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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgaaagttacagctgcttcagtcatttgaacaagacatccccgtcttttctaggtaacttcgaactagagatctcatgctatttcatctctcctttcagAGTGATTCTGCAGAAGTATTCATTCTACTGGCGTGCTGAGCAGGTGCAGGAGCTCTAATAAGCCTAGTGCGCACTTCAGTCATCAGCCAAGTGATTGAAA

Basic information

species Zea mays
transcript GRMZM2G011588_T03
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|28984342|gb|BQ539412.2|BQ539412
EST:     CAGCAATCCCTGCCGTCTTGCCATGCTCCCCACGAGGAGCACACCGTCAG                         AGTGATTCTGCAGAAGTATTCATTCTACTGGCGTGCTGAGCAGGTGCAGGA
genomic: CAGCAATCCCTGCCGTCTTGCCATGCTCCCCACGAGGAGCACACCGTCAGgtccgcctcc ... ctcctttcagAGTGATTCTGCAGAAGTATTCATTCTACTGGCGTGCTGAGCAGGTGCAGGA
EST: gi|211331079|gb|FL338526.1|FL338526
EST:     CAGCAATCCCTGCCGTCTTGCCATGCTCCCCACGAGGAGCACATCGTCAG                         AGTGATTCTGCAGAAGTATTCATTCTACTGGCGTGCTGAGCAGGTGCAGGA
genomic: CAGCAATCCCTGCCGTCTTGCCATGCTCCCCACGAGGAGCACACCGTCAGgtccgcctcc ... ctcctttcagAGTGATTCTGCAGAAGTATTCATTCTACTGGCGTGCTGAGCAGGTGCAGGA

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), 43 (downstream exon)
Score: 28

CACCCTCTTCTCCTCCCAAGGCTGACTGGCCGTCGGCTCGGGTCTGGGGACAGCAATCCCTGCCGTCTTGCCATGCTCCCCACGAGGAGCACACCGTCAGgtccgcctcc ... ctcctttcagAGTGATTCTGCAGAAGTATTCATTCTACTGGCGTGCTGAGCAGGTGCAGGAGCTCTAATAAGCCTAGTGCGCACTTCAGTCATCAGCCAAGTGATTGAAA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 174

CACCCTCTTCTCCTCCCAAGGCTGACTGGCCGTCGGCTCGGGTCTGGGGACAGCAATCCCTGCCGTCTTGCCATGCTCCCCACGAGGAGCACACCGTCAGgtccgcctcc ... ctcctttcagAGTGATTCTGCAGAAGTATTCATTCTACTGGCGTGCTGAGCAGGTGCAGGAGCTCTAATAAGCCTAGTGCGCACTTCAGTCATCAGCCAAGTGATTGAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 177

CACCCTCTTCTCCTCCCAAGGCTGACTGGCCGTCGGCTCGGGTCTGGGGACAGCAATCCCTGCCGTCTTGCCATGCTCCCCACGAGGAGCACACCGTCAGgtccgcctcc ... ctcctttcagAGTGATTCTGCAGAAGTATTCATTCTACTGGCGTGCTGAGCAGGTGCAGGAGCTCTAATAAGCCTAGTGCGCACTTCAGTCATCAGCCAAGTGATTGAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 181

CACCCTCTTCTCCTCCCAAGGCTGACTGGCCGTCGGCTCGGGTCTGGGGACAGCAATCCCTGCCGTCTTGCCATGCTCCCCACGAGGAGCACACCGTCAGgtccgcctcc ... ctcctttcagAGTGATTCTGCAGAAGTATTCATTCTACTGGCGTGCTGAGCAGGTGCAGGAGCTCTAATAAGCCTAGTGCGCACTTCAGTCATCAGCCAAGTGATTGAAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttttctaggtaacttcgaactagagatctcatgctatttcatctctcctttcagAGTGATTCTGCAGAAGTATTCATTCTACTGGCGTGCTGAGCAGGTGCAGGAGCTCTAATAAGCCTAGTGCGCACTTCAGTCATCAGCCAAGTGATTGAAA
       aggtaac  putative branch site (score: 181)
                                tgctatttcatctctc  putative PPT
                                   tatttcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgaaagttacagctgcttcagtcatttgaacaagacatccccgtcttttctaggtaacttcgaactagagatctcatgctatttcatctctcctttcagAGTGATTCTGCAGAAGTATTCATTCTACTGGCGTGCTGAGCAGGTGCAGGAGCTCTAATAAGCCTAGTGCGCACTTCAGTCATCAGCCAAGTGATTGAAA

- - - - - - gctgctt
- - - - - - - - - - - tcatttg
- - - - - - - - - - - - - - -aacaaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgcta