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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagccgcgcgcttacatttttctgatacgctctctcttgcgcccgcggcgagtggctaaaactaggggcattcccttcttccgttcgacagACCGGAGGAAGCGTACATTGCGGCGGAGCCCGTTGCCGAGGCCGCTGTCGAAAGTGAAG

Basic information

species Zea mays
transcript GRMZM2G133749_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|37420996|gb|CF648194.1|CF648194
EST:     TCCTCCTTCCTCACCAGCTCCGACGATAACTCCCTCCGCTTGTTTTACTT                         ACCGGAGGAAGCGTACATTGCGGCGGAGCCCGTTGCCGAGGCCGCTGTCGA
genomic: TCCTCCTTCCTCACCAGCTCCGACGATAACTCCCTCCGCTTGTTTTACTTgtaagccgcg ... cgttcgacagACCGGAGGAAGCGTACATTGCGGCGGAGCCCGTTGCCGAGGCCGCTGTCGA
EST: gi|78120250|gb|DV538634.1|DV538634
EST:     TCCTCCTTCCTCACCAGCTCCGACGATAACTCCCTCCGCTTGTTTTACTT                         ACCGGAGGAAGCGTACATTGCGGCGGAGCCCGTTGCCGAGGCCGCTGTCGA
genomic: TCCTCCTTCCTCACCAGCTCCGACGATAACTCCCTCCGCTTGTTTTACTTgtaagccgcg ... cgttcgacagACCGGAGGAAGCGTACATTGCGGCGGAGCCCGTTGCCGAGGCCGCTGTCGA
EST: gi|211122217|gb|FL355462.1|FL355462
EST:     TCCTCCTTCCTCACCAGCTCCGACGATAACTCCCTCCGCTTGTTTTACTT                         ACCGGAGGAAGCGTACATTGCGGCGGAGCCCGTTGCCGAGGCCGCTGTCGA
genomic: TCCTCCTTCCTCACCAGCTCCGACGATAACTCCCTCCGCTTGTTTTACTTgtaagccgcg ... cgttcgacagACCGGAGGAAGCGTACATTGCGGCGGAGCCCGTTGCCGAGGCCGCTGTCGA
EST: gi|71437477|gb|DR818527.1|DR818527
EST:     TCCTCCTTCCTCACCAGCTCCGACGATAACTCCCTCCGCTTGTTTTACTT                         ACCGGAGGAAGCGTACATTGCGGCGGAGCCCGTTGCCGAGGCCGCTGTCGA
genomic: TCCTCCTTCCTCACCAGCTCCGACGATAACTCCCTCCGCTTGTTTTACTTgtaagccgcg ... cgttcgacagACCGGAGGAAGCGTACATTGCGGCGGAGCCCGTTGCCGAGGCCGCTGTCGA
EST: gi|71449230|gb|DR830280.1|DR830280
EST:     TCCTCCTTCCTCACCAGCTCCGACGATAACTCCCTCCGCTTGTTTTACTT                         ACCGGAGGAAGCGTACATTGCGGCGGAGCCCGTTGCCGAGGCCGCTGTCGA
genomic: TCCTCCTTCCTCACCAGCTCCGACGATAACTCCCTCCGCTTGTTTTACTTgtaagccgcg ... cgttcgacagACCGGAGGAAGCGTACATTGCGGCGGAGCCCGTTGCCGAGGCCGCTGTCGA
EST: gi|31558468|gb|CD527680.1|CD527680
EST:     TCCTCCTTCCTCACCAGCTCCGACGATAACTCCCTCCGCTTGTTTTACTT                         ACCGGAGGAAGCGTACATTGCGGCGGAGCCCGTTGCCGAGGCCGCTGTCGA
genomic: TCCTCCTTCCTCACCAGCTCCGACGATAACTCCCTCCGCTTGTTTTACTTgtaagccgcg ... cgttcgacagACCGGAGGAAGCGTACATTGCGGCGGAGCCCGTTGCCGAGGCCGCTGTCGA
EST: gi|76287082|gb|DV026650.1|DV026650
EST:     TCCTCCTTCCTCACCAGCTCCGACGATAACTCCCTCCGCTTGTTTTACTT                         ACCGGAGGAAGCGTACATTGCGGCGGAGCCCGTTGCCGAGGCCGCTGTCGA
genomic: TCCTCCTTCCTCACCAGCTCCGACGATAACTCCCTCCGCTTGTTTTACTTgtaagccgcg ... cgttcgacagACCGGAGGAAGCGTACATTGCGGCGGAGCCCGTTGCCGAGGCCGCTGTCGA
EST: gi|86475107|gb|DY241477.1|DY241477
EST:     TCCTCCTTCCTCACCAGCTCCGAAGATAACTCCCTCCGCTTGTTTTACTT                         ACCGGAGGAAGCGTACATTGCGGCGGAGCCCGTTGCCGAGGCCGCTGTCAA
genomic: TCCTCCTTCCTCACCAGCTCCGACGATAACTCCCTCCGCTTGTTTTACTTgtaagccgcg ... cgttcgacagACCGGAGGAAGCGTACATTGCGGCGGAGCCCGTTGCCGAGGCCGCTGTCGA
EST: gi|60394554|gb|DN227424.1|DN227424
EST:     TCCTCCTTCCTCACCAGCTCCGACGATAACTCCCTCCGCTTGTTTTACTT                         ACCGGAGGAAGCGTACATTGCGGCGGAGCCCGTTGCCGAGGCCGCTGTCGA
genomic: TCCTCCTTCCTCACCAGCTCCGACGATAACTCCCTCCGCTTGTTTTACTTgtaagccgcg ... cgttcgacagACCGGAGGAAGCGTACATTGCGGCGGAGCCCGTTGCCGAGGCCGCTGTCGA
EST: gi|211186698|gb|FL366147.1|FL366147
EST:     TCCTCCTTCCTCACCAGCTCCGACGATAACTCCCTCCGCTTGTTTTACTT                         ACCGGAGGAAGCGTACATTGCGGCGGAGCC-GTTGCCGAGGC-GCTGTCGA
genomic: TCCTCCTTCCTCACCAGCTCCGACGATAACTCCCTCCGCTTGTTTTACTTgtaagccgcg ... cgttcgacagACCGGAGGAAGCGTACATTGCGGCGGAGCCCGTTGCCGAGGCCGCTGTCGA
EST: gi|211132517|gb|FL346748.1|FL346748
EST:     TCCTCCTTCCTCACCAGCTCCGACGATAACTCCCTCCGCTTGTTTTACTT                         ACCGGAAGGAAGCGTACATTGCGGCGGAGCCCGTTGCCGAGGCCGCTGTCG
genomic: TCCTCCTTCCTCACCAGCTCCGACGATAACTCCCTCCGCTTGTTTTACTTgtaagccgcg ... cgttcgacagACCGGA-GGAAGCGTACATTGCGGCGGAGCCCGTTGCCGAGGCCGCTGTCG
EST: gi|78084101|gb|DV512494.1|DV512494
EST:     TCCTCCTTCCTCACCAGCTCCGACGATAACTCCCTCCGCTTGTTTTACTT                         ACCGGAGGAAGCGTACATTGCGGCGGAGCCCGTTGCCGAGGCCGCTGTCGA
genomic: TCCTCCTTCCTCACCAGCTCCGACGATAACTCCCTCCGCTTGTTTTACTTgtaagccgcg ... cgttcgacagACCGGAGGAAGCGTACATTGCGGCGGAGCCCGTTGCCGAGGCCGCTGTCGA
EST: gi|94478312|gb|EB707270.1|EB707270
EST:     TCCTCCTTCCTCACCAGCTCCGACGATAACTCCCTCCGCTTGTTTTACTT                         ACCGGAGGAAGCGTACATTGCGGCGGAGCCCGTTGCCGAGGCCGCTGTCGA
genomic: TCCTCCTTCCTCACCAGCTCCGACGATAACTCCCTCCGCTTGTTTTACTTgtaagccgcg ... cgttcgacagACCGGAGGAAGCGTACATTGCGGCGGAGCCCGTTGCCGAGGCCGCTGTCGA
EST: gi|211083828|gb|FL344180.1|FL344180
EST:     TCCTCCTTCCTCACCAGCTCCGACGATAACTCCCTCCGCTTGTTTTACTT                         ACCGGAGGAAGCGTACATTGCGGCGGAGCCCGTTGCCGAGGCCGCTGTCAG
genomic: TCCTCCTTCCTCACCAGCTCCGACGATAACTCCCTCCGCTTGTTTTACTTgtaagccgcg ... cgttcgacagACCGGAGGAAGCGTACATTGCGGCGGAGCCCGTTGCCGAGGCCGCTGTC-G
EST: gi|78112774|gb|DV531168.1|DV531168
EST:     TCCTCCTTCCTCACCAGCTCCGACGATAACTCCCTCCGCTTGTTTTACTT                         ACCGGAGGAAGCGTACATTGCGGCGGAGCCCGTTGCCGAGGCCGCTGTCGA
genomic: TCCTCCTTCCTCACCAGCTCCGACGATAACTCCCTCCGCTTGTTTTACTTgtaagccgcg ... cgttcgacagACCGGAGGAAGCGTACATTGCGGCGGAGCCCGTTGCCGAGGCCGCTGTCGA

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), 41 (downstream exon)
Score: 28

ATAGTAGCGGCGAGAACTTCCTCAAGGGCGTAAAGTGGTCGCCCGACGGGTCCTCCTTCCTCACCAGCTCCGACGATAACTCCCTCCGCTTGTTTTACTTgtaagccgcg ... cgttcgacagACCGGAGGAAGCGTACATTGCGGCGGAGCCCGTTGCCGAGGCCGCTGTCGAAAGTGAAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 17

ATAGTAGCGGCGAGAACTTCCTCAAGGGCGTAAAGTGGTCGCCCGACGGGTCCTCCTTCCTCACCAGCTCCGACGATAACTCCCTCCGCTTGTTTTACTTgtaagccgcg ... cgttcgacagACCGGAGGAAGCGTACATTGCGGCGGAGCCCGTTGCCGAGGCCGCTGTCGAAAGTGAAG


Block sizes: 42 (upstream exon), 47 (downstream exon)
Score: 12

ATAGTAGCGGCGAGAACTTCCTCAAGGGCGTAAAGTGGTCGCCCGACGGGTCCTCCTTCCTCACCAGCTCCGACGATAACTCCCTCCGCTTGTTTTACTTgtaagccgcg ... cgttcgacagACCGGAGGAAGCGTACATTGCGGCGGAGCCCGTTGCCGAGGCCGCTGTCGAAAGTGAAG


Block sizes: 46 (upstream exon), 38 (downstream exon)
Score: 8

ATAGTAGCGGCGAGAACTTCCTCAAGGGCGTAAAGTGGTCGCCCGACGGGTCCTCCTTCCTCACCAGCTCCGACGATAACTCCCTCCGCTTGTTTTACTTgtaagccgcg ... cgttcgacagACCGGAGGAAGCGTACATTGCGGCGGAGCCCGTTGCCGAGGCCGCTGTCGAAAGTGAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcgcccgcggcgagtggctaaaactaggggcattcccttcttccgttcgacagACCGGAGGAAGCGTACATTGCGGCGGAGCCCGTTGCCGAGGCCGCTGTCGAAAGTGAAG
                 ggctaaa  putative branch site (score: 8)
                                cattcccttcttccgt  putative PPT
                    taaaacta  TA-rich tract