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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaagccgtgtagtgacgcgaagggttgtggcgtgcttccggatttgtgttgtattgattgattggtgttctcccggatttgtgctgttttgattgatgttatggctcgtcaatcggcgtggtgttctggacgtggtttaccatcgtcttttcgtgggcagAGGAAGCCGTAGCTGAGAGCGACTGCAAGGTTTCCAGAATATACGGCGTGGTCGGCACCATAAGATTGCTCGCTG

Basic information

species Zea mays
transcript GRMZM2G047894_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|71428423|gb|DR809473.1|DR809473
EST:     CGCTTTCGCCGTCCTTCGCTCCGGCGGCTCCATCCGCCCTCTCTCCCCAG                         AGGAAGCCGTAGCTGAGAGCGACTGCAAGGTTTCCAGAATATACGGCGTGG
genomic: CGCTTTCGCCGTCCTTCGCTCCGGCGGCTCCATCCGCCCTCTCTCCCCAGgtgaagccgt ... tcgtgggcagAGGAAGCCGTAGCTGAGAGCGACTGCAAGGTTTCCAGAATATACGGCGTGG
EST: gi|211511662|gb|FL408088.1|FL408088
EST:     CGCTTTCGCCGTCCTTCGCTCCGGCGGCTCCATCCGCCCTCTCTCCCCAG                         AGGAAGCCGTAGCTGAGAGCGACTGCAAGGTTTCCAGAATATACGGGGTGG
genomic: CGCTTTCGCCGTCCTTCGCTCCGGCGGCTCCATCCGCCCTCTCTCCCCAGgtgaagccgt ... tcgtgggcagAGGAAGCCGTAGCTGAGAGCGACTGCAAGGTTTCCAGAATATACGGCGTGG
EST: gi|211285033|gb|FK988595.1|FK988595
EST:     CGCTTTCGCCGTCCTTCGCTCCGGCGGCTCCATCCGCCCTCTCTCCCCAG                         AGGAAGCCGTAGCTGAGAGCGACTGCAAGGTTTCCAGAATATACGGCGTGG
genomic: CGCTTTCGCCGTCCTTCGCTCCGGCGGCTCCATCCGCCCTCTCTCCCCAGgtgaagccgt ... tcgtgggcagAGGAAGCCGTAGCTGAGAGCGACTGCAAGGTTTCCAGAATATACGGCGTGG
EST: gi|211199436|gb|FL401716.1|FL401716
EST:     CGCTTTCGCCGTCCTTCGCTCCGGCGGCTCCATCCGCCCTCTCTCCCCAG                         AGGAAGCCGTAGCTGAGAGCGACTGCAAGGTTTCCAGAATATACGGGGTGG
genomic: CGCTTTCGCCGTCCTTCGCTCCGGCGGCTCCATCCGCCCTCTCTCCCCAGgtgaagccgt ... tcgtgggcagAGGAAGCCGTAGCTGAGAGCGACTGCAAGGTTTCCAGAATATACGGCGTGG
EST: gi|211223965|gb|FL409228.1|FL409228
EST:     CGCTTTCGCCGTCCTTCGCTCCGGCGGCTCCATCCGCCCTCTCTCCCCAG                         AGGAAGCCGTAGCTGAGAGCGACTGCAAGGTTTCCAGAATATACGGGGTGG
genomic: CGCTTTCGCCGTCCTTCGCTCCGGCGGCTCCATCCGCCCTCTCTCCCCAGgtgaagccgt ... tcgtgggcagAGGAAGCCGTAGCTGAGAGCGACTGCAAGGTTTCCAGAATATACGGCGTGG
EST: gi|211348875|gb|FL413241.1|FL413241
EST:     CGCTTTCGCCGTCCTTCGCTCCGGCGGCTCCATCCGCCCTCTCTCCCCAG                         AGGAAGCCGTAGCTGAGAGCGACTGCAAGGTTTCCAGAATATACGGGGTGG
genomic: CGCTTTCGCCGTCCTTCGCTCCGGCGGCTCCATCCGCCCTCTCTCCCCAGgtgaagccgt ... tcgtgggcagAGGAAGCCGTAGCTGAGAGCGACTGCAAGGTTTCCAGAATATACGGCGTGG
EST: gi|78086850|gb|DV515243.1|DV515243
EST:     CGCTTTCGCCGTCCTTCGCTCCGGCGGCTCCATCCGCCCTCTCTCCCCAG                         AGGAAGCCGTAGCTGAGAGCGACTGCAAGGTTTCCAGAATATACGGCGTGG
genomic: CGCTTTCGCCGTCCTTCGCTCCGGCGGCTCCATCCGCCCTCTCTCCCCAGgtgaagccgt ... tcgtgggcagAGGAAGCCGTAGCTGAGAGCGACTGCAAGGTTTCCAGAATATACGGCGTGG
EST: gi|211285032|gb|FK988594.1|FK988594
EST:     CGCTTTCGCCGTCCTTCGCTCCGGCGGCTCCATCCGCCCTCTCTCCCCAG                         AGGAAGCCGTAGCTGAGAGCGACTGCAAGGTTTCCAGAATATACGGGGTGG
genomic: CGCTTTCGCCGTCCTTCGCTCCGGCGGCTCCATCCGCCCTCTCTCCCCAGgtgaagccgt ... tcgtgggcagAGGAAGCCGTAGCTGAGAGCGACTGCAAGGTTTCCAGAATATACGGCGTGG
EST: gi|71325385|gb|DR799370.1|DR799370
EST:     CGCTTTCGCCGTCCTTCGCTCCGGCGGCTCCATCCGCCCTCTCTCCCCAG                         AGGAAGCCGTAGCTGAGAGCGACTGCAAGGTTTCCAGAATATACGGCGTGG
genomic: CGCTTTCGCCGTCCTTCGCTCCGGCGGCTCCATCCGCCCTCTCTCCCCAGgtgaagccgt ... tcgtgggcagAGGAAGCCGTAGCTGAGAGCGACTGCAAGGTTTCCAGAATATACGGCGTGG

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: 143

CTGCGGGAGTTCCGCGACCGCTACGTGATCCGTTCGCTCGACGGCGCCGCCGCTTTCGCCGTCCTTCGCTCCGGCGGCTCCATCCGCCCTCTCTCCCCAGgtgaagccgt ... tcgtgggcagAGGAAGCCGTAGCTGAGAGCGACTGCAAGGTTTCCAGAATATACGGCGTGGTCGGCACCATAAGATTGCTCGCTG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 81

CTGCGGGAGTTCCGCGACCGCTACGTGATCCGTTCGCTCGACGGCGCCGCCGCTTTCGCCGTCCTTCGCTCCGGCGGCTCCATCCGCCCTCTCTCCCCAGgtgaagccgt ... tcgtgggcagAGGAAGCCGTAGCTGAGAGCGACTGCAAGGTTTCCAGAATATACGGCGTGGTCGGCACCATAAGATTGCTCGCTG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 143

CTGCGGGAGTTCCGCGACCGCTACGTGATCCGTTCGCTCGACGGCGCCGCCGCTTTCGCCGTCCTTCGCTCCGGCGGCTCCATCCGCCCTCTCTCCCCAGgtgaagccgt ... tcgtgggcagAGGAAGCCGTAGCTGAGAGCGACTGCAAGGTTTCCAGAATATACGGCGTGGTCGGCACCATAAGATTGCTCGCTG


Block sizes: 44 (upstream exon), 46 (downstream exon)
Score: 153

CTGCGGGAGTTCCGCGACCGCTACGTGATCCGTTCGCTCGACGGCGCCGCCGCTTTCGCCGTCCTTCGCTCCGGCGGCTCCATCCGCCCTCTCTCCCCAGgtgaagccgt ... tcgtgggcagAGGAAGCCGTAGCTGAGAGCGACTGCAAGGTTTCCAGAATATACGGCGTGGTCGGCACCATAAGATTGCTCGCTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgtcaatcggcgtggtgttctggacgtggtttaccatcgtcttttcgtgggcagAGGAAGCCGTAGCTGAGAGCGACTGCAAGGTTTCCAGAATATACGGCGTGGTCGGCACCATAAGATTGCTCGCTG
                                     tcgtcttttc  CT-rich tract