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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgttgtcttctttctttgccccccgtctctgtctctctctctctctgtttgtttctttctgttcttggcctcagattggatctctcatctacccggcctttcttaccatagttttataatccctgcagGTTTCCACCTAGGCAGAGATAAATAAGATCTGCGGAATCAAGAAGCTCTGTCCAAGGAGGAAGCCAGCGGCACGGCAGTGCCCTCGGCGGTGATGAAGTA

Basic information

species Zea mays
transcript GRMZM2G089102_T01
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|12058201|gb|BF728063.2|BF728063
EST:     GCCGCGCCGGCGACCCGCGGCGTCGCATGTGAACACGGGGCGCGTTCCTC                         GTTTCCACCTAGGCAGAGATAAATAAGATCGGCGGAATCAAGAAGCTCTGT
genomic: GCCGCGCCGGCGACCCGCGGCGTCGCATGTGAACACGGGGCGCGTTCATCgtgttgtctt ... atccctgcagGTTTCCACCTAGGCAGAGATAAATAAGATCTGCGGAATCAAGAAGCTCTGT
EST: gi|149009060|gb|EE041232.2|EE041232
EST:     GCCGCGCCGGCGACCCGCGGCGTCGCATGTGAACACGGGGCGCGTTCATC                         GTTTCCACCTAGGCAGAGATAAATAAGATCTGCGGAATCAAGAAGCTCTGT
genomic: GCCGCGCCGGCGACCCGCGGCGTCGCATGTGAACACGGGGCGCGTTCATCgtgttgtctt ... atccctgcagGTTTCCACCTAGGCAGAGATAAATAAGATCTGCGGAATCAAGAAGCTCTGT
EST: gi|211118243|gb|FL244856.1|FL244856
EST:     GCCGCGCCGGCGACCCGCGGCGTCGCATGTGAACACGGGGCGCGTTCATC                         GTTTCCACCTAGGCAGAGATAAATAAGATCTGCGGAATCAAGAAGCTCTGT
genomic: GCCGCGCCGGCGACCCGCGGCGTCGCATGTGAACACGGGGCGCGTTCATCgtgttgtctt ... atccctgcagGTTTCCACCTAGGCAGAGATAAATAAGATCTGCGGAATCAAGAAGCTCTGT
EST: gi|149089807|gb|EE179083.2|EE179083
EST:     GCCGCGCCGGCGACCCGCGGCGTCGCATGTGAACACGGGGCGCGTTCATC                         GTTTCCACCTAGGCAGAGATAAATAAGATCTGCGGAATCAAGAAGCTCTGT
genomic: GCCGCGCCGGCGACCCGCGGCGTCGCATGTGAACACGGGGCGCGTTCATCgtgttgtctt ... atccctgcagGTTTCCACCTAGGCAGAGATAAATAAGATCTGCGGAATCAAGAAGCTCTGT
EST: gi|148960170|gb|EE153420.2|EE153420
EST:     GCCGCGCCGGCGACCCGCGGCGTCGCATGTGAACACGGGGCGCGTTCATC                         GTTTCCACCTAGGCAGAGATAAATAAGATCTGCGGAATCAAGAAGCTCTGT
genomic: GCCGCGCCGGCGACCCGCGGCGTCGCATGTGAACACGGGGCGCGTTCATCgtgttgtctt ... atccctgcagGTTTCCACCTAGGCAGAGATAAATAAGATCTGCGGAATCAAGAAGCTCTGT

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 2 RNA-Seq libraries.


Block sizes: 16 (upstream exon), 42 (downstream exon)
Score: 2

GGTGATATCCCGCGTCCCCAGCGAGGATGCTGTCATTGCGCTGCCACGCCGCCGCGCCGGCGACCCGCGGCGTCGCATGTGAACACGGGGCGCGTTCATCgtgttgtctt ... atccctgcagGTTTCCACCTAGGCAGAGATAAATAAGATCTGCGGAATCAAGAAGCTCTGTCCAAGGAGGAAGCCAGCGGCACGGCAGTGCCCTCGGCGGTGATGAAGTA


Block sizes: 44 (upstream exon), 47 (downstream exon)
Score: 30

GGTGATATCCCGCGTCCCCAGCGAGGATGCTGTCATTGCGCTGCCACGCCGCCGCGCCGGCGACCCGCGGCGTCGCATGTGAACACGGGGCGCGTTCATCgtgttgtctt ... atccctgcagGTTTCCACCTAGGCAGAGATAAATAAGATCTGCGGAATCAAGAAGCTCTGTCCAAGGAGGAAGCCAGCGGCACGGCAGTGCCCTCGGCGGTGATGAAGTA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattggatctctcatctacccggcctttcttaccatagttttataatccctgcagGTTTCCACCTAGGCAGAGATAAATAAGATCTGCGGAATCAAGAAGCTCTGTCCAAGGAGGAAGCCAGCGGCACGGCAGTGCCCTCGGCGGTGATGAAGTA
                          ttcttac  putative branch site (score: 30)
                                              tccctgc  putative PPT
                                  atagttttataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgttgtcttctttctttgccccccgtctctgtctctctctctctctgtttgtttctttctgttcttggcctcagattggatctctcatctacccggcctttcttaccatagttttataatccctgcagGTTTCCACCTAGGCAGAGATAAATAAGATCTGCGGAATCAAGAAGCTCTGTCCAAGGAGGAAGCCAGCGGCACGGCAGTGCCCTCGGCGGTGATGAAGTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA