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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actcttgccaaaaaaaaaatgtagagccaaaacgaccccacaaaacatgtatgatccttcaaatccaatttgttgaaggcttgtttttattctaatgcagGAAAAGGATGATCTCTCATTCACGGATAGCGACCTGGGGTGCGACTTCTTTCCACTCGGTGCTTGCATATGAGACCTCTTAACAACCCCTCGTGCAGATT

Basic information

species Zea mays
transcript GRMZM2G409974_T01
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|74235132|gb|DT643046.1|DT643046
EST:     GCTTTAGTAGCTGCAATTTTGATGGTCTTCTCAATTCCATGATCAAAGCG                         GAAAAGGATGATCTTTCATTCACGGATAGCGACCTGGGGTGCGACTTCTTT
genomic: GCTCTAGTAGCTGCAATTTTGATGGTCTTCTCAATTCCATGATCAAAGCGgtatggacct ... tctaatgcagGAAAAGGATGATCTCTCATTCACGGATAGCGACCTGGGGTGCGACTTCTTT
EST: gi|211312347|gb|FL453730.1|FL453730
EST:     GCTCTAGTAGCTGCAATTTTGATGGTCTTCTCAATTCCATGATCAAAGCG                         GAAAAGGATGATCTCTCATTCACGGATAGCGACCTGGGGTGCGACTTCTTT
genomic: GCTCTAGTAGCTGCAATTTTGATGGTCTTCTCAATTCCATGATCAAAGCGgtatggacct ... tctaatgcagGAAAAGGATGATCTCTCATTCACGGATAGCGACCTGGGGTGCGACTTCTTT
EST: gi|91049187|gb|EB159605.1|EB159605
EST:     GCTCTAGTAGCTGCAATTTTGATGGTCTTCTCAATTCCATGATCAAAGCG                         GAAAAGGATGATCTCTCATTCACGGATAGCGACCTGGGGTGGGACTTCTTT
genomic: GCTCTAGTAGCTGCAATTTTGATGGTCTTCTCAATTCCATGATCAAAGCGgtatggacct ... tctaatgcagGAAAAGGATGATCTCTCATTCACGGATAGCGACCTGGGGTGCGACTTCTTT
EST: gi|32800998|gb|CD953234.1|CD953234
EST:     GCTCTAGTAGCTGCAATTTTGATGGTCTTCTCAATTCCATGATCAAAGCG                         GAAAAGGATGATCTCTCATTCACGGATAGCGACCTGGGGTGCGACTTCTTT
genomic: GCTCTAGTAGCTGCAATTTTGATGGTCTTCTCAATTCCATGATCAAAGCGgtatggacct ... tctaatgcagGAAAAGGATGATCTCTCATTCACGGATAGCGACCTGGGGTGCGACTTCTTT
EST: gi|60337935|gb|DN204908.1|DN204908
EST:     GCTCTAGTAGCTGCAATTTTGATGGTCTTCTCAATTCCATGATCAAAGCG                         GAAAAGGATGATCTCTCATTCACGGATAGCGACCTGGGGTGCGACTTCTTT
genomic: GCTCTAGTAGCTGCAATTTTGATGGTCTTCTCAATTCCATGATCAAAGCGgtatggacct ... tctaatgcagGAAAAGGATGATCTCTCATTCACGGATAGCGACCTGGGGTGCGACTTCTTT
EST: gi|6127270|gb|AW129795.1|AW129795
EST:     GCTCTAGTAGCTGCAATTTTGATGGTCTTCTCAATTCCATGATCAAAGCG                         GAAAAGGATGATCTCTCATTCACGGATAGCGACCTGGGGTGCGACTTCTTT
genomic: GCTCTAGTAGCTGCAATTTTGATGGTCTTCTCAATTCCATGATCAAAGCGgtatggacct ... tctaatgcagGAAAAGGATGATCTCTCATTCACGGATAGCGACCTGGGGTGCGACTTCTTT
EST: gi|32789012|gb|CD941248.1|CD941248
EST:     GCTCTAGTAGCTGCAATTTTGATGGTCTTCTCAATTCCATGATCAAAGCG                         GAAAAGGATGATCTCTCATTCACGGATAGCGACCTGGGGTGCGACTTCTTA
genomic: GCTCTAGTAGCTGCAATTTTGATGGTCTTCTCAATTCCATGATCAAAGCGgtatggacct ... tctaatgcagGAAAAGGATGATCTCTCATTCACGGATAGCGACCTGGGGTGCGACTTCTTT
EST: gi|74235133|gb|DT643047.1|DT643047
EST:     GCTCTAGTAGCTGCAATTTTGATGGTCTTCTCAATTCCATGATCAAAGCG                         GAAAAGGATGATCTCTCATTCACGGATAGCGACCTGGGGTGCGACTTCTTT
genomic: GCTCTAGTAGCTGCAATTTTGATGGTCTTCTCAATTCCATGATCAAAGCGgtatggacct ... tctaatgcagGAAAAGGATGATCTCTCATTCACGGATAGCGACCTGGGGTGCGACTTCTTT
EST: gi|60346510|gb|DN213483.1|DN213483
EST:     GCTTTAGTAGCTGCAATTTTGATGGTCTTCTCAATTCCATGATCAAAGCG                         GAAAAGGATGATCTCTCATTCACGGATAGCGACCTGGGGTGCGACTTCTTT
genomic: GCTCTAGTAGCTGCAATTTTGATGGTCTTCTCAATTCCATGATCAAAGCGgtatggacct ... tctaatgcagGAAAAGGATGATCTCTCATTCACGGATAGCGACCTGGGGTGCGACTTCTTT
EST: gi|32800976|gb|CD953212.1|CD953212
EST:     GCTCTAGTAGCTGCAATTTTGATGGTCTTCTCAATTCCATGATCAAAGCG                         GAAAAGGATGATCTCTCATTCACGGATAGCGACCTGGGGTGCGACTTCTTT
genomic: GCTCTAGTAGCTGCAATTTTGATGGTCTTCTCAATTCCATGATCAAAGCGgtatggacct ... tctaatgcagGAAAAGGATGATCTCTCATTCACGGATAGCGACCTGGGGTGCGACTTCTTT

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: 49 (upstream exon), 49 (downstream exon)
Score: 43

GCAGAGGAATATTTATGATTTGGGGATTCCAAAGCTCCATGGTGGTTTTAGCTCTAGTAGCTGCAATTTTGATGGTCTTCTCAATTCCATGATCAAAGCGgtatggacct ... tctaatgcagGAAAAGGATGATCTCTCATTCACGGATAGCGACCTGGGGTGCGACTTCTTTCCACTCGGTGCTTGCATATGAGACCTCTTAACAACCCCTCGTGCAGATT


Block sizes: 44 (upstream exon), 47 (downstream exon)
Score: 9

GCAGAGGAATATTTATGATTTGGGGATTCCAAAGCTCCATGGTGGTTTTAGCTCTAGTAGCTGCAATTTTGATGGTCTTCTCAATTCCATGATCAAAGCGgtatggacct ... tctaatgcagGAAAAGGATGATCTCTCATTCACGGATAGCGACCTGGGGTGCGACTTCTTTCCACTCGGTGCTTGCATATGAGACCTCTTAACAACCCCTCGTGCAGATT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 21

GCAGAGGAATATTTATGATTTGGGGATTCCAAAGCTCCATGGTGGTTTTAGCTCTAGTAGCTGCAATTTTGATGGTCTTCTCAATTCCATGATCAAAGCGgtatggacct ... tctaatgcagGAAAAGGATGATCTCTCATTCACGGATAGCGACCTGGGGTGCGACTTCTTTCCACTCGGTGCTTGCATATGAGACCTCTTAACAACCCCTCGTGCAGATT


Block sizes: 33 (upstream exon), 44 (downstream exon)
Score: 10

GCAGAGGAATATTTATGATTTGGGGATTCCAAAGCTCCATGGTGGTTTTAGCTCTAGTAGCTGCAATTTTGATGGTCTTCTCAATTCCATGATCAAAGCGgtatggacct ... tctaatgcagGAAAAGGATGATCTCTCATTCACGGATAGCGACCTGGGGTGCGACTTCTTTCCACTCGGTGCTTGCATATGAGACCTCTTAACAACCCCTCGTGCAGATT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgtatgatccttcaaatccaatttgttgaaggcttgtttttattctaatgcagGAAAAGGATGATCTCTCATTCACGGATAGCGACCTGGGGTGCGACTTCTTTCCACTCGGTGCTTGCATATGAGACCTCTTAACAACCCCTCGTGCAGATT
                                            ttctaat  putative branch site (score: 10)
                                  cttgtttttattct  CT-rich tract
                                   ttgtttttattctaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
actcttgccaaaaaaaaaatgtagagccaaaacgaccccacaaaacatgtatgatccttcaaatccaatttgttgaaggcttgtttttattctaatgcagGAAAAGGATGATCTCTCATTCACGGATAGCGACCTGGGGTGCGACTTCTTTCCACTCGGTGCTTGCATATGAGACCTCTTAACAACCCCTCGTGCAGATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- -cttgcca
- - - - -aaaaaaa
- - - - - - - - - - - - - - -aaacgac
- - - - - - - - - - - - - - - - - - -ccacaaa
- - - - - - - - - - - - - - - - - - - - - - - atgtatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tttgttg