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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgggtgatgaattgctttctttcatatgttcatattccttcttcctttatgatcaattagtgaatttgatgcatttttattgttttgcagACCCAGCCACTTGTGTATTTGCAAGCACCAGTCGTGATCATCCGATACACCTTTGGGATGCCACCAGTGGGGAA

Basic information

species Zea mays
transcript GRMZM2G133749_T02
intron # 3
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:     GGGTGAGCCAGTGTACGATTTCTGCTGGTACCCGTGTATGTCCTTGTCTG                         ACCCAGCCACTTGTGTATTTGCAAGCACCAGTCGTGATCATCCGATACACC
genomic: GGGTGAGCCAGTGTACGATTTCTGCTGGTACCCGTGTATGTCCTTGTCTGgtgggtgatg ... tgttttgcagACCCAGCCACTTGTGTATTTGCAAGCACCAGTCGTGATCATCCGATACACC
EST: gi|78120250|gb|DV538634.1|DV538634
EST:     GGGTGAGCCAGTGTACGATTTCTGCTGGTACCCGTGTATGTCCTTGTCTG                         ACCCAGCCACTTGTGTATTTGCAAGCACCAGTCGTGATCATCCGATACACC
genomic: GGGTGAGCCAGTGTACGATTTCTGCTGGTACCCGTGTATGTCCTTGTCTGgtgggtgatg ... tgttttgcagACCCAGCCACTTGTGTATTTGCAAGCACCAGTCGTGATCATCCGATACACC
EST: gi|211122217|gb|FL355462.1|FL355462
EST:     GGGTGAGCCAGTGTACGATTTCTGCTGGTACCCGTGTATGTCCTTGTCTG                         ACCCAGCCACTTGTGTATTTGCAAGCACCAGTCGTGATCATCCGATACACC
genomic: GGGTGAGCCAGTGTACGATTTCTGCTGGTACCCGTGTATGTCCTTGTCTGgtgggtgatg ... tgttttgcagACCCAGCCACTTGTGTATTTGCAAGCACCAGTCGTGATCATCCGATACACC
EST: gi|78110507|gb|DV528917.1|DV528917
EST:     GGGTGAGCCAGTGTACGATTTCTGCTGGTACCCGTGTATGTCCTTGTCTG                         ACCCAGCCACTTGTGTATTTGCAAGCACCAGTCGTGATCATCCGATACACC
genomic: GGGTGAGCCAGTGTACGATTTCTGCTGGTACCCGTGTATGTCCTTGTCTGgtgggtgatg ... tgttttgcagACCCAGCCACTTGTGTATTTGCAAGCACCAGTCGTGATCATCCGATACACC
EST: gi|71437477|gb|DR818527.1|DR818527
EST:     GGGTGAGCCAGTGTACGATTTCTGCTGGTACCCGTGTATGTCCTTGTCTG                         ACCCAGCCACTTGTGTATTTGCAAGCACCAGTCGTGATCATCCGATACACC
genomic: GGGTGAGCCAGTGTACGATTTCTGCTGGTACCCGTGTATGTCCTTGTCTGgtgggtgatg ... tgttttgcagACCCAGCCACTTGTGTATTTGCAAGCACCAGTCGTGATCATCCGATACACC
EST: gi|71449230|gb|DR830280.1|DR830280
EST:     GGGTGAGCCAGTGTACGATTTCTGCTGGTACCCGTGTATGTCCTTGTCTG                         ACCCAGCCACTTGTGTATTTGCAAGCACCAGTCGTGATCATCCGATACACC
genomic: GGGTGAGCCAGTGTACGATTTCTGCTGGTACCCGTGTATGTCCTTGTCTGgtgggtgatg ... tgttttgcagACCCAGCCACTTGTGTATTTGCAAGCACCAGTCGTGATCATCCGATACACC
EST: gi|31558468|gb|CD527680.1|CD527680
EST:     GGGTGAGCCAGTGTACGATTTCTGCTGGTACCCGTGTATGTCCTTGTCTG                         ACCCAGCCACTTGTGTATTTGCAAGCACCAGTCGTGATCATCCGATACACC
genomic: GGGTGAGCCAGTGTACGATTTCTGCTGGTACCCGTGTATGTCCTTGTCTGgtgggtgatg ... tgttttgcagACCCAGCCACTTGTGTATTTGCAAGCACCAGTCGTGATCATCCGATACACC
EST: gi|76287082|gb|DV026650.1|DV026650
EST:     GGGTGAGCCAGTGTACGATTTCTGCTGGTACCCGTGTATGTCCTTGTCTG                         ACCCAGCCACTTGTGTATTTGCAAGCACCAGTCGTGATCATCCGATACACC
genomic: GGGTGAGCCAGTGTACGATTTCTGCTGGTACCCGTGTATGTCCTTGTCTGgtgggtgatg ... tgttttgcagACCCAGCCACTTGTGTATTTGCAAGCACCAGTCGTGATCATCCGATACACC
EST: gi|86475107|gb|DY241477.1|DY241477
EST:     GGGTGAGCCAGTGTACGATTTCTGCTGGTACCCGTGTATGTCCTTGTCTG                         ACCCAGCCACTTGTGTATTTGCAAGCACCACTCGTGATCATCCGATACACC
genomic: GGGTGAGCCAGTGTACGATTTCTGCTGGTACCCGTGTATGTCCTTGTCTGgtgggtgatg ... tgttttgcagACCCAGCCACTTGTGTATTTGCAAGCACCAGTCGTGATCATCCGATACACC
EST: gi|60394554|gb|DN227424.1|DN227424
EST:     GGGTGAGCCAGTGTACGATTTCTGCTGGTACCCGTGTATGTCCTTGTCTG                         ACCCAGCCACTTGTGTATTTGCAAGCACCAGTCGTGATCATCCGATACACC
genomic: GGGTGAGCCAGTGTACGATTTCTGCTGGTACCCGTGTATGTCCTTGTCTGgtgggtgatg ... tgttttgcagACCCAGCCACTTGTGTATTTGCAAGCACCAGTCGTGATCATCCGATACACC
EST: gi|211132517|gb|FL346748.1|FL346748
EST:     GGGTGAGCCAGTGTACGATTTCTGCTGGTACCCGTGTATGTCCTTGTCTG                         ACCCAGCCACTTGTGTATTTGCAAGCACCAGTCGTGATCATCCGATACACC
genomic: GGGTGAGCCAGTGTACGATTTCTGCTGGTACCCGTGTATGTCCTTGTCTGgtgggtgatg ... tgttttgcagACCCAGCCACTTGTGTATTTGCAAGCACCAGTCGTGATCATCCGATACACC
EST: gi|37418378|gb|CF646857.1|CF646857
EST:     GGGTGAGCCAGTGTACGATTTCTGCTGGTACCCGTGTATGTCCTTGTCTG                         ACCCAGCCACTTGTGTATTTGCAAGCACCAGTCGTGATCATCCGATACACC
genomic: GGGTGAGCCAGTGTACGATTTCTGCTGGTACCCGTGTATGTCCTTGTCTGgtgggtgatg ... tgttttgcagACCCAGCCACTTGTGTATTTGCAAGCACCAGTCGTGATCATCCGATACACC
EST: gi|78084101|gb|DV512494.1|DV512494
EST:     GGGTGAGCCAGTGTACGATTTCTGCTGGTACCCGTGTATGTCCTTGTCTG                         ACCCAGCCACTTGTGTATTTGCAAGCACCAGTCGTGATCATCCGATACACC
genomic: GGGTGAGCCAGTGTACGATTTCTGCTGGTACCCGTGTATGTCCTTGTCTGgtgggtgatg ... tgttttgcagACCCAGCCACTTGTGTATTTGCAAGCACCAGTCGTGATCATCCGATACACC
EST: gi|94478312|gb|EB707270.1|EB707270
EST:     GGGTGAGCCAGTGTACGATTTCTGCTGGTACCCGTGTATGTCCTTGTCTG                         ACCCAGCCACTTGTGTATTTGCAAGCACCAGTCGTGATCATCCGATACACC
genomic: GGGTGAGCCAGTGTACGATTTCTGCTGGTACCCGTGTATGTCCTTGTCTGgtgggtgatg ... tgttttgcagACCCAGCCACTTGTGTATTTGCAAGCACCAGTCGTGATCATCCGATACACC
EST: gi|211083828|gb|FL344180.1|FL344180
EST:     GGTGAGCCAGTGTACGATTTCTGCTGGGTACC-GTGTATGTCCTTGTCTG                         ACCCAGC-ACTTGTGTATTTGCAAGCCCCAGTCGTGATCATCCGATAC
genomic: GGTGAGCCAGTGTACGATTTCTGCTGG-TACCCGTGTATGTCCTTGTCTGgtgggtgatg ... tgttttgcagACCCAGCCACTTGTGTATTTGCAAGCACCAGTCGTGATCATCCGATAC
EST: gi|78112774|gb|DV531168.1|DV531168
EST:     GGGTGAGCCAGTGTACGATTTCTGCTGGTACCCGTGTATGTCCTTGTCTG                         ACCCAGCCACTTGTGTATTTGCAAGCACCAGTCGTGATCATCCGATACACC
genomic: GGGTGAGCCAGTGTACGATTTCTGCTGGTACCCGTGTATGTCCTTGTCTGgtgggtgatg ... tgttttgcagACCCAGCCACTTGTGTATTTGCAAGCACCAGTCGTGATCATCCGATACACC

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), 45 (downstream exon)
Score: 132

ATTCTTATGGAGCTTTCATTCAGGCGAACGAGGGTGAGCCAGTGTACGATTTCTGCTGGTACCCGTGTATGTCCTTGTCTGgtgggtgatg ... tgttttgcagACCCAGCCACTTGTGTATTTGCAAGCACCAGTCGTGATCATCCGATACACCTTTGGGATGCCACCAGTGGGGAA


Block sizes: 48 (upstream exon), 42 (downstream exon)
Score: 40

ATTCTTATGGAGCTTTCATTCAGGCGAACGAGGGTGAGCCAGTGTACGATTTCTGCTGGTACCCGTGTATGTCCTTGTCTGgtgggtgatg ... tgttttgcagACCCAGCCACTTGTGTATTTGCAAGCACCAGTCGTGATCATCCGATACACCTTTGGGATGCCACCAGTGGGGAA


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 53

ATTCTTATGGAGCTTTCATTCAGGCGAACGAGGGTGAGCCAGTGTACGATTTCTGCTGGTACCCGTGTATGTCCTTGTCTGgtgggtgatg ... tgttttgcagACCCAGCCACTTGTGTATTTGCAAGCACCAGTCGTGATCATCCGATACACCTTTGGGATGCCACCAGTGGGGAA


Block sizes: 45 (upstream exon), 47 (downstream exon)
Score: 60

ATTCTTATGGAGCTTTCATTCAGGCGAACGAGGGTGAGCCAGTGTACGATTTCTGCTGGTACCCGTGTATGTCCTTGTCTGgtgggtgatg ... tgttttgcagACCCAGCCACTTGTGTATTTGCAAGCACCAGTCGTGATCATCCGATACACCTTTGGGATGCCACCAGTGGGGAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccttcttcctttatgatcaattagtgaatttgatgcatttttattgttttgcagACCCAGCCACTTGTGTATTTGCAAGCACCAGTCGTGATCATCCGATACACCTTTGGGATGCCACCAGTGGGGAA
                            atttgat  putative branch site (score: 60)
                                      tttttatt  putative PPT
                                     atttttattgtttt  TA-rich tract