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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAGAGATTCGAAGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAGACAAGGACGCTgtaagttctttaacgagtgacgttatattcagactcagttttgttgggcagtgccaagtaaatagttaacattggcatattcggttcctttgaattactg...

Basic information

species Zea mays
transcript GRMZM2G010754_T01
intron # 3
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|8665254|gb|BE186070.1|BE186070
EST:     AGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAGACAAGGACGCT                         GCCTTCAAAGAAATATCCAAGGATGACTACTTTGCAAAGAACAACGAGTTC
genomic: AGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAGACAAGGACGCTgtaagttctt ... tctgaaacagGCCTTCAAAGAAATATCCAAGGATGACTACTTTGCAAAGAACAACGAGTTC
EST: gi|60352925|gb|DN219898.1|DN219898
EST:     AGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAGACAAGGACGCT                         GCCTTCAAAGAAATATCCAAGGATGACTACTTTGCAAAGAACAACGAGTTC
genomic: AGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAGACAAGGACGCTgtaagttctt ... tctgaaacagGCCTTCAAAGAAATATCCAAGGATGACTACTTTGCAAAGAACAACGAGTTC
EST: gi|20301418|gb|BQ164361.1|BQ164361
EST:     TCCAAGGAGAAGACGAGCAAGAGAAAAGACAAGGACGCT                         GCCTTCAATATGAAATATCCAAGGATGACTACTTTGCAAAGAACAACGAGT
genomic: TCCAAGGAGAAGACGAGCAAGAGAAAAGACAAGGACGCTgtaagttctt ... tctgaaacagGCCTTCAA-A-GAAATATCCAAGGATGACTACTTTGCAAAGAACAACGAGT
EST: gi|211198262|gb|FL232390.1|FL232390
EST:     AGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAGACAAGGACGCT                         GCCTTCAAAGAAATATCCAAGGATGACTACTTTGCAAAGAACAACGAGTTC
genomic: AGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAGACAAGGACGCTgtaagttctt ... tctgaaacagGCCTTCAAAGAAATATCCAAGGATGACTACTTTGCAAAGAACAACGAGTTC
EST: gi|60344656|gb|DN211629.1|DN211629
EST:     AGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAGACAAGGACGCT                         GCCTTCAAAGAAATATCCAAGGATGACTACTTTGCAAAGAACAACGAGTTC
genomic: AGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAGACAAGGACGCTgtaagttctt ... tctgaaacagGCCTTCAAAGAAATATCCAAGGATGACTACTTTGCAAAGAACAACGAGTTC
EST: gi|8665559|gb|BE186375.1|BE186375
EST:     AGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAGACAAGGACGCT                         GCCTTCAAAGAAATATCCAAGGATGACTACTTTGCAAAGAACAACGAGTTC
genomic: AGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAGACAAGGACGCTgtaagttctt ... tctgaaacagGCCTTCAAAGAAATATCCAAGGATGACTACTTTGCAAAGAACAACGAGTTC
EST: gi|5018459|gb|AI714652.1|AI714652
EST:     AGGATAGGCATTCCAAGGAGAAGNCGAGCAAGAGAAAAGNCAAGGACGCT                         GCCTTCAAAGAAATATCCAAGGATGACTACTTTGCAAAGAACAACGAGTTC
genomic: AGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAGACAAGGACGCTgtaagttctt ... tctgaaacagGCCTTCAAAGAAATATCCAAGGATGACTACTTTGCAAAGAACAACGAGTTC
EST: gi|211200810|gb|FL232404.1|FL232404
EST:     AGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAGACAAGGACGCG                         GCCTTCAAAGAAATATCCAAGGATGACTACTTTGCAAAGAACAACGAGTTC
genomic: AGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAGACAAGGACGCTgtaagttctt ... tctgaaacagGCCTTCAAAGAAATATCCAAGGATGACTACTTTGCAAAGAACAACGAGTTC
EST: gi|60343805|gb|DN210778.1|DN210778
EST:     AGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAGACAAGGACGCT                         GCCTTCAAAGAAATATCCAAGGATGACTACTTTGCAAAGAACAACGAGTTC
genomic: AGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAGACAAGGACGCTgtaagttctt ... tctgaaacagGCCTTCAAAGAAATATCCAAGGATGACTACTTTGCAAAGAACAACGAGTTC
EST: gi|60339898|gb|DN206871.1|DN206871
EST:     AGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAGACAAGGACGCT                         GCCTTCAAAGAAATATCCAAGGATGACTACTTTGCAAAGAACAACGAGTTC
genomic: AGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAGACAAGGACGCTgtaagttctt ... tctgaaacagGCCTTCAAAGAAATATCCAAGGATGACTACTTTGCAAAGAACAACGAGTTC
EST: gi|78024507|gb|DV492894.1|DV492894
EST:     AGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAGACAAGGACGCT                         GCCTTCAAAGAAATATCCAAGGATGACTACTTTGCAAAGAACAACGAGTTC
genomic: AGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAGACAAGGACGCTgtaagttctt ... tctgaaacagGCCTTCAAAGAAATATCCAAGGATGACTACTTTGCAAAGAACAACGAGTTC
EST: gi|5456187|gb|AI833877.1|AI833877
EST:     AGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAGACAAGGACGCT                         GCCTTCAAAGAAATATCCAAGGATGACTACTTTGCAAAGAACAACGAGTTC
genomic: AGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAGACAAGGACGCTgtaagttctt ... tctgaaacagGCCTTCAAAGAAATATCCAAGGATGACTACTTTGCAAAGAACAACGAGTTC
EST: gi|26456161|gb|CA827744.1|CA827744
EST:     AGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAGACAAGGACGCT                         GCCTTCAAAGAAATATCCAAGGATGACTACTTTGCAAAGAACAACGAGTTC
genomic: AGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAGACAAGGACGCTgtaagttctt ... tctgaaacagGCCTTCAAAGAAATATCCAAGGATGACTACTTTGCAAAGAACAACGAGTTC
EST: gi|149076085|gb|EE164662.2|EE164662
EST:     AGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAGACAAGGACGCT                         GCCTTCAAAGAAATATCCAAGGATGACTACTTTGCAAAGAACAACGAGTTC
genomic: AGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAGACAAGGACGCTgtaagttctt ... tctgaaacagGCCTTCAAAGAAATATCCAAGGATGACTACTTTGCAAAGAACAACGAGTTC
EST: gi|213172009|gb|FM190576.1|FM190576
EST:     AGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAGACAAGGACGCT                         GCCTTCAAAGAAATATCCAAGGATGACTACTTTGCAAAGAACAACGAGTTC
genomic: AGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAGACAAGGACGCTgtaagttctt ... tctgaaacagGCCTTCAAAGAAATATCCAAGGATGACTACTTTGCAAAGAACAACGAGTTC
EST: gi|211198269|gb|FL232397.1|FL232397
EST:     AGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAGACAAGGACGCG                         GCCTTCAAAGAAATATCCAAGGATGACTACTTTGCAAAGAACAACGAGTTC
genomic: AGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAGACAAGGACGCTgtaagttctt ... tctgaaacagGCCTTCAAAGAAATATCCAAGGATGACTACTTTGCAAAGAACAACGAGTTC
EST: gi|211103961|gb|FL232383.1|FL232383
EST:     AGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAGACAAGGACGCT                         GCCTTCAAAGAAATATCCAAGGATGACTACTTTGCAAAGAACAACGAGTTC
genomic: AGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAGACAAGGACGCTgtaagttctt ... tctgaaacagGCCTTCAAAGAAATATCCAAGGATGACTACTTTGCAAAGAACAACGAGTTC
EST: gi|149076084|gb|EE164661.2|EE164661
EST:     AGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAGACAAGGACGCT                         GCCTTCAAAGAAATATCCAAGGATGACTACTTTGCAAAGAACAACGAGTTC
genomic: AGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAGACAAGGACGCTgtaagttctt ... tctgaaacagGCCTTCAAAGAAATATCCAAGGATGACTACTTTGCAAAGAACAACGAGTTC
EST: gi|211101495|gb|FL232372.1|FL232372
EST:     AGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAGACAAGGACGCT                         GCCTTCAAAGAAATATCCAAGGATGACTACTTTGCAAAGAACAACGAGTTC
genomic: AGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAGACAAGGACGCTgtaagttctt ... tctgaaacagGCCTTCAAAGAAATATCCAAGGATGACTACTTTGCAAAGAACAACGAGTTC
EST: gi|211101493|gb|FL232370.1|FL232370
EST:     AGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAGACAAGGACGCT                         GCCTTCAAAGAAATATCCAAGGATGACTACTTTGCAAAGAACAACGAGTTC
genomic: AGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAGACAAGGACGCTgtaagttctt ... tctgaaacagGCCTTCAAAGAAATATCCAAGGATGACTACTTTGCAAAGAACAACGAGTTC
EST: gi|211386269|gb|FL454547.1|FL454547
EST:     AGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAGACAAGGACGCG                         GCCTTCAAAGAAATATCCAAGGATGACTACTTTGCAAAGAACAACGAGTTC
genomic: AGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAGACAAGGACGCTgtaagttctt ... tctgaaacagGCCTTCAAAGAAATATCCAAGGATGACTACTTTGCAAAGAACAACGAGTTC
EST: gi|211103965|gb|FL232387.1|FL232387
EST:     AGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAGACAAGGACGCT                         GCCTTCAAAGAAATATCCAAGGATGACTACTTTGCAAAGAACAACGAGTTC
genomic: AGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAGACAAGGACGCTgtaagttctt ... tctgaaacagGCCTTCAAAGAAATATCCAAGGATGACTACTTTGCAAAGAACAACGAGTTC
EST: gi|67011144|gb|CO439893.1|CO439893
EST:     AGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAGACAAGGACGCT                         GCCTTCAAAGAAATATCCAAGGATGACTACTTTGCAAAGAACAACGAGTTC
genomic: AGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAGACAAGGACGCTgtaagttctt ... tctgaaacagGCCTTCAAAGAAATATCCAAGGATGACTACTTTGCAAAGAACAACGAGTTC

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: 45 (upstream exon), 49 (downstream exon)
Score: 80

AGAGAGATTCGAAGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAGACAAGGACGCTgtaagttctt ... tctgaaacagGCCTTCAAAGAAATATCCAAGGATGACTACTTTGCAAAGAACAACGAGTTCGCTACCTGGTTGAAGGAGGAAAAGGGCAAATATTTCTCAGATTTGTCTT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 32

AGAGAGATTCGAAGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAGACAAGGACGCTgtaagttctt ... tctgaaacagGCCTTCAAAGAAATATCCAAGGATGACTACTTTGCAAAGAACAACGAGTTCGCTACCTGGTTGAAGGAGGAAAAGGGCAAATATTTCTCAGATTTGTCTT


Block sizes: 44 (upstream exon), 47 (downstream exon)
Score: 18

AGAGAGATTCGAAGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAGACAAGGACGCTgtaagttctt ... tctgaaacagGCCTTCAAAGAAATATCCAAGGATGACTACTTTGCAAAGAACAACGAGTTCGCTACCTGGTTGAAGGAGGAAAAGGGCAAATATTTCTCAGATTTGTCTT


Block sizes: 44 (upstream exon), 48 (downstream exon)
Score: 60

AGAGAGATTCGAAGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAGACAAGGACGCTgtaagttctt ... tctgaaacagGCCTTCAAAGAAATATCCAAGGATGACTACTTTGCAAAGAACAACGAGTTCGCTACCTGGTTGAAGGAGGAAAAGGGCAAATATTTCTCAGATTTGTCTT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAGAGATTCGAAGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAGACAAGGACGCTgtaagttctttaacgagtgacgttatattcagactcagttttgttgggcagtgccaagtaaatagttaacattggcatattcggttcctttgaattactg

- - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caagtaaa