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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattcatctgatctgtttaacatattgcttttgttcctagaactgtaatatcatgtttttttttggctctggtactctaatactgtacaatttatcctcagtgtgtcatttcagattttacttgactacaaatgtgtttccattgttgcagCATGATGATGCCACTAAGGGTTGGAAAGACATTGGTGTTGGTCAGCTCTCTATCAGAAGTAAAGAAGGCACAGAGAAAGCTTCCAAAGAATCCACTCCTA

Basic information

species Zea mays
transcript GRMZM2G086484_T03
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|31351667|gb|CD436024.1|CD436024
EST:     AGAAGGGGGTAGTTGTTGTTCATGAAACCAAATGCAAGGTGTATGTCAAG                         CATGATGATGCCACTAAGGGTTGGAAAGACATTGGTGTTGGTCAGCTCTCT
genomic: AGAAGGGGGTAGTTGTCGTTCATGAAACCAAATGCAAGGTGTATGTCAAGgtattcatct ... attgttgcagCATGATGATGCCACTAAGGGTTGGAAAGACATTGGTGTTGGTCAGCTCTCT
EST: gi|71311912|gb|DR792439.1|DR792439
EST:     AGAAGGGGGTAGTTGTCGTTCATGAAACCAAATGCAAGGTGTATGTCAAG                         CATGATGATGCCACTAAGGGTTGGAAAGACATTGGTGTTGGTCAGCTCTCT
genomic: AGAAGGGGGTAGTTGTCGTTCATGAAACCAAATGCAAGGTGTATGTCAAGgtattcatct ... attgttgcagCATGATGATGCCACTAAGGGTTGGAAAGACATTGGTGTTGGTCAGCTCTCT
EST: gi|22491304|gb|BU051227.1|BU051227
EST:     AGAAGGGGGTAGTTGTTGTTCATGAAACCAAATGCAAGGTGTATGTCAAG                         CATGATGATGCCACTAAGGGTTGGAAAGACATTGGTGTTGGTCAGCTCTCT
genomic: AGAAGGGGGTAGTTGTCGTTCATGAAACCAAATGCAAGGTGTATGTCAAGgtattcatct ... attgttgcagCATGATGATGCCACTAAGGGTTGGAAAGACATTGGTGTTGGTCAGCTCTCT
EST: gi|71762836|gb|DR960773.1|DR960773
EST:     AGAAGGGGGTAGTTGTCGTTCATGAAACCAAATGCAAGGTGTATGTCAAG                         CATGATGATGCCACTAAGGGTTGGAAAGACATTGGTGTTGGTCAGCTCTCT
genomic: AGAAGGGGGTAGTTGTCGTTCATGAAACCAAATGCAAGGTGTATGTCAAGgtattcatct ... attgttgcagCATGATGATGCCACTAAGGGTTGGAAAGACATTGGTGTTGGTCAGCTCTCT
EST: gi|33091533|gb|CF051527.1|CF051527
EST:     AGAAGGGGGTAGTTGTTGTTCATGAAACCAAATGCAAGGTGTATGTCAAG                         CATGATGATGCCACTAAGGGTTGGAAAGACATTGGTGTTGGTCAGCTCTCT
genomic: AGAAGGGGGTAGTTGTCGTTCATGAAACCAAATGCAAGGTGTATGTCAAGgtattcatct ... attgttgcagCATGATGATGCCACTAAGGGTTGGAAAGACATTGGTGTTGGTCAGCTCTCT
EST: gi|83278326|gb|DV942334.1|DV942334
EST:     AGAAGGGGGTAGTTGTCGTTCATGAAACCAAATGCAAGGTGTATGTCAAG                         CATGATGATGCCACTAAGGGTTGGAAAGACATTGGTGTTGGTCAGCTCTCT
genomic: AGAAGGGGGTAGTTGTCGTTCATGAAACCAAATGCAAGGTGTATGTCAAGgtattcatct ... attgttgcagCATGATGATGCCACTAAGGGTTGGAAAGACATTGGTGTTGGTCAGCTCTCT
EST: gi|19770206|gb|BQ034927.1|BQ034927
EST:     AGAAGGGGGTAGTTGTTGTTCATGAAACCAAATGCAAGGTGTATGTCAAG                         CATGATGATGCCACTAAGGGTTGGAAAGACATTGGTGTTGGTCAGCTCTCT
genomic: AGAAGGGGGTAGTTGTCGTTCATGAAACCAAATGCAAGGTGTATGTCAAGgtattcatct ... attgttgcagCATGATGATGCCACTAAGGGTTGGAAAGACATTGGTGTTGGTCAGCTCTCT
EST: gi|40334296|gb|CK368366.1|CK368366
EST:     GAAGGGGGGTAGTTGTTGTTCATGAAACCAAATGCAAGGTGTATGTCAAG                         CATGATGATGCCACTAAGGGTTGGAAAGACATTGGTGTTGGTCAGCTCTCT
genomic: GAAGGGGG-TAGTTGTCGTTCATGAAACCAAATGCAAGGTGTATGTCAAGgtattcatct ... attgttgcagCATGATGATGCCACTAAGGGTTGGAAAGACATTGGTGTTGGTCAGCTCTCT

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: 48 (upstream exon), 49 (downstream exon)
Score: 164

ATGCTGAACCTGAGAAGCCAAGCAGCCCTTCTGTAAAGAAGGCAGAAGAGAAGGGGGTAGTTGTCGTTCATGAAACCAAATGCAAGGTGTATGTCAAGgtattcatct ... attgttgcagCATGATGATGCCACTAAGGGTTGGAAAGACATTGGTGTTGGTCAGCTCTCTATCAGAAGTAAAGAAGGCACAGAGAAAGCTTCCAAAGAATCCACTCCTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 72

ATGCTGAACCTGAGAAGCCAAGCAGCCCTTCTGTAAAGAAGGCAGAAGAGAAGGGGGTAGTTGTCGTTCATGAAACCAAATGCAAGGTGTATGTCAAGgtattcatct ... attgttgcagCATGATGATGCCACTAAGGGTTGGAAAGACATTGGTGTTGGTCAGCTCTCTATCAGAAGTAAAGAAGGCACAGAGAAAGCTTCCAAAGAATCCACTCCTA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 83

ATGCTGAACCTGAGAAGCCAAGCAGCCCTTCTGTAAAGAAGGCAGAAGAGAAGGGGGTAGTTGTCGTTCATGAAACCAAATGCAAGGTGTATGTCAAGgtattcatct ... attgttgcagCATGATGATGCCACTAAGGGTTGGAAAGACATTGGTGTTGGTCAGCTCTCTATCAGAAGTAAAGAAGGCACAGAGAAAGCTTCCAAAGAATCCACTCCTA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 66

ATGCTGAACCTGAGAAGCCAAGCAGCCCTTCTGTAAAGAAGGCAGAAGAGAAGGGGGTAGTTGTCGTTCATGAAACCAAATGCAAGGTGTATGTCAAGgtattcatct ... attgttgcagCATGATGATGCCACTAAGGGTTGGAAAGACATTGGTGTTGGTCAGCTCTCTATCAGAAGTAAAGAAGGCACAGAGAAAGCTTCCAAAGAATCCACTCCTA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcagtgtgtcatttcagattttacttgactacaaatgtgtttccattgttgcagCATGATGATGCCACTAAGGGTTGGAAAGACATTGGTGTTGGTCAGCTCTCTATCAGAAGTAAAGAAGGCACAGAGAAAGCTTCCAAAGAATCCACTCCTA
                       acttgac  putative branch site (score: 66)
                                        tttccatt  putative PPT
                  attttactt  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
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gtattcatctgatctgtttaacatattgcttttgttcctagaactgtaatatcatgtttttttttggctctggtactctaatactgtacaatttatcctcagtgtgtcatttcagattttacttgactacaaatgtgtttccattgttgcagCATGATGATGCCACTAAGGGTTGGAAAGACATTGGTGTTGGTCAGCTCTCTATCAGAAGTAAAGAAGGCACAGAGAAAGCTTCCAAAGAATCCACTCCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
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