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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatatcacccttattttgagttaatgttttaactcccttacccttcaaacatcatgttgttttattgttagtagtttttgatgatagatctgctagacatcactcctttttaatcatattctgaatcagatgatccctaaatgcatcaatttttaatcaaattgcagAAACGGAGGGCTCTAGAAGAAAGTGAGGAAGGTCTTAAG

Basic information

species Zea mays
transcript GRMZM2G003692_T07
intron # 5
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|14244326|gb|BG842296.2|BG842296
EST:     CTAATGCAGGCGTTGACTATATGGTCCATAATGCAGCCTTCGAACGTCCT                         AAACGGAGGGCTCTAGAAGAAAGTGAGGAAGGTCTTAAG
genomic: CTAATGCAGGCGTTGACTATATGGTCCATAATGCAGCCTTCGAACGTCCTgtaaatatca ... caaattgcagAAACGGAGGGCTCTAGAAGAAAGTGAGGAAGGTCTTAAG
EST: gi|14208321|gb|BG842006.1|BG842006
EST:     CTAATGCAGGCGTTGACTATATGGTCCATAATGCAGCCTTCGAACGTCCT                         AAACGGAGGGCTCTAGAAGAAAGTGAGGAAGGTCTTAAG
genomic: CTAATGCAGGCGTTGACTATATGGTCCATAATGCAGCCTTCGAACGTCCTgtaaatatca ... caaattgcagAAACGGAGGGCTCTAGAAGAAAGTGAGGAAGGTCTTAAG
EST: gi|37397592|gb|CF636096.1|CF636096
EST:     CTAATGCAGGCGTTGACTATATGGTCCATAATGCAGCCTTCGAACGTCCT                         AAACGGAGGGCTCTAGAAGAAAGTGAGGAAGGTCTTAAG
genomic: CTAATGCAGGCGTTGACTATATGGTCCATAATGCAGCCTTCGAACGTCCTgtaaatatca ... caaattgcagAAACGGAGGGCTCTAGAAGAAAGTGAGGAAGGTCTTAAG
EST: gi|149101270|gb|EE187382.2|EE187382
EST:     CTAATGCAGGCGTTGACTATATGGTCCATAATGCAGCCTTCGAACGTCCT                         AAACGGAGGGCTCTAGAAGAAAGTGAGGAAGGTCTTAAG
genomic: CTAATGCAGGCGTTGACTATATGGTCCATAATGCAGCCTTCGAACGTCCTgtaaatatca ... caaattgcagAAACGGAGGGCTCTAGAAGAAAGTGAGGAAGGTCTTAAG
EST: gi|32856130|gb|CD995811.1|CD995811
EST:     CTAATGCAGGCGTTGACTATATGGTCCATAATGCAGCCTTCGAACGTCCT                         AAACGGAGGGCTCTAGAAGAGAGTGAGGAAGGTCTTAAG
genomic: CTAATGCAGGCGTTGACTATATGGTCCATAATGCAGCCTTCGAACGTCCTgtaaatatca ... caaattgcagAAACGGAGGGCTCTAGAAGAAAGTGAGGAAGGTCTTAAG
EST: gi|32840502|gb|CD980183.1|CD980183
EST:     GCAGGCGTTGACTATATGGTCCATAATGCAGCCTTCGAACGTCCT                         AAACGGAGGGCTCTAGAAGAAAGTGAGGAAGGTCTTAAG
genomic: GCAGGCGTTGACTATATGGTCCATAATGCAGCCTTCGAACGTCCTgtaaatatca ... caaattgcagAAACGGAGGGCTCTAGAAGAAAGTGAGGAAGGTCTTAAG
EST: gi|40337101|gb|CK371171.1|CK371171
EST:     CTAATGCAGGCGTTGACTATATGGTCCATAATGCAGCCTTCGAACGTCCT                         AAACGGAGGGCTCTAGAAGAAAGTGAGGAAGGTCTTAAG
genomic: CTAATGCAGGCGTTGACTATATGGTCCATAATGCAGCCTTCGAACGTCCTgtaaatatca ... caaattgcagAAACGGAGGGCTCTAGAAGAAAGTGAGGAAGGTCTTAAG
EST: gi|71759817|gb|DR957754.1|DR957754
EST:     CTAATGCAGGCGTTGACTATATGGTCCATAATGCAGCCTTCGAACGTCCT                         AAACGGAGGGCTCTAGAAGAAAGTGAGGAAGGTCTTAAG
genomic: CTAATGCAGGCGTTGACTATATGGTCCATAATGCAGCCTTCGAACGTCCTgtaaatatca ... caaattgcagAAACGGAGGGCTCTAGAAGAAAGTGAGGAAGGTCTTAAG
EST: gi|71438969|gb|DR820019.1|DR820019
EST:     CTAATGCAGGCGTTGACTATATGGTCCATAATGCAGCCTTCGAACGTCCT                         AAACGGAGGGCTCTAGAAGAAAGTGAGGAAGGTCTTAAG
genomic: CTAATGCAGGCGTTGACTATATGGTCCATAATGCAGCCTTCGAACGTCCTgtaaatatca ... caaattgcagAAACGGAGGGCTCTAGAAGAAAGTGAGGAAGGTCTTAAG

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: 46 (upstream exon), 39 (downstream exon)
Score: 104

TGGTGAAGAATCTCTGAAAGAAGTCGTACATGTGGCAGAATCATTTTTTTCTAATGCAGGCGTTGACTATATGGTCCATAATGCAGCCTTCGAACGTCCTgtaaatatca ... caaattgcagAAACGGAGGGCTCTAGAAGAAAGTGAGGAAGGTCTTAAG


Block sizes: 47 (upstream exon), 39 (downstream exon)
Score: 367

TGGTGAAGAATCTCTGAAAGAAGTCGTACATGTGGCAGAATCATTTTTTTCTAATGCAGGCGTTGACTATATGGTCCATAATGCAGCCTTCGAACGTCCTgtaaatatca ... caaattgcagAAACGGAGGGCTCTAGAAGAAAGTGAGGAAGGTCTTAAG


Block sizes: 49 (upstream exon), 39 (downstream exon)
Score: 329

TGGTGAAGAATCTCTGAAAGAAGTCGTACATGTGGCAGAATCATTTTTTTCTAATGCAGGCGTTGACTATATGGTCCATAATGCAGCCTTCGAACGTCCTgtaaatatca ... caaattgcagAAACGGAGGGCTCTAGAAGAAAGTGAGGAAGGTCTTAAG


Block sizes: 49 (upstream exon), 39 (downstream exon)
Score: 334

TGGTGAAGAATCTCTGAAAGAAGTCGTACATGTGGCAGAATCATTTTTTTCTAATGCAGGCGTTGACTATATGGTCCATAATGCAGCCTTCGAACGTCCTgtaaatatca ... caaattgcagAAACGGAGGGCTCTAGAAGAAAGTGAGGAAGGTCTTAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcatattctgaatcagatgatccctaaatgcatcaatttttaatcaaattgcagAAACGGAGGGCTCTAGAAGAAAGTGAGGAAGGTCTTAAG
                                      ttttaat  putative branch site (score: 334)
                                atcaatttttaatcaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatatcacccttattttgagttaatgttttaactcccttacccttcaaacatcatgttgttttattgttagtagtttttgatgatagatctgctagacatcactcctttttaatcatattctgaatcagatgatccctaaatgcatcaatttttaatcaaattgcagAAACGGAGGGCTCTAGAAGAAAGTGAGGAAGGTCTTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA