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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttctagcctgtgttacttctttgttttatgttacttgttgaactgatcctagcgttacttttcctccttttgtctgtctgtttgtttgtctgtggcagTAGTTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCTACTTTTCAAATCACTATGGTTACCCTTTCCTACAGCTGGGCAAGCGTAG

Basic information

species Zea mays
transcript GRMZM2G049382_T02
intron # 1
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|76286587|gb|DV026155.1|DV026155
EST:     CGCAAGCCGTGCGTGCCCGCGGGTTCCCCGATTTG                         TAGTTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCT
genomic: CGCAAGCCGTGCGTGCCCGCGGGTTCCCCGATTTGgtaactgctc ... tctgtggcagTAGTTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCT
EST: gi|93016747|gb|EB642267.1|EB642267
EST:     GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGA-TT-                         T-GTTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCT
genomic: GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGATTTGgtaactgctc ... tctgtggcagTAGTTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCT
EST: gi|71775361|gb|DR973239.1|DR973239
EST:     GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGA-TT-                         T-GTTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCT
genomic: GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGATTTGgtaactgctc ... tctgtggcagTAGTTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCT
EST: gi|211441856|gb|FL182593.1|FL182593
EST:     GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGA-TT-                         T-GTTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCT
genomic: GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGATTTGgtaactgctc ... tctgtggcagTAGTTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCT
EST: gi|22489209|gb|BU049119.1|BU049119
EST:     GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGA-TT-                         T-GTTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCT
genomic: GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGATTTGgtaactgctc ... tctgtggcagTAGTTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCT
EST: gi|101389927|gb|EB816894.1|EB816894
EST:     CGCAAGCCGTGCGTGCCCGCGGGTTCCCCGATTTG                         TAGTTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCT
genomic: CGCAAGCCGTGCGTGCCCGCGGGTTCCCCGATTTGgtaactgctc ... tctgtggcagTAGTTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCT
EST: gi|71444264|gb|DR825314.1|DR825314
EST:     GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGATTTG                         TAGTTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCT
genomic: GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGATTTGgtaactgctc ... tctgtggcagTAGTTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCT
EST: gi|32918957|gb|CF023769.1|CF023769
EST:     CCGCCTGCGGGCGCCGCAAGGCCGTGCGTGCCCGCGGGTTCCCCGA-TT-                         T-GTTTATTTACGGAAGTTTACAATTGGTCAACAAGACTTAGTCCAACCCT
genomic: CCGCCTGCGGGCGCCGCAA-GCCGTGCGTGCCCGCGGGTTCCCCGATTTGgtaactgctc ... tctgtggcagTAGTTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCT
EST: gi|76015122|gb|DT942292.1|DT942292
EST:     GCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGA-TT-                         T-GTTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCT
genomic: GCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGATTTGgtaactgctc ... tctgtggcagTAGTTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCT
EST: gi|94476136|gb|EB705094.1|EB705094
EST:     GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGATTTG                         TAGTTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCT
genomic: GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGATTTGgtaactgctc ... tctgtggcagTAGTTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCT
EST: gi|211441855|gb|FL182592.1|FL182592
EST:     GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGA-TT-                         T-GTTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCT
genomic: GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGATTTGgtaactgctc ... tctgtggcagTAGTTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCT
EST: gi|71437491|gb|DR818541.1|DR818541
EST:     GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGATTTG                         TAGTTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCT
genomic: GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGATTTGgtaactgctc ... tctgtggcagTAGTTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCT
EST: gi|74237928|gb|DT645842.1|DT645842
EST:     GCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGA-TT-                         T-GTTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCT
genomic: GCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGATTTGgtaactgctc ... tctgtggcagTAGTTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCT
EST: gi|74241229|gb|DT649143.1|DT649143
EST:     GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGA-TT-                         T-GTTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCT
genomic: GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGATTTGgtaactgctc ... tctgtggcagTAGTTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCT
EST: gi|211441853|gb|FL182590.1|FL182590
EST:     GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGATTTG                         T--TT-ATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCT
genomic: GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGATTTGgtaactgctc ... tctgtggcagTAGTTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCT
EST: gi|78109421|gb|DV527837.1|DV527837
EST:     GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGATTTG                         TAGTTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCT
genomic: GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGATTTGgtaactgctc ... tctgtggcagTAGTTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCT
EST: gi|30306535|gb|CD001208.1|CD001208
EST:     GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGATTTG                         TAGTTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCT
genomic: GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGATTTGgtaactgctc ... tctgtggcagTAGTTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCT
EST: gi|211441854|gb|FL182591.1|FL182591
EST:     GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGA-TT-                         T-GTTTATTTACGGAAG-TTACAATTGATCAACAAGACTTAGTCCAACCCT
genomic: GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGATTTGgtaactgctc ... tctgtggcagTAGTTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCT
EST: gi|71437490|gb|DR818540.1|DR818540
EST:     GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGATTTG                         TAGTTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCT
genomic: GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGATTTGgtaactgctc ... tctgtggcagTAGTTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCT
EST: gi|76015982|gb|DT943152.1|DT943152
EST:     GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGATTTG                         TAGTTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCT
genomic: GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGATTTGgtaactgctc ... tctgtggcagTAGTTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCT
EST: gi|32919043|gb|CF023855.1|CF023855
EST:     CCGCCTGCGGGCGCCGCAAGGCCGTGCGTGCCCGCGGGTTCCCCGA-TT-                         T-GTTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCT
genomic: CCGCCTGCGGGCGCCGCAA-GCCGTGCGTGCCCGCGGGTTCCCCGATTTGgtaactgctc ... tctgtggcagTAGTTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCT
EST: gi|211441852|gb|FL182589.1|FL182589
EST:     GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGA-TT-                         T-GTTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCT
genomic: GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGATTTGgtaactgctc ... tctgtggcagTAGTTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCT
EST: gi|93014379|gb|EB639899.1|EB639899
EST:     GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGATTTG                         TAGTTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCT
genomic: GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGATTTGgtaactgctc ... tctgtggcagTAGTTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCT
EST: gi|78109677|gb|DV528093.1|DV528093
EST:     GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGA-TT-                         T-GTTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCT
genomic: GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGATTTGgtaactgctc ... tctgtggcagTAGTTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCT
EST: gi|32943700|gb|CF048519.1|CF048519
EST:     CCGCCTGCGGGCGCCGCAAGGCCGTGCGTGCCCGCGGGTTCCCCGA-TT-                         T-GTTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCT
genomic: CCGCCTGCGGGCGCCGCAA-GCCGTGCGTGCCCGCGGGTTCCCCGATTTGgtaactgctc ... tctgtggcagTAGTTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCT
EST: gi|17970113|gb|BM276864.1|BM276864
EST:     GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGA-TT-                         T-GTTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCT
genomic: GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGATTTGgtaactgctc ... tctgtggcagTAGTTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCT
EST: gi|149081435|gb|EE170555.2|EE170555
EST:     GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGATTTG                         TAGTTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCT
genomic: GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGATTTGgtaactgctc ... tctgtggcagTAGTTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCT
EST: gi|87298772|gb|DY470775.1|DY470775
EST:     GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGA-TT-                         T-GTTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCT
genomic: GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGATTTGgtaactgctc ... tctgtggcagTAGTTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCT
EST: gi|50330365|gb|CO525491.1|CO525491
EST:     GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGATTTG                         TAGTTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCT
genomic: GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGATTTGgtaactgctc ... tctgtggcagTAGTTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCT
EST: gi|78077755|gb|DV506187.1|DV506187
EST:     GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGATTTG                         TAGTTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCCACCCT
genomic: GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGATTTGgtaactgctc ... tctgtggcagTAGTTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCT
EST: gi|149015537|gb|EE045415.2|EE045415
EST:     GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGA-TT-                         T-GTTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCT
genomic: GCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGATTTGgtaactgctc ... tctgtggcagTAGTTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCT

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: 39

ACTCGGAGTCTTCCCCCACCCCCATAACGTCCTCTTCCGTGCTCTGCGTTGCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGATTTGgtaactgctc ... tctgtggcagTAGTTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCTACTTTTCAAATCACTATGGTTACCCTTTCCTACAGCTGGGCAAGCGTAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 26

ACTCGGAGTCTTCCCCCACCCCCATAACGTCCTCTTCCGTGCTCTGCGTTGCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGATTTGgtaactgctc ... tctgtggcagTAGTTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCTACTTTTCAAATCACTATGGTTACCCTTTCCTACAGCTGGGCAAGCGTAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 12

ACTCGGAGTCTTCCCCCACCCCCATAACGTCCTCTTCCGTGCTCTGCGTTGCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGATTTGgtaactgctc ... tctgtggcagTAGTTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCTACTTTTCAAATCACTATGGTTACCCTTTCCTACAGCTGGGCAAGCGTAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 18

ACTCGGAGTCTTCCCCCACCCCCATAACGTCCTCTTCCGTGCTCTGCGTTGCCGCCTGCGGGCGCCGCAAGCCGTGCGTGCCCGCGGGTTCCCCGATTTGgtaactgctc ... tctgtggcagTAGTTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCTACTTTTCAAATCACTATGGTTACCCTTTCCTACAGCTGGGCAAGCGTAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatcctagcgttacttttcctccttttgtctgtctgtttgtttgtctgtggcagTAGTTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCTACTTTTCAAATCACTATGGTTACCCTTTCCTACAGCTGGGCAAGCGTAG
 aactgat  putative branch site (score: 18)
              cttttcctccttttgt  putative PPT
           ttactttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttctagcctgtgttacttctttgttttatgttacttgttgaactgatcctagcgttacttttcctccttttgtctgtctgtttgtttgtctgtggcagTAGTTTATTTACGGAAGTTTACAATTGATCAACAAGACTTAGTCCAACCCTACTTTTCAAATCACTATGGTTACCCTTTCCTACAGCTGGGCAAGCGTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - tgttact
- - - - - - - - - - - - - - - - - - -tgttgaa
- - - - - - - - - - - - - - - - - - - - - - ctgatcc