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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cactagtgcatttatgtcatattttggaacgaattactgttcatgatgttgattctaaatgttgatgttgtgttttcttgtttctgatgaatctctctagATGAAGCTGCTGATTGACTGGAAAATCTGGATCGGACTTTTTCCAAATTTCTGTTTCCTGATGTTGCTGCAATTTGTCACCAATGAACTGAAACTCACCG

Basic information

species Zea mays
transcript GRMZM2G412888_T01
intron # 7
splice site 3'
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|113703814|gb|EE681318.1|EE681318
EST:     TGGAGTGCAGAATCATGATGCCAGCTTCAAAAGTGAAATTACCGAGGATG                         ATGAAGCTGCTGATTGACTGGAAAATCTGGATCGGACTTTTTCCAAATTTC
genomic: TGGAGTGCAGAATCATGATGCCAGCTTCAAAAGTGAAATTACCGAGGATGgtaatttaat ... atctctctagATGAAGCTGCTGATTGACTGGAAAATCTGGATCGGACTTTTTCCAAATTTC
EST: gi|30087676|gb|CB885882.1|CB885882
EST:     TGGAGTGCAGAATCATGATGCCAGCTTCAAAAGTGAAATTACCGAGGATG                         ATGAAGCTGCTGATTGACTGGAAAATCTGGATCGGACTTTTTCCAAATTTC
genomic: TGGAGTGCAGAATCATGATGCCAGCTTCAAAAGTGAAATTACCGAGGATGgtaatttaat ... atctctctagATGAAGCTGCTGATTGACTGGAAAATCTGGATCGGACTTTTTCCAAATTTC
EST: gi|110540523|gb|EE044443.1|EE044443
EST:     TGGAGTGCAGAATCATGATGCCAGCTTCAAAAGTGAAATTACCGAGGATG                         ATGAAGCTGCTGATTGACTGGAAAATCTGGATCGGACTTTTTCCAAATTTC
genomic: TGGAGTGCAGAATCATGATGCCAGCTTCAAAAGTGAAATTACCGAGGATGgtaatttaat ... atctctctagATGAAGCTGCTGATTGACTGGAAAATCTGGATCGGACTTTTTCCAAATTTC
EST: gi|37381733|gb|CF627768.1|CF627768
EST:     TGGAGTGCAGAATCATGATGCCAGCTTCAAAAGTGAAATTACCGAGGATG                         ATGAAGCTGCTGATTGACTGGAAAATCTGGATCGGACTTTTTCCAAATTTC
genomic: TGGAGTGCAGAATCATGATGCCAGCTTCAAAAGTGAAATTACCGAGGATGgtaatttaat ... atctctctagATGAAGCTGCTGATTGACTGGAAAATCTGGATCGGACTTTTTCCAAATTTC
EST: gi|37382993|gb|CF628471.1|CF628471
EST:     TGGAGTGCAGAATCATGATGCCAGCTTCAAAAGTGAAATTACCGAGGATG                         ATGAAGCTGCTGATTGACTGGAAAATCTGGATCGGACTTTTTCCAAATTTC
genomic: TGGAGTGCAGAATCATGATGCCAGCTTCAAAAGTGAAATTACCGAGGATGgtaatttaat ... atctctctagATGAAGCTGCTGATTGACTGGAAAATCTGGATCGGACTTTTTCCAAATTTC
EST: gi|71425139|gb|DR806558.1|DR806558
EST:     TGGAGTGCAGAATCATGATGCCAGCTTCAAAAGTGAAATTACCGAGGATG                         ATGAAGCTGCTGATTGACTGGAAAATCTGGATCGGACTTTTTCCAAATTTC
genomic: TGGAGTGCAGAATCATGATGCCAGCTTCAAAAGTGAAATTACCGAGGATGgtaatttaat ... atctctctagATGAAGCTGCTGATTGACTGGAAAATCTGGATCGGACTTTTTCCAAATTTC
EST: gi|60338445|gb|DN205418.1|DN205418
EST:     TGGAGTGCAGAATCATGATGCCAGCTTCAAAAGTGAAATTACCGAGGATG                         ATGAAGCTGCTGATTGACTGGAAAATCTGGATCGGACTTTTTCCAAATTTC
genomic: TGGAGTGCAGAATCATGATGCCAGCTTCAAAAGTGAAATTACCGAGGATGgtaatttaat ... atctctctagATGAAGCTGCTGATTGACTGGAAAATCTGGATCGGACTTTTTCCAAATTTC
EST: gi|110195540|gb|EC877437.1|EC877437
EST:     TGGAGTGCAGAATCATGATGCCAGCTTCAAAAGTGAAATTACCGAGGATG                         ATGAAGCTGCTGATTGACTGGAAAATCTGGATCGGACTTTTTCCAAATTTC
genomic: TGGAGTGCAGAATCATGATGCCAGCTTCAAAAGTGAAATTACCGAGGATGgtaatttaat ... atctctctagATGAAGCTGCTGATTGACTGGAAAATCTGGATCGGACTTTTTCCAAATTTC
EST: gi|148977665|gb|EE026090.2|EE026090
EST:     TGGAGTGCAGAATCATGATGCCAGCTTCAAAAGTGAAATTACCGAGGATG                         ATGAAGCTGCTGATTGACTGGAAAATCTGGATCGGACTTTTTCCAAATTTC
genomic: TGGAGTGCAGAATCATGATGCCAGCTTCAAAAGTGAAATTACCGAGGATGgtaatttaat ... atctctctagATGAAGCTGCTGATTGACTGGAAAATCTGGATCGGACTTTTTCCAAATTTC
EST: gi|71448310|gb|DR829360.1|DR829360
EST:     TGGAGTGCAGAATCATGATGCCAGCTTCAAAAGTGAAATTACCGAGGATG                         ATGAAGCTGCTGATTGACTGGAAAATCTGGATCGGACTTTTTCCAAATTTC
genomic: TGGAGTGCAGAATCATGATGCCAGCTTCAAAAGTGAAATTACCGAGGATGgtaatttaat ... atctctctagATGAAGCTGCTGATTGACTGGAAAATCTGGATCGGACTTTTTCCAAATTTC
EST: gi|71427906|gb|DR808956.1|DR808956
EST:     TGGAGTGCAGAATCATGATGCCAGCTTCAAAAGTGAAATTACCGAGGATG                         ATGAAGCTGCTGATTGACTGGAAAATCTGGATCGGACTTTTTCCAAATTTC
genomic: TGGAGTGCAGAATCATGATGCCAGCTTCAAAAGTGAAATTACCGAGGATGgtaatttaat ... atctctctagATGAAGCTGCTGATTGACTGGAAAATCTGGATCGGACTTTTTCCAAATTTC
EST: gi|78026668|gb|DV495055.1|DV495055
EST:     TGGAGTGCAGAATCATGATGCCAGCTTCAAAAGTGAAATTACCGAGGATG                         ATGAAGCTGCTGATTGACTGGAAAATCTGGATCGGACTTTTTCCAAATTTC
genomic: TGGAGTGCAGAATCATGATGCCAGCTTCAAAAGTGAAATTACCGAGGATGgtaatttaat ... atctctctagATGAAGCTGCTGATTGACTGGAAAATCTGGATCGGACTTTTTCCAAATTTC
EST: gi|31997570|gb|CD661661.1|CD661661
EST:     TGGAGTGCAGAATCATGATGCCAGCTTCAAAAGTGAAATTACCGAGGATG                         ATGAAGCTGCTGATTGACTGGAAAATCTGGATCGGACTTTTTCCAAATTTC
genomic: TGGAGTGCAGAATCATGATGCCAGCTTCAAAAGTGAAATTACCGAGGATGgtaatttaat ... atctctctagATGAAGCTGCTGATTGACTGGAAAATCTGGATCGGACTTTTTCCAAATTTC
EST: gi|5108468|gb|AI740181.1|AI740181
EST:     TGGAGTGCAGAATCATGATGCCAGCTTCAAAAGTGAAATTACCGAGGATG                         ATGAAGCTGCTGATTGACTGGAAAATCTGGATCGGACTTTTTCCAAATTTC
genomic: TGGAGTGCAGAATCATGATGCCAGCTTCAAAAGTGAAATTACCGAGGATGgtaatttaat ... atctctctagATGAAGCTGCTGATTGACTGGAAAATCTGGATCGGACTTTTTCCAAATTTC
EST: gi|5607937|gb|AI901604.1|AI901604
EST:     TGGAGTGCAGAATCATGATGCCAGCTTCAAAAGTGAAATTACCGAGGATG                         ATGAAGCTGCTGATTGACTGGAAAATCTGGATCGGACTTTTTCCAAATTTC
genomic: TGGAGTGCAGAATCATGATGCCAGCTTCAAAAGTGAAATTACCGAGGATGgtaatttaat ... atctctctagATGAAGCTGCTGATTGACTGGAAAATCTGGATCGGACTTTTTCCAAATTTC
EST: gi|211038059|gb|FL324598.1|FL324598
EST:     TGGAGTGCAGAATCATGATGCCAGCTTCAAAAGTGAAATTACCGAGGATG                         ATGAAGCTGCTGATTGACTGGAAAATYTGGATCGGACTTTTTCCAAATTTC
genomic: TGGAGTGCAGAATCATGATGCCAGCTTCAAAAGTGAAATTACCGAGGATGgtaatttaat ... atctctctagATGAAGCTGCTGATTGACTGGAAAATCTGGATCGGACTTTTTCCAAATTTC
EST: gi|28986954|gb|CB351391.1|CB351391
EST:     TGGAGTGCAGAATCATGATGCCAGCTTCAAAAGTGAAATTACCGAGGATG                         ATGAAGCTGCTGATTGACTGGAAAATCTGGATCGGACTTTTTCCAAATTTC
genomic: TGGAGTGCAGAATCATGATGCCAGCTTCAAAAGTGAAATTACCGAGGATGgtaatttaat ... atctctctagATGAAGCTGCTGATTGACTGGAAAATCTGGATCGGACTTTTTCCAAATTTC
EST: gi|71316273|gb|DR794813.1|DR794813
EST:     TGGAGTGCAGAATCATGATGCCAGCTTCAAAAGTGAAATTACCGAGGATG                         ATGAAGCTGCTGATTGACTGGAAAATCTGGATCGGACTTTTTCCAAATTTC
genomic: TGGAGTGCAGAATCATGATGCCAGCTTCAAAAGTGAAATTACCGAGGATGgtaatttaat ... atctctctagATGAAGCTGCTGATTGACTGGAAAATCTGGATCGGACTTTTTCCAAATTTC
EST: gi|37374218|gb|CF623453.1|CF623453
EST:     TGGAGTGCAGAATCATGATGCCAGCTTCAAAAGTGAAATTACCGAGGATG                         ATGAAGCTGCTGATTGACTGGAAAATCTGGATCGGACTTTTTCCAAATTTC
genomic: TGGAGTGCAGAATCATGATGCCAGCTTCAAAAGTGAAATTACCGAGGATGgtaatttaat ... atctctctagATGAAGCTGCTGATTGACTGGAAAATCTGGATCGGACTTTTTCCAAATTTC
EST: gi|30705914|gb|CD058968.1|CD058968
EST:     TGGAGTGCAGAATCATGATGCCAGCTTCAAAAGTGAAATTACCGAGGATG                         ATGAAGCTGCTGATTGACTGGAAAATCTGGATCGGACTTTTTCCAAATTTC
genomic: TGGAGTGCAGAATCATGATGCCAGCTTCAAAAGTGAAATTACCGAGGATGgtaatttaat ... atctctctagATGAAGCTGCTGATTGACTGGAAAATCTGGATCGGACTTTTTCCAAATTTC
EST: gi|5108429|gb|AI740142.1|AI740142
EST:     TGGAGTGCAGAATCATGATGCCAGCTTCAAAAGTGAAATTACCGAGGATG                         ATGAAGCTGCTGATTGACTGGAAAATCTGGATCGGACTTTTTCCAAATTTC
genomic: TGGAGTGCAGAATCATGATGCCAGCTTCAAAAGTGAAATTACCGAGGATGgtaatttaat ... atctctctagATGAAGCTGCTGATTGACTGGAAAATCTGGATCGGACTTTTTCCAAATTTC
EST: gi|60354852|gb|DN221825.1|DN221825
EST:     TGGAGTGCAGAATCATGATGCCAGCTTCAAAAGTGAAATTACCGAGGATG                         ATGAAGCTGCTGATTGACTGGAAAATCTGGATCGGACTTTTTCCAAATTTC
genomic: TGGAGTGCAGAATCATGATGCCAGCTTCAAAAGTGAAATTACCGAGGATGgtaatttaat ... atctctctagATGAAGCTGCTGATTGACTGGAAAATCTGGATCGGACTTTTTCCAAATTTC

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: 177

GGGGACCGCTACTGGAGGACAATCCAATTGTTCTTGGATCAATACGCTCCTGGAGTGCAGAATCATGATGCCAGCTTCAAAAGTGAAATTACCGAGGATGgtaatttaat ... atctctctagATGAAGCTGCTGATTGACTGGAAAATCTGGATCGGACTTTTTCCAAATTTCTGTTTCCTGATGTTGCTGCAATTTGTCACCAATGAACTGAAACTCACCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 278

GGGGACCGCTACTGGAGGACAATCCAATTGTTCTTGGATCAATACGCTCCTGGAGTGCAGAATCATGATGCCAGCTTCAAAAGTGAAATTACCGAGGATGgtaatttaat ... atctctctagATGAAGCTGCTGATTGACTGGAAAATCTGGATCGGACTTTTTCCAAATTTCTGTTTCCTGATGTTGCTGCAATTTGTCACCAATGAACTGAAACTCACCG


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

GGGGACCGCTACTGGAGGACAATCCAATTGTTCTTGGATCAATACGCTCCTGGAGTGCAGAATCATGATGCCAGCTTCAAAAGTGAAATTACCGAGGATGgtaatttaat ... atctctctagATGAAGCTGCTGATTGACTGGAAAATCTGGATCGGACTTTTTCCAAATTTCTGTTTCCTGATGTTGCTGCAATTTGTCACCAATGAACTGAAACTCACCG


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 180

GGGGACCGCTACTGGAGGACAATCCAATTGTTCTTGGATCAATACGCTCCTGGAGTGCAGAATCATGATGCCAGCTTCAAAAGTGAAATTACCGAGGATGgtaatttaat ... atctctctagATGAAGCTGCTGATTGACTGGAAAATCTGGATCGGACTTTTTCCAAATTTCTGTTTCCTGATGTTGCTGCAATTTGTCACCAATGAACTGAAACTCACCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgttgattctaaatgttgatgttgtgttttcttgtttctgatgaatctctctagATGAAGCTGCTGATTGACTGGAAAATCTGGATCGGACTTTTTCCAAATTTCTGTTTCCTGATGTTGCTGCAATTTGTCACCAATGAACTGAAACTCACCG
                                              tctctct  CT-rich tract
      attctaaat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cactagtgcatttatgtcatattttggaacgaattactgttcatgatgttgattctaaatgttgatgttgtgttttcttgtttctgatgaatctctctagATGAAGCTGCTGATTGACTGGAAAATCTGGATCGGACTTTTTCCAAATTTCTGTTTCCTGATGTTGCTGCAATTTGTCACCAATGAACTGAAACTCACCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - -gtgcatt
- - - - - - - - - - - - - gaacgaa
- - - - - - - - - - - - - - - - - - - gttcatg
- - - - - - - - - - - - - - - - - - - - - - - tgttgat