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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGTGGTCACTGCAAGCATCTTGCTCCGgttagtagagtattagcttgaaaatttccaaattattgcagcggtcttcattttttttgtggactgaacatgtacttaaatttag

Basic information

species Zea mays
transcript GRMZM2G159369_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G159369_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os05g06430.1 (Oryza sativa), 5'ss of exon 6
GTGTGGTCACTGCAAGCATCTTGCTCCGgttagtagagtat-----tagcttgaaaatttccaaattattgca--gcggtcttcattttttttgtggact-gaacatgtacttaaatttag
||||||||||||||||||||||||||||||||||||   |      ||  ||| ||| || |||| || ||||  |   | ||  | |||| | |  |||  ||| || ||||   |||||
GTGTGGTCACTGCAAGCATCTTGCTCCGgttagtagtacacctcagtattttgcaaagttgcaaaataatgcattgtcatttttctattttgtctaaactcaaacttgcacttgt-tttag
















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|22819386|gb|BU499476.1|BU499476
EST:     GTGTGGTCACTGCAAGCATCTTGCTCCG                         ATTTATGAGAAGCTGGCTTCAG
genomic: GTGTGGTCACTGCAAGCATCTTGCTCCGgttagtagag ... ttaaatttagATTTATGAGAAGCTGGCTTCAG
EST: gi|32847846|gb|CD987527.1|CD987527
EST:     GTGTGGTCACTGCAAGCATCTTGCTCCG                         ATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATT
genomic: GTGTGGTCACTGCAAGCATCTTGCTCCGgttagtagag ... ttaaatttagATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATT
EST: gi|32837026|gb|CD976704.1|CD976704
EST:     GTGTGGTCACTGCAAGCATCTTGCTCCG                         ATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATT
genomic: GTGTGGTCACTGCAAGCATCTTGCTCCGgttagtagag ... ttaaatttagATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATT
EST: gi|148929737|gb|EC876638.2|EC876638
EST:     GTGTGGTCACTGCAAGCATCTTGCTCCG                         ATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATT
genomic: GTGTGGTCACTGCAAGCATCTTGCTCCGgttagtagag ... ttaaatttagATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATT
EST: gi|32849063|gb|CD988744.1|CD988744
EST:     GTGTGGTCACTGCAAGCATCTTGCTCCG                         ATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATT
genomic: GTGTGGTCACTGCAAGCATCTTGCTCCGgttagtagag ... ttaaatttagATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATT
EST: gi|24934298|gb|CA452516.1|CA452516
EST:     GTGTGGTCACTGCAAGCATCTTGCTCCG                         ATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATT
genomic: GTGTGGTCACTGCAAGCATCTTGCTCCGgttagtagag ... ttaaatttagATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATT
EST: gi|20507142|gb|BQ279504.1|BQ279504
EST:     GTGTGGTCACTGCAAGCATCTTGCTCCG                         ATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATT
genomic: GTGTGGTCACTGCAAGCATCTTGCTCCGgttagtagag ... ttaaatttagATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATT
EST: gi|74239675|gb|DT647589.1|DT647589
EST:     GTGTGGTCACTGCAAGCATCTTGCTCCG                         ATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATT
genomic: GTGTGGTCACTGCAAGCATCTTGCTCCGgttagtagag ... ttaaatttagATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATT
EST: gi|28575999|gb|CB281891.1|CB281891
EST:     GTGTGGTCACTGCAAGCATCTTGCTCCG                         ATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATT
genomic: GTGTGGTCACTGCAAGCATCTTGCTCCGgttagtagag ... ttaaatttagATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATT
EST: gi|32858375|gb|CD998056.1|CD998056
EST:     GTGTGGTCACTGCAAGCATCTTGCTCCG                         ATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGAC
genomic: GTGTGGTCACTGCAAGCATCTTGCTCCGgttagtagag ... ttaaatttagATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGAC
EST: gi|9254368|gb|BE344836.1|BE344836
EST:     GTGTGGTCACTGCAAGCATCTTGCTCCG                         ATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATT
genomic: GTGTGGTCACTGCAAGCATCTTGCTCCGgttagtagag ... ttaaatttagATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATT
EST: gi|88755206|gb|DY539347.1|DY539347
EST:     GTGTGGTCACTGCAAGCATCTTGCTCCG                         ATTTATGAGAAGCTGGCTTCAGTTTTTCAAGCAG
genomic: GTGTGGTCACTGCAAGCATCTTGCTCCGgttagtagag ... ttaaatttagATTTATGAGAAGCTGGCTTCAGTTTT-CAAGCAG
EST: gi|5922104|gb|AW055498.1|AW055498
EST:     GTGTGGTCACTGCAAGCATCTTGCTCCG                         ATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATT
genomic: GTGTGGTCACTGCAAGCATCTTGCTCCGgttagtagag ... ttaaatttagATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATT
EST: gi|67039449|gb|CO465704.1|CO465704
EST:     CCCCATGG-GTGGTCACTGCAAGCAT-TTGTTCCG                         A-TTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGAGCGGTGTTGTGAT
genomic: CCCCATGGTGTGGTCACTGCAAGCATCTTGCTCCGgttagtagag ... ttaaatttagATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGA-CGGTGTTGTGAT
EST: gi|32848046|gb|CD987727.1|CD987727
EST:     GTGTGGTCACTGCAAGCATCTTGCTCCG                         ATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATT
genomic: GTGTGGTCACTGCAAGCATCTTGCTCCGgttagtagag ... ttaaatttagATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATT
EST: gi|111145784|gb|EE258169.1|EE258169
EST:     GTGTGGTCACTGCAAGCATCTTTGCTCCG                         ATTTATGAGAAAGCTGGCTTCAGTTTTCAAGCAAGACG
genomic: GTGTGGTCACTGCAAGCATCTT-GCTCCGgttagtagag ... ttaaatttagATTTATGAGAA-GCTGGCTTCAGTTTTCAAGCAGGACG
EST: gi|71445959|gb|DR827009.1|DR827009
EST:     GTGTGGTCACTGCGAGCATCTTGCTCCG                         ATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATT
genomic: GTGTGGTCACTGCAAGCATCTTGCTCCGgttagtagag ... ttaaatttagATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATT
EST: gi|31355506|gb|CD439863.1|CD439863
EST:     GTGTGGTCACTGCAAGCATCTTGCTCCG                         ATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATT
genomic: GTGTGGTCACTGCAAGCATCTTGCTCCGgttagtagag ... ttaaatttagATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATT
EST: gi|148961930|gb|EE012722.2|EE012722
EST:     GTGTGGTCACTGCAAGCATCTTGCTCCG                         ATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATT
genomic: GTGTGGTCACTGCAAGCATCTTGCTCCGgttagtagag ... ttaaatttagATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATT
EST: gi|31360143|gb|CD444500.1|CD444500
EST:     GTGTGGTCACTGCAAGCATCTTGCTCCG                         ATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGAC
genomic: GTGTGGTCACTGCAAGCATCTTGCTCCGgttagtagag ... ttaaatttagATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGAC
EST: gi|211334955|gb|FK966344.1|FK966344
EST:     GTGTGGTCACTGCAAGCATCTTGCTCCG                         ATTTATGAGAAGCTGGCTTCAGTTTTCA-GCAGGACGACGGGTGT-GTGAT
genomic: GTGTGGTCACTGCAAGCATCTTGCTCCGgttagtagag ... ttaaatttagATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGG-TGTTGTGAT
EST: gi|6994161|gb|AW453375.1|AW453375
EST:     GTGTGGTCACTGCAAGCATCTTGCTCCG                         ATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATT
genomic: GTGTGGTCACTGCAAGCATCTTGCTCCGgttagtagag ... ttaaatttagATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATT
EST: gi|71326461|gb|DR799910.1|DR799910
EST:     GTGTGGTCACTGCAAGCATCTTGCTCCG                         ATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATT
genomic: GTGTGGTCACTGCAAGCATCTTGCTCCGgttagtagag ... ttaaatttagATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATT
EST: gi|32933996|gb|CF038808.1|CF038808
EST:     GTGTGGTCACTGCAAGCATCTTGCTCCG                         ATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATT
genomic: GTGTGGTCACTGCAAGCATCTTGCTCCGgttagtagag ... ttaaatttagATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATT
EST: gi|26457090|gb|CA828673.1|CA828673
EST:     GTGTGGTCACTGCAAGCATCTTGCTCCG                         ATTTATGAGAAGCTGGC
genomic: GTGTGGTCACTGCAAGCATCTTGCTCCGgttagtagag ... ttaaatttagATTTATGAGAAGCTGGC
EST: gi|32846747|gb|CD986428.1|CD986428
EST:     GTGTGGTCACTGCAAGCATCTTGCTCCG                         ATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATT
genomic: GTGTGGTCACTGCAAGCATCTTGCTCCGgttagtagag ... ttaaatttagATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATT
EST: gi|148929195|gb|EC874742.2|EC874742
EST:     GTGTGGTCACTGCAAGCATCTTGCTCCG                         ATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATT
genomic: GTGTGGTCACTGCAAGCATCTTGCTCCGgttagtagag ... ttaaatttagATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATT
EST: gi|33285626|gb|CF075421.1|CF075421
EST:     GTGTGGTCACTGCAAGCATCTTGCTCCG                         ATTTATGAGAAGCTGGCTTCAGTTTTCANGCAGGACGACGGTGTTGTGATT
genomic: GTGTGGTCACTGCAAGCATCTTGCTCCGgttagtagag ... ttaaatttagATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATT
EST: gi|211001445|gb|FL439450.1|FL439450
EST:     GTGTGGTCACTGCAAGCATCTTGCTCCG                         ATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATT
genomic: GTGTGGTCACTGCAAGCATCTTGCTCCGgttagtagag ... ttaaatttagATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATT
EST: gi|24763723|gb|CA398894.1|CA398894
EST:     GTGTGGTCACTGCAAGCATCTTGCTCCG                         ATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATT
genomic: GTGTGGTCACTGCAAGCATCTTGCTCCGgttagtagag ... ttaaatttagATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATT
EST: gi|211497907|gb|FK991939.1|FK991939
EST:     GTGTGGTCACTGCAAGCATCTTGCTCCG                         ATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATT
genomic: GTGTGGTCACTGCAAGCATCTTGCTCCGgttagtagag ... ttaaatttagATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATT
EST: gi|149096330|gb|EE182049.2|EE182049
EST:     GTGTGGTCACTGCAAGCATCTTGCTCCG                         ATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATT
genomic: GTGTGGTCACTGCAAGCATCTTGCTCCGgttagtagag ... ttaaatttagATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATT
EST: gi|149044453|gb|EE047574.2|EE047574
EST:     GTGTGGTCACTGCAAGCATCTTGCTCCG                         ATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATT
genomic: GTGTGGTCACTGCAAGCATCTTGCTCCGgttagtagag ... ttaaatttagATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATT
EST: gi|32849041|gb|CD988722.1|CD988722
EST:     GTGTGGTCACTGCAAGCATCTTGCTCCG                         ATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATT
genomic: GTGTGGTCACTGCAAGCATCTTGCTCCGgttagtagag ... ttaaatttagATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATT
EST: gi|32864543|gb|CF004225.1|CF004225
EST:     GTGTGGTCACTGCAAGCATCTTGCTCCG                         ATTTATGAGAAGCTGGCTTCAGTTNTCAAGCAGGACGACGGTGTTGTGATT
genomic: GTGTGGTCACTGCAAGCATCTTGCTCCGgttagtagag ... ttaaatttagATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATT
EST: gi|78084675|gb|DV513068.1|DV513068
EST:     GTGTGGTCACTGCAAGCATCTTGCTCCG                         ATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATT
genomic: GTGTGGTCACTGCAAGCATCTTGCTCCGgttagtagag ... ttaaatttagATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATT
EST: gi|32846337|gb|CD986018.1|CD986018
EST:     GTGTGGTCACTGCAAGCATCTTGCTCCG                         ATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATT
genomic: GTGTGGTCACTGCAAGCATCTTGCTCCGgttagtagag ... ttaaatttagATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATT
EST: gi|40336546|gb|CK370616.1|CK370616
EST:     GTGTGGTCACTGCAAGCATCTTGCTCCG                         ATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATT
genomic: GTGTGGTCACTGCAAGCATCTTGCTCCGgttagtagag ... ttaaatttagATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATT
EST: gi|33101223|gb|CF061183.1|CF061183
EST:     GTGTGGTCACTGCAAGCATCTTGCTCCG                         ATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATT
genomic: GTGTGGTCACTGCAAGCATCTTGCTCCGgttagtagag ... ttaaatttagATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATT
EST: gi|22935460|gb|BU571735.1|BU571735
EST:     GTGTGGTCACTGCAAGCATCTTGCTCCG                         ATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATT
genomic: GTGTGGTCACTGCAAGCATCTTGCTCCGgttagtagag ... ttaaatttagATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATT
EST: gi|37393543|gb|CF634037.1|CF634037
EST:     GTGTGGTCACTGCAAGCATCTTGCTCCG                         ATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATT
genomic: GTGTGGTCACTGCAAGCATCTTGCTCCGgttagtagag ... ttaaatttagATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATT
EST: gi|21891538|gb|BQ744751.1|BQ744751
EST:     GTGTGGTCACTGCAAGCATCTTGCTCCG                         ATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATT
genomic: GTGTGGTCACTGCAAGCATCTTGCTCCGgttagtagag ... ttaaatttagATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATT
EST: gi|148955860|gb|EC901555.2|EC901555
EST:     GTGTGGTCACTGCAAGCATCTTGCTCCG                         ATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATT
genomic: GTGTGGTCACTGCAAGCATCTTGCTCCGgttagtagag ... ttaaatttagATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATT
EST: gi|213192265|gb|FM195988.1|FM195988
EST:     GTGTGGTCACTGCAAGCATCTTGCTCCG                         ATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATT
genomic: GTGTGGTCACTGCAAGCATCTTGCTCCGgttagtagag ... ttaaatttagATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATT

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: 39 (upstream exon), 49 (downstream exon)
Score: 838

GTGTGGTCACTGCAAGCATCTTGCTCCGgttagtagag ... ttaaatttagATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATTGCCAATATTGATGCTGACAAGCACACTGACTTGGCTGAAAA


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 782

GTGTGGTCACTGCAAGCATCTTGCTCCGgttagtagag ... ttaaatttagATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATTGCCAATATTGATGCTGACAAGCACACTGACTTGGCTGAAAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 648

GTGTGGTCACTGCAAGCATCTTGCTCCGgttagtagag ... ttaaatttagATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATTGCCAATATTGATGCTGACAAGCACACTGACTTGGCTGAAAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 1176

GTGTGGTCACTGCAAGCATCTTGCTCCGgttagtagag ... ttaaatttagATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATTGCCAATATTGATGCTGACAAGCACACTGACTTGGCTGAAAA