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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gctgtgatcactgatcaccatcagcttctgtgcagttgcacatgcatgattcagactttggcccacgatgattattgttgatctcgattctgccttgcagGAAAAGCAGGATGGTTTAAAAGCAGATGGAACCAGCAAACCTTCAGAGGATGAACTAACATGTAGTGTTTGCTTAGAGCAAGTCACGGTGGGTGATCTGT

Basic information

species Zea mays
transcript GRMZM2G337425_T03
intron # 6
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|18166650|gb|BM336489.1|BM336489
EST:     TGATGGGCCATCTCAGCTATCGGTTTCTTCAACTGGGTCCGGCAATGAG                         GAAAAGCAGGATGGTTTAAAAGCAGATGGAACCAGCAAACCTTCAGAGGAT
genomic: TGATGGGCCATCTCAGCTATCGGTTTCTTCAACTGGGTCCGGCAATGAGgtaattgata ... tgccttgcagGAAAAGCAGGATGGTTTAAAAGCAGATGGAACCAGCAAACCTTCAGAGGAT
EST: gi|148928861|gb|EC873779.2|EC873779
EST:     TGATGGGCCATCTCAGCTATCGGTTTCTTCAACTGGGTCCGGCAATGAG                         GAAAAGCAGGATGGTTTAAAAGCAGATGGAACCAGCAAACCTTCAGAGGAT
genomic: TGATGGGCCATCTCAGCTATCGGTTTCTTCAACTGGGTCCGGCAATGAGgtaattgata ... tgccttgcagGAAAAGCAGGATGGTTTAAAAGCAGATGGAACCAGCAAACCTTCAGAGGAT
EST: gi|18164717|gb|BM334556.1|BM334556
EST:     TGATGGGCCATCTCAGCTATCGGTTTCTTCAACTGGGTCCGGCAATGAG                         GAAAAGCAGGATGGTTTAAAAGCAGATGGAACCAGCAAACCTTCAGAGGAT
genomic: TGATGGGCCATCTCAGCTATCGGTTTCTTCAACTGGGTCCGGCAATGAGgtaattgata ... tgccttgcagGAAAAGCAGGATGGTTTAAAAGCAGATGGAACCAGCAAACCTTCAGAGGAT
EST: gi|71760470|gb|DR958407.1|DR958407
EST:     TGATGGGCCATCTCAGCTATCGGTTTCTTCAACTGGGTCCGGCAATGAG                         GAAAAGCAGGATGGTTTAAAAGCAGATGGAACCAGCAAACCTTCAGAGGAT
genomic: TGATGGGCCATCTCAGCTATCGGTTTCTTCAACTGGGTCCGGCAATGAGgtaattgata ... tgccttgcagGAAAAGCAGGATGGTTTAAAAGCAGATGGAACCAGCAAACCTTCAGAGGAT
EST: gi|78083978|gb|DV512371.1|DV512371
EST:     TGATGGGCCATCTCAGCTATCGGTTTCTTCAACTGGGTCCGGCAATGAG                         GAAAAGCAGGATGGTTTAAAAGCAGATGGAACCAGCAAACCTTCAGAGGAT
genomic: TGATGGGCCATCTCAGCTATCGGTTTCTTCAACTGGGTCCGGCAATGAGgtaattgata ... tgccttgcagGAAAAGCAGGATGGTTTAAAAGCAGATGGAACCAGCAAACCTTCAGAGGAT
EST: gi|78085072|gb|DV513465.1|DV513465
EST:     TGATGGGCCATCTCAGCTATCGGTTTCTTCAACTGGGTCCGGCAATGAG                         GAAAAGCAGGATGGTTTAAAAGCAGATGGAACCAGCAAACCTTCAGAGGAT
genomic: TGATGGGCCATCTCAGCTATCGGTTTCTTCAACTGGGTCCGGCAATGAGgtaattgata ... tgccttgcagGAAAAGCAGGATGGTTTAAAAGCAGATGGAACCAGCAAACCTTCAGAGGAT
EST: gi|76288197|gb|DV027765.1|DV027765
EST:     TGATGGGCCATCTCAGCTATCGGTTTCTTCAACTGGGTCCGGCAATGAG                         GAAAAGCAGGATGGTTTAAAAGCAGATGGAACCAGCAAACCTTCAGAGGAT
genomic: TGATGGGCCATCTCAGCTATCGGTTTCTTCAACTGGGTCCGGCAATGAGgtaattgata ... tgccttgcagGAAAAGCAGGATGGTTTAAAAGCAGATGGAACCAGCAAACCTTCAGAGGAT
EST: gi|86467324|gb|DY233694.1|DY233694
EST:     TGATGGGCCATCTCAGCTATCGGTTTCTTCAACTGGGTCCGGCAATGAG                         GAAAAGCAGGATGGTTTAAAAGCAGATGGAACCAGCAAACCTTCAGAGGAT
genomic: TGATGGGCCATCTCAGCTATCGGTTTCTTCAACTGGGTCCGGCAATGAGgtaattgata ... tgccttgcagGAAAAGCAGGATGGTTTAAAAGCAGATGGAACCAGCAAACCTTCAGAGGAT

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: 87

TGATGGGCCATCTCAGCTATCGGTTTCTTCAACTGGGTCCGGCAATGAGgtaattgata ... tgccttgcagGAAAAGCAGGATGGTTTAAAAGCAGATGGAACCAGCAAACCTTCAGAGGATGAACTAACATGTAGTGTTTGCTTAGAGCAAGTCACGGTGGGTGATCTGT


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 41

TGATGGGCCATCTCAGCTATCGGTTTCTTCAACTGGGTCCGGCAATGAGgtaattgata ... tgccttgcagGAAAAGCAGGATGGTTTAAAAGCAGATGGAACCAGCAAACCTTCAGAGGATGAACTAACATGTAGTGTTTGCTTAGAGCAAGTCACGGTGGGTGATCTGT


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 52

TGATGGGCCATCTCAGCTATCGGTTTCTTCAACTGGGTCCGGCAATGAGgtaattgata ... tgccttgcagGAAAAGCAGGATGGTTTAAAAGCAGATGGAACCAGCAAACCTTCAGAGGATGAACTAACATGTAGTGTTTGCTTAGAGCAAGTCACGGTGGGTGATCTGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 60

TGATGGGCCATCTCAGCTATCGGTTTCTTCAACTGGGTCCGGCAATGAGgtaattgata ... tgccttgcagGAAAAGCAGGATGGTTTAAAAGCAGATGGAACCAGCAAACCTTCAGAGGATGAACTAACATGTAGTGTTTGCTTAGAGCAAGTCACGGTGGGTGATCTGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgattcagactttggcccacgatgattattgttgatctcgattctgccttgcagGAAAAGCAGGATGGTTTAAAAGCAGATGGAACCAGCAAACCTTCAGAGGATGAACTAACATGTAGTGTTTGCTTAGAGCAAGTCACGGTGGGTGATCTGT
                              tgttgat  putative branch site (score: 60)
                                          ttctgcctt  putative PPT
                      atgattatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gctgtgatcactgatcaccatcagcttctgtgcagttgcacatgcatgattcagactttggcccacgatgattattgttgatctcgattctgccttgcagGAAAAGCAGGATGGTTTAAAAGCAGATGGAACCAGCAAACCTTCAGAGGATGAACTAACATGTAGTGTTTGCTTAGAGCAAGTCACGGTGGGTGATCTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG