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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATACAAGGGAGTTTATGAATACTGTAGATCAAAAGGGATAGATCTGGGCAAACCTGTTGCGCTTGACGTCGTTGTTGATGGCACAGTTCCTCAAGgtttgatttagtgctttgggtgtacaaatatatccttctgttcatgtttataaaaataaaggattgctgctgttatttctcctgttag

Basic information

species Zea mays
transcript GRMZM2G458549_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G458549_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os03g61710.1 (Oryza sativa), 5'ss of exon 4
ATACAAGGGAGTTTATGAATACTGTAGATCAAAAGGGATAGATCTGGGCAAACCTGTTGCGCTTGACGTCGTTGTTGATGGCACAGTTCCTCAAGgtttgatttagtgctttgggtgtacaaatatatc--cttctgttcatgtttataa-aaataaaggattgctgc-tgttatttctcctgt-tag
|||||||||||||||||| || ||||| ||||||||||||||| ||||   ||||||||  ||||| || |||||||||||||||||||||  |||| |  ||| |   ||| | | |   | | | ||   | |   | ||    ||   || |     ||   ||| |||| || ||| | | |||
ATACAAGGGAGTTTATGAGTATTGTAGGTCAAAAGGGATAGATATGGGTGGACCTGTTGGCCTTGATGTAGTTGTTGATGGCACAGTTCCTACAGgtatatttttgatattttgttttgggattctttcacttccaaataataagcatgttaagtttgacatgattgcgtgttgttactcttatgtag
















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|76290432|gb|DV030000.1|DV030000
EST:     GGGCAAACCTGTTGCGCTTGACGTCGTTGTTGATGGCACAGTTCCTCAAG                         GCTCTGGACTGTCAAGCTCAGCAGCATTTGTCTGTTCAGCAACAATTGCTA
genomic: GGGCAAACCTGTTGCGCTTGACGTCGTTGTTGATGGCACAGTTCCTCAAGgtttgattta ... ctcctgttagGCTCTGGACTGTCAAGCTCAGCAGCATTTGTCTGTTCAGCAACAATTGCTA
EST: gi|50330093|gb|CO525219.1|CO525219
EST:     GGGCAAACCTGTTGCGCTTGACGTCGTTGTTGATGGCACAGTTCCTCAAG                         GCTCTGGACTGTCAAGCTCAGCAGCATTTGTCTGTTCAGCAACAATTGCTA
genomic: GGGCAAACCTGTTGCGCTTGACGTCGTTGTTGATGGCACAGTTCCTCAAGgtttgattta ... ctcctgttagGCTCTGGACTGTCAAGCTCAGCAGCATTTGTCTGTTCAGCAACAATTGCTA
EST: gi|148960156|gb|EE153406.2|EE153406
EST:     GGGCAAACCTGTTGCGCTTGACGTCGTTGTTGATGGCACAGTTCCTCAAG                         GCTCTGGACTGTCAAGCTCAGCAGCATTTGTCTGTTCAGCAACAATTGCTA
genomic: GGGCAAACCTGTTGCGCTTGACGTCGTTGTTGATGGCACAGTTCCTCAAGgtttgattta ... ctcctgttagGCTCTGGACTGTCAAGCTCAGCAGCATTTGTCTGTTCAGCAACAATTGCTA
EST: gi|32806294|gb|CD958528.1|CD958528
EST:     GGGCAAACCTGTTGCGCTTGACGTCGTTGTTGATGGCACAGTTCCTCAAG                         GCTCTGGACTGTCAAGCTCAGCAGCATTTGTCTGTTCAGCAACAATTGCTA
genomic: GGGCAAACCTGTTGCGCTTGACGTCGTTGTTGATGGCACAGTTCCTCAAGgtttgattta ... ctcctgttagGCTCTGGACTGTCAAGCTCAGCAGCATTTGTCTGTTCAGCAACAATTGCTA
EST: gi|76283981|gb|DV023549.1|DV023549
EST:     GGGCAAACCTGTTGCGCTTGACGTCGTTGTTGATGGCACAGTTCCTCAAG                         GCTCTGGACTGTCAAGCTCAGCAGCATTTGTCTGTTCAGCAACAATTGCTA
genomic: GGGCAAACCTGTTGCGCTTGACGTCGTTGTTGATGGCACAGTTCCTCAAGgtttgattta ... ctcctgttagGCTCTGGACTGTCAAGCTCAGCAGCATTTGTCTGTTCAGCAACAATTGCTA
EST: gi|89764289|gb|DY691150.1|DY691150
EST:     GGGCAAACCTGTTGCGCTTGACGTCGTTGTTGATGGCACAGTTCCTCAAG                         GCTCTGGACTGTCAAGCTCAGCAGCATTTGTCTGTTCAGCAACAATTGCTA
genomic: GGGCAAACCTGTTGCGCTTGACGTCGTTGTTGATGGCACAGTTCCTCAAGgtttgattta ... ctcctgttagGCTCTGGACTGTCAAGCTCAGCAGCATTTGTCTGTTCAGCAACAATTGCTA
EST: gi|93014044|gb|EB639564.1|EB639564
EST:     GGGCAAACCTGTTGCGCTTGACGTCGTTGTTGATGGCACAGTTCCTCAAG                         GCTCTGGACTGTCAGGCTCAGCAGCATTTTGTCTG
genomic: GGGCAAACCTGTTGCGCTTGACGTCGTTGTTGATGGCACAGTTCCTCAAGgtttgattta ... ctcctgttagGCTCTGGACTGTCAAGCTCAGCAGCATTT-GTCTG
EST: gi|148955644|gb|EC901316.2|EC901316
EST:     GGGCAAACCTGTTGCGCTTGACGTCGTTGTTGATGGCACAGTTCCTCAAG                         GCTCTGGACTGTCAAGCTCAGCAGCATTTGTCTGTTCAGCAACAATTGCTA
genomic: GGGCAAACCTGTTGCGCTTGACGTCGTTGTTGATGGCACAGTTCCTCAAGgtttgattta ... ctcctgttagGCTCTGGACTGTCAAGCTCAGCAGCATTTGTCTGTTCAGCAACAATTGCTA
EST: gi|149070820|gb|EE159229.2|EE159229
EST:     GGGCAAACCTGTTGCGCTTGACGTCGTTGTTGATGGCACAGTTCCTCAAG                         GCTCTGGACTGTCAAGCTCAGCAGCATTTGTCTGTTCAGCAACAATTGCTA
genomic: GGGCAAACCTGTTGCGCTTGACGTCGTTGTTGATGGCACAGTTCCTCAAGgtttgattta ... ctcctgttagGCTCTGGACTGTCAAGCTCAGCAGCATTTGTCTGTTCAGCAACAATTGCTA
EST: gi|74231838|gb|DT639752.1|DT639752
EST:     GGGCAAACCTGTTGCGCTTGACGTCGTTGTTGATGGCACAGTTCCTCAAG                         GCTCTGGACTGTCAAGCTCAGCAGCATTTGTCTGTTCAGCAACATTTGCTA
genomic: GGGCAAACCTGTTGCGCTTGACGTCGTTGTTGATGGCACAGTTCCTCAAGgtttgattta ... ctcctgttagGCTCTGGACTGTCAAGCTCAGCAGCATTTGTCTGTTCAGCAACAATTGCTA
EST: gi|148972046|gb|EE022887.2|EE022887
EST:     GGGCAAACCTGTTGCGCTTGACGTCGTTGTTGATGGCACAGTTCCTCAAG                         GCTCTGGACTGTCAAGCTCAGCAGCATTTGTCTGTTCAGCAACAATTGCTA
genomic: GGGCAAACCTGTTGCGCTTGACGTCGTTGTTGATGGCACAGTTCCTCAAGgtttgattta ... ctcctgttagGCTCTGGACTGTCAAGCTCAGCAGCATTTGTCTGTTCAGCAACAATTGCTA
EST: gi|149071533|gb|EE159924.2|EE159924
EST:     GGGCAAACCTGTTGCGCTTGACGTCGTTGTTGATGGCACAGTTCCTCAAG                         GCTCTGGACTGTCAAGCTCAGCAGCATTTGTCTGTTCAGCAACAATTGCTA
genomic: GGGCAAACCTGTTGCGCTTGACGTCGTTGTTGATGGCACAGTTCCTCAAGgtttgattta ... ctcctgttagGCTCTGGACTGTCAAGCTCAGCAGCATTTGTCTGTTCAGCAACAATTGCTA
EST: gi|76912626|gb|DV164825.1|DV164825
EST:     GGGCAAACCTGTTGCGCTTGACGTCGTTGTTGATGGCACAGTTCCTCAAG                         GCTCTGGACTGTCAAGCTCAGCAGCATTTGTCTGTTCAGCAACAATTGCTA
genomic: GGGCAAACCTGTTGCGCTTGACGTCGTTGTTGATGGCACAGTTCCTCAAGgtttgattta ... ctcctgttagGCTCTGGACTGTCAAGCTCAGCAGCATTTGTCTGTTCAGCAACAATTGCTA
EST: gi|148965140|gb|EE015956.2|EE015956
EST:     GGGCAAACCTGTTGCGCTTGACGTCGTTGTTGATGGCACAGTTCCTCAAG                         GCTCTGGACTGTCAAGCTCAGCAGCATTTGTCTGTTCAGCAACAATTGCTA
genomic: GGGCAAACCTGTTGCGCTTGACGTCGTTGTTGATGGCACAGTTCCTCAAGgtttgattta ... ctcctgttagGCTCTGGACTGTCAAGCTCAGCAGCATTTGTCTGTTCAGCAACAATTGCTA
EST: gi|78085244|gb|DV513637.1|DV513637
EST:     GGGCAAACCTGTTGCGCTTGACGTCGTTGTTGATGGCACAGTTCCTCAAG                         GCTCTGGACTGTCAAGCTCAGCAGCATTTGTCTGTTCAGCAACAATTGCTA
genomic: GGGCAAACCTGTTGCGCTTGACGTCGTTGTTGATGGCACAGTTCCTCAAGgtttgattta ... ctcctgttagGCTCTGGACTGTCAAGCTCAGCAGCATTTGTCTGTTCAGCAACAATTGCTA
EST: gi|93282954|gb|EB675218.1|EB675218
EST:     GGGCAAACCTGTTGCGCTTGACGTCGTTGTTGATGGCACAGTTCCTCAAG                         GCTCTGGACTGTCAAGCTCAGCAGCATTTGTCTGTTCAGCAACAATTGCTA
genomic: GGGCAAACCTGTTGCGCTTGACGTCGTTGTTGATGGCACAGTTCCTCAAGgtttgattta ... ctcctgttagGCTCTGGACTGTCAAGCTCAGCAGCATTTGTCTGTTCAGCAACAATTGCTA
EST: gi|148991238|gb|EE032704.2|EE032704
EST:     GGGCAAACCTGTTGCGCTTGACGTCGTTGTTGATGGCACAGTTCCTCAAG                         GCTCTGGACTGTCAAGCTCAGCAGCATTTGTCTGTTCAGCAACAATTGCTA
genomic: GGGCAAACCTGTTGCGCTTGACGTCGTTGTTGATGGCACAGTTCCTCAAGgtttgattta ... ctcctgttagGCTCTGGACTGTCAAGCTCAGCAGCATTTGTCTGTTCAGCAACAATTGCTA
EST: gi|148951727|gb|EC897480.2|EC897480
EST:     GGGCAAACCTGTTGCGCTTGACGTCGTTGTTGATGGCACAGTTCCTCAAG                         GCTCTGGACTGTCAAGCTCAGCAGCATTTGTCTGTTCAGCAACAATTGCTA
genomic: GGGCAAACCTGTTGCGCTTGACGTCGTTGTTGATGGCACAGTTCCTCAAGgtttgattta ... ctcctgttagGCTCTGGACTGTCAAGCTCAGCAGCATTTGTCTGTTCAGCAACAATTGCTA
EST: gi|71318360|gb|DR795942.1|DR795942
EST:     GGGCAAACCTGTTGCGCTTGACGTCGTTGTTGATGGCACAGTTCCTCAAG                         GCTCTGGACTGTCAAGCTCAGCAGCATTTGTCTGTTCAGCAACAATTGCTA
genomic: GGGCAAACCTGTTGCGCTTGACGTCGTTGTTGATGGCACAGTTCCTCAAGgtttgattta ... ctcctgttagGCTCTGGACTGTCAAGCTCAGCAGCATTTGTCTGTTCAGCAACAATTGCTA
EST: gi|148973013|gb|EE024065.2|EE024065
EST:     GGCAAACCTGTTGCGCTTGACGTCGTTGTTGATGGTC-CAGTTCCTCAAG                         GCTCTGGACTGTCAAGCTCAGCAGCTTTTGTCTGTTCAGCAACAATTGCTA
genomic: GGCAAACCTGTTGCGCTTGACGTCGTTGTTGATGG-CACAGTTCCTCAAGgtttgattta ... ctcctgttagGCTCTGGACTGTCAAGCTCAGCAGCATTTGTCTGTTCAGCAACAATTGCTA
EST: gi|148942675|gb|EC887696.2|EC887696
EST:     GGGCAAACCTGTTGCGCTTGACGTCGTTGTTGATGGCACAGTTCCTCAAG                         GCTCTGGACTGTCCAGCTCAGCAGCATTTGTCTGTTCAGCAACAATTGCTA
genomic: GGGCAAACCTGTTGCGCTTGACGTCGTTGTTGATGGCACAGTTCCTCAAGgtttgattta ... ctcctgttagGCTCTGGACTGTCAAGCTCAGCAGCATTTGTCTGTTCAGCAACAATTGCTA
EST: gi|148967123|gb|EE018297.2|EE018297
EST:     GGGCAAACCTGTTGCGCTTGACGTCGTTGTTGATGGCACAGTTCCTCAAG                         GCTCTGGACTGTCAAGCTCAGCAGCATTTGTCTGTTCAGCAACAATTGCTA
genomic: GGGCAAACCTGTTGCGCTTGACGTCGTTGTTGATGGCACAGTTCCTCAAGgtttgattta ... ctcctgttagGCTCTGGACTGTCAAGCTCAGCAGCATTTGTCTGTTCAGCAACAATTGCTA
EST: gi|108824283|gb|EC278291.1|EC278291
EST:     GGGCAAACCTGTTGCGCTTGACGTCGTTGTTGATGGCACAGTTCCTCAAG                         GCTCTGGACTGTCAAGCTCAGCAGCCTTTGTCTGTTCAGCAACAATTGCTA
genomic: GGGCAAACCTGTTGCGCTTGACGTCGTTGTTGATGGCACAGTTCCTCAAGgtttgattta ... ctcctgttagGCTCTGGACTGTCAAGCTCAGCAGCATTTGTCTGTTCAGCAACAATTGCTA

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: 47 (upstream exon), 48 (downstream exon)
Score: 118

ATACAAGGGAGTTTATGAATACTGTAGATCAAAAGGGATAGATCTGGGCAAACCTGTTGCGCTTGACGTCGTTGTTGATGGCACAGTTCCTCAAGgtttgattta ... ctcctgttagGCTCTGGACTGTCAAGCTCAGCAGCATTTGTCTGTTCAGCAACAATTGCTATCATGGGAATCCTTGACAAAAACTTTCCAAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 335

ATACAAGGGAGTTTATGAATACTGTAGATCAAAAGGGATAGATCTGGGCAAACCTGTTGCGCTTGACGTCGTTGTTGATGGCACAGTTCCTCAAGgtttgattta ... ctcctgttagGCTCTGGACTGTCAAGCTCAGCAGCATTTGTCTGTTCAGCAACAATTGCTATCATGGGAATCCTTGACAAAAACTTTCCAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 327

ATACAAGGGAGTTTATGAATACTGTAGATCAAAAGGGATAGATCTGGGCAAACCTGTTGCGCTTGACGTCGTTGTTGATGGCACAGTTCCTCAAGgtttgattta ... ctcctgttagGCTCTGGACTGTCAAGCTCAGCAGCATTTGTCTGTTCAGCAACAATTGCTATCATGGGAATCCTTGACAAAAACTTTCCAAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 292

ATACAAGGGAGTTTATGAATACTGTAGATCAAAAGGGATAGATCTGGGCAAACCTGTTGCGCTTGACGTCGTTGTTGATGGCACAGTTCCTCAAGgtttgattta ... ctcctgttagGCTCTGGACTGTCAAGCTCAGCAGCATTTGTCTGTTCAGCAACAATTGCTATCATGGGAATCCTTGACAAAAACTTTCCAAAG