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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaagttgttttttacaatgatcatgtactgagtcttgacagataaaaactgaatgtattcatccctgaacgctttgtcaactgatcacataccatgcagGAATTGCATAATGGAGTGGTGCAATGAGAAGCCTGAGTGCCCCCTATGCAGAACTCCGATTACCCATTCGAGTTTGATTTGTATATATCATTCAGATTTC

Basic information

species Zea mays
transcript GRMZM2G111614_T01
intron # 10
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|78026945|gb|DV495332.1|DV495332
EST:     AGCATCCGGCAAAATCCTACTGCCACAACCTGTGGACATGTTTTCTGCTG                         GAATTGCATAATGGAGTGGTGCAATGAGAAGCCTGAGTGCCCCCTATGCAG
genomic: AGCATCCGGCAAAATCCTACTGCCACAACCTGTGGACATGTTTTCTGCTGgtaaaagttg ... taccatgcagGAATTGCATAATGGAGTGGTGCAATGAGAAGCCTGAGTGCCCCCTATGCAG
EST: gi|166589460|gb|EG256282.1|EG256282
EST:     ACTGCCACAACCTGTGGACATGTTTTCTGCTG                         GAATTGCATTAATGGAGTGGTGCAATGAGAAGCCTGAGTGCCCCCTATGCA
genomic: ACTGCCACAACCTGTGGACATGTTTTCTGCTGgtaaaagttg ... taccatgcagGAATTGCA-TAATGGAGTGGTGCAATGAGAAGCCTGAGTGCCCCCTATGCA
EST: gi|78027265|gb|DV495652.1|DV495652
EST:     AGCATCCGGCAAAATCCTACTGCCACAACCTGTGGACATGTTTTCTGCTG                         GAATTGCATAATGGAGTGGTGCAATGAGAAGCCTGAGTGCCCCCTATGCAG
genomic: AGCATCCGGCAAAATCCTACTGCCACAACCTGTGGACATGTTTTCTGCTGgtaaaagttg ... taccatgcagGAATTGCATAATGGAGTGGTGCAATGAGAAGCCTGAGTGCCCCCTATGCAG
EST: gi|211263166|gb|FL356033.1|FL356033
EST:     AGCATCCGGCAAAATCCTACTGCCACAACCTGTGGACATGTTTTCTGCTG                         GAATTGCATAATGGAGTGGTGCAATGAGAAGCCTGAGTGCCCCCTATGCAG
genomic: AGCATCCGGCAAAATCCTACTGCCACAACCTGTGGACATGTTTTCTGCTGgtaaaagttg ... taccatgcagGAATTGCATAATGGAGTGGTGCAATGAGAAGCCTGAGTGCCCCCTATGCAG
EST: gi|78111108|gb|DV529505.1|DV529505
EST:     AGCATCCGGCAAAATCCTACTGCCACAACCTGTGGACATGTTTTCTGCTG                         GAATTGCATAATGGAGTGGTGCAATGAGAAGCCTGAGTGCCCCCTATGCAG
genomic: AGCATCCGGCAAAATCCTACTGCCACAACCTGTGGACATGTTTTCTGCTGgtaaaagttg ... taccatgcagGAATTGCATAATGGAGTGGTGCAATGAGAAGCCTGAGTGCCCCCTATGCAG
EST: gi|78026036|gb|DV494423.1|DV494423
EST:     AGCATCCGGCAAAATCCTACTGCCACAACCTGTGGACATGTTTTCTGCTG                         GAATTGCATAATGGAGTGGTGCAATGAGAAGCCTGAGTGCCCCCTATGCAG
genomic: AGCATCCGGCAAAATCCTACTGCCACAACCTGTGGACATGTTTTCTGCTGgtaaaagttg ... taccatgcagGAATTGCATAATGGAGTGGTGCAATGAGAAGCCTGAGTGCCCCCTATGCAG
EST: gi|94474488|gb|EB703446.1|EB703446
EST:     AGCATCCGGCAAAATCCTACTGCCACAACCTGTGGACATGTTTTTTGCTG                         GAATTGCATAATGGAGTGGTGCAATGAGAAGCCTGAGTGCCCCCTATGCAG
genomic: AGCATCCGGCAAAATCCTACTGCCACAACCTGTGGACATGTTTTCTGCTGgtaaaagttg ... taccatgcagGAATTGCATAATGGAGTGGTGCAATGAGAAGCCTGAGTGCCCCCTATGCAG
EST: gi|78025723|gb|DV494110.1|DV494110
EST:     AGCATCCGGCAAAATCCTACTGCCACAACCTGTGGACATGTTTTCTGCTG                         GAATTGCATAATGGAGTGGTGCAATGAGAAGCCTGAGTGCCCCCTATGCAG
genomic: AGCATCCGGCAAAATCCTACTGCCACAACCTGTGGACATGTTTTCTGCTGgtaaaagttg ... taccatgcagGAATTGCATAATGGAGTGGTGCAATGAGAAGCCTGAGTGCCCCCTATGCAG
EST: gi|6654164|gb|AW267569.1|AW267569
EST:     AGCATCCGGCAAAATCCTACTGCCNCAACCTGTGGACATGTTTTCTGCTG                         GAATTGCATAATGGAGTGGTGCAATGAGAAGCCTGAGTGCCCCCTATGCAG
genomic: AGCATCCGGCAAAATCCTACTGCCACAACCTGTGGACATGTTTTCTGCTGgtaaaagttg ... taccatgcagGAATTGCATAATGGAGTGGTGCAATGAGAAGCCTGAGTGCCCCCTATGCAG
EST: gi|78104551|gb|DV522969.1|DV522969
EST:     AGCATCCGGCAAAATCCTACTGCCACAACCTGTGGACATGTTTTTTGCTG                         GAATTGCATAATGGAGTGGTGCAATGAGAAGCCTGAGTGCCCCCTATGCAG
genomic: AGCATCCGGCAAAATCCTACTGCCACAACCTGTGGACATGTTTTCTGCTGgtaaaagttg ... taccatgcagGAATTGCATAATGGAGTGGTGCAATGAGAAGCCTGAGTGCCCCCTATGCAG
EST: gi|78026496|gb|DV494883.1|DV494883
EST:     AGCATCCGGCAAAATCCTACTGCCACAACCTGTGGACATGTTTTCTGCTG                         GAATTGCATAATGGAGTGGTGCAATGAGAAGCCTGAGTGCCCCCTATGCAG
genomic: AGCATCCGGCAAAATCCTACTGCCACAACCTGTGGACATGTTTTCTGCTGgtaaaagttg ... taccatgcagGAATTGCATAATGGAGTGGTGCAATGAGAAGCCTGAGTGCCCCCTATGCAG
EST: gi|78081930|gb|DV510342.1|DV510342
EST:     AGCATCCGGCAAAATCCTACTGCCACAACCTGTGGACATGTTTTCTGCTG                         GAATTGCATAATGGAGTGGTGCAATGAGAAGCCTGAGTGCCCCCTATGCAG
genomic: AGCATCCGGCAAAATCCTACTGCCACAACCTGTGGACATGTTTTCTGCTGgtaaaagttg ... taccatgcagGAATTGCATAATGGAGTGGTGCAATGAGAAGCCTGAGTGCCCCCTATGCAG
EST: gi|78027056|gb|DV495443.1|DV495443
EST:     AGCATCCGGCAAAATCCTATTGCCACAACTTGTGGACATGTTTTCTGCTG                         GAATTGCATAATGGAGTGGTGCAATGAGAAGCCTGAGTGCCCCCTATGCAG
genomic: AGCATCCGGCAAAATCCTACTGCCACAACCTGTGGACATGTTTTCTGCTGgtaaaagttg ... taccatgcagGAATTGCATAATGGAGTGGTGCAATGAGAAGCCTGAGTGCCCCCTATGCAG

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: 42 (upstream exon), 47 (downstream exon)
Score: 27

ACCTCCAATGGCAAGAGCAAATGCACCCTTTGTCTCAGCATCCGGCAAAATCCTACTGCCACAACCTGTGGACATGTTTTCTGCTGgtaaaagttg ... taccatgcagGAATTGCATAATGGAGTGGTGCAATGAGAAGCCTGAGTGCCCCCTATGCAGAACTCCGATTACCCATTCGAGTTTGATTTGTATATATCATTCAGATTTC


Block sizes: 45 (upstream exon), 47 (downstream exon)
Score: 13

ACCTCCAATGGCAAGAGCAAATGCACCCTTTGTCTCAGCATCCGGCAAAATCCTACTGCCACAACCTGTGGACATGTTTTCTGCTGgtaaaagttg ... taccatgcagGAATTGCATAATGGAGTGGTGCAATGAGAAGCCTGAGTGCCCCCTATGCAGAACTCCGATTACCCATTCGAGTTTGATTTGTATATATCATTCAGATTTC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 40

ACCTCCAATGGCAAGAGCAAATGCACCCTTTGTCTCAGCATCCGGCAAAATCCTACTGCCACAACCTGTGGACATGTTTTCTGCTGgtaaaagttg ... taccatgcagGAATTGCATAATGGAGTGGTGCAATGAGAAGCCTGAGTGCCCCCTATGCAGAACTCCGATTACCCATTCGAGTTTGATTTGTATATATCATTCAGATTTC


Block sizes: 34 (upstream exon), 47 (downstream exon)
Score: 24

ACCTCCAATGGCAAGAGCAAATGCACCCTTTGTCTCAGCATCCGGCAAAATCCTACTGCCACAACCTGTGGACATGTTTTCTGCTGgtaaaagttg ... taccatgcagGAATTGCATAATGGAGTGGTGCAATGAGAAGCCTGAGTGCCCCCTATGCAGAACTCCGATTACCCATTCGAGTTTGATTTGTATATATCATTCAGATTTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaactgaatgtattcatccctgaacgctttgtcaactgatcacataccatgcagGAATTGCATAATGGAGTGGTGCAATGAGAAGCCTGAGTGCCCCCTATGCAGAACTCCGATTACCCATTCGAGTTTGATTTGTATATATCATTCAGATTTC
                                  aactgat  putative branch site (score: 24)
       aatgtatt  TA-rich tract