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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCGCACGTTCCCCTTTTCCGCCGCAGCGATGGTGTACGTGGATTCCTGGGACGAGTTCGTGGAGCGGTCCGTGCAGCTCTTCCGCGCCGACCCCAACACCgtacgccgtcgtcgcccgatcccctctcttctccaaattccttcctgctccattccgtgtgtctgatcctacctaacctgtttgtgcgcgtgtgtctgcag

Basic information

species Zea mays
transcript GRMZM2G058407_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|44682050|gb|CK787098.1|CK787098
EST:     ACGAGTTCGTGGAGCGGTCCGTGCAGCTCTTCCGCGCCGACCCCAACACC                         ACCCGCTACGTGATGAAGTATCGGCACTGCGAGGGGAAGCTCGTGCTCAAG
genomic: ACGAGTTCGTGGAGCGGTCCGTGCAGCTCTTCCGCGCCGACCCCAACACCgtacgccgtc ... gtgtctgcagACCCGCTACGTGATGAAGTATCGGCACTGCGAGGGGAAGCTCGTGCTCAAG
EST: gi|211186460|gb|FL239191.1|FL239191
EST:     ACGAGTTCGTGGAGCGGTCCGTGCAGCTCTTCCGCGCCGACCCCAACACC                         ACCCGCTACGTGATGAAGTATCGGCACTGCGAGGGGAAGCTCGTGCTCAAG
genomic: ACGAGTTCGTGGAGCGGTCCGTGCAGCTCTTCCGCGCCGACCCCAACACCgtacgccgtc ... gtgtctgcagACCCGCTACGTGATGAAGTATCGGCACTGCGAGGGGAAGCTCGTGCTCAAG
EST: gi|32863264|gb|CF002946.1|CF002946
EST:     ACGAGTTCGTGGAGCGGTCCGTGCAGCTGTTCCGCGCCGACCCCAACACC                         ACCCGCTACGTGATGAAGTATCGGCACTGCGAGGGGAAGCTCGTGCTCAAG
genomic: ACGAGTTCGTGGAGCGGTCCGTGCAGCTCTTCCGCGCCGACCCCAACACCgtacgccgtc ... gtgtctgcagACCCGCTACGTGATGAAGTATCGGCACTGCGAGGGGAAGCTCGTGCTCAAG
EST: gi|211188850|gb|FL239192.1|FL239192
EST:     ACGAGTTCGTGGAGCGGTCCGTGCAGCTCTTCCGCGCCGACCCCAACACC                         ACCCGCTACGTGATGAAGTATCGGCACTGCGAGGGGAAGCTCGTGCTCAAG
genomic: ACGAGTTCGTGGAGCGGTCCGTGCAGCTCTTCCGCGCCGACCCCAACACCgtacgccgtc ... gtgtctgcagACCCGCTACGTGATGAAGTATCGGCACTGCGAGGGGAAGCTCGTGCTCAAG
EST: gi|32936820|gb|CF041639.1|CF041639
EST:     ACGAGTTCGTGGAGCGGTCCGTGCAGCTGTTCCGCGCCGACCCCAACACC                         ACCCGCTACGTGATGAAGTATCGGCACTGCGAGGGGAAGCTCGTGCTCAAG
genomic: ACGAGTTCGTGGAGCGGTCCGTGCAGCTCTTCCGCGCCGACCCCAACACCgtacgccgtc ... gtgtctgcagACCCGCTACGTGATGAAGTATCGGCACTGCGAGGGGAAGCTCGTGCTCAAG
EST: gi|211186450|gb|FL239181.1|FL239181
EST:     ACGAGTTCGTGGAGCGGTCCGTGCAGCTCTTCCGCGCCGACCCCAACACC                         ACCCGCTACGTGATGAAGTATCGGCACTGCGAGGGGAAGCTCGTGCTCAAG
genomic: ACGAGTTCGTGGAGCGGTCCGTGCAGCTCTTCCGCGCCGACCCCAACACCgtacgccgtc ... gtgtctgcagACCCGCTACGTGATGAAGTATCGGCACTGCGAGGGGAAGCTCGTGCTCAAG
EST: gi|45213689|gb|CK849962.1|CK849962
EST:     ACGAGTTCGTGGAGCGGTCCGTGCAGCTCTTCCGCGCCGACCCCAACACC                         ACCCGCTACGTGATGAAGTATCGGCACTGCGAGGGGAAGCTCGTGCTCAAG
genomic: ACGAGTTCGTGGAGCGGTCCGTGCAGCTCTTCCGCGCCGACCCCAACACCgtacgccgtc ... gtgtctgcagACCCGCTACGTGATGAAGTATCGGCACTGCGAGGGGAAGCTCGTGCTCAAG
EST: gi|211186452|gb|FL239183.1|FL239183
EST:     ACGAGTTCGTGGAGCGGTCCGTGCAGCTCTTCCGCGCCGACCCCAACACC                         ACCCGCTACGTGATGAAGTATCGGCACTGCGAGGGGAAGCTCGTGCTCAAG
genomic: ACGAGTTCGTGGAGCGGTCCGTGCAGCTCTTCCGCGCCGACCCCAACACCgtacgccgtc ... gtgtctgcagACCCGCTACGTGATGAAGTATCGGCACTGCGAGGGGAAGCTCGTGCTCAAG
EST: gi|32937577|gb|CF042396.1|CF042396
EST:     ACGAGTTCGTGGAGCGGTCCGTGCAGCTGTTCCGCGCCGACCCCAACACC                         ACCCGCTACGTGATGAAGTATCGGCACTGCGAGGGGAAGCTCGTGCTCAAG
genomic: ACGAGTTCGTGGAGCGGTCCGTGCAGCTCTTCCGCGCCGACCCCAACACCgtacgccgtc ... gtgtctgcagACCCGCTACGTGATGAAGTATCGGCACTGCGAGGGGAAGCTCGTGCTCAAG
EST: gi|211186458|gb|FL239189.1|FL239189
EST:     ACGAGTTCGTGGAGCGGTCCGTGCAGCTCTTCCGCGCCGACCCCAACACC                         ACCCGCTACGTGATGAAGTATCGGCACTGCGAGGGGAAGCTCGTGCTCAAG
genomic: ACGAGTTCGTGGAGCGGTCCGTGCAGCTCTTCCGCGCCGACCCCAACACCgtacgccgtc ... gtgtctgcagACCCGCTACGTGATGAAGTATCGGCACTGCGAGGGGAAGCTCGTGCTCAAG
EST: gi|211186455|gb|FL239186.1|FL239186
EST:     ACGAGTTCGTGGAGCGGTCCGTGCAGCTCTTCCGCGCCGACCCCAACACC                         ACCCGCTACGTGATGAAGTATCGGCACTGCGAGGGGAAGCTCGTGCTCAAG
genomic: ACGAGTTCGTGGAGCGGTCCGTGCAGCTCTTCCGCGCCGACCCCAACACCgtacgccgtc ... gtgtctgcagACCCGCTACGTGATGAAGTATCGGCACTGCGAGGGGAAGCTCGTGCTCAAG
EST: gi|32864829|gb|CF004511.1|CF004511
EST:     ACGAGTTCGTGGAGCGGTCCGTGCAGCTGTTCCGCGCCGACCCCAACACC                         ACCCGCTACGTGATGAAGTATCGGCACTGCGAGGGGAAGCTCGTGCTCAAG
genomic: ACGAGTTCGTGGAGCGGTCCGTGCAGCTCTTCCGCGCCGACCCCAACACCgtacgccgtc ... gtgtctgcagACCCGCTACGTGATGAAGTATCGGCACTGCGAGGGGAAGCTCGTGCTCAAG
EST: gi|116818620|gb|EC861668.1|EC861668
EST:     ACGAGTTCGTGGAGCGGTCCGTGCAGCTCTTCCGCGCCGACCCCAACACC                         ACCCGCTACGTGATGAAGTATCGGCACTGCGAGGGGAAGCTCGTGCTCAAG
genomic: ACGAGTTCGTGGAGCGGTCCGTGCAGCTCTTCCGCGCCGACCCCAACACCgtacgccgtc ... gtgtctgcagACCCGCTACGTGATGAAGTATCGGCACTGCGAGGGGAAGCTCGTGCTCAAG
EST: gi|211186449|gb|FL239180.1|FL239180
EST:     ACGAGTTCGTGGAGCGGTCCGTGCAGCTCTTCCGCGCCGACCCCAACACC                         ACCCGCTACGTGATGAAGTATCGGCACTGCGAGGGGAAGCTCGTGCTCAAG
genomic: ACGAGTTCGTGGAGCGGTCCGTGCAGCTCTTCCGCGCCGACCCCAACACCgtacgccgtc ... gtgtctgcagACCCGCTACGTGATGAAGTATCGGCACTGCGAGGGGAAGCTCGTGCTCAAG
EST: gi|32936664|gb|CF041483.1|CF041483
EST:     ACGAGTTCGTGGAGCGGTCCGTGCAGCTGTTCCGCGCCGACCCCAACACC                         ACCCGCTACGTGATGAAGTATCGGCACTGCGAGGGGAAGCTCGTGCTCAAG
genomic: ACGAGTTCGTGGAGCGGTCCGTGCAGCTCTTCCGCGCCGACCCCAACACCgtacgccgtc ... gtgtctgcagACCCGCTACGTGATGAAGTATCGGCACTGCGAGGGGAAGCTCGTGCTCAAG
EST: gi|32906973|gb|CF011786.1|CF011786
EST:     ACGAGTTCGTGGAGCGGTCCGTGCAGCTGTTCCGCGCCGACCCCAACACC                         ACCCGCTACGTGATGAAGTATCGGCACTGCGAGGGGAAGCTCGTGCTCAAG
genomic: ACGAGTTCGTGGAGCGGTCCGTGCAGCTCTTCCGCGCCGACCCCAACACCgtacgccgtc ... gtgtctgcagACCCGCTACGTGATGAAGTATCGGCACTGCGAGGGGAAGCTCGTGCTCAAG
EST: gi|211186448|gb|FL239179.1|FL239179
EST:     ACGAGTTCGTGGAGCGGTCCGTGCAGCTCTTCCGCGCCGACCCCAACACC                         ACCCGCTACGTGATGAAGTATCGGCACTGCGAGGGGAAGCTCGTGCTCAAG
genomic: ACGAGTTCGTGGAGCGGTCCGTGCAGCTCTTCCGCGCCGACCCCAACACCgtacgccgtc ... gtgtctgcagACCCGCTACGTGATGAAGTATCGGCACTGCGAGGGGAAGCTCGTGCTCAAG
EST: gi|211186459|gb|FL239190.1|FL239190
EST:     ACGAGTTCGTGGAGCGGTCCGTGCAGCTCTTCCGCGCCGACCCCAACACC                         ACCCGCTACGTGATGAAGTATCGGCACTGCGAGGGGAAGCTCGTGCTCAAG
genomic: ACGAGTTCGTGGAGCGGTCCGTGCAGCTCTTCCGCGCCGACCCCAACACCgtacgccgtc ... gtgtctgcagACCCGCTACGTGATGAAGTATCGGCACTGCGAGGGGAAGCTCGTGCTCAAG
EST: gi|211186451|gb|FL239182.1|FL239182
EST:     ACGAGTTCGTGGAGCGGTCCGTGCAGCTCTTCCGCGCCGACCCCAACACC                         ACCCGCTACGTGATGAAGTATCGGCACTGCGAGGGGAAGCTCGTGCTCAAG
genomic: ACGAGTTCGTGGAGCGGTCCGTGCAGCTCTTCCGCGCCGACCCCAACACCgtacgccgtc ... gtgtctgcagACCCGCTACGTGATGAAGTATCGGCACTGCGAGGGGAAGCTCGTGCTCAAG
EST: gi|211186454|gb|FL239185.1|FL239185
EST:     ACGAGTTCGTGGAGCGGTCCGTGCAGCTCTTCCGCGCCGACCCCAACACC                         ACCCGCTACGTGATGAAGTATCGGCACTGCGAGGGGAAGCTCGTGCTCAAG
genomic: ACGAGTTCGTGGAGCGGTCCGTGCAGCTCTTCCGCGCCGACCCCAACACCgtacgccgtc ... gtgtctgcagACCCGCTACGTGATGAAGTATCGGCACTGCGAGGGGAAGCTCGTGCTCAAG
EST: gi|44681672|gb|CK786720.1|CK786720
EST:     ACGAGTTCGTGGAGCGGTCCGTGCAGCTCTTCCGCGCCGACCCCAACACC                         ACCCGCTACGTGATGAAGTATCGGCACTGCGAGGGGAAGCTCGTGCTCAAG
genomic: ACGAGTTCGTGGAGCGGTCCGTGCAGCTCTTCCGCGCCGACCCCAACACCgtacgccgtc ... gtgtctgcagACCCGCTACGTGATGAAGTATCGGCACTGCGAGGGGAAGCTCGTGCTCAAG
EST: gi|33942654|gb|CF349254.1|CF349254
EST:     ACGAGTTCGTGGAGCGGTCCGTGCAGCTCTTCCGCGCCGACCCCAACACC                         ACCCGCTACGTGATGAAGTATCGGCACTGCGAGGGGAAGCTCGTGCTCAAG
genomic: ACGAGTTCGTGGAGCGGTCCGTGCAGCTCTTCCGCGCCGACCCCAACACCgtacgccgtc ... gtgtctgcagACCCGCTACGTGATGAAGTATCGGCACTGCGAGGGGAAGCTCGTGCTCAAG
EST: gi|211186453|gb|FL239184.1|FL239184
EST:     ACGAGTTCGTGGAGCGGTCCGTGCAGCTCTTCCGCGCCGACCCCAACACC                         ACCCGCTACGTGATGAAGTATCGGCACTGCGAGGGGAAGCTCGTGCTCAAG
genomic: ACGAGTTCGTGGAGCGGTCCGTGCAGCTCTTCCGCGCCGACCCCAACACCgtacgccgtc ... gtgtctgcagACCCGCTACGTGATGAAGTATCGGCACTGCGAGGGGAAGCTCGTGCTCAAG
EST: gi|211089528|gb|FL476391.1|FL476391
EST:     ACGAGTTCGTGGAGCGGTCCGTGCAGCTCTTCCGCGCCGACCCCAACACC                         ACCCGCTACGTGATGAAGTATCGGCACTGCGAGGGGAAGCTCGTGCTCAAG
genomic: ACGAGTTCGTGGAGCGGTCCGTGCAGCTCTTCCGCGCCGACCCCAACACCgtacgccgtc ... gtgtctgcagACCCGCTACGTGATGAAGTATCGGCACTGCGAGGGGAAGCTCGTGCTCAAG
EST: gi|211186456|gb|FL239187.1|FL239187
EST:     ACGAGTTCGTGGAGCGGTCCGTGCAGCTCTTCCGCGCCGACCCCAACACC                         ACCCGCTACGTGATGAAGTATCGGCACTGCGAGGGGAAGCTCGTGCTCAAG
genomic: ACGAGTTCGTGGAGCGGTCCGTGCAGCTCTTCCGCGCCGACCCCAACACCgtacgccgtc ... gtgtctgcagACCCGCTACGTGATGAAGTATCGGCACTGCGAGGGGAAGCTCGTGCTCAAG
EST: gi|211186447|gb|FL239178.1|FL239178
EST:     ACGAGTTCGTGGAGCGGTCCGTGCAGCTCTTCCGCGCCGACCCCAACACC                         ACCCGCTACGTGATGAAGTATCGGCACTGCGAGGGGAAGCTCGTGCTCAAG
genomic: ACGAGTTCGTGGAGCGGTCCGTGCAGCTCTTCCGCGCCGACCCCAACACCgtacgccgtc ... gtgtctgcagACCCGCTACGTGATGAAGTATCGGCACTGCGAGGGGAAGCTCGTGCTCAAG
EST: gi|76292026|gb|DV031594.1|DV031594
EST:     ACGAGTTCGTGGAGCGGTCCGTGCAGCTCTTCCGCGCCGACCCCAACACC                         ACCCGCTACGTGATGAAGTATCGGCACTGCGAGGGGAAGCTCGTGCTCAAG
genomic: ACGAGTTCGTGGAGCGGTCCGTGCAGCTCTTCCGCGCCGACCCCAACACCgtacgccgtc ... gtgtctgcagACCCGCTACGTGATGAAGTATCGGCACTGCGAGGGGAAGCTCGTGCTCAAG

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), 46 (downstream exon)
Score: 68

CCGCACGTTCCCCTTTTCCGCCGCAGCGATGGTGTACGTGGATTCCTGGGACGAGTTCGTGGAGCGGTCCGTGCAGCTCTTCCGCGCCGACCCCAACACCgtacgccgtc ... gtgtctgcagACCCGCTACGTGATGAAGTATCGGCACTGCGAGGGGAAGCTCGTGCTCAAGGTCACTGATGACCGCGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 59

CCGCACGTTCCCCTTTTCCGCCGCAGCGATGGTGTACGTGGATTCCTGGGACGAGTTCGTGGAGCGGTCCGTGCAGCTCTTCCGCGCCGACCCCAACACCgtacgccgtc ... gtgtctgcagACCCGCTACGTGATGAAGTATCGGCACTGCGAGGGGAAGCTCGTGCTCAAGGTCACTGATGACCGCGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 64

CCGCACGTTCCCCTTTTCCGCCGCAGCGATGGTGTACGTGGATTCCTGGGACGAGTTCGTGGAGCGGTCCGTGCAGCTCTTCCGCGCCGACCCCAACACCgtacgccgtc ... gtgtctgcagACCCGCTACGTGATGAAGTATCGGCACTGCGAGGGGAAGCTCGTGCTCAAGGTCACTGATGACCGCGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 141

CCGCACGTTCCCCTTTTCCGCCGCAGCGATGGTGTACGTGGATTCCTGGGACGAGTTCGTGGAGCGGTCCGTGCAGCTCTTCCGCGCCGACCCCAACACCgtacgccgtc ... gtgtctgcagACCCGCTACGTGATGAAGTATCGGCACTGCGAGGGGAAGCTCGTGCTCAAGGTCACTGATGACCGCGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCGCACGTTCCCCTTTTCCGCCGCAGCGATGGTGTACGTGGATTCCTGGGACGAGTTCGTGGAGCGGTCCGTGCAGCTCTTCCGCGCCGACCCCAACACCgtacgccgtcgtcgcccgatcccctctcttctccaaattccttcctgctccattccgtgtgtctgatcctacctaacctgtttgtgcgcgtgtgtctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC