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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCCATGCCTCCACCGCCTGCATATGAAGAAGTCAATGGTATATTCATGAGGAATACGGTCGCAGAGTTGGTCGAGACCGTGGAGTATTTCCTGGCTGAGgtgatctgtttcgttacattgaacaagtttgaagctgcgctaggcactagatcttagtttgtacccataataatctgtgtatgtattgccatttttctttggtag

Basic information

species Zea mays
transcript GRMZM2G123624_T01
intron # 8
splice site 5'
intron type U2

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|60398124|gb|DN230940.1|DN230940
EST:     GGAATACGGTCGCAGAGTTGGTCGAGACCGTGGAGTATTTCCTGGCTGAG                         GCAATCCAATCATATCGAGCAGAGAGCGACACTGAGCTCAACCTTTCAGCT
genomic: GGAATACGGTCGCAGAGTTGGTCGAGACCGTGGAGTATTTCCTGGCTGAGgtgatctgtt ... tctttggtagGCAATCCAATCATATCGAGCAGAGAGCGACACTGAGCTCAACCTTTCAGCT
EST: gi|28985206|gb|BQ539380.2|BQ539380
EST:     GGAATACGGTCGCAGAGTTGGTCGAGACCGTGGAGTATTTCCTGGCTGAG                         GCAATCCAATCATATCGAGCAGAGAGCGACACTGAGCTCAACCTTTCAGCT
genomic: GGAATACGGTCGCAGAGTTGGTCGAGACCGTGGAGTATTTCCTGGCTGAGgtgatctgtt ... tctttggtagGCAATCCAATCATATCGAGCAGAGAGCGACACTGAGCTCAACCTTTCAGCT
EST: gi|78545157|gb|DV622655.1|DV622655
EST:     GGAATACGGTCGCAGAGTTGGTCGAGACCGTGGAGTATTTCCTGGCTGAG                         GCAATCCAATCATATCGAGCAGAGAGCGACACTGAGCTCAACCTTTCAGCT
genomic: GGAATACGGTCGCAGAGTTGGTCGAGACCGTGGAGTATTTCCTGGCTGAGgtgatctgtt ... tctttggtagGCAATCCAATCATATCGAGCAGAGAGCGACACTGAGCTCAACCTTTCAGCT
EST: gi|32919380|gb|CF024192.1|CF024192
EST:     GGAATACGGTCGCAGAGTTGGTCGAGACCGTGGAGTATTTCCTGGCTGAG                         GCAATCCAATCATATCGAGCAGAGAGCGACACTGAGCTCAACCTTTCAGCT
genomic: GGAATACGGTCGCAGAGTTGGTCGAGACCGTGGAGTATTTCCTGGCTGAGgtgatctgtt ... tctttggtagGCAATCCAATCATATCGAGCAGAGAGCGACACTGAGCTCAACCTTTCAGCT
EST: gi|71768413|gb|DR966350.1|DR966350
EST:     GGAATACGGTCGCAGAGTTGGTCGAGACCGTGGAGTATTTCCTGGCTGAG                         GCAATCCAATCATATCGAGCAGAGAGCGACACTGAGCTCAACCTTTCAGCT
genomic: GGAATACGGTCGCAGAGTTGGTCGAGACCGTGGAGTATTTCCTGGCTGAGgtgatctgtt ... tctttggtagGCAATCCAATCATATCGAGCAGAGAGCGACACTGAGCTCAACCTTTCAGCT
EST: gi|60341099|gb|DN208072.1|DN208072
EST:     GGAATACGGTCGCAGAGTTGGTCGAGACCGTGGAGTATTTCCTGGCTGAG                         GCAATCCAATCATATCGAGCAGAGAGCGACACTGAGCTCAACCTTTCAGCT
genomic: GGAATACGGTCGCAGAGTTGGTCGAGACCGTGGAGTATTTCCTGGCTGAGgtgatctgtt ... tctttggtagGCAATCCAATCATATCGAGCAGAGAGCGACACTGAGCTCAACCTTTCAGCT
EST: gi|74239023|gb|DT646937.1|DT646937
EST:     GGAATACGGTCGCAGAGTTGGTCGAGACCGTGGAGTATTTCCTGGCTGAG                         GCAATCCAATCATATCGAGCAGAGAGCGACACTGAGCTCAACCTTTCAGCT
genomic: GGAATACGGTCGCAGAGTTGGTCGAGACCGTGGAGTATTTCCTGGCTGAGgtgatctgtt ... tctttggtagGCAATCCAATCATATCGAGCAGAGAGCGACACTGAGCTCAACCTTTCAGCT
EST: gi|211106266|gb|FL250478.1|FL250478
EST:     GGAATACGGTCGCAGAGTTGGTCGAGACCGTGGAGTATTTCCTGGCTGAG                         GCAATCCAATCATATCGAGCAGAGAGCGACACTGAGCTCAACCTTTCAGCT
genomic: GGAATACGGTCGCAGAGTTGGTCGAGACCGTGGAGTATTTCCTGGCTGAGgtgatctgtt ... tctttggtagGCAATCCAATCATATCGAGCAGAGAGCGACACTGAGCTCAACCTTTCAGCT
EST: gi|78074542|gb|DV502976.1|DV502976
EST:     GGAATACGGTCGCAGAGTTGGTCGAGACCGTGGAGTATTTCCTGGCTGAG                         GCAATCCAATCATATCGAGCAGAGAGCGACACTGAGCTCAACCTTTCAGCT
genomic: GGAATACGGTCGCAGAGTTGGTCGAGACCGTGGAGTATTTCCTGGCTGAGgtgatctgtt ... tctttggtagGCAATCCAATCATATCGAGCAGAGAGCGACACTGAGCTCAACCTTTCAGCT
EST: gi|76019273|gb|DT946443.1|DT946443
EST:     GGAATACGGTCGCAGAGTTGGTCGAGACCGTGGAGTATTTCCTGGCTGAG                         GCAATCCAATCATATCGAGCAGAGAGCGACACTGAGCTCAACCTTTCAGCT
genomic: GGAATACGGTCGCAGAGTTGGTCGAGACCGTGGAGTATTTCCTGGCTGAGgtgatctgtt ... tctttggtagGCAATCCAATCATATCGAGCAGAGAGCGACACTGAGCTCAACCTTTCAGCT
EST: gi|60358710|gb|DN225683.1|DN225683
EST:     GGAATACGGTCGCAGAGTTGGTCGAGACCGTGGAGTATTTCCTGGCTGAG                         GCAATCCAATCATATCGAGCAGAGAGCGACACTGAGCTCAACCTTTCAGCT
genomic: GGAATACGGTCGCAGAGTTGGTCGAGACCGTGGAGTATTTCCTGGCTGAGgtgatctgtt ... tctttggtagGCAATCCAATCATATCGAGCAGAGAGCGACACTGAGCTCAACCTTTCAGCT
EST: gi|211409238|gb|FL441029.1|FL441029
EST:     GGAATACGGTCGCAGAGTTGGTCGAGACCGTGGAGTATTTCCTGGCTGAG                         GCAATCCAATCATATCGAGCAGAGAGCGACACTGAGCTCAACCTTTCAGCT
genomic: GGAATACGGTCGCAGAGTTGGTCGAGACCGTGGAGTATTTCCTGGCTGAGgtgatctgtt ... tctttggtagGCAATCCAATCATATCGAGCAGAGAGCGACACTGAGCTCAACCTTTCAGCT
EST: gi|71765023|gb|DR962960.1|DR962960
EST:     GGAATACGGTCGCAGAGTTGGTCGAGACCGTGGAGTATTTCCTGGCTGAG                         GCAATCCAATCATATCGAGCAGAGAGCGACACTGAGCTCAACCTTTCAGCT
genomic: GGAATACGGTCGCAGAGTTGGTCGAGACCGTGGAGTATTTCCTGGCTGAGgtgatctgtt ... tctttggtagGCAATCCAATCATATCGAGCAGAGAGCGACACTGAGCTCAACCTTTCAGCT
EST: gi|78026827|gb|DV495214.1|DV495214
EST:     GGAATACGGTCGCAGAGTTGGTCGAGACCGTGGAGTATTTCCTGGCTGAG                         GCAATCCAATCATATCGAGCAGAGAGCGACACTGAGCTCAACCTTTCAGCT
genomic: GGAATACGGTCGCAGAGTTGGTCGAGACCGTGGAGTATTTCCTGGCTGAGgtgatctgtt ... tctttggtagGCAATCCAATCATATCGAGCAGAGAGCGACACTGAGCTCAACCTTTCAGCT
EST: gi|71756340|gb|DR954277.1|DR954277
EST:     GGAATACGGTCGCAGAGTTGGTCGAGACCGTGGAGTATTTCCTGGCTGAG                         GCAATCCAATCATATCGAGCAGAGAGCGACACTGAGCTCAACCTTTCAGCT
genomic: GGAATACGGTCGCAGAGTTGGTCGAGACCGTGGAGTATTTCCTGGCTGAGgtgatctgtt ... tctttggtagGCAATCCAATCATATCGAGCAGAGAGCGACACTGAGCTCAACCTTTCAGCT
EST: gi|149085094|gb|EE174601.2|EE174601
EST:     GGAATACGGTCGCAGAGTTGGTCGAGACCGTGGAGTATTTCCTGGCTGAG                         GCAATCCAATCATATCGAGCAGAGAGCGACACTGAGCTCAACCTTTCAGCT
genomic: GGAATACGGTCGCAGAGTTGGTCGAGACCGTGGAGTATTTCCTGGCTGAGgtgatctgtt ... tctttggtagGCAATCCAATCATATCGAGCAGAGAGCGACACTGAGCTCAACCTTTCAGCT
EST: gi|71328409|gb|DR800841.1|DR800841
EST:     GGAATACGGTCGCAGAGTTGGTCGAGACCGTGGAGTATTTCCTGGCTGAG                         GCAATCCAATCATATCGAGCAGAGAGCGACACTGAGCTCAACCTTTCAGCT
genomic: GGAATACGGTCGCAGAGTTGGTCGAGACCGTGGAGTATTTCCTGGCTGAGgtgatctgtt ... tctttggtagGCAATCCAATCATATCGAGCAGAGAGCGACACTGAGCTCAACCTTTCAGCT

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: 115

TTCCATGCCTCCACCGCCTGCATATGAAGAAGTCAATGGTATATTCATGAGGAATACGGTCGCAGAGTTGGTCGAGACCGTGGAGTATTTCCTGGCTGAGgtgatctgtt ... tctttggtagGCAATCCAATCATATCGAGCAGAGAGCGACACTGAGCTCAACCTTTCAGCTGGTGACTACATAGTGGTCCGAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 83

TTCCATGCCTCCACCGCCTGCATATGAAGAAGTCAATGGTATATTCATGAGGAATACGGTCGCAGAGTTGGTCGAGACCGTGGAGTATTTCCTGGCTGAGgtgatctgtt ... tctttggtagGCAATCCAATCATATCGAGCAGAGAGCGACACTGAGCTCAACCTTTCAGCTGGTGACTACATAGTGGTCCGAAAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 72

TTCCATGCCTCCACCGCCTGCATATGAAGAAGTCAATGGTATATTCATGAGGAATACGGTCGCAGAGTTGGTCGAGACCGTGGAGTATTTCCTGGCTGAGgtgatctgtt ... tctttggtagGCAATCCAATCATATCGAGCAGAGAGCGACACTGAGCTCAACCTTTCAGCTGGTGACTACATAGTGGTCCGAAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 74

TTCCATGCCTCCACCGCCTGCATATGAAGAAGTCAATGGTATATTCATGAGGAATACGGTCGCAGAGTTGGTCGAGACCGTGGAGTATTTCCTGGCTGAGgtgatctgtt ... tctttggtagGCAATCCAATCATATCGAGCAGAGAGCGACACTGAGCTCAACCTTTCAGCTGGTGACTACATAGTGGTCCGAAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCCATGCCTCCACCGCCTGCATATGAAGAAGTCAATGGTATATTCATGAGGAATACGGTCGCAGAGTTGGTCGAGACCGTGGAGTATTTCCTGGCTGAGgtgatctgtttcgttacattgaacaagtttgaagctgcgctaggcactagatcttagtttgtacccataataatctgtgtatgtattgccatttttctttggtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG