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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTTGTTCGTGACCACAATGTCGAGCTGCGCAGCACGCTCCACGATCTCCTTGCGCTTCTTAGTGGACACGTTGTGAGCAATTTCAGCGCAGTAGGTCCTgcatgtgcaagggaaggaagtttaagtcagtaaaacgaactgtcctgattacaaacacacaaacagatcacaaccagcagacattgttaatgacaaaagacagaattgcaatgagaatcaatacct

Basic information

species Zea mays
transcript GRMZM5G803927_T02
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|211530927|gb|FL079614.1|FL079614
EST:     TTGCGCTTCTTGGTGGACACGTTGTGAGCAATTTCAGCGCAGTAGGTCCT                         GTTGTGCATCATGAGCAACTCCAGCTCAGAAACGTTGTGGACCACAAACTT
genomic: TTGCGCTTCTTAGTGGACACGTTGTGAGCAATTTCAGCGCAGTAGGTCCTgcatgtgcaa ... atcaatacctGTTGTGCATCATGAGCAACTCCAGCTCAGAAACGTTGTGGACCACAAACTT
EST: gi|211530921|gb|FL079608.1|FL079608
EST:     TTGCGCTTCTTGGTGGACACGTTGTGAGCAATTTCAGCGCAGTAGGTCCT                         GTTGTGCATCATGAGCAACTCCAGCTCAGAAACGTTGTGGACCACAAACTT
genomic: TTGCGCTTCTTAGTGGACACGTTGTGAGCAATTTCAGCGCAGTAGGTCCTgcatgtgcaa ... atcaatacctGTTGTGCATCATGAGCAACTCCAGCTCAGAAACGTTGTGGACCACAAACTT
EST: gi|166571044|gb|EG154522.1|EG154522
EST:     GTTGTGAGCAATTTCAGCGCAGTAGGTCCT                         GTTGTGCATCATGAGCAACTCCAGCTCAGAAACGTTGTGGACCACAAACTT
genomic: GTTGTGAGCAATTTCAGCGCAGTAGGTCCTgcatgtgcaa ... atcaatacctGTTGTGCATCATGAGCAACTCCAGCTCAGAAACGTTGTGGACCACAAACTT
EST: gi|9254539|gb|BE345007.1|BE345007
EST:     TTGCGCTTCTTAGTGGACACGTTGTGAGCAATTTCAGCGCAGTAGGTCCT                         GTTGTGCATCATGAGCAACTCCAGCTCAGAAACGTTGTGGACCACAAACTT
genomic: TTGCGCTTCTTAGTGGACACGTTGTGAGCAATTTCAGCGCAGTAGGTCCTgcatgtgcaa ... atcaatacctGTTGTGCATCATGAGCAACTCCAGCTCAGAAACGTTGTGGACCACAAACTT
EST: gi|92088057|gb|EB484288.1|EB484288
EST:     TTGCGCTTCTTGGTGGACACGTTGTGAGCAATTTCAGCGCAGTAGGTCCT                         GTTGTGCATCATGAGCAACTCCAGCTCAGAAACGTTGTGGACCACAAACTT
genomic: TTGCGCTTCTTAGTGGACACGTTGTGAGCAATTTCAGCGCAGTAGGTCCTgcatgtgcaa ... atcaatacctGTTGTGCATCATGAGCAACTCCAGCTCAGAAACGTTGTGGACCACAAACTT
EST: gi|211044025|gb|FL231327.1|FL231327
EST:     TTGCGCTTCTTGGTGGACACGTTGTGAGCAATTTCAGCGCAGTAGGTCCT                         GTTGTGCATCATGAGCAACTCCAGCTCAGAAACGTTGTGGACCACAAACTT
genomic: TTGCGCTTCTTAGTGGACACGTTGTGAGCAATTTCAGCGCAGTAGGTCCTgcatgtgcaa ... atcaatacctGTTGTGCATCATGAGCAACTCCAGCTCAGAAACGTTGTGGACCACAAACTT
EST: gi|211285282|gb|FL231180.1|FL231180
EST:     TTGCGCTTCTTGGTGGACACGTTGTGAGCAATTTCAGCGCAGTAGGTCCT                         GTTGTGCATCATGAGCAACTCCAGCTCAGAAACGTTGTGGACCACAAACTT
genomic: TTGCGCTTCTTAGTGGACACGTTGTGAGCAATTTCAGCGCAGTAGGTCCTgcatgtgcaa ... atcaatacctGTTGTGCATCATGAGCAACTCCAGCTCAGAAACGTTGTGGACCACAAACTT
EST: gi|29130397|gb|CB381101.1|CB381101
EST:     TTGCGCTTCTTAGTGGACCCGTTGTGAGCAATTTCAGCGCAGTAGGTCCT                         GTTGTGCATCATGAGCAACTCCAGCTCAGAAACGTTGTGGACCACAAACTT
genomic: TTGCGCTTCTTAGTGGACACGTTGTGAGCAATTTCAGCGCAGTAGGTCCTgcatgtgcaa ... atcaatacctGTTGTGCATCATGAGCAACTCCAGCTCAGAAACGTTGTGGACCACAAACTT
EST: gi|32911306|gb|CF016118.1|CF016118
EST:     TTGCGCTTCTTGGTGGACACGTTGTGAGCAATTTCAGCGCAGTAGGTCCT                         GTTGTGCATCATGAGCAACTCCAGCTCAGAAACGTTGTGGACCACAAACTT
genomic: TTGCGCTTCTTAGTGGACACGTTGTGAGCAATTTCAGCGCAGTAGGTCCTgcatgtgcaa ... atcaatacctGTTGTGCATCATGAGCAACTCCAGCTCAGAAACGTTGTGGACCACAAACTT

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 8 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 162

GCTTGTTCGTGACCACAATGTCGAGCTGCGCAGCACGCTCCACGATCTCCTTGCGCTTCTTAGTGGACACGTTGTGAGCAATTTCAGCGCAGTAGGTCCTgcatgtgcaa ... atcaatacctGTTGTGCATCATGAGCAACTCCAGCTCAGAAACGTTGTGGACCACAAACTTCTTGAACTTGTTGGGGAGGTAGTGCCTGGTCGACTTGTCAGAACCATAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 2215

GCTTGTTCGTGACCACAATGTCGAGCTGCGCAGCACGCTCCACGATCTCCTTGCGCTTCTTAGTGGACACGTTGTGAGCAATTTCAGCGCAGTAGGTCCTgcatgtgcaa ... atcaatacctGTTGTGCATCATGAGCAACTCCAGCTCAGAAACGTTGTGGACCACAAACTTCTTGAACTTGTTGGGGAGGTAGTGCCTGGTCGACTTGTCAGAACCATAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 69

GCTTGTTCGTGACCACAATGTCGAGCTGCGCAGCACGCTCCACGATCTCCTTGCGCTTCTTAGTGGACACGTTGTGAGCAATTTCAGCGCAGTAGGTCCTgcatgtgcaa ... atcaatacctGTTGTGCATCATGAGCAACTCCAGCTCAGAAACGTTGTGGACCACAAACTTCTTGAACTTGTTGGGGAGGTAGTGCCTGGTCGACTTGTCAGAACCATAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1234

GCTTGTTCGTGACCACAATGTCGAGCTGCGCAGCACGCTCCACGATCTCCTTGCGCTTCTTAGTGGACACGTTGTGAGCAATTTCAGCGCAGTAGGTCCTgcatgtgcaa ... atcaatacctGTTGTGCATCATGAGCAACTCCAGCTCAGAAACGTTGTGGACCACAAACTTCTTGAACTTGTTGGGGAGGTAGTGCCTGGTCGACTTGTCAGAACCATAA


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

GCTTGTTCGTGACCACAATGTCGAGCTGCGCAGCACGCTCCACGATCTCCTTGCGCTTCTTAGTGGACACGTTGTGAGCAATTTCAGCGCAGTAGGTCCTgcatgtgcaa ... atcaatacctGTTGTGCATCATGAGCAACTCCAGCTCAGAAACGTTGTGGACCACAAACTTCTTGAACTTGTTGGGGAGGTAGTGCCTGGTCGACTTGTCAGAACCATAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 913

GCTTGTTCGTGACCACAATGTCGAGCTGCGCAGCACGCTCCACGATCTCCTTGCGCTTCTTAGTGGACACGTTGTGAGCAATTTCAGCGCAGTAGGTCCTgcatgtgcaa ... atcaatacctGTTGTGCATCATGAGCAACTCCAGCTCAGAAACGTTGTGGACCACAAACTTCTTGAACTTGTTGGGGAGGTAGTGCCTGGTCGACTTGTCAGAACCATAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 67

GCTTGTTCGTGACCACAATGTCGAGCTGCGCAGCACGCTCCACGATCTCCTTGCGCTTCTTAGTGGACACGTTGTGAGCAATTTCAGCGCAGTAGGTCCTgcatgtgcaa ... atcaatacctGTTGTGCATCATGAGCAACTCCAGCTCAGAAACGTTGTGGACCACAAACTTCTTGAACTTGTTGGGGAGGTAGTGCCTGGTCGACTTGTCAGAACCATAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 920

GCTTGTTCGTGACCACAATGTCGAGCTGCGCAGCACGCTCCACGATCTCCTTGCGCTTCTTAGTGGACACGTTGTGAGCAATTTCAGCGCAGTAGGTCCTgcatgtgcaa ... atcaatacctGTTGTGCATCATGAGCAACTCCAGCTCAGAAACGTTGTGGACCACAAACTTCTTGAACTTGTTGGGGAGGTAGTGCCTGGTCGACTTGTCAGAACCATAA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTTGTTCGTGACCACAATGTCGAGCTGCGCAGCACGCTCCACGATCTCCTTGCGCTTCTTAGTGGACACGTTGTGAGCAATTTCAGCGCAGTAGGTCCTgcatgtgcaagggaaggaagtttaagtcagtaaaacgaactgtcctgattacaaacacacaaacagatcacaaccagcagacattgttaatgacaaaagacagaattgcaatgagaatcaatacct

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA