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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTCGTTTGGTTGCACCTACTTGTTTGTATTTGGCATCTAAGGTGGAGGAGAGTACAGTGCAAGCCCGACTTCTTGTATTTTATATAAAAAAGATGTGTGgtgtgtcttataaccatatttatcgccatatttacatgtaaaaactgcagtagatgaccttctctctctctctccctctcttcaaagtgcag

Basic information

species Zea mays
transcript GRMZM2G408242_T03
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G408242_T03 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os09g32680.4 (Oryza sativa), 5'ss of exon 4
CCTCGTTTGGTTGCACCTACTTGTTTGTATTTGGCATCTAAGGTGGAGGAGAGTACAGTGCAAGCCCGACTTCTTGTATTTTATATAAAAAAGATGTGTGgtgtgtcttataaccatatttatcgccatatttacatgtaaaaactgcagtagatgaccttctctctctctctccctctcttcaaagtgcag
|||||| |||| ||||| || ||||||||||||||||| |||||||| ||||| |||||||||||  |||||||||| ||||| ||||||||||||||||||  | || |||| ||||  |     ||||||||   | || ||||||| ||    |        |     ||| | | |  |||| || ||
CCTCGTCTGGTAGCACCAACCTGTTTGTATTTGGCATCAAAGGTGGAAGAGAGCACAGTGCAAGCAAGACTTCTTGTCTTTTACATAAAAAAGATGTGTGgtaaggctcataatcataaatggacacatatttatcgggaagaactgcactaacctaaaactaaacatgtgctctccccccgcaaaatgtag
















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|211116525|gb|FL229714.1|FL229714
EST:     GAGTACAGTGCAAGCCCGACTTCTTGTATTTTAYATAAAAAAGATGTGTG                         GTTCCGATGATAAGTATCGGT
genomic: GAGTACAGTGCAAGCCCGACTTCTTGTATTTTATATAAAAAAGATGTGTGgtgtgtctta ... caaagtgcagGTTCCGATGATAAGTATCGGT
EST: gi|88748070|gb|DY532211.1|DY532211
EST:     GAGTACAGTGCAAGCCCGACTTCTTGTATTTTATATAAAAAAGATGTGTG                         GTTCCAGATGATAAGTATCGGTTTGAAAT
genomic: GAGTACAGTGCAAGCCCGACTTCTTGTATTTTATATAAAAAAGATGTGTGgtgtgtctta ... caaagtgcagGTTCC-GATGATAAGTATCGGTTTGAAAT
EST: gi|211115731|gb|FL229702.1|FL229702
EST:     GAGTACAGTGCAAGCCCGACTTCTTGTATTTTATATAAAANAGATGTGTG                         GTTCCGATGATAAGTATCGGTTTG
genomic: GAGTACAGTGCAAGCCCGACTTCTTGTATTTTATATAAAAAAGATGTGTGgtgtgtctta ... caaagtgcagGTTCCGATGATAAGTATCGGTTTG
EST: gi|22521611|gb|BU080422.1|BU080422
EST:     GAGTACAGTGCAAGCCCGACTTCTTGTATTTTATATAAAAAAGATGTGTG                         GTTCCGATGATAAGTATCGGTTTGAAATTAAGGATATTCTTGAAATGGAAA
genomic: GAGTACAGTGCAAGCCCGACTTCTTGTATTTTATATAAAAAAGATGTGTGgtgtgtctta ... caaagtgcagGTTCCGATGATAAGTATCGGTTTGAAATTAAGGATATTCTTGAAATGGAAA
EST: gi|60352426|gb|DN219399.1|DN219399
EST:     GAGTACAGTGCAAGCCCGACTTCTTGTATTTTATATAAAAAAGATGTGTG                         GTTCCGATGATAAGTATCGGTTTGAAATTAAGGATATTCTTGAAATGGAAA
genomic: GAGTACAGTGCAAGCCCGACTTCTTGTATTTTATATAAAAAAGATGTGTGgtgtgtctta ... caaagtgcagGTTCCGATGATAAGTATCGGTTTGAAATTAAGGATATTCTTGAAATGGAAA
EST: gi|211117332|gb|FL229741.1|FL229741
EST:     GAGTACAGTGCAAGCCCGACTTCTTGTATTTTATATAAAAAAGATGTGTG                         GTTCCGATGATAAGTATCGG
genomic: GAGTACAGTGCAAGCCCGACTTCTTGTATTTTATATAAAAAAGATGTGTGgtgtgtctta ... caaagtgcagGTTCCGATGATAAGTATCGG
EST: gi|211116530|gb|FL229719.1|FL229719
EST:     GAGTACAGTGCAAGCCCGACTTCTTGTATTTTATATAAAAAAGATGTGTG                         GTTCCGATGATAAGTATCGGTTTGAAATTAAGGATATTCTTGAAATGGAAA
genomic: GAGTACAGTGCAAGCCCGACTTCTTGTATTTTATATAAAAAAGATGTGTGgtgtgtctta ... caaagtgcagGTTCCGATGATAAGTATCGGTTTGAAATTAAGGATATTCTTGAAATGGAAA
EST: gi|211115740|gb|FL229711.1|FL229711
EST:     GAGTACAGTGCAAGCCCGACTTCTTGTATTTYATATAAAAAAGATGTGTG                         GTTCCGATGAT
genomic: GAGTACAGTGCAAGCCCGACTTCTTGTATTTTATATAAAAAAGATGTGTGgtgtgtctta ... caaagtgcagGTTCCGATGAT
EST: gi|37373889|gb|CF623269.1|CF623269
EST:     GAGTACAGTGCAAGCCCGACTTCTTGTATTTTATATAAAAAAGATGTGTG                         GTTCCGATGATAAGTATCGGTTGGAAATTAAGGATATTCTTGAAATGGAAA
genomic: GAGTACAGTGCAAGCCCGACTTCTTGTATTTTATATAAAAAAGATGTGTGgtgtgtctta ... caaagtgcagGTTCCGATGATAAGTATCGGTTTGAAATTAAGGATATTCTTGAAATGGAAA
EST: gi|78022288|gb|DV490675.1|DV490675
EST:     AAAGATGTGTG                         GTTCCGATGATAAGTATCGGTTTGAAATTAAGGATATTCTTGAAATGGAAA
genomic: AAAGATGTGTGgtgtgtctta ... caaagtgcagGTTCCGATGATAAGTATCGGTTTGAAATTAAGGATATTCTTGAAATGGAAA
EST: gi|211116524|gb|FL229713.1|FL229713
EST:     GAGTACAGTGCAAGCCCGACTTCTTGTATTTTATATAAAAA-GATGTGTG                         GTTCCGATGATAAGTATCGGGTTGAAATTAAG
genomic: GAGTACAGTGCAAGCCCGACTTCTTGTATTTTATATAAAAAAGATGTGTGgtgtgtctta ... caaagtgcagGTTCCGATGATAAGTATCGGTTTGAAATTAAG
EST: gi|211117330|gb|FL229739.1|FL229739
EST:     GAGTACAGTGCAAGCCCGACTTCTTGTATTTTATATAAAAAAGATGTGTG                         GTTCCGATGATAAGTATCGGTTTGAAATTAAGGATATTCTTGAAATGGAAA
genomic: GAGTACAGTGCAAGCCCGACTTCTTGTATTTTATATAAAAAAGATGTGTGgtgtgtctta ... caaagtgcagGTTCCGATGATAAGTATCGGTTTGAAATTAAGGATATTCTTGAAATGGAAA
EST: gi|211116534|gb|FL229723.1|FL229723
EST:     GAGTACAGTGCAAGCCCGACTTCTTGTATTTTATATAAAAAAGATGTGTG                         GTTCCGATGATAAGTATCGG
genomic: GAGTACAGTGCAAGCCCGACTTCTTGTATTTTATATAAAAAAGATGTGTGgtgtgtctta ... caaagtgcagGTTCCGATGATAAGTATCGG
EST: gi|22818772|gb|BU498862.1|BU498862
EST:     GAGTACAGTGCAAGCCCGACTTCTTGTATTTTATATAAAAAAGATGTGTG                         GTTCCGATGATAAGTATCGGTTTGAAATTAAGGATATTCTTGAAATGGAAA
genomic: GAGTACAGTGCAAGCCCGACTTCTTGTATTTTATATAAAAAAGATGTGTGgtgtgtctta ... caaagtgcagGTTCCGATGATAAGTATCGGTTTGAAATTAAGGATATTCTTGAAATGGAAA
EST: gi|17970138|gb|BM276903.1|BM276903
EST:     GAGTACAGTGCAAGCCCGACTTCTTGTATTTTATATAAAAAAGATGTGTG                         GTTCCGATGATAAGTATCGGTTTGAAATTAAGGATATTCTTGAAATGGAAA
genomic: GAGTACAGTGCAAGCCCGACTTCTTGTATTTTATATAAAAAAGATGTGTGgtgtgtctta ... caaagtgcagGTTCCGATGATAAGTATCGGTTTGAAATTAAGGATATTCTTGAAATGGAAA
EST: gi|5325108|gb|AI783299.1|AI783299
EST:     GAGTACAGTGCAAGCCCGACTTCTTGTATTTTATATAAAAAAGATGTGTG                         GTTCCGATGATAAGTATCGGTTTGAAATTAAGGATATTCTTGAAATGGAAA
genomic: GAGTACAGTGCAAGCCCGACTTCTTGTATTTTATATAAAAAAGATGTGTGgtgtgtctta ... caaagtgcagGTTCCGATGATAAGTATCGGTTTGAAATTAAGGATATTCTTGAAATGGAAA
EST: gi|211114947|gb|FL229695.1|FL229695
EST:     GAGTACAGTGCAAGCCCGACTTCTTGTATTTTATATAAAAAAGATGTGTG                         GTTCCGATGATAAGTATCGGTTTGAAATTAAGGATATTCTTGA
genomic: GAGTACAGTGCAAGCCCGACTTCTTGTATTTTATATAAAAAAGATGTGTGgtgtgtctta ... caaagtgcagGTTCCGATGATAAGTATCGGTTTGAAATTAAGGATATTCTTGA
EST: gi|60346539|gb|DN213512.1|DN213512
EST:     GAGTACAGTGCAAGCCCGACTTCTTGTATTTTATATAAAAAAGATGTGTG                         GTTCCGATGATAAGTATCGGTTTGAAATTAAGGATATTCTTGAAATGGAAA
genomic: GAGTACAGTGCAAGCCCGACTTCTTGTATTTTATATAAAAAAGATGTGTGgtgtgtctta ... caaagtgcagGTTCCGATGATAAGTATCGGTTTGAAATTAAGGATATTCTTGAAATGGAAA
EST: gi|22818771|gb|BU498861.1|BU498861
EST:     GAGTACAGTGCAAGCCCGACTTCTTGTATTTTATATAAAAAAGATGTGTG                         GTTCCGATGATAAGTATCGGTTTGAAATTAAGGATATTCTTGAAATGGAAA
genomic: GAGTACAGTGCAAGCCCGACTTCTTGTATTTTATATAAAAAAGATGTGTGgtgtgtctta ... caaagtgcagGTTCCGATGATAAGTATCGGTTTGAAATTAAGGATATTCTTGAAATGGAAA
EST: gi|74235410|gb|DT643324.1|DT643324
EST:     GAGTACAGTGCAAGCCCGACTTCTTGTATTTTATATAAAAAAGATGTGTG                         GTTCCGATGATAAGTATCGGTTTGAAATTAAGGATATTCTTGAAATGGAAA
genomic: GAGTACAGTGCAAGCCCGACTTCTTGTATTTTATATAAAAAAGATGTGTGgtgtgtctta ... caaagtgcagGTTCCGATGATAAGTATCGGTTTGAAATTAAGGATATTCTTGAAATGGAAA
EST: gi|211115727|gb|FL229698.1|FL229698
EST:     GAGTACAGTGCAAGCCCGACTTCTTGTATTTTATATAAAAAAGATGTGTG                         GTTCCGATGATAAGTATCGGTTTGAAATTAAGGATATTCTTGAAATGGAAA
genomic: GAGTACAGTGCAAGCCCGACTTCTTGTATTTTATATAAAAAAGATGTGTGgtgtgtctta ... caaagtgcagGTTCCGATGATAAGTATCGGTTTGAAATTAAGGATATTCTTGAAATGGAAA
EST: gi|50333682|gb|CO528808.1|CO528808
EST:     GAGTACAGTGCAAGCCCGACTTCTTGTATTTTATATAAAAAAGATGTGTG                         GTTCCGATGATAAGTATCGGTTTGAAATTAAGGATATTCTTGAAATGGAAA
genomic: GAGTACAGTGCAAGCCCGACTTCTTGTATTTTATATAAAAAAGATGTGTGgtgtgtctta ... caaagtgcagGTTCCGATGATAAGTATCGGTTTGAAATTAAGGATATTCTTGAAATGGAAA
EST: gi|211117325|gb|FL229734.1|FL229734
EST:     GAGTACAGTGCAAGCCCGACTTCTTGTATTTTATATAAAAAAGATGTGTG                         GTTCCGATGATAAGTATCGGTT
genomic: GAGTACAGTGCAAGCCCGACTTCTTGTATTTTATATAAAAAAGATGTGTGgtgtgtctta ... caaagtgcagGTTCCGATGATAAGTATCGGTT
EST: gi|6020447|gb|AW065375.1|AW065375
EST:     GAGTACAGGGCAAGCCCGACTTCTTGTATTTTATATAAAAAAGATGTGTG                         GTTCCGATGATAAGTATCGGTTTGAAATTAAGGATATTCTTGAAATGGAAA
genomic: GAGTACAGTGCAAGCCCGACTTCTTGTATTTTATATAAAAAAGATGTGTGgtgtgtctta ... caaagtgcagGTTCCGATGATAAGTATCGGTTTGAAATTAAGGATATTCTTGAAATGGAAA
EST: gi|149084617|gb|EE174095.2|EE174095
EST:     GAGTACAGTGCAAGCCCGACTTCTTGTATTTTATATAAAAAAGATGTGTG                         GTTCCGATGATAAGTATCGGTTTGAAATTAAGGATATTCTTGAAATGGAAA
genomic: GAGTACAGTGCAAGCCCGACTTCTTGTATTTTATATAAAAAAGATGTGTGgtgtgtctta ... caaagtgcagGTTCCGATGATAAGTATCGGTTTGAAATTAAGGATATTCTTGAAATGGAAA
EST: gi|148990759|gb|EE032170.2|EE032170
EST:     GAGTACAGTGCAAGCCCGACTTCTTGTATTTTATATAAAAAAGATGTGTG                         GTTCCGATGATAAGTATCGGTTTGAAATTAAGGATATTCTTGAAATGGAAA
genomic: GAGTACAGTGCAAGCCCGACTTCTTGTATTTTATATAAAAAAGATGTGTGgtgtgtctta ... caaagtgcagGTTCCGATGATAAGTATCGGTTTGAAATTAAGGATATTCTTGAAATGGAAA
EST: gi|93015766|gb|EB641286.1|EB641286
EST:     GAGTACAGTGCAAGCCCGACTTCTTGTATTTTATATAAAAAAGATGTGTG                         GTTCCGATGATAAGTATCGGGTTTGAAATTAAG
genomic: GAGTACAGTGCAAGCCCGACTTCTTGTATTTTATATAAAAAAGATGTGTGgtgtgtctta ... caaagtgcagGTTCCGATGATAAGTATCGG-TTTGAAATTAAG
EST: gi|211115729|gb|FL229700.1|FL229700
EST:     GAGTACAGTGCAAGCCCGACTTCTTGTATTTTATATAAAAAAGATGTGTG                         GTTCCGATGATAAGTATCGGTTTGAAA
genomic: GAGTACAGTGCAAGCCCGACTTCTTGTATTTTATATAAAAAAGATGTGTGgtgtgtctta ... caaagtgcagGTTCCGATGATAAGTATCGGTTTGAAA
EST: gi|26456727|gb|CA828310.1|CA828310
EST:     GAGTACAGTGCAAGCCCGACTTCTTGTATTTTATATAAAAAAGATGTGTG                         GTTCCGATGATAAGTATCGGTTTGAAATTAAGGATATTCTTGAAATGGAAA
genomic: GAGTACAGTGCAAGCCCGACTTCTTGTATTTTATATAAAAAAGATGTGTGgtgtgtctta ... caaagtgcagGTTCCGATGATAAGTATCGGTTTGAAATTAAGGATATTCTTGAAATGGAAA
EST: gi|60339571|gb|DN206544.1|DN206544
EST:     TTTATATAAAAAAGATGTGTG                         GTTCCGATGATAAGTATCGGTTTGAAATTAAGGATATTCTTGAAATGGAAA
genomic: TTTATATAAAAAAGATGTGTGgtgtgtctta ... caaagtgcagGTTCCGATGATAAGTATCGGTTTGAAATTAAGGATATTCTTGAAATGGAAA
EST: gi|20803321|gb|BQ294371.1|BQ294371
EST:     GAGTACAGTGCAAGCCCGACTTCTTGTATTTTATATAAAAAAGATGTGTG                         GTTCCGATGATAAGTATCGGTTTGAAATTAAGGATATTCTTGAAATGGAAA
genomic: GAGTACAGTGCAAGCCCGACTTCTTGTATTTTATATAAAAAAGATGTGTGgtgtgtctta ... caaagtgcagGTTCCGATGATAAGTATCGGTTTGAAATTAAGGATATTCTTGAAATGGAAA
EST: gi|74235409|gb|DT643323.1|DT643323
EST:     GAGTACAGTGCAAGCCCGACTTCTTGTATTTTATATAAAAAAGATGTGTG                         GTTCCGATGATAAGTATCGGTTTGAAATTAAGGATATTCTTGAAATGGAAA
genomic: GAGTACAGTGCAAGCCCGACTTCTTGTATTTTATATAAAAAAGATGTGTGgtgtgtctta ... caaagtgcagGTTCCGATGATAAGTATCGGTTTGAAATTAAGGATATTCTTGAAATGGAAA
EST: gi|22521612|gb|BU080423.1|BU080423
EST:     GAGTACAGTGCAAGCCCGACTTCTTGTATTTTATATAAAAAAGATGTGTG                         GTTCCGATGATAAGTATCGGTTTGAAATTAAGGATATTCTTGAAATGGAAA
genomic: GAGTACAGTGCAAGCCCGACTTCTTGTATTTTATATAAAAAAGATGTGTGgtgtgtctta ... caaagtgcagGTTCCGATGATAAGTATCGGTTTGAAATTAAGGATATTCTTGAAATGGAAA
EST: gi|211114945|gb|FL229693.1|FL229693
EST:     GAGTACAGTGCAAGCCCGACTTCTTGTATTTTATATAAAADAGATGTGTG                         GTTCCGATGATAAGTATCCGGTTTGAAATTAAGGATAT
genomic: GAGTACAGTGCAAGCCCGACTTCTTGTATTTTATATAAAAAAGATGTGTGgtgtgtctta ... caaagtgcagGTTCCGATGATAAGTATC-GGTTTGAAATTAAGGATAT
EST: gi|211115726|gb|FL229697.1|FL229697
EST:     GAGTACAGTGCAAGCCCGACTTCTTGTATTTTATATAAAAAAGATGTGTG                         GTTCCGATGATAAGTATCGGTTTGAAATTAAAGGATATTCTTGAAATGGAA
genomic: GAGTACAGTGCAAGCCCGACTTCTTGTATTTTATATAAAAAAGATGTGTGgtgtgtctta ... caaagtgcagGTTCCGATGATAAGTATCGGTTTGAAATTAA-GGATATTCTTGAAATGGAA
EST: gi|148937775|gb|EC881986.2|EC881986
EST:     GAGTACAGTGCAAGCCCGACTTCTTGTATTTTATATAAAAAAGATGTGTG                         GTTCCGATGATAAGTATCGGTTTGAAATTAAGGATATTCTTGAAATGGAAA
genomic: GAGTACAGTGCAAGCCCGACTTCTTGTATTTTATATAAAAAAGATGTGTGgtgtgtctta ... caaagtgcagGTTCCGATGATAAGTATCGGTTTGAAATTAAGGATATTCTTGAAATGGAAA

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), 48 (downstream exon)
Score: 134

CCTCGTTTGGTTGCACCTACTTGTTTGTATTTGGCATCTAAGGTGGAGGAGAGTACAGTGCAAGCCCGACTTCTTGTATTTTATATAAAAAAGATGTGTGgtgtgtctta ... caaagtgcagGTTCCGATGATAAGTATCGGTTTGAAATTAAGGATATTCTTGAAATGGAAATGAAGCTCCTGGAAGCTCTCGACTATTATTTGGTTGTTTTCCATCCATA


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 124

CCTCGTTTGGTTGCACCTACTTGTTTGTATTTGGCATCTAAGGTGGAGGAGAGTACAGTGCAAGCCCGACTTCTTGTATTTTATATAAAAAAGATGTGTGgtgtgtctta ... caaagtgcagGTTCCGATGATAAGTATCGGTTTGAAATTAAGGATATTCTTGAAATGGAAATGAAGCTCCTGGAAGCTCTCGACTATTATTTGGTTGTTTTCCATCCATA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 125

CCTCGTTTGGTTGCACCTACTTGTTTGTATTTGGCATCTAAGGTGGAGGAGAGTACAGTGCAAGCCCGACTTCTTGTATTTTATATAAAAAAGATGTGTGgtgtgtctta ... caaagtgcagGTTCCGATGATAAGTATCGGTTTGAAATTAAGGATATTCTTGAAATGGAAATGAAGCTCCTGGAAGCTCTCGACTATTATTTGGTTGTTTTCCATCCATA


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 119

CCTCGTTTGGTTGCACCTACTTGTTTGTATTTGGCATCTAAGGTGGAGGAGAGTACAGTGCAAGCCCGACTTCTTGTATTTTATATAAAAAAGATGTGTGgtgtgtctta ... caaagtgcagGTTCCGATGATAAGTATCGGTTTGAAATTAAGGATATTCTTGAAATGGAAATGAAGCTCCTGGAAGCTCTCGACTATTATTTGGTTGTTTTCCATCCATA


Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCTCGTTTGGTTGCACCTACTTGTTTGTATTTGGCATCTAAGGTGGAGGAGAGTACAGTGCAAGCCCGACTTCTTGTATTTTATATAAAAAAGATGTGTGgtgtgtcttataaccatatttatcgccatatttacatgtaaaaactgcagtagatgaccttctctctctctctccctctcttcaaagtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG