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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactaaaaacgctagatgtatgtatgcccactttgacgtaaacgtactgttccgttactgatttcatgcaagtgctgccagCTGCAAGAAACAAGTCCGCAGAATGTGATCCACGACGTCTCCTGGGAGGAAGGCGGGCACAGTGGGAGTAGTGTTCTTGGTCCGTTCCAGGGACTCCTTC

Basic information

species Zea mays
transcript GRMZM2G102161_T01
intron # 6
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|32828018|gb|CD967696.1|CD967696
EST:     GATCTCAACAAAGACCTAAGGAAAAAG                         CTGCAAGAAACAAGTCCGCAGAATGTGATCCACGACGTCTCCTGGGAGGAA
genomic: GATCTCAACAAAGACCTAAGGAAAAAGgtaactaaaa ... gtgctgccagCTGCAAGAAACAAGTCCGCAGAATGTGATCCACGACGTCTCCTGGGAGGAA
EST: gi|32837918|gb|CD977596.1|CD977596
EST:     GAACAAGAGTTGCAGGATCTCAACAAAGACCTAAGGAAAAAG                         CTGCAAGAAACAAGTCCGCAGAATGTGATCCACGACGTCTCCTGGGAGGAA
genomic: GAACAAGAGTTGCAGGATCTCAACAAAGACCTAAGGAAAAAGgtaactaaaa ... gtgctgccagCTGCAAGAAACAAGTCCGCAGAATGTGATCCACGACGTCTCCTGGGAGGAA
EST: gi|32847423|gb|CD987104.1|CD987104
EST:     GAACAAGAGTTGCAGGATCTCAACAAAGACCTAAGGAAAAAG                         CTGCAAGAAACAAGTCCGCAGAATGTGATCCACGACGTCTCCTGGGAGGAA
genomic: GAACAAGAGTTGCAGGATCTCAACAAAGACCTAAGGAAAAAGgtaactaaaa ... gtgctgccagCTGCAAGAAACAAGTCCGCAGAATGTGATCCACGACGTCTCCTGGGAGGAA
EST: gi|18178380|gb|BM379590.1|BM379590
EST:     GAACAAGAGTTGCAGGATCTCAACAAAGACTTAAGGAAAAAG                         CTGCAAGAAACAAGTCCGCAGAATGTGATCCACGACGTCTCCTGGGAGGAA
genomic: GAACAAGAGTTGCAGGATCTCAACAAAGACCTAAGGAAAAAGgtaactaaaa ... gtgctgccagCTGCAAGAAACAAGTCCGCAGAATGTGATCCACGACGTCTCCTGGGAGGAA
EST: gi|67011315|gb|CO440064.1|CO440064
EST:     GAACAAGAGTTGCAGGATCTCAACAAAGACCTAAGGAAAAAG                         CTGCAAGAAACAAGTCCGCAGAATGTGATCCACGACGTCTCCTGGGAGGAA
genomic: GAACAAGAGTTGCAGGATCTCAACAAAGACCTAAGGAAAAAGgtaactaaaa ... gtgctgccagCTGCAAGAAACAAGTCCGCAGAATGTGATCCACGACGTCTCCTGGGAGGAA
EST: gi|32810400|gb|CD962634.1|CD962634
EST:     GATCTCAACAAAGACCTAAGGAAAAAG                         CTGCAAGAAACAAGTCCGCAGAATGTGATCCACGACGTCTCCTGGGAGGAA
genomic: GATCTCAACAAAGACCTAAGGAAAAAGgtaactaaaa ... gtgctgccagCTGCAAGAAACAAGTCCGCAGAATGTGATCCACGACGTCTCCTGGGAGGAA
EST: gi|32847744|gb|CD987425.1|CD987425
EST:     GAACAAGAGTTGCAGGATCTCAACAAAGACCTAAGGAAAAAG                         CTGCAAGAAACAAGTCCGCAGAATGTGATCCACGACGTCTCCTGGGAGGAA
genomic: GAACAAGAGTTGCAGGATCTCAACAAAGACCTAAGGAAAAAGgtaactaaaa ... gtgctgccagCTGCAAGAAACAAGTCCGCAGAATGTGATCCACGACGTCTCCTGGGAGGAA
EST: gi|32845819|gb|CD985500.1|CD985500
EST:     GAACAAGAGTTGCAGGATCTCAACAAAGACCTAAGGAAAAAG                         CTGCAAGAAACAAGTCCGCAGAATGTGATCCACGACGTCTCCTGGGAGGAA
genomic: GAACAAGAGTTGCAGGATCTCAACAAAGACCTAAGGAAAAAGgtaactaaaa ... gtgctgccagCTGCAAGAAACAAGTCCGCAGAATGTGATCCACGACGTCTCCTGGGAGGAA
EST: gi|16917809|gb|BM073443.1|BM073443
EST:     GAACAAGAGTTGCAGGATCTCAACAAAGACCTAAGGAAAAAG                         CTGCAAGAAACAAGTCCGCAGAATGTGATCCACGACGTCTCCTGGGAGGAA
genomic: GAACAAGAGTTGCAGGATCTCAACAAAGACCTAAGGAAAAAGgtaactaaaa ... gtgctgccagCTGCAAGAAACAAGTCCGCAGAATGTGATCCACGACGTCTCCTGGGAGGAA
EST: gi|211408737|gb|FL193400.1|FL193400
EST:     GAACAAGAGTTGCAGGATCTCAACAAAGACCTAAGGAAAAAG                         CTGCAAGAAACAAGTCCGCAGAATGTGATCCACGACGTCTCCTGGGAGGAA
genomic: GAACAAGAGTTGCAGGATCTCAACAAAGACCTAAGGAAAAAGgtaactaaaa ... gtgctgccagCTGCAAGAAACAAGTCCGCAGAATGTGATCCACGACGTCTCCTGGGAGGAA
EST: gi|32824768|gb|CD964490.1|CD964490
EST:     GATCTCAACAAAGACCTAAGGAAAAAG                         CTGCAAGAAACAAGTCTGCAGAATGTGATCCACGACGTCTCCTGGGAGAAA
genomic: GATCTCAACAAAGACCTAAGGAAAAAGgtaactaaaa ... gtgctgccagCTGCAAGAAACAAGTCCGCAGAATGTGATCCACGACGTCTCCTGGGAGGAA
EST: gi|32866292|gb|CF005974.1|CF005974
EST:     GAACAAGAGTTGCAGGATCTCAACAAAGACCTAAGGAAAAAG                         CTGCAAGAAACAAGTCCGCAGAATGTGATCCACGACGTCTCCTGGGAGGAA
genomic: GAACAAGAGTTGCAGGATCTCAACAAAGACCTAAGGAAAAAGgtaactaaaa ... gtgctgccagCTGCAAGAAACAAGTCCGCAGAATGTGATCCACGACGTCTCCTGGGAGGAA
EST: gi|32847872|gb|CD987553.1|CD987553
EST:     GAACAAGAGTTGCAGGATCTCAACAAAGACCTAAGGAAAAAG                         CTGCAAGAAACAAGTCCGCAGAATGTGATCCACGACGTCTCCTGGGAGGAA
genomic: GAACAAGAGTTGCAGGATCTCAACAAAGACCTAAGGAAAAAGgtaactaaaa ... gtgctgccagCTGCAAGAAACAAGTCCGCAGAATGTGATCCACGACGTCTCCTGGGAGGAA

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 2 RNA-Seq libraries.


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 328

GAACAAGAGTTGCAGGATCTCAACAAAGACCTAAGGAAAAAGgtaactaaaa ... gtgctgccagCTGCAAGAAACAAGTCCGCAGAATGTGATCCACGACGTCTCCTGGGAGGAAGGCGGGCACAGTGGGAGTAGTGTTCTTGGTCCGTTCCAGGGACTCCTTC


Block sizes: 42 (upstream exon), 48 (downstream exon)
Score: 193

GAACAAGAGTTGCAGGATCTCAACAAAGACCTAAGGAAAAAGgtaactaaaa ... gtgctgccagCTGCAAGAAACAAGTCCGCAGAATGTGATCCACGACGTCTCCTGGGAGGAAGGCGGGCACAGTGGGAGTAGTGTTCTTGGTCCGTTCCAGGGACTCCTTC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cccactttgacgtaaacgtactgttccgttactgatttcatgcaagtgctgccagCTGCAAGAAACAAGTCCGCAGAATGTGATCCACGACGTCTCCTGGGAGGAAGGCGGGCACAGTGGGAGTAGTGTTCTTGGTCCGTTCCAGGGACTCCTTC
                             tactgat  putative branch site (score: 193)
                                  atttcat  TA-rich tract