG                         GTGCTCCACGCGATGGCGCAGAAGGAGACTAATGGCAGCAACGGCGATCAC
genomic: CGTGTCCGTGCCAAGCAAGCCGAGCCCAACCCCCAAGAGCCAGCTGCTCGgtgagtgccg ... gtcggaccagGTGCTCCACGCGATGGCGCAGAAGGAGACTAATGGCAGCAACGGCGATCAC
EST: gi|211225658|gb|FL394160.1|FL394160
EST:     CGTGTCCGTGCCAAGCAAGCCGAGCCCAA-CCCCAAGAGCCAGCTGCTCG                         GTGCTCCACGCGATGGCGCAGAAGGAGACTAATGGCAGCAACGGCGATCAC
genomic: CGTGTCCGTGCCAAGCAAGCCGAGCCCAACCCCCAAGAGCCAGCTGCTCGgtgagtgccg ... gtcggaccagGTGCTCCACGCGATGGCGCAGAAGGAGACTAATGGCAGCAACGGCGATCAC
EST: gi|211102135|gb|FL378499.1|FL378499
EST:     CGTGTCCGTGCCAAGCAAGCCGAGCCCAACCCCCAAGAGCCAGCTGCTCG                         GTGCTCCACGCGATGGCGCAGAAGGAGACTAATGGCAGCAACGGCGATCAC
genomic: CGTGTCCGTGCCAAGCAAGCCGAGCCCAACCCCCAAGAGCCAGCTGCTCGgtgagtgccg ... gtcggaccagGTGCTCCACGCGATGGCGCAGAAGGAGACTAATGGCAGCAACGGCGATCAC
EST: gi|211513418|gb|FL378838.1|FL378838
EST:     CGTGTCCGTGCCAAGCAAGCCGAGCCCAACCCCCAAGAGCCAGCTGCTCG                         GTGCTCCACGCGATGGCGCAGAAGGAGACTAATGGCAGCAACGGCGATCAC
genomic: CGTGTCCGTGCCAAGCAAGCCGAGCCCAACCCCCAAGAGCCAGCTGCTCGgtgagtgccg ... gtcggaccagGTGCTCCACGCGATGGCGCAGAAGGAGACTAATGGCAGCAACGGCGATCAC
EST: gi|211182716|gb|FL410032.1|FL410032
EST:     AAGCCGAGCCCAA-CCCCAAGAGCCAGCTGCTCG                         GTGCTCCACGCGATGGCGCAGAAGGAGACTAATGGCAGCAACGGCGATCAC
genomic: AAGCCGAGCCCAACCCCCAAGAGCCAGCTGCTCGgtgagtgccg ... gtcggaccagGTGCTCCACGCGATGGCGCAGAAGGAGACTAATGGCAGCAACGGCGATCAC
EST: gi|211479897|gb|FL423797.1|FL423797
EST:     CGTGTCCGTGCCAAGCAAGCCGAGCCCAACCCCCAAGAGCCAGCTGCTCG                         GTGCTCCACGCGATGGCGCAGAAGGAGACTAATGGCAGCAACGGCGATCAC
genomic: CGTGTCCGTGCCAAGCAAGCCGAGCCCAACCCCCAAGAGCCAGCTGCTCGgtgagtgccg ... gtcggaccagGTGCTCCACGCGATGGCGCAGAAGGAGACTAATGGCAGCAACGGCGATCAC
EST: gi|211264125|gb|FL402706.1|FL402706
EST:     CGTGTCCGTGCCAAGCAAGCCGAGCCCAA-CCCCAAGAGCCAGCTGCTCG                         GTGCTCCACGCGATGGCGCAGAAGGAGACTAATGGCAGCAACGGCGATCAC
genomic: CGTGTCCGTGCCAAGCAAGCCGAGCCCAACCCCCAAGAGCCAGCTGCTCGgtgagtgccg ... gtcggaccagGTGCTCCACGCGATGGCGCAGAAGGAGACTAATGGCAGCAACGGCGATCAC
EST: gi|211355257|gb|FL372995.1|FL372995
EST:     CGTGTCCGTGCCAAGCAAGCCGAGCCCAA-CCCCAAGAGCCAGCTGCTCG                         GTGCTCCACGCGATGGCGCAGAAGGAGACTAATGGCAGCAACGGCGATCAC
genomic: CGTGTCCGTGCCAAGCAAGCCGAGCCCAACCCCCAAGAGCCAGCTGCTCGgtgagtgccg ... gtcggaccagGTGCTCCACGCGATGGCGCAGAAGGAGACTAATGGCAGCAACGGCGATCAC
EST: gi|211057982|gb|FL426572.1|FL426572
EST:     CGTGTCCGTGCCAAGCAAGCCGAGCCCAACCCCCAAGAGCCAGCTGCTCG                         GTGCTCCACGCGATGGCGCAGAAGGAGACTAATGGCAGCAACGGCGATCAC
genomic: CGTGTCCGTGCCAAGCAAGCCGAGCCCAACCCCCAAGAGCCAGCTGCTCGgtgagtgccg ... gtcggaccagGTGCTCCACGCGATGGCGCAGAAGGAGACTAATGGCAGCAACGGCGATCAC
EST: gi|71444250|gb|DR825300.1|DR825300
EST:     CGTGTCCGTGCCAAGCAAGCCGAGCCCAACCCCCAAGAGCCAGCTGCTCG                         GTGCTCCACGCGATGGCGCAGAAGGAGACTAATGGCAGCAACGGCGATCAC
genomic: CGTGTCCGTGCCAAGCAAGCCGAGCCCAACCCCCAAGAGCCAGCTGCTCGgtgagtgccg ... gtcggaccagGTGCTCCACGCGATGGCGCAGAAGGAGACTAATGGCAGCAACGGCGATCAC
EST: gi|149082965|gb|EE172201.2|EE172201
EST:     CGTGTCCGTGCCAAGCAAGCCGAGCCCAACCCCCAAGAGCCAGCTGCTCG                         GTGCTCCACGCGATGGCGCAGAAGGAGACTAATGGCAGCAACGGCGATCAC
genomic: CGTGTCCGTGCCAAGCAAGCCGAGCCCAACCCCCAAGAGCCAGCTGCTCGgtgagtgccg ... gtcggaccagGTGCTCCACGCGATGGCGCAGAAGGAGACTAATGGCAGCAACGGCGATCAC
EST: gi|71449953|gb|DR831003.1|DR831003
EST:     CGTGTCCGTGCCAAGCAAGCCGAGCCCAACCCCCAAGAGCCAGCTGCTCG                         GTGCTCCACGCGATGGCGCAGAAGGAGACTAATGGCAGCAACGGCGATCAC
genomic: CGTGTCCGTGCCAAGCAAGCCGAGCCCAACCCCCAAGAGCCAGCTGCTCGgtgagtgccg ... gtcggaccagGTGCTCCACGCGATGGCGCAGAAGGAGACTAATGGCAGCAACGGCGATCAC
EST: gi|211143536|gb|FL424879.1|FL424879
EST:     CGTGTCCGTGCCAAGCAAGCCGAGCCCAACCCCCAAGAGCCAGCTGCTCG                         GTGCTCCACGCGATGGCGCAGAAGGAGACTAATGGCAGCAACGGCGATCAC
genomic: CGTGTCCGTGCCAAGCAAGCCGAGCCCAACCCCCAAGAGCCAGCTGCTCGgtgagtgccg ... gtcggaccagGTGCTCCACGCGATGGCGCAGAAGGAGACTAATGGCAGCAACGGCGATCAC
EST: gi|211479918|gb|FL425086.1|FL425086
EST:     CGTGTCCGTGCCAAGCAAGCCGAGCCCAACCCCCAAGAGCCAGCTGCTCG                         GTGCTCCACGCGATGGCGCAGAAGGAGACTAATGGCAGCAACGGCGATCAC
genomic: CGTGTCCGTGCCAAGCAAGCCGAGCCCAACCCCCAAGAGCCAGCTGCTCGgtgagtgccg ... gtcggaccagGTGCTCCACGCGATGGCGCAGAAGGAGACTAATGGCAGCAACGGCGATCAC
EST: gi|211084498|gb|FL378036.1|FL378036
EST:     CGTGTCCGTGCCAAGCAAGCCGAGCCCAACCCCCAAGAGCCAGCTGCTCG                         GTGCTCCACGCGATGGCGCAGAAGGAGACTAATGGCAGCAACGGCGATCAC
genomic: CGTGTCCGTGCCAAGCAAGCCGAGCCCAACCCCCAAGAGCCAGCTGCTCGgtgagtgccg ... gtcggaccagGTGCTCCACGCGATGGCGCAGAAGGAGACTAATGGCAGCAACGGCGATCAC
EST: gi|149070980|gb|EE159385.2|EE159385
EST:     CGTGTCCGTGCCAAGCAAGCCGAGCCCAACCCCCAAGAGCCAGCTGCTCG                         GTGCTCCACGCGATGGCGCAGAAGGAGACTAATGGCAGCAACGGCGATCAC
genomic: CGTGTCCGTGCCAAGCAAGCCGAGCCCAACCCCCAAGAGCCAGCTGCTCGgtgagtgccg ... gtcggaccagGTGCTCCACGCGATGGCGCAGAAGGAGACTAATGGCAGCAACGGCGATCAC
EST: gi|211256579|gb|FL391909.1|FL391909
EST:     CGTGTCCGTGCCAAGCAAGCCGAGCCCAA-CCCCAAGAGCCAGCTGCTCG                         GTGCTCCACGCGATGGCGCAGAAAGAGACTAATGGCAGCAACGGCGATCAC
genomic: CGTGTCCGTGCCAAGCAAGCCGAGCCCAACCCCCAAGAGCCAGCTGCTCGgtgagtgccg ... gtcggaccagGTGCTCCACGCGATGGCGCAGAAGGAGACTAATGGCAGCAACGGCGATCAC
EST: gi|211441206|gb|FL381374.1|FL381374
EST:     CGTGTCCGTGCCAAGCAAGCCGAGCCCAACCCCCAAGAGCCAGCTGCTCG                         GTGCTCCACGCGATGGCGCAGAAGGAGACTAATGGCAGCAACGGCGATCAC
genomic: CGTGTCCGTGCCAAGCAAGCCGAGCCCAACCCCCAAGAGCCAGCTGCTCGgtgagtgccg ... gtcggaccagGTGCTCCACGCGATGGCGCAGAAGGAGACTAATGGCAGCAACGGCGATCAC
EST: gi|211021925|gb|FL369377.1|FL369377
EST:     CGTGTCCGTGCCAAGCAAGCCGAGCCCAACCCCCAAGAGCCAGCTGCTCG                         GTGCTCCACGCGATGGCGCAGAAGGAGACTAATGGCAGCAACGGCGATCAC
genomic: CGTGTCCGTGCCAAGCAAGCCGAGCCCAACCCCCAAGAGCCAGCTGCTCGgtgagtgccg ... gtcggaccagGTGCTCCACGCGATGGCGCAGAAGGAGACTAATGGCAGCAACGGCGATCAC
EST: gi|211108221|gb|FL373168.1|FL373168
EST:     CGTGTCCGTGCCAAGCAAGCCGAGCCCAACCCCCAAGAGCCAGCTGCTCG                         GTGCTCCACGCGATGGCGCAGAAGGAGACTAATGGCAGCAACGGCGATCAC
genomic: CGTGTCCGTGCCAAGCAAGCCGAGCCCAACCCCCAAGAGCCAGCTGCTCGgtgagtgccg ... gtcggaccagGTGCTCCACGCGATGGCGCAGAAGGAGACTAATGGCAGCAACGGCGATCAC
EST: gi|149070503|gb|EE158907.2|EE158907
EST:     CGTGTCCGTGCCAAGCAAGCCGAGCCCAACCCCCAAGAGCCAGCTGCTCG                         GTGCTCCACGCGATGGCGCAGAAGGAGACTAATGGCAGCAACGGCGATCAC
genomic: CGTGTCCGTGCCAAGCAAGCCGAGCCCAACCCCCAAGAGCCAGCTGCTCGgtgagtgccg ... gtcggaccagGTGCTCCACGCGATGGCGCAGAAGGAGACTAATGGCAGCAACGGCGATCAC
EST: gi|211042612|gb|FL405104.1|FL405104
EST:     CGTGTCCGTGCCAAGCAAGCCGAGCCCAACCCCCAAGAGCCAGCTGCTCG                         GTGCTCCACGCGATGGCGCAGAAGGAGACTAATGGCAGCAACGGCGATCAC
genomic: CGTGTCCGTGCCAAGCAAGCCGAGCCCAACCCCCAAGAGCCAGCTGCTCGgtgagtgccg ... gtcggaccagGTGCTCCACGCGATGGCGCAGAAGGAGACTAATGGCAGCAACGGCGATCAC
EST: gi|211535769|gb|FL372741.1|FL372741
EST:     CGTGTCCGTGCCAAGCAAGCCGAGCCCAACCCCCAAGAGCCAGCTGCTCG                         GTGCTCCACGCGATGGCGCAGAAGGAGACTAATGGCAGCAACGGCGATCAC
genomic: CGTGTCCGTGCCAAGCAAGCCGAGCCCAACCCCCAAGAGCCAGCTGCTCGgtgagtgccg ... gtcggaccagGTGCTCCACGCGATGGCGCAGAAGGAGACTAATGGCAGCAACGGCGATCAC

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), 48 (downstream exon)
Score: 367

GCCTTCTCCTCGTCCGCCCCAGTCTAATCCGATTCAAACCGCCCGTTCCCCGTGTCCGTGCCAAGCAAGCCGAGCCCAACCCCCAAGAGCCAGCTGCTCGgtgagtgccg ... gtcggaccagGTGCTCCACGCGATGGCGCAGAAGGAGACTAATGGCAGCAACGGCGATCACATCTCCACCCGCCCGCCGCCGACCCCCTCGCCCCTCCGCTTCTCCAAGT


Block sizes: 49 (upstream exon), 41 (downstream exon)
Score: 887

GCCTTCTCCTCGTCCGCCCCAGTCTAATCCGATTCAAACCGCCCGTTCCCCGTGTCCGTGCCAAGCAAGCCGAGCCCAACCCCCAAGAGCCAGCTGCTCGgtgagtgccg ... gtcggaccagGTGCTCCACGCGATGGCGCAGAAGGAGACTAATGGCAGCAACGGCGATCACATCTCCACCCGCCCGCCGCCGACCCCCTCGCCCCTCCGCTTCTCCAAGT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 1057

GCCTTCTCCTCGTCCGCCCCAGTCTAATCCGATTCAAACCGCCCGTTCCCCGTGTCCGTGCCAAGCAAGCCGAGCCCAACCCCCAAGAGCCAGCTGCTCGgtgagtgccg ... gtcggaccagGTGCTCCACGCGATGGCGCAGAAGGAGACTAATGGCAGCAACGGCGATCACATCTCCACCCGCCCGCCGCCGACCCCCTCGCCCCTCCGCTTCTCCAAGT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 2026

GCCTTCTCCTCGTCCGCCCCAGTCTAATCCGATTCAAACCGCCCGTTCCCCGTGTCCGTGCCAAGCAAGCCGAGCCCAACCCCCAAGAGCCAGCTGCTCGgtgagtgccg ... gtcggaccagGTGCTCCACGCGATGGCGCAGAAGGAGACTAATGGCAGCAACGGCGATCACATCTCCACCCGCCCGCCGCCGACCCCCTCGCCCCTCCGCTTCTCCAAGT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCTTCTCCTCGTCCGCCCCAGTCTAATCCGATTCAAACCGCCCGTTCCCCGTGTCCGTGCCAAGCAAGCCGAGCCCAACCCCCAAGAGCCAGCTGCTCGgtgagtgccgcgccccgtcgcctcctcacgcttcgttgcttgcaatcaacgcgatcgtctggtctcgtcttgttccagtgtgtcatttctctctgacgggtgagatttggtttggatctggtcggaccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT