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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgccatgccttcttctgcccgactttgcgcactcgctctgcgcctctccctcatctgtttgagatctgaaattacgcgagctgcagGAGGGCGAGCTTGAAGAGCTCGAGAAGGGCATCGAGCCCACGTGGGCGAAGCTGGTCGAGCCGCTAGAACGCATCACCGACAGGCTCGAGGTGATCTGGG

Basic information

species Zea mays
transcript GRMZM2G133919_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G133919_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g58340.1 (Oryza sativa), 3'ss of exon 1
gtacgccatgccttcttctgccc-gactttgcgcactcgctctgcgcctctccctcatctgtttgagatctgaaattac---gcgagctgcagGAGGGCGAGCTTGAAGAGCTCGAGAAGGGCATCGAGCCCACGTGGGCGAAGCTGGTCGAGCCGCTAGAACGCATCACCGACAGGCTCGAGGTGATCTGGG
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gtacgtc---ccctgccctgccctggatccaccagcttccttcccgcaaatttaatttccgatct-gacccgacccttccttgttgcatgcagGAGGGCGAGCTCACCGACCTCGAGAAGGGCGTGCAGCCCACCTGGGGGAAGCTGGTCGAGCCGCTCGAGCGGATCGTCGACAGCCTCGAGGTCGTCTGGG
















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|211451544|gb|FL256607.1|FL256607
EST:     TCGAGCCCAGCCACGTCCGCCCCGGCATCCACGAACTGCTAACACGACTC                         GAGGGCGAGCTTGAAGAGCTCGAGAAGGGCATCGAGCCCACGTGGGCGAAG
genomic: TCGAGCCCAGCCACGTCCGCCCCGGCATCCACGAACTGCTAACACGACTCgtacgccatg ... cgagctgcagGAGGGCGAGCTTGAAGAGCTCGAGAAGGGCATCGAGCCCACGTGGGCGAAG
EST: gi|149009256|gb|EE041351.2|EE041351
EST:     TCGAGCCCAGCCACGTCCGCCCCGGCATCCACGAACTGCTAACACGACTC                         GAGGGCGAGCTTGAAGAGCTCGAGAAGGGCATCGAGCCCACGTGGGCGAAG
genomic: TCGAGCCCAGCCACGTCCGCCCCGGCATCCACGAACTGCTAACACGACTCgtacgccatg ... cgagctgcagGAGGGCGAGCTTGAAGAGCTCGAGAAGGGCATCGAGCCCACGTGGGCGAAG
EST: gi|74240585|gb|DT648499.1|DT648499
EST:     TCGAGCCCAGCCACGTCCGCCCCGGCATCCACGAACTGCTAACACGACTC                         GAGGGCGAGCTTGAAGAGCTCGAGAAGGGCATCGAGCCCACGTGGGCGAAG
genomic: TCGAGCCCAGCCACGTCCGCCCCGGCATCCACGAACTGCTAACACGACTCgtacgccatg ... cgagctgcagGAGGGCGAGCTTGAAGAGCTCGAGAAGGGCATCGAGCCCACGTGGGCGAAG
EST: gi|211451543|gb|FL256606.1|FL256606
EST:     TCGAGCCCAGCCACGTCCGCCCCGGCATCCACGAACTGCTAACACGACTC                         GAGGGCGAGCTTGAAGAGCTCGAGAAGGGCATCTAGCCCACGTGGGCGAAG
genomic: TCGAGCCCAGCCACGTCCGCCCCGGCATCCACGAACTGCTAACACGACTCgtacgccatg ... cgagctgcagGAGGGCGAGCTTGAAGAGCTCGAGAAGGGCATCGAGCCCACGTGGGCGAAG
EST: gi|148950560|gb|EC896140.2|EC896140
EST:     TCGAGCCCAGCCACGTCCGCCCCGGCATCCACGAACTGCTAACACGACTC                         GAGGGCGAGCTTGAAGAGCTCGAGAAGGGCATCGAGCCCACGTGGGCGAAG
genomic: TCGAGCCCAGCCACGTCCGCCCCGGCATCCACGAACTGCTAACACGACTCgtacgccatg ... cgagctgcagGAGGGCGAGCTTGAAGAGCTCGAGAAGGGCATCGAGCCCACGTGGGCGAAG
EST: gi|211453674|gb|FL256610.1|FL256610
EST:     TCGAGCCCAGCCACGTCCGCCCCGGCATCCACGAACTGCTAACACGACTC                         GAGGGCGAGCTTGAAGAGCTCGAGAAGGGCATCTAGCCCACGTGGGCGAAG
genomic: TCGAGCCCAGCCACGTCCGCCCCGGCATCCACGAACTGCTAACACGACTCgtacgccatg ... cgagctgcagGAGGGCGAGCTTGAAGAGCTCGAGAAGGGCATCGAGCCCACGTGGGCGAAG
EST: gi|148960061|gb|EE153304.2|EE153304
EST:     TCGAGCCCAGCCACGTCCGCCCCGGCATCCACGAACTGCTAACACGACTC                         GAGGGCGAGCTTGAAGAGCTCGAGAAGGGCATCGAGCCCACGTGGGCGAAG
genomic: TCGAGCCCAGCCACGTCCGCCCCGGCATCCACGAACTGCTAACACGACTCgtacgccatg ... cgagctgcagGAGGGCGAGCTTGAAGAGCTCGAGAAGGGCATCGAGCCCACGTGGGCGAAG
EST: gi|149072691|gb|EE160926.2|EE160926
EST:     TCGAGCCCAGCCACGTCCGCCCCGGCATCCACGAACTGCTAACACGACTC                         GAGGGCGAGCTTGAAGAGCTCGAGAAGGGCATCGAGCCCACGTGGGCGAAG
genomic: TCGAGCCCAGCCACGTCCGCCCCGGCATCCACGAACTGCTAACACGACTCgtacgccatg ... cgagctgcagGAGGGCGAGCTTGAAGAGCTCGAGAAGGGCATCGAGCCCACGTGGGCGAAG
EST: gi|76020481|gb|DT947651.1|DT947651
EST:     TCGAGCCCAGCCACGTCCGCCCCGGCATCCACGAACTGCTAACACGACTC                         GAGGGCGAGCTTGAAGAGCTCGAGAAGGGCATCGAGCCCACGTGGGCGAAG
genomic: TCGAGCCCAGCCACGTCCGCCCCGGCATCCACGAACTGCTAACACGACTCgtacgccatg ... cgagctgcagGAGGGCGAGCTTGAAGAGCTCGAGAAGGGCATCGAGCCCACGTGGGCGAAG
EST: gi|211451546|gb|FL256609.1|FL256609
EST:     TCGAGCCCAGCCACGTCCGCCCCGGCATCCACGAACTGCTAACACGACTC                         GAGGGCGAGCTTGAAGAGCTCGAGAAGGGCATCTAGCCCACGTGGGCGAAG
genomic: TCGAGCCCAGCCACGTCCGCCCCGGCATCCACGAACTGCTAACACGACTCgtacgccatg ... cgagctgcagGAGGGCGAGCTTGAAGAGCTCGAGAAGGGCATCGAGCCCACGTGGGCGAAG
EST: gi|71437686|gb|DR818736.1|DR818736
EST:     TCGAGCCCAGCCACGTCCGCCCCGGCATCCACGAACTGCTAACACGACTC                         GAGGGCGAGCTTGAAGAGCTCGAGAAGGGCATCGAGCCCACGTGGGCGAAG
genomic: TCGAGCCCAGCCACGTCCGCCCCGGCATCCACGAACTGCTAACACGACTCgtacgccatg ... cgagctgcagGAGGGCGAGCTTGAAGAGCTCGAGAAGGGCATCGAGCCCACGTGGGCGAAG
EST: gi|148956895|gb|EC902819.2|EC902819
EST:     TCGAGCCCAGCCACGTCCGCCCCGGCATCCACGAACTGCTAACACGACTC                         GAGGGCGAGCTTGAAGAGCTCGAGAAGGGCATCGAGCCCACGTGGGCGAAG
genomic: TCGAGCCCAGCCACGTCCGCCCCGGCATCCACGAACTGCTAACACGACTCgtacgccatg ... cgagctgcagGAGGGCGAGCTTGAAGAGCTCGAGAAGGGCATCGAGCCCACGTGGGCGAAG
EST: gi|31354902|gb|CD439259.1|CD439259
EST:     ACGAGCCCAGCCACGTCCGCCCCGGCATCCACGAACTGCTAACACGACTC                         GAGGGCGAGCTTGAAGAGCTCGAGAAGGGCATCGAGCCCACGTGGGCGAAG
genomic: TCGAGCCCAGCCACGTCCGCCCCGGCATCCACGAACTGCTAACACGACTCgtacgccatg ... cgagctgcagGAGGGCGAGCTTGAAGAGCTCGAGAAGGGCATCGAGCCCACGTGGGCGAAG
EST: gi|148983362|gb|EE029348.2|EE029348
EST:     TCGAGCCCAGCCACGTCCGCCCCGGCATCCACGAACTGCTAACACGACTC                         GAGGGCGAGCTTGAAGAGCTCGAGAAGGGCATCGAGCCCACGTGGGCGAAG
genomic: TCGAGCCCAGCCACGTCCGCCCCGGCATCCACGAACTGCTAACACGACTCgtacgccatg ... cgagctgcagGAGGGCGAGCTTGAAGAGCTCGAGAAGGGCATCGAGCCCACGTGGGCGAAG
EST: gi|149075398|gb|EE163912.2|EE163912
EST:     TCGAGCCCAGCCACGTCCGCCCCGGCATCCACGAACTGCTAACACGACTC                         GAGGGCGAGCTTGAAGAGCTCGAGAAGGGCATCGAGCCCACGTGGGCGAAG
genomic: TCGAGCCCAGCCACGTCCGCCCCGGCATCCACGAACTGCTAACACGACTCgtacgccatg ... cgagctgcagGAGGGCGAGCTTGAAGAGCTCGAGAAGGGCATCGAGCCCACGTGGGCGAAG

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: 200

CGACAACCCCCTCCTCGTCGCCGACTTCGACTTCCCGCCCTTCGACCGCGTCGAGCCCAGCCACGTCCGCCCCGGCATCCACGAACTGCTAACACGACTCgtacgccatg ... cgagctgcagGAGGGCGAGCTTGAAGAGCTCGAGAAGGGCATCGAGCCCACGTGGGCGAAGCTGGTCGAGCCGCTAGAACGCATCACCGACAGGCTCGAGGTGATCTGGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 213

CGACAACCCCCTCCTCGTCGCCGACTTCGACTTCCCGCCCTTCGACCGCGTCGAGCCCAGCCACGTCCGCCCCGGCATCCACGAACTGCTAACACGACTCgtacgccatg ... cgagctgcagGAGGGCGAGCTTGAAGAGCTCGAGAAGGGCATCGAGCCCACGTGGGCGAAGCTGGTCGAGCCGCTAGAACGCATCACCGACAGGCTCGAGGTGATCTGGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 212

CGACAACCCCCTCCTCGTCGCCGACTTCGACTTCCCGCCCTTCGACCGCGTCGAGCCCAGCCACGTCCGCCCCGGCATCCACGAACTGCTAACACGACTCgtacgccatg ... cgagctgcagGAGGGCGAGCTTGAAGAGCTCGAGAAGGGCATCGAGCCCACGTGGGCGAAGCTGGTCGAGCCGCTAGAACGCATCACCGACAGGCTCGAGGTGATCTGGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 175

CGACAACCCCCTCCTCGTCGCCGACTTCGACTTCCCGCCCTTCGACCGCGTCGAGCCCAGCCACGTCCGCCCCGGCATCCACGAACTGCTAACACGACTCgtacgccatg ... cgagctgcagGAGGGCGAGCTTGAAGAGCTCGAGAAGGGCATCGAGCCCACGTGGGCGAAGCTGGTCGAGCCGCTAGAACGCATCACCGACAGGCTCGAGGTGATCTGGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcgctctgcgcctctccctcatctgtttgagatctgaaattacgcgagctgcagGAGGGCGAGCTTGAAGAGCTCGAGAAGGGCATCGAGCCCACGTGGGCGAAGCTGGTCGAGCCGCTAGAACGCATCACCGACAGGCTCGAGGTGATCTGGG
                                   tgaaatta  TA-rich tract