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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catgtagaatttatttgttctcttgtaactggaaagttttggttcttaagagttaagagtgactttaatcatatgatgcatggcattttttttcctgcagTGGAATTTGATTTTAGTGGAAACTATCTTGCCATTGGTGGTTCAGATATAAG

Basic information

species Zea mays
transcript GRMZM2G037698_T02
intron # 15
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|6022161|gb|AW067089.1|AW067089
EST:     AAATTTTAGGACCTTCTCTCCCTATGATTCAGATACGCCAACAAATACTG                         TGGAATTTGATTTTAGTGGAAACTATCTTGCCATTGGTGGTTCAGATATAA
genomic: AAATTTTAGGACCTTCTCTCCCTATGATTCAGATACGCCAACAAATACTGgtaagtaact ... tttcctgcagTGGAATTTGATTTTAGTGGAAACTATCTTGCCATTGGTGGTTCAGATATAA
EST: gi|32908360|gb|CF013173.1|CF013173
EST:     AAATTTTAGGACCTTCTCTCCCTATGATTCAGATACGCCAACAAATACTG                         TGGAATTTGATTTTAGTGGAAACTATCTTGCCATTGGTGGTTCAGATATAA
genomic: AAATTTTAGGACCTTCTCTCCCTATGATTCAGATACGCCAACAAATACTGgtaagtaact ... tttcctgcagTGGAATTTGATTTTAGTGGAAACTATCTTGCCATTGGTGGTTCAGATATAA
EST: gi|5055844|gb|AI734731.1|AI734731
EST:     TTCAGATACGCCAACAAATACTG                         TGGAATTTGATTTTAGTGGAAACTATCTTGCCATTGGTGGTTCAGATATAA
genomic: TTCAGATACGCCAACAAATACTGgtaagtaact ... tttcctgcagTGGAATTTGATTTTAGTGGAAACTATCTTGCCATTGGTGGTTCAGATATAA
EST: gi|32934237|gb|CF039049.1|CF039049
EST:     AAATTTTAGGACCTTCTCTCCCTATGATTCAGATACGCCAACAAATACTG                         TGGAATTTGATTTTAGTGGAAACTATCTTGCCATTGGTGGTTCAGATATAA
genomic: AAATTTTAGGACCTTCTCTCCCTATGATTCAGATACGCCAACAAATACTGgtaagtaact ... tttcctgcagTGGAATTTGATTTTAGTGGAAACTATCTTGCCATTGGTGGTTCAGATATAA
EST: gi|20811259|gb|BQ295737.1|BQ295737
EST:     AAATTTTAGGACCTTCTCTCCCTATGATTCAGATACGCCAACAAATACTG                         TGGAATTTGATTTTAGTGGAAACTATCTTGCCATTGGTGGTTCAGATATAA
genomic: AAATTTTAGGACCTTCTCTCCCTATGATTCAGATACGCCAACAAATACTGgtaagtaact ... tttcctgcagTGGAATTTGATTTTAGTGGAAACTATCTTGCCATTGGTGGTTCAGATATAA
EST: gi|24764727|gb|CA399890.1|CA399890
EST:     AAATTTTAGGACCTTCTCTCCCTATGATTCAGATACGCCAACAAATACTG                         TGGAATTTGATTTTAGTGGAAACTATCTTGCCATTGGTGGTTCAGATATAA
genomic: AAATTTTAGGACCTTCTCTCCCTATGATTCAGATACGCCAACAAATACTGgtaagtaact ... tttcctgcagTGGAATTTGATTTTAGTGGAAACTATCTTGCCATTGGTGGTTCAGATATAA
EST: gi|211335935|gb|FL468899.1|FL468899
EST:     AAATTTTAGGACCTTCTCTCCCTATGATTCAGATACGCCAACAAATACTG                         TGGAATTTGATTTTAGTGGAAACTATCTTGCCATTGGTGGTTCAGATATAA
genomic: AAATTTTAGGACCTTCTCTCCCTATGATTCAGATACGCCAACAAATACTGgtaagtaact ... tttcctgcagTGGAATTTGATTTTAGTGGAAACTATCTTGCCATTGGTGGTTCAGATATAA
EST: gi|33090853|gb|CF050847.1|CF050847
EST:     AAATTTTAGGACCTTCTCTCCCTATGATTCAGATACGCCAACAAATACTG                         TGGAATTTGATTTTAGTGGAAACTATCTTGCCATTGGTGGTTCAGATATAA
genomic: AAATTTTAGGACCTTCTCTCCCTATGATTCAGATACGCCAACAAATACTGgtaagtaact ... tttcctgcagTGGAATTTGATTTTAGTGGAAACTATCTTGCCATTGGTGGTTCAGATATAA
EST: gi|32933281|gb|CF038093.1|CF038093
EST:     AAATTTTAGGACCTTCTCTCCCTATGATTCAGATACGCCAACAAATACTG                         TGGAATTTGATTTTAGTGGAAACTATCTTGCCATTGGTGGTTCAGATATAA
genomic: AAATTTTAGGACCTTCTCTCCCTATGATTCAGATACGCCAACAAATACTGgtaagtaact ... tttcctgcagTGGAATTTGATTTTAGTGGAAACTATCTTGCCATTGGTGGTTCAGATATAA
EST: gi|148987119|gb|EE030947.2|EE030947
EST:     AAATTTTAGGACCTTCTCTCCCTATGATTCAGATACGCCAACAAATACTG                         TGGAATTTGATTTTAGTGGAAACTATCTTGCCATTGGTGGTTCAGATATAA
genomic: AAATTTTAGGACCTTCTCTCCCTATGATTCAGATACGCCAACAAATACTGgtaagtaact ... tttcctgcagTGGAATTTGATTTTAGTGGAAACTATCTTGCCATTGGTGGTTCAGATATAA
EST: gi|8577012|gb|BE129649.1|BE129649
EST:     AAATTTTAGGACCTTCTCTCCCTATGATTCAGATACGCCAACAAATACTG                         TGGAATTTGATTTTAGTGGAAACTATCTTGCCATTGGTGGTTCAGATATAA
genomic: AAATTTTAGGACCTTCTCTCCCTATGATTCAGATACGCCAACAAATACTGgtaagtaact ... tttcctgcagTGGAATTTGATTTTAGTGGAAACTATCTTGCCATTGGTGGTTCAGATATAA
EST: gi|78024591|gb|DV492978.1|DV492978
EST:     TACGCCAACAAATACTG                         TGGAATTTGATTTTAGTGGAAACTATCTTGCCATTGGTGGTTCAGATATAA
genomic: TACGCCAACAAATACTGgtaagtaact ... tttcctgcagTGGAATTTGATTTTAGTGGAAACTATCTTGCCATTGGTGGTTCAGATATAA
EST: gi|32837457|gb|CD977135.1|CD977135
EST:     AAATTTTAGGACCTTCTCTCCCTATGATTCAGATACGCCAACAAATACTG                         TGGAATTTGATTTTAGTGGAAACTATCTTGCCATTGGTGGTTCAAATATAA
genomic: AAATTTTAGGACCTTCTCTCCCTATGATTCAGATACGCCAACAAATACTGgtaagtaact ... tttcctgcagTGGAATTTGATTTTAGTGGAAACTATCTTGCCATTGGTGGTTCAGATATAA
EST: gi|60341462|gb|DN208435.1|DN208435
EST:     AAATTTTAGGACCTTCTCTCCCTATGATTCAGATACGCCAACAAATACTG                         TGGAATTTGATTTTAGTGGAAACTATCTTGCCATTGGTGGTTCAGATATAA
genomic: AAATTTTAGGACCTTCTCTCCCTATGATTCAGATACGCCAACAAATACTGgtaagtaact ... tttcctgcagTGGAATTTGATTTTAGTGGAAACTATCTTGCCATTGGTGGTTCAGATATAA
EST: gi|5607968|gb|AI901635.1|AI901635
EST:     AAATTTTAGGACCTTCTCTCCCTATGATTCAGATACGCCAACAAATACTG                         TGGAATTTGATTTTAGTGGAAACTATCTTGCCATTGGTGGTTCAGATATAA
genomic: AAATTTTAGGACCTTCTCTCCCTATGATTCAGATACGCCAACAAATACTGgtaagtaact ... tttcctgcagTGGAATTTGATTTTAGTGGAAACTATCTTGCCATTGGTGGTTCAGATATAA
EST: gi|32936163|gb|CF040975.1|CF040975
EST:     AAATTTTAGGACCTTCTCTCCCTATGATTCAGATACGCCAACAAATACTG                         TGGAATTTGATTTTAGTGGAAACTATCTTGCCATTGGTGGTTCAGATATAA
genomic: AAATTTTAGGACCTTCTCTCCCTATGATTCAGATACGCCAACAAATACTGgtaagtaact ... tttcctgcagTGGAATTTGATTTTAGTGGAAACTATCTTGCCATTGGTGGTTCAGATATAA
EST: gi|33103734|gb|CF063694.1|CF063694
EST:     AAATTTTAGGACCTTCTCTCCCTATGATTCAGATACGCCAACAAATACTG                         TGGAATTTGATTTTAGTGGAAACTATCTTGCCATTGGTGGTTCAGATATAA
genomic: AAATTTTAGGACCTTCTCTCCCTATGATTCAGATACGCCAACAAATACTGgtaagtaact ... tttcctgcagTGGAATTTGATTTTAGTGGAAACTATCTTGCCATTGGTGGTTCAGATATAA

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: 242

ACTGCTGCTCATGATGGTGTCAAGCTTTGGGATCTTCGGAAATTAAGAAATTTTAGGACCTTCTCTCCCTATGATTCAGATACGCCAACAAATACTGgtaagtaact ... tttcctgcagTGGAATTTGATTTTAGTGGAAACTATCTTGCCATTGGTGGTTCAGATATAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 121

ACTGCTGCTCATGATGGTGTCAAGCTTTGGGATCTTCGGAAATTAAGAAATTTTAGGACCTTCTCTCCCTATGATTCAGATACGCCAACAAATACTGgtaagtaact ... tttcctgcagTGGAATTTGATTTTAGTGGAAACTATCTTGCCATTGGTGGTTCAGATATAAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 83

ACTGCTGCTCATGATGGTGTCAAGCTTTGGGATCTTCGGAAATTAAGAAATTTTAGGACCTTCTCTCCCTATGATTCAGATACGCCAACAAATACTGgtaagtaact ... tttcctgcagTGGAATTTGATTTTAGTGGAAACTATCTTGCCATTGGTGGTTCAGATATAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 96

ACTGCTGCTCATGATGGTGTCAAGCTTTGGGATCTTCGGAAATTAAGAAATTTTAGGACCTTCTCTCCCTATGATTCAGATACGCCAACAAATACTGgtaagtaact ... tttcctgcagTGGAATTTGATTTTAGTGGAAACTATCTTGCCATTGGTGGTTCAGATATAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaagagttaagagtgactttaatcatatgatgcatggcattttttttcctgcagTGGAATTTGATTTTAGTGGAAACTATCTTGCCATTGGTGGTTCAGATATAAG
                 ctttaat  putative branch site (score: 96)
                                      cattttttttcctgc  putative PPT
                  tttaatcatatgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catgtagaatttatttgttctcttgtaactggaaagttttggttcttaagagttaagagtgactttaatcatatgatgcatggcattttttttcctgcagTGGAATTTGATTTTAGTGGAAACTATCTTGCCATTGGTGGTTCAGATATAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
catgtag
- - - - - - - - - - - - - - - - - - - -tggttct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcatgg