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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCCGCGGTCCCGGGTGCTCGGGAGGCCGATCCGGGTGGCGCCACCCGCCGCGGCCCGGCCGGGCGGTGCGTCCGCGGGTAGCATACGCGCCGTCTCCGCGgtgagtctgcgtcgattggtttcgagccttcgcctcgggagattcctcgggctggggcgttccgggcgccgccatttctaggggatcatgggttccgttt...

Basic information

species Zea mays
transcript GRMZM2G090338_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G090338_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os05g42350.1 (Oryza sativa), 5'ss of exon 1
CCCGCGGTCCCGGGTGCTCGGGAGGCCGATCCGGGTGGCG---CCACCCGCCGCGGCCCGGCCGGGCGGTG------CGTCCGCGGGTAGCATACGCGCCGTCTCCGCGgtgagtctgcgtcg--attggtttcgagccttcgcctcgggagattcctcgggctggggcgttccgggcgccgccatttctaggggatcatgggttccgttt
          ||| ||||||| |||||| |||| ||||||   || | ||| |||||||   | ||||| |      ||||  |||  ||||||||||||||||||||||||||| | |   |   || ||||     | |    ||  |    || |  |   | |   || ||||     || | |  ||  |    |   ||    | 
---------GCGGATGCTCGGAAGGCCGCTCCGTGTGGCGACCCCTCACGCGGCGGCCCCCGCTGGCGGCGGCGGGTCGTCGTCGGCCAGCATACGCGCCGTCTCCGCGgtgagtttccagtgctgtttgttttctctcgtgatttctcgt--ctcgtgcgagagagagatttcgggttttaccgtctggagaaggatttttttttatctc
















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|71437599|gb|DR818649.1|DR818649
EST:     CGGCCCGGCCGGGCGGTGCGTCCGCGGGTAGCATACGCGCCGTCTCCGCG                         CCTGCGAAGAAGGACGCTTCTGAAGTTAAGCGAAGCAAGGTTGAGATAATC
genomic: CGGCCCGGCCGGGCGGTGCGTCCGCGGGTAGCATACGCGCCGTCTCCGCGgtgagtctgc ... atgcctgcagCCTGCGAAGAAGGACGCTTCTGAAGTTAAGCGAAGCAAGGTTGAGATAATC
EST: gi|211421434|gb|FL301670.1|FL301670
EST:     CGGCCCGGCCGGGCGGTGCGTCCGCGGGTAGCATACGCGCCGTCTCCGCG                         CCTGCGAAGAAGGACGCTTCTGAAGTTAAGCGAAGCAAGGTTGAGATAATC
genomic: CGGCCCGGCCGGGCGGTGCGTCCGCGGGTAGCATACGCGCCGTCTCCGCGgtgagtctgc ... atgcctgcagCCTGCGAAGAAGGACGCTTCTGAAGTTAAGCGAAGCAAGGTTGAGATAATC
EST: gi|91877462|gb|EB407419.1|EB407419
EST:     CGGCCCGGCCGGGCGGTGCGTCCGCGGGTAGCATACGCGCCGTCTCCGCG                         CCTGCGAAGAAGGACGCTTCTGAAGTTAAGCGAAGCAAGGTTGAGATAATC
genomic: CGGCCCGGCCGGGCGGTGCGTCCGCGGGTAGCATACGCGCCGTCTCCGCGgtgagtctgc ... atgcctgcagCCTGCGAAGAAGGACGCTTCTGAAGTTAAGCGAAGCAAGGTTGAGATAATC
EST: gi|148995109|gb|EE034403.2|EE034403
EST:     CGGCCCGGCCGGGCGGTGCGTCCGCGGGTAGCATACGCGCCGTCTCCGCG                         CCTGCGAAGAAGGACGCTTCTGAAGTTAAGCGAAGCAAGGTTGAGATAATC
genomic: CGGCCCGGCCGGGCGGTGCGTCCGCGGGTAGCATACGCGCCGTCTCCGCGgtgagtctgc ... atgcctgcagCCTGCGAAGAAGGACGCTTCTGAAGTTAAGCGAAGCAAGGTTGAGATAATC
EST: gi|18649814|gb|BM498633.1|BM498633
EST:     GCCGTCTCCGCG                         CCTGCGAAGAAGGACGCTTCTGAAGTTAAGCGAAGCAAGGTTGAGATAATC
genomic: GCCGTCTCCGCGgtgagtctgc ... atgcctgcagCCTGCGAAGAAGGACGCTTCTGAAGTTAAGCGAAGCAAGGTTGAGATAATC
EST: gi|211286336|gb|FL301657.1|FL301657
EST:     CGGCCCGGCCGGGCGGTGCGTCCGCGGGTAGCATACGCGCCGTCTCCGCG                         CCTGCGAAGAAGGACGCTTCTGAAAGTTAAGCGA-GCAAGGGTTGAGATAA
genomic: CGGCCCGGCCGGGCGGTGCGTCCGCGGGTAGCATACGCGCCGTCTCCGCGgtgagtctgc ... atgcctgcagCCTGCGAAGAAGGACGCTTCTGAA-GTTAAGCGAAGCAAGG-TTGAGATAA
EST: gi|149079519|gb|EE168499.2|EE168499
EST:     CGGCCCGGCCGGGCGGTGCGTCCGCGGGTAGCATACGCGCCGTCTCCGCG                         CCTGCGAAGAAGGACGCTTCTGAAGTTAAGCGAAGCAAGGTTGAGATAATC
genomic: CGGCCCGGCCGGGCGGTGCGTCCGCGGGTAGCATACGCGCCGTCTCCGCGgtgagtctgc ... atgcctgcagCCTGCGAAGAAGGACGCTTCTGAAGTTAAGCGAAGCAAGGTTGAGATAATC
EST: gi|31351460|gb|CD435817.1|CD435817
EST:     CGGCCCGGCCGGGCGGCGCGTCCGCGGGTAGCATACGAGCCGTCTCCGCG                         CCTGCGAAGAAGGACGCTTCTGAAGTTAAGCGAAGCAAGGTTGAGATAATC
genomic: CGGCCCGGCCGGGCGGTGCGTCCGCGGGTAGCATACGCGCCGTCTCCGCGgtgagtctgc ... atgcctgcagCCTGCGAAGAAGGACGCTTCTGAAGTTAAGCGAAGCAAGGTTGAGATAATC
EST: gi|76917904|gb|DV167066.1|DV167066
EST:     CGGCCCGGCCGGGCGGTGCGTCCGCGGGTAGCATACGCGCCGTCTCCGCG                         CCTGCGAAGAAGGACGCTTCTGAAGTTAAGCGAAGCAAGGTTGAGATAATC
genomic: CGGCCCGGCCGGGCGGTGCGTCCGCGGGTAGCATACGCGCCGTCTCCGCGgtgagtctgc ... atgcctgcagCCTGCGAAGAAGGACGCTTCTGAAGTTAAGCGAAGCAAGGTTGAGATAATC
EST: gi|101384564|gb|EB814327.1|EB814327
EST:     CGGCCCGGCCGGGCGGTGCGTCCGCGGGTAGCATACGCGCCGTCTCCGCG                         CCTGCGAAGAAGGACGCTTCTGAAGTTAAGCGAAGCAAGGTTGAGATAATC
genomic: CGGCCCGGCCGGGCGGTGCGTCCGCGGGTAGCATACGCGCCGTCTCCGCGgtgagtctgc ... atgcctgcagCCTGCGAAGAAGGACGCTTCTGAAGTTAAGCGAAGCAAGGTTGAGATAATC
EST: gi|12047113|gb|BF729252.1|BF729252
EST:     GCATACGCGCCGTCTCCGCG                         CCTGCGAAGAAGGATGCTTCTGAAGTTAAGCGAAGCAAGGTTGAGATAATC
genomic: GCATACGCGCCGTCTCCGCGgtgagtctgc ... atgcctgcagCCTGCGAAGAAGGACGCTTCTGAAGTTAAGCGAAGCAAGGTTGAGATAATC
EST: gi|148947630|gb|EC893110.2|EC893110
EST:     CGGCCCGGCCGGGCGGTGCGTCCGCGGGTAGCATACGCGCCGTCTCCGCG                         CCTGCGAAGAAGGACGCTTCTGAAGTTAAGCGAAGCAAGGTTGAGATAATC
genomic: CGGCCCGGCCGGGCGGTGCGTCCGCGGGTAGCATACGCGCCGTCTCCGCGgtgagtctgc ... atgcctgcagCCTGCGAAGAAGGACGCTTCTGAAGTTAAGCGAAGCAAGGTTGAGATAATC
EST: gi|211501913|gb|FL162222.1|FL162222
EST:     CGGCCCGGCCGGGCGGTGCGTCCGCGGGTAGCATACGCGCCGTCTCCGCG                         CCTGCGAAGAAGGACGCTTCTGAAGTTAAGCGAAGCAAGGTTGAGATAATC
genomic: CGGCCCGGCCGGGCGGTGCGTCCGCGGGTAGCATACGCGCCGTCTCCGCGgtgagtctgc ... atgcctgcagCCTGCGAAGAAGGACGCTTCTGAAGTTAAGCGAAGCAAGGTTGAGATAATC
EST: gi|211319289|gb|FL162214.1|FL162214
EST:     CGGCCCGGCCGGGCGGTGCGTCCGCGGGTAGCATACGCGCCGTCTCCGCG                         CCTGCGAAGAAGGACGCTTCTGAAGTTAAGCGAAGCAAGGTTGAGATAATC
genomic: CGGCCCGGCCGGGCGGTGCGTCCGCGGGTAGCATACGCGCCGTCTCCGCGgtgagtctgc ... atgcctgcagCCTGCGAAGAAGGACGCTTCTGAAGTTAAGCGAAGCAAGGTTGAGATAATC
EST: gi|149085315|gb|EE174821.2|EE174821
EST:     CGGCCCGGCCGGGCGGTGCGTCCGCGGGTAGCATACGCGCCGTCTCCGCG                         CCTGCGAAGAAGGACGCTTCTGAAGTTAAGCGAAGCAAGGTTGAGATAATC
genomic: CGGCCCGGCCGGGCGGTGCGTCCGCGGGTAGCATACGCGCCGTCTCCGCGgtgagtctgc ... atgcctgcagCCTGCGAAGAAGGACGCTTCTGAAGTTAAGCGAAGCAAGGTTGAGATAATC
EST: gi|87153847|gb|DY398636.1|DY398636
EST:     GCCGTCTCCGCG                         CCTGCGAAGAAGGACGCTTCTGAAGTTAAGCGAAGCAAGGTTGAGATAATC
genomic: GCCGTCTCCGCGgtgagtctgc ... atgcctgcagCCTGCGAAGAAGGACGCTTCTGAAGTTAAGCGAAGCAAGGTTGAGATAATC
EST: gi|149014457|gb|EE044072.2|EE044072
EST:     CGGCCCGGCCGGGCGGTGCGTCCGCGGGTAGCATACGCGCCGTCTCCGCG                         CCTGCGAAGAAGGACGCTTCTGAAGTTAAGCGAAGCAAGGTTGAGATAATC
genomic: CGGCCCGGCCGGGCGGTGCGTCCGCGGGTAGCATACGCGCCGTCTCCGCGgtgagtctgc ... atgcctgcagCCTGCGAAGAAGGACGCTTCTGAAGTTAAGCGAAGCAAGGTTGAGATAATC
EST: gi|211286335|gb|FL301656.1|FL301656
EST:     CGGCCCGGCCGGGCGGTGCGTCCGCGGGTAGCATACGCGCCGTCTCCGCG                         CCTGCGAAGAAGGACGCTTCTGAAGTTAAGCGAAGCAAGGTTGAGATAATC
genomic: CGGCCCGGCCGGGCGGTGCGTCCGCGGGTAGCATACGCGCCGTCTCCGCGgtgagtctgc ... atgcctgcagCCTGCGAAGAAGGACGCTTCTGAAGTTAAGCGAAGCAAGGTTGAGATAATC
EST: gi|211286345|gb|FL301666.1|FL301666
EST:     CGGCCCGGCCGGGCGGTGCGTCCGCGGGTAGCATACGCGCCGTCTCCGCG                         CCTGCGAAGAAG-ACGCTTCCTGAAGT-AAGCGAAGCAAGG
genomic: CGGCCCGGCCGGGCGGTGCGTCCGCGGGTAGCATACGCGCCGTCTCCGCGgtgagtctgc ... atgcctgcagCCTGCGAAGAAGGACGCTTC-TGAAGTTAAGCGAAGCAAGG
EST: gi|71330580|gb|DR802058.1|DR802058
EST:     CGGCCCGGCCGGGCGGTGCGTCCGCGGGTAGCATACGCGCCGTCTCCGCG                         CCTGCGAAGAAGGACGCTTCTGAAGTTAAGCGAAGCAAGGTTGAGATAATC
genomic: CGGCCCGGCCGGGCGGTGCGTCCGCGGGTAGCATACGCGCCGTCTCCGCGgtgagtctgc ... atgcctgcagCCTGCGAAGAAGGACGCTTCTGAAGTTAAGCGAAGCAAGGTTGAGATAATC
EST: gi|76015452|gb|DT942622.1|DT942622
EST:     CGGCCCGGCCGGGCGGTGCGTCCGCGGGTAGCATACGCGCCGTCTCCGCG                         CCTGCGAAGAAGGACGCTTCTGAAGTTAAGCGAAGCAAGGTTGAGATAATC
genomic: CGGCCCGGCCGGGCGGTGCGTCCGCGGGTAGCATACGCGCCGTCTCCGCGgtgagtctgc ... atgcctgcagCCTGCGAAGAAGGACGCTTCTGAAGTTAAGCGAAGCAAGGTTGAGATAATC
EST: gi|78179648|gb|DV550021.1|DV550021
EST:     GGCGGCGCGTCCGCGGGTAGCATACGCGCCGTCTCCGCG                         CCTGCGAAGAAGGATGCTTCTGAAGTTAAGCGAAGCAAGGTTGAGATAATC
genomic: GGCGGTGCGTCCGCGGGTAGCATACGCGCCGTCTCCGCGgtgagtctgc ... atgcctgcagCCTGCGAAGAAGGACGCTTCTGAAGTTAAGCGAAGCAAGGTTGAGATAATC
EST: gi|211319287|gb|FL162212.1|FL162212
EST:     CGGCCCGGCCGGGCGGTGCGTCCGCGGGCAGCATACGCGCCGTCTCCGCG                         CCTGCGAAGAAGGATGCTTCTGAAGTTAAGCGAAGCAAGGTTGAGATAATC
genomic: CGGCCCGGCCGGGCGGTGCGTCCGCGGGTAGCATACGCGCCGTCTCCGCGgtgagtctgc ... atgcctgcagCCTGCGAAGAAGGACGCTTCTGAAGTTAAGCGAAGCAAGGTTGAGATAATC

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: 48 (upstream exon), 49 (downstream exon)
Score: 265

CCCGCGGTCCCGGGTGCTCGGGAGGCCGATCCGGGTGGCGCCACCCGCCGCGGCCCGGCCGGGCGGTGCGTCCGCGGGTAGCATACGCGCCGTCTCCGCGgtgagtctgc ... atgcctgcagCCTGCGAAGAAGGACGCTTCTGAAGTTAAGCGAAGCAAGGTTGAGATAATCAAGGAAAAGAGCAACTTCCTCCGGTACCCTTTGAACGAGGAGTTGGTCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1208

CCCGCGGTCCCGGGTGCTCGGGAGGCCGATCCGGGTGGCGCCACCCGCCGCGGCCCGGCCGGGCGGTGCGTCCGCGGGTAGCATACGCGCCGTCTCCGCGgtgagtctgc ... atgcctgcagCCTGCGAAGAAGGACGCTTCTGAAGTTAAGCGAAGCAAGGTTGAGATAATCAAGGAAAAGAGCAACTTCCTCCGGTACCCTTTGAACGAGGAGTTGGTCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1510

CCCGCGGTCCCGGGTGCTCGGGAGGCCGATCCGGGTGGCGCCACCCGCCGCGGCCCGGCCGGGCGGTGCGTCCGCGGGTAGCATACGCGCCGTCTCCGCGgtgagtctgc ... atgcctgcagCCTGCGAAGAAGGACGCTTCTGAAGTTAAGCGAAGCAAGGTTGAGATAATCAAGGAAAAGAGCAACTTCCTCCGGTACCCTTTGAACGAGGAGTTGGTCT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 268

CCCGCGGTCCCGGGTGCTCGGGAGGCCGATCCGGGTGGCGCCACCCGCCGCGGCCCGGCCGGGCGGTGCGTCCGCGGGTAGCATACGCGCCGTCTCCGCGgtgagtctgc ... atgcctgcagCCTGCGAAGAAGGACGCTTCTGAAGTTAAGCGAAGCAAGGTTGAGATAATCAAGGAAAAGAGCAACTTCCTCCGGTACCCTTTGAACGAGGAGTTGGTCT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCCGCGGTCCCGGGTGCTCGGGAGGCCGATCCGGGTGGCGCCACCCGCCGCGGCCCGGCCGGGCGGTGCGTCCGCGGGTAGCATACGCGCCGTCTCCGCGgtgagtctgcgtcgattggtttcgagccttcgcctcgggagattcctcgggctggggcgttccgggcgccgccatttctaggggatcatgggttccgttt

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