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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTACAATGTTTTCCAGTATGGCTTTGTTGCTCTTGCCATCCTCACTCTCTTCTACTATGCTATATTTgtaagtcattttcatcaagtgcttagtcattcacattaacaactataaaagaaatcatgcacaactgtgttattcccactacttgttag

Basic information

species Zea mays
transcript GRMZM2G012284_T01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G012284_T01 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os06g03760.2 (Oryza sativa), 5'ss of exon 13
GTACAATGTTTTCCAGTATGGCTTTGTTGCTCTTGCCATCCTCACTCTCTTCTACTATGCTATATTTgtaagt-cattttcatcaagtgcttagtca-ttcacattaacaactataaaagaaatcatgcacaactgtgttattcccactacttgttag-
||||||||||||||||||||||||||| |||||||| || ||||| ||||| |||||||| |||||||||||| |||| |    ||||  | ||||| |||  || || | ||  ||||    |      |   | |||  |    |||  |||||   
GTACAATGTTTTCCAGTATGGCTTTGTGGCTCTTGCGATACTCACACTCTTTTACTATGCAATATTTgtaagtgcattcttccaaagtattcagtcaattcgtatgaaaatctggaaaaatgttggcttgcttatttgtcctga--actgtttgttcag
















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|76288405|gb|DV027973.1|DV027973
EST:     ATGGCTTTGTTGCTCTTGCCATCCTCACTCTCTTCTACTATGCTATATTT                         GGATGGAGAAAGAGGAAACCAACAGGAAGATTCCAGCTCTCAAATTGATTT
genomic: ATGGCTTTGTTGCTCTTGCCATCCTCACTCTCTTCTACTATGCTATATTTgtaagtcatt ... tacttgttagGGATGGAGAAAGAGGAAACCAACAGGAAGATTCCAGCTCTCAAATTGATTT
EST: gi|67039856|gb|CO466111.1|CO466111
EST:     ATGGCTTTGTTGCTCTTGCCATCCTCACTCTCTTCTACTATGCTATATTT                         GGATGGAGAAAGAGGAAACCAACAGGAAGATTCCAGCTCTCAAATTGATTT
genomic: ATGGCTTTGTTGCTCTTGCCATCCTCACTCTCTTCTACTATGCTATATTTgtaagtcatt ... tacttgttagGGATGGAGAAAGAGGAAACCAACAGGAAGATTCCAGCTCTCAAATTGATTT
EST: gi|91872772|gb|EB402729.1|EB402729
EST:     ATGGCTTTGTTGCTCTTGCCATCCTCACTCTCTTCTACTATGCTATATTT                         GGATGGAGAAAGAGGAAACCAACAGGAAGATTCCAGCTCTCAAATTGATTT
genomic: ATGGCTTTGTTGCTCTTGCCATCCTCACTCTCTTCTACTATGCTATATTTgtaagtcatt ... tacttgttagGGATGGAGAAAGAGGAAACCAACAGGAAGATTCCAGCTCTCAAATTGATTT
EST: gi|32942701|gb|CF047520.1|CF047520
EST:     ATGGCTTTGTTGCTCTTGCCATCCTCACTCTCTTCTACTATGCTATATTT                         GGATGGAGAAAGAGGAAACCAACAGGAAGATTCCAGCTCTCAAATTGATTT
genomic: ATGGCTTTGTTGCTCTTGCCATCCTCACTCTCTTCTACTATGCTATATTTgtaagtcatt ... tacttgttagGGATGGAGAAAGAGGAAACCAACAGGAAGATTCCAGCTCTCAAATTGATTT
EST: gi|67024981|gb|CO453730.1|CO453730
EST:     ATGGCTTTGTTGCTCTTGCCATCCTCACTCTCTTCTACTATGCTATATTT                         GGATGGAGAAAGAGGAAACCAACAGGAAGATTCCAGCTCTCAAATTGATTT
genomic: ATGGCTTTGTTGCTCTTGCCATCCTCACTCTCTTCTACTATGCTATATTTgtaagtcatt ... tacttgttagGGATGGAGAAAGAGGAAACCAACAGGAAGATTCCAGCTCTCAAATTGATTT
EST: gi|32942658|gb|CF047477.1|CF047477
EST:     ATGGCTTTGTTGCTCTTGCCATCCTCACTCTCTTCTACTATGCTATATTT                         GGATGGAGAAAGAGGAAACCAACAGGAAGATTCCAGCTCTCAAATTGATTT
genomic: ATGGCTTTGTTGCTCTTGCCATCCTCACTCTCTTCTACTATGCTATATTTgtaagtcatt ... tacttgttagGGATGGAGAAAGAGGAAACCAACAGGAAGATTCCAGCTCTCAAATTGATTT
EST: gi|71763789|gb|DR961726.1|DR961726
EST:     ATGGCTTTGTTGCTCTTGCCATCCTCACTCTCTTCTACTATGCTATATTT                         GGATGGAGAAAGAGGAAACCAACAGGAAGATTCCAGCTCTCAAATTGATTT
genomic: ATGGCTTTGTTGCTCTTGCCATCCTCACTCTCTTCTACTATGCTATATTTgtaagtcatt ... tacttgttagGGATGGAGAAAGAGGAAACCAACAGGAAGATTCCAGCTCTCAAATTGATTT
EST: gi|6952443|gb|AW424511.1|AW424511
EST:     ATGGCTTTGTTGCTCTTGCCATCCTCACTCTCTTCTACTATGCTATATTT                         GGATGGAGAAAGAGGAAACCAACAGGAAGATTCCAGCTCTCAAATTGATTT
genomic: ATGGCTTTGTTGCTCTTGCCATCCTCACTCTCTTCTACTATGCTATATTTgtaagtcatt ... tacttgttagGGATGGAGAAAGAGGAAACCAACAGGAAGATTCCAGCTCTCAAATTGATTT
EST: gi|71449543|gb|DR830593.1|DR830593
EST:     ATGGCTTTGTTGCTCTTGCCATCCTCACTCTCTTCTACTATGCTATATTT                         GGATGGAGAAAGAGGAAACCAACAGGAAGATTCCAGCTCTCAAATTGATTT
genomic: ATGGCTTTGTTGCTCTTGCCATCCTCACTCTCTTCTACTATGCTATATTTgtaagtcatt ... tacttgttagGGATGGAGAAAGAGGAAACCAACAGGAAGATTCCAGCTCTCAAATTGATTT
EST: gi|148962661|gb|EE013558.2|EE013558
EST:     ATGGCTTTGTTGCTCTTGCCATCCTCACTCTCTTTTACTATGCTATATTT                         GGATGGAGAAAGAGGAAACCAACAGGAAGATTCCAGCTCTCAAATTGATTT
genomic: ATGGCTTTGTTGCTCTTGCCATCCTCACTCTCTTCTACTATGCTATATTTgtaagtcatt ... tacttgttagGGATGGAGAAAGAGGAAACCAACAGGAAGATTCCAGCTCTCAAATTGATTT
EST: gi|33942467|gb|CF349067.1|CF349067
EST:     ATGGCTTTGTTGCTCTTGCCATCCTCACTCTCTTCTACTATGCTATATTT                         GGATGGGAGAAAGAGGAA
genomic: ATGGCTTTGTTGCTCTTGCCATCCTCACTCTCTTCTACTATGCTATATTTgtaagtcatt ... tacttgttagGGATGG-AGAAAGAGGAA

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: 49 (upstream exon), 47 (downstream exon)
Score: 313

GTACAATGTTTTCCAGTATGGCTTTGTTGCTCTTGCCATCCTCACTCTCTTCTACTATGCTATATTTgtaagtcatt ... tacttgttagGGATGGAGAAAGAGGAAACCAACAGGAAGATTCCAGCTCTCAAATTGATTTGCTCTGTAAGTGAAGTTTGACGGATTCATCATATGTGCCCCCTGAGTGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 248

GTACAATGTTTTCCAGTATGGCTTTGTTGCTCTTGCCATCCTCACTCTCTTCTACTATGCTATATTTgtaagtcatt ... tacttgttagGGATGGAGAAAGAGGAAACCAACAGGAAGATTCCAGCTCTCAAATTGATTTGCTCTGTAAGTGAAGTTTGACGGATTCATCATATGTGCCCCCTGAGTGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 268

GTACAATGTTTTCCAGTATGGCTTTGTTGCTCTTGCCATCCTCACTCTCTTCTACTATGCTATATTTgtaagtcatt ... tacttgttagGGATGGAGAAAGAGGAAACCAACAGGAAGATTCCAGCTCTCAAATTGATTTGCTCTGTAAGTGAAGTTTGACGGATTCATCATATGTGCCCCCTGAGTGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 457

GTACAATGTTTTCCAGTATGGCTTTGTTGCTCTTGCCATCCTCACTCTCTTCTACTATGCTATATTTgtaagtcatt ... tacttgttagGGATGGAGAAAGAGGAAACCAACAGGAAGATTCCAGCTCTCAAATTGATTTGCTCTGTAAGTGAAGTTTGACGGATTCATCATATGTGCCCCCTGAGTGG