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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCATCCGTCCACTATTCAACTACCGAACTACGACCAACTGGTCACATCTGCTATCACTTGGAATAACCCACATGATGGGAACACTTACATGAAAATAAAGgtgatctctttctcttacttaggaccttagctctgcgaataaaaatgaaaaaaaaaacttggctaagaaaatttcttttgcag

Basic information

species Zea mays
transcript GRMZM2G180889_T01
intron # 4
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|32840433|gb|CD980114.1|CD980114
EST:     CTATCACTTGGAATAACCCACATGATGGGAACACTTACATGAAAATAAAG                         GGTGTAAATTTTGGAAGCAAAGCTGGTAGTCTGAATATATCTGTAACTGGG
genomic: CTATCACTTGGAATAACCCACATGATGGGAACACTTACATGAAAATAAAGgtgatctctt ... tcttttgcagGTTGTAAATTTTGGAAGCAAAGCTGTTAGTCTGAATATATCTGTAACTGGG
EST: gi|211495745|gb|FL475524.1|FL475524
EST:     CTATCACTTGGAATAACCCACATGATGGGAACACTTACATGAAAATAAAG                         GTTGTAAATTTTGGAAGCAAAGCTGTTAGTCTGAATATATCTGTAACTGGG
genomic: CTATCACTTGGAATAACCCACATGATGGGAACACTTACATGAAAATAAAGgtgatctctt ... tcttttgcagGTTGTAAATTTTGGAAGCAAAGCTGTTAGTCTGAATATATCTGTAACTGGG
EST: gi|40335824|gb|CK369894.1|CK369894
EST:     GAACACTTACATGAAAATAAAG                         GTTGTAAATTTTGGAAGCAAAGCTGTTAGTCTGAATATATCTGTAACTGGG
genomic: GAACACTTACATGAAAATAAAGgtgatctctt ... tcttttgcagGTTGTAAATTTTGGAAGCAAAGCTGTTAGTCTGAATATATCTGTAACTGGG
EST: gi|32841988|gb|CD981669.1|CD981669
EST:     CTATCACTTGGAATAACCCACATGATGGGAACACTTACATGAAAATAAAG                         GTTGTAAATTTTGGAAGCAAAGCTGTTAGTCTGAATATATCTGTAACTGGG
genomic: CTATCACTTGGAATAACCCACATGATGGGAACACTTACATGAAAATAAAGgtgatctctt ... tcttttgcagGTTGTAAATTTTGGAAGCAAAGCTGTTAGTCTGAATATATCTGTAACTGGG
EST: gi|26558128|gb|CA830363.1|CA830363
EST:     CTATCACTTGGAATAACCCACATGATGGGAACACTTACATGAAAATAAAG                         GTTGTAAATTTTGGAAGCAAAGCTGTTAGTCTGAATATATCTGTAACTGGG
genomic: CTATCACTTGGAATAACCCACATGATGGGAACACTTACATGAAAATAAAGgtgatctctt ... tcttttgcagGTTGTAAATTTTGGAAGCAAAGCTGTTAGTCTGAATATATCTGTAACTGGG
EST: gi|37387566|gb|CF630980.1|CF630980
EST:     CTATCACTTGGAATAACCCACATGATGGGAACACTTACATGAAAATAAAG                         GTTGTAAATTTTGGAAGCAAAGCTGTTAGTCTGAATATATCGGTAACTGGG
genomic: CTATCACTTGGAATAACCCACATGATGGGAACACTTACATGAAAATAAAGgtgatctctt ... tcttttgcagGTTGTAAATTTTGGAAGCAAAGCTGTTAGTCTGAATATATCTGTAACTGGG
EST: gi|211495744|gb|FL475523.1|FL475523
EST:     ACCCACATGATGGGAACACTTACATGAAAATAAAG                         GTTGTAAATTTTGGAAGCAAAGCTGTTAGTCTGAATATATCTGTAACTGGG
genomic: ACCCACATGATGGGAACACTTACATGAAAATAAAGgtgatctctt ... tcttttgcagGTTGTAAATTTTGGAAGCAAAGCTGTTAGTCTGAATATATCTGTAACTGGG
EST: gi|21987659|gb|BQ779187.1|BQ779187
EST:     CTATCACTTGGAATAACCCACATGATGGGAACACTTACATGAAAATAAAG                         GTTGTAAATTTTGGAAGCAAAGCTGTTAGTCTGAATATATCTGTAACTGGG
genomic: CTATCACTTGGAATAACCCACATGATGGGAACACTTACATGAAAATAAAGgtgatctctt ... tcttttgcagGTTGTAAATTTTGGAAGCAAAGCTGTTAGTCTGAATATATCTGTAACTGGG
EST: gi|32842541|gb|CD982222.1|CD982222
EST:     CTATCACTTGGAATAACCCACATGATGGGAACACTTACATGAAAATAAAG                         GTTGTAAATTTTGGAAGCAAAGCTGGTAGTCTGAATATATCTGTAACTGGG
genomic: CTATCACTTGGAATAACCCACATGATGGGAACACTTACATGAAAATAAAGgtgatctctt ... tcttttgcagGTTGTAAATTTTGGAAGCAAAGCTGTTAGTCTGAATATATCTGTAACTGGG
EST: gi|87155463|gb|DY400252.1|DY400252
EST:     TTATCACTTGGAATAACCCACATGATGGGAACACTTACATGAAAATAAAG                         GTTGTAAATTTTGGAAGCAAAGCTGTTAGTCTGAATATATCTGTAACTGGG
genomic: CTATCACTTGGAATAACCCACATGATGGGAACACTTACATGAAAATAAAGgtgatctctt ... tcttttgcagGTTGTAAATTTTGGAAGCAAAGCTGTTAGTCTGAATATATCTGTAACTGGG
EST: gi|32842248|gb|CD981929.1|CD981929
EST:     CTATCACTTGGAATAACCCACATGATGGGAACACTTACATGAAAATAAAG                         GTTGTAAATTTTGGAAGCAAAGCTGTTAGTCTGAATATATCTGTAACTGGG
genomic: CTATCACTTGGAATAACCCACATGATGGGAACACTTACATGAAAATAAAGgtgatctctt ... tcttttgcagGTTGTAAATTTTGGAAGCAAAGCTGTTAGTCTGAATATATCTGTAACTGGG
EST: gi|32842540|gb|CD982221.1|CD982221
EST:     CTATCACTTGGAATAACCCACATGATGGGAACACTTACATGAAAATAAAG                         GTTGTAAATTTTGGAAGCAAAGCTGTTAGTCTGAATATATCTGTACCTGGG
genomic: CTATCACTTGGAATAACCCACATGATGGGAACACTTACATGAAAATAAAGgtgatctctt ... tcttttgcagGTTGTAAATTTTGGAAGCAAAGCTGTTAGTCTGAATATATCTGTAACTGGG
EST: gi|32842247|gb|CD981928.1|CD981928
EST:     CTATCACTTGGAATAACCCACATGATGGGAACACTTACATGAAAATAAAG                         GTTGTAAATTTTGGAAGCAAAGCTGTTAGTCTGAATATATCTGTAACTGGG
genomic: CTATCACTTGGAATAACCCACATGATGGGAACACTTACATGAAAATAAAGgtgatctctt ... tcttttgcagGTTGTAAATTTTGGAAGCAAAGCTGTTAGTCTGAATATATCTGTAACTGGG
EST: gi|32841989|gb|CD981670.1|CD981670
EST:     CTATCACTTGGAATAACCCACATGATGGGAACACTTACATGAAAATAAAG                         GTTGTAAATTTTGGAAGCAAAGCTGTTAGTCTGAATATATCTGTAACTGGG
genomic: CTATCACTTGGAATAACCCACATGATGGGAACACTTACATGAAAATAAAGgtgatctctt ... tcttttgcagGTTGTAAATTTTGGAAGCAAAGCTGTTAGTCTGAATATATCTGTAACTGGG

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: 34

TCATCCGTCCACTATTCAACTACCGAACTACGACCAACTGGTCACATCTGCTATCACTTGGAATAACCCACATGATGGGAACACTTACATGAAAATAAAGgtgatctctt ... tcttttgcagGTTGTAAATTTTGGAAGCAAAGCTGTTAGTCTGAATATATCTGTAACTGGGTTGGAAACTGATATTCAGACATTTGGATCCATAAAGACGGTTCTCACGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 664

TCATCCGTCCACTATTCAACTACCGAACTACGACCAACTGGTCACATCTGCTATCACTTGGAATAACCCACATGATGGGAACACTTACATGAAAATAAAGgtgatctctt ... tcttttgcagGTTGTAAATTTTGGAAGCAAAGCTGTTAGTCTGAATATATCTGTAACTGGGTTGGAAACTGATATTCAGACATTTGGATCCATAAAGACGGTTCTCACGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 400

TCATCCGTCCACTATTCAACTACCGAACTACGACCAACTGGTCACATCTGCTATCACTTGGAATAACCCACATGATGGGAACACTTACATGAAAATAAAGgtgatctctt ... tcttttgcagGTTGTAAATTTTGGAAGCAAAGCTGTTAGTCTGAATATATCTGTAACTGGGTTGGAAACTGATATTCAGACATTTGGATCCATAAAGACGGTTCTCACGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 336

TCATCCGTCCACTATTCAACTACCGAACTACGACCAACTGGTCACATCTGCTATCACTTGGAATAACCCACATGATGGGAACACTTACATGAAAATAAAGgtgatctctt ... tcttttgcagGTTGTAAATTTTGGAAGCAAAGCTGTTAGTCTGAATATATCTGTAACTGGGTTGGAAACTGATATTCAGACATTTGGATCCATAAAGACGGTTCTCACGT