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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaatatcttgtaagttggaaccgagggagtacatattttcccagtttggcatgctttgtatatgcaggatcaacactaaatgtgcaaactgattttcagCCTGGAACATACATAGACCAACGTGAGAAACAAGTCAAGTATAGTGATTTCATCAACAAAGAGCTGATACTCTTCTCAATGGCGGACCTGCAGCGATCAA

Basic information

species Zea mays
transcript GRMZM2G021270_T01
intron # 9
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|18654823|gb|BM499628.1|BM499628
EST:     TCAGCAAGAAACGGATTGCTGATAGGAAACAGTGGCTTACAAATTTTCAG                         CCTGGAACATACATAGACCAACGTGAGAAACAAGTCAAGTATAGGGATTTC
genomic: TCAGCAAGAAACGGATTGCTGATAGGAAACAGTGGCTTACAAATTTTCAGgttagctctc ... tgattttcagCCTGGAACATACATAGACCAACGTGAGAAACAAGTCAAGTATAGTGATTTC
EST: gi|18963118|gb|BM660250.1|BM660250
EST:     TCAGCAAGAAACGGATTGCTGATAGGAAACAGTGGCTTACAAATTTTCAG                         CCTGGAACATACATAGACCAACGTGAGAAACAAGTCAAGTATAGTGATTTC
genomic: TCAGCAAGAAACGGATTGCTGATAGGAAACAGTGGCTTACAAATTTTCAGgttagctctc ... tgattttcagCCTGGAACATACATAGACCAACGTGAGAAACAAGTCAAGTATAGTGATTTC
EST: gi|31354680|gb|CD439037.1|CD439037
EST:     TCAGCAAGAAACGGATTGCTGATAGGAAACAGTGGCTTACAAATTTTCAG                         CCTGGAACATACATAGACCAACGTGAGAAACAAGTCAAGTATAGTGATTTC
genomic: TCAGCAAGAAACGGATTGCTGATAGGAAACAGTGGCTTACAAATTTTCAGgttagctctc ... tgattttcagCCTGGAACATACATAGACCAACGTGAGAAACAAGTCAAGTATAGTGATTTC
EST: gi|18655210|gb|BM500015.1|BM500015
EST:     TCAGCAAGAAACGGATTGCTGATAGGAAACAGTGGCTTACAAATTTTCAG                         CCTGGAACATACATAGACCAACGTGAGAAACAAGTCAAGTATAGTGATTTC
genomic: TCAGCAAGAAACGGATTGCTGATAGGAAACAGTGGCTTACAAATTTTCAGgttagctctc ... tgattttcagCCTGGAACATACATAGACCAACGTGAGAAACAAGTCAAGTATAGTGATTTC
EST: gi|18662206|gb|BM501800.1|BM501800
EST:     TCAGCAAGAAACGGATTGCTGATAGGAAACAGTGGCTTACAAATTTTCAG                         CCTGGAACATACATAGACCAACGTGAGAAACAAGTCAAGTATAGTGATTTC
genomic: TCAGCAAGAAACGGATTGCTGATAGGAAACAGTGGCTTACAAATTTTCAGgttagctctc ... tgattttcagCCTGGAACATACATAGACCAACGTGAGAAACAAGTCAAGTATAGTGATTTC
EST: gi|18661837|gb|BM501604.1|BM501604
EST:     TCAGCAAGAAACGGATTGCTGATAGGAAACAGTGGCTTACAAATTTTCAG                         CCTGGAACATACATAGACCAACGTGAGAAACAAGTCAAGTATAGTGATTTC
genomic: TCAGCAAGAAACGGATTGCTGATAGGAAACAGTGGCTTACAAATTTTCAGgttagctctc ... tgattttcagCCTGGAACATACATAGACCAACGTGAGAAACAAGTCAAGTATAGTGATTTC

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: 559

GGATTTTGTCTGGGTAGATGACCAAGATGGCAACCATATTGAGTTAGCATTCAGCAAGAAACGGATTGCTGATAGGAAACAGTGGCTTACAAATTTTCAGgttagctctc ... tgattttcagCCTGGAACATACATAGACCAACGTGAGAAACAAGTCAAGTATAGTGATTTCATCAACAAAGAGCTGATACTCTTCTCAATGGCGGACCTGCAGCGATCAA


Block sizes: 48 (upstream exon), 44 (downstream exon)
Score: 25

GGATTTTGTCTGGGTAGATGACCAAGATGGCAACCATATTGAGTTAGCATTCAGCAAGAAACGGATTGCTGATAGGAAACAGTGGCTTACAAATTTTCAGgttagctctc ... tgattttcagCCTGGAACATACATAGACCAACGTGAGAAACAAGTCAAGTATAGTGATTTCATCAACAAAGAGCTGATACTCTTCTCAATGGCGGACCTGCAGCGATCAA


Block sizes: 39 (upstream exon), 47 (downstream exon)
Score: 24

GGATTTTGTCTGGGTAGATGACCAAGATGGCAACCATATTGAGTTAGCATTCAGCAAGAAACGGATTGCTGATAGGAAACAGTGGCTTACAAATTTTCAGgttagctctc ... tgattttcagCCTGGAACATACATAGACCAACGTGAGAAACAAGTCAAGTATAGTGATTTCATCAACAAAGAGCTGATACTCTTCTCAATGGCGGACCTGCAGCGATCAA


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 27

GGATTTTGTCTGGGTAGATGACCAAGATGGCAACCATATTGAGTTAGCATTCAGCAAGAAACGGATTGCTGATAGGAAACAGTGGCTTACAAATTTTCAGgttagctctc ... tgattttcagCCTGGAACATACATAGACCAACGTGAGAAACAAGTCAAGTATAGTGATTTCATCAACAAAGAGCTGATACTCTTCTCAATGGCGGACCTGCAGCGATCAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttggcatgctttgtatatgcaggatcaacactaaatgtgcaaactgattttcagCCTGGAACATACATAGACCAACGTGAGAAACAAGTCAAGTATAGTGATTTCATCAACAAAGAGCTGATACTCTTCTCAATGGCGGACCTGCAGCGATCAA
                                                ttttc  CT-rich tract
          tttgtatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaaatatcttgtaagttggaaccgagggagtacatattttcccagtttggcatgctttgtatatgcaggatcaacactaaatgtgcaaactgattttcagCCTGGAACATACATAGACCAACGTGAGAAACAAGTCAAGTATAGTGATTTCATCAACAAAGAGCTGATACTCTTCTCAATGGCGGACCTGCAGCGATCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG