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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtgaacaggtgaaacgtgaagagcaacttgagtatgcccaaagtatcatttcaggactgaagagaaatgctaaccttccccgattcccccctcttgcagTCTCGCTTGGCAACCGGCGCCGCCGAAGCCGACAAGGGAGGCACGTGCGCCCAGCGAACACCAAGCTCAAGGTGGGTGATCGTACTGGCGAACCGCTGCA

Basic information

species Zea mays
transcript GRMZM2G069865_T02
intron # 1
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|71315085|gb|DR794171.1|DR794171
EST:     GCTAGATCTGCACCTGTTCATTCCTCTCCAGTCCCTAGCGAGAGATTCAG                         TCTCGCTTGGCAACCGGCGCCGCCGAAGCCGACAAGGGAGGCACGTGCGCC
genomic: GCTAGATCTGCACCTGTTCATTCCTCTCCAGTCCCTAGCGAGAGATTCAGgtaaggagta ... cctcttgcagTCTCGCTTGGCAACCGGCGCCGCCGAAGCCGACAAGGGAGGCACGTGCGCC
EST: gi|211107330|gb|FL033707.1|FL033707
EST:     GCTAGATCTGCACCTGTTCATTCCTCTCCAGTCCCTAGCGAGAGATTCAG                         TCTCGCTTGGCAACCGGCGCCGC-GAAGCCGACAAGGGAGGCACGTGCGCC
genomic: GCTAGATCTGCACCTGTTCATTCCTCTCCAGTCCCTAGCGAGAGATTCAGgtaaggagta ... cctcttgcagTCTCGCTTGGCAACCGGCGCCGCCGAAGCCGACAAGGGAGGCACGTGCGCC
EST: gi|148990983|gb|EE032418.2|EE032418
EST:     GCTAGATCTGCACCTGTTCATTCCTCTCCAGTCCCTAGCGAGAGATTCAG                         TCTCGCTTGGCAACCGGCGCCGCCGAAGCCGACAAGGGAGGCACGTGCGCC
genomic: GCTAGATCTGCACCTGTTCATTCCTCTCCAGTCCCTAGCGAGAGATTCAGgtaaggagta ... cctcttgcagTCTCGCTTGGCAACCGGCGCCGCCGAAGCCGACAAGGGAGGCACGTGCGCC
EST: gi|211107333|gb|FL033710.1|FL033710
EST:     CTAGATCTGCACCTGTTCATTCCTCTCCAGTCCCTAGCGAGAGATTTCAG                         TCTCGCTTGGCAACCGGCGCCGCCGAAGCCGACAAGGGAGGCACGTGCGC
genomic: CTAGATCTGCACCTGTTCATTCCTCTCCAGTCCCTAGCGAGAGATT-CAGgtaaggagta ... cctcttgcagTCTCGCTTGGCAACCGGCGCCGCCGAAGCCGACAAGGGAGGCACGTGCGC
EST: gi|211107332|gb|FL033709.1|FL033709
EST:     GCTAGATCTGCACCTGTTCATTCCTCTCCAGTCCCTAGCGAGAGATTCAG                         TCTCGCTTGGCAACCGGCGCCGCCGAAGCCGACAAGGGAGGCACGTGCGCC
genomic: GCTAGATCTGCACCTGTTCATTCCTCTCCAGTCCCTAGCGAGAGATTCAGgtaaggagta ... cctcttgcagTCTCGCTTGGCAACCGGCGCCGCCGAAGCCGACAAGGGAGGCACGTGCGCC
EST: gi|91872241|gb|EB402198.1|EB402198
EST:     GCTAGATCTGCACCTGTTCATTCCTCTCCAGTCCCTAGCGAGAGATTCAG                         TCTCGCTTGGCAACCGGCGCCGCCGAAGCCGACAAGGGAGGCACGTGCGCC
genomic: GCTAGATCTGCACCTGTTCATTCCTCTCCAGTCCCTAGCGAGAGATTCAGgtaaggagta ... cctcttgcagTCTCGCTTGGCAACCGGCGCCGCCGAAGCCGACAAGGGAGGCACGTGCGCC

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), 38 (downstream exon)
Score: 19

AGCGCCCTGATCCTCCCTCTCCCTGACTCCCTCCTCACGTTCTCCGCACGGCTAGATCTGCACCTGTTCATTCCTCTCCAGTCCCTAGCGAGAGATTCAGgtaaggagta ... cctcttgcagTCTCGCTTGGCAACCGGCGCCGCCGAAGCCGACAAGGGAGGCACGTGCGCCCAGCGAACACCAAGCTCAAGGTGGGTGATCGTACTGGCGAACCGCTGCA


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 24

AGCGCCCTGATCCTCCCTCTCCCTGACTCCCTCCTCACGTTCTCCGCACGGCTAGATCTGCACCTGTTCATTCCTCTCCAGTCCCTAGCGAGAGATTCAGgtaaggagta ... cctcttgcagTCTCGCTTGGCAACCGGCGCCGCCGAAGCCGACAAGGGAGGCACGTGCGCCCAGCGAACACCAAGCTCAAGGTGGGTGATCGTACTGGCGAACCGCTGCA


Block sizes: 48 (upstream exon), 44 (downstream exon)
Score: 17

AGCGCCCTGATCCTCCCTCTCCCTGACTCCCTCCTCACGTTCTCCGCACGGCTAGATCTGCACCTGTTCATTCCTCTCCAGTCCCTAGCGAGAGATTCAGgtaaggagta ... cctcttgcagTCTCGCTTGGCAACCGGCGCCGCCGAAGCCGACAAGGGAGGCACGTGCGCCCAGCGAACACCAAGCTCAAGGTGGGTGATCGTACTGGCGAACCGCTGCA


Block sizes: 45 (upstream exon), 44 (downstream exon)
Score: 29

AGCGCCCTGATCCTCCCTCTCCCTGACTCCCTCCTCACGTTCTCCGCACGGCTAGATCTGCACCTGTTCATTCCTCTCCAGTCCCTAGCGAGAGATTCAGgtaaggagta ... cctcttgcagTCTCGCTTGGCAACCGGCGCCGCCGAAGCCGACAAGGGAGGCACGTGCGCCCAGCGAACACCAAGCTCAAGGTGGGTGATCGTACTGGCGAACCGCTGCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcatttcaggactgaagagaaatgctaaccttccccgattcccccctcttgcagTCTCGCTTGGCAACCGGCGCCGCCGAAGCCGACAAGGGAGGCACGTGCGCCCAGCGAACACCAAGCTCAAGGTGGGTGATCGTACTGGCGAACCGCTGCA
                       tgctaac  putative branch site (score: 29)
                             ccttccccgattcccc  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtgaacaggtgaaacgtgaagagcaacttgagtatgcccaaagtatcatttcaggactgaagagaaatgctaaccttccccgattcccccctcttgcagTCTCGCTTGGCAACCGGCGCCGCCGAAGCCGACAAGGGAGGCACGTGCGCCCAGCGAACACCAAGCTCAAGGTGGGTGATCGTACTGGCGAACCGCTGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - gtatgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaagagaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atgctaa