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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttatttactgaactgtcaattcagatcatatctgacaaacttattgtattatattttcaccatttttaaccgtttccacttttagTTATGTGTTTGGAACACGGATGGATGGGAAAAGCAAAAGAACAGATTTTTGCAGATACCGTCAGGTCGCCAATCTAATATCTTGGACACTCGTGTTCAGT

Basic information

species Zea mays
transcript GRMZM2G550865_T01
intron # 9
splice site 3'
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|211016175|gb|FL013379.1|FL013379
EST:     CCTTTTCAAATGTGCTAAATGTCTTAGTCTCTTCCGGAGCTGATGCTCAG                         TTATGTGTTTGGAACACGGATGGATGGGAAAAGCAAAAGAACAGATTTTTG
genomic: CCTTTTCAAATGTGCTAAATGTCTTAGTCTCTTCCGGAGCTGATGCTCAGgttatttact ... ccacttttagTTATGTGTTTGGAACACGGATGGATGGGAAAAGCAAAAGAACAGATTTTTG
EST: gi|22546038|gb|BU098359.1|BU098359
EST:     CCTTTTCAAATGTGCTAAATGTCTTAGTCTCTTCCGGAGCTGATGCTCAG                         TTATGTGTTTGGAACACGGATGGATGGGAAAAGCAAAAGAACAGATTTTTG
genomic: CCTTTTCAAATGTGCTAAATGTCTTAGTCTCTTCCGGAGCTGATGCTCAGgttatttact ... ccacttttagTTATGTGTTTGGAACACGGATGGATGGGAAAAGCAAAAGAACAGATTTTTG
EST: gi|67024360|gb|CO453109.1|CO453109
EST:     CCTTTTCAAATGTGCTAAATGTCTTAGTCTCTTCCGGAGCTGATGCTCAG                         TTATGTGTTTGGAACACGGATGGATGGGAAAAGCAAAAGAACAGATTTTTG
genomic: CCTTTTCAAATGTGCTAAATGTCTTAGTCTCTTCCGGAGCTGATGCTCAGgttatttact ... ccacttttagTTATGTGTTTGGAACACGGATGGATGGGAAAAGCAAAAGAACAGATTTTTG
EST: gi|67032677|gb|CO461426.1|CO461426
EST:     CCTTTTCAAATGTGCTAAATGTCTTAGTCTCTTCCGGAGCTGATGCTCAG                         TTATGTGTTTGGAACACGGATGGATGGGAAAAGCAAAAGAACAGATTTTTG
genomic: CCTTTTCAAATGTGCTAAATGTCTTAGTCTCTTCCGGAGCTGATGCTCAGgttatttact ... ccacttttagTTATGTGTTTGGAACACGGATGGATGGGAAAAGCAAAAGAACAGATTTTTG
EST: gi|87157645|gb|DY402434.1|DY402434
EST:     CCTTTTCAAATGTGCTAAATGTCTTAGTCTCTTCCGGAGCTGATGCTCAG                         TTATGTGTTTGGAACACGGATGGATGGGAAAAGCAAAAGAACAGATTTTTG
genomic: CCTTTTCAAATGTGCTAAATGTCTTAGTCTCTTCCGGAGCTGATGCTCAGgttatttact ... ccacttttagTTATGTGTTTGGAACACGGATGGATGGGAAAAGCAAAAGAACAGATTTTTG
EST: gi|78083755|gb|DV512148.1|DV512148
EST:     CCTTTTCAAATGTGCTAAATGTCTTAGTCTCTTCCGGAGCTGATGCTCAG                         TTATGTGTTTGGAACACGGATGGATGGGAAAAGCAAAAGAACAGATTTTTG
genomic: CCTTTTCAAATGTGCTAAATGTCTTAGTCTCTTCCGGAGCTGATGCTCAGgttatttact ... ccacttttagTTATGTGTTTGGAACACGGATGGATGGGAAAAGCAAAAGAACAGATTTTTG
EST: gi|26558945|gb|CA831180.1|CA831180
EST:     CCTTTTCAAATGTGCTAAATGTCTTAGTCTCTTCCGGAGCTGATGCTCAG                         TTATGTGTTTGGAACACGGATGGATGGGAAAAGCAAAAGAACAGATTTTTG
genomic: CCTTTTCAAATGTGCTAAATGTCTTAGTCTCTTCCGGAGCTGATGCTCAGgttatttact ... ccacttttagTTATGTGTTTGGAACACGGATGGATGGGAAAAGCAAAAGAACAGATTTTTG

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), 49 (downstream exon)
Score: 296

GTCAAAAGCAAGCTCAGGGGTCACTCTAAGAGAATCACGGGTCTTGCCTTTTCAAATGTGCTAAATGTCTTAGTCTCTTCCGGAGCTGATGCTCAGgttatttact ... ccacttttagTTATGTGTTTGGAACACGGATGGATGGGAAAAGCAAAAGAACAGATTTTTGCAGATACCGTCAGGTCGCCAATCTAATATCTTGGACACTCGTGTTCAGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 183

GTCAAAAGCAAGCTCAGGGGTCACTCTAAGAGAATCACGGGTCTTGCCTTTTCAAATGTGCTAAATGTCTTAGTCTCTTCCGGAGCTGATGCTCAGgttatttact ... ccacttttagTTATGTGTTTGGAACACGGATGGATGGGAAAAGCAAAAGAACAGATTTTTGCAGATACCGTCAGGTCGCCAATCTAATATCTTGGACACTCGTGTTCAGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 275

GTCAAAAGCAAGCTCAGGGGTCACTCTAAGAGAATCACGGGTCTTGCCTTTTCAAATGTGCTAAATGTCTTAGTCTCTTCCGGAGCTGATGCTCAGgttatttact ... ccacttttagTTATGTGTTTGGAACACGGATGGATGGGAAAAGCAAAAGAACAGATTTTTGCAGATACCGTCAGGTCGCCAATCTAATATCTTGGACACTCGTGTTCAGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 159

GTCAAAAGCAAGCTCAGGGGTCACTCTAAGAGAATCACGGGTCTTGCCTTTTCAAATGTGCTAAATGTCTTAGTCTCTTCCGGAGCTGATGCTCAGgttatttact ... ccacttttagTTATGTGTTTGGAACACGGATGGATGGGAAAAGCAAAAGAACAGATTTTTGCAGATACCGTCAGGTCGCCAATCTAATATCTTGGACACTCGTGTTCAGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgacaaacttattgtattatattttcaccatttttaaccgtttccacttttagTTATGTGTTTGGAACACGGATGGATGGGAAAAGCAAAAGAACAGATTTTTGCAGATACCGTCAGGTCGCCAATCTAATATCTTGGACACTCGTGTTCAGT
                                 ttttaac  putative branch site (score: 159)
                                       ccgtttccactttt  CT-rich tract
          ttattgtattatattt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttatttactgaactgtcaattcagatcatatctgacaaacttattgtattatattttcaccatttttaaccgtttccacttttagTTATGTGTTTGGAACACGGATGGATGGGAAAAGCAAAAGAACAGATTTTTGCAGATACCGTCAGGTCGCCAATCTAATATCTTGGACACTCGTGTTCAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT