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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcttctttcttattttgtgatttgtgggcaatttctattaataattgatcctagaactaactagcacatttatttatttattcagaaaaaaatactcattgtatatttctcacttcagGTGTTTGACATATCATCACTGCAAATATTTTCTCCTCAAGAACTTGATTATCTGATTTGTGGTCGCTGTGAACTTTGGGAG

Basic information

species Zea mays
transcript GRMZM2G049141_T02
intron # 12
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|211176318|gb|FL281704.1|FL281704
EST:     AGACCGGCATAATGCGGCAAGTAGAGGCATTTAAGGCAGGATTCAATCAG                         GTGTTTGACATATCATCACTGCAAATATTTTCTCCTCAAGAACTTGATTAT
genomic: AGACCGGCATAATGCGGCAAGTAGAGGCATTTAAGGCAGGATTCAATCAGgtcttctttc ... ctcacttcagGTGTTTGACATATCATCACTGCAAATATTTTCTCCTCAAGAACTTGATTAT
EST: gi|211174649|gb|FL281699.1|FL281699
EST:     AGACCGGCATAATGCGGCAAGTAGAGGCATTTAAGGCAGGATTCAATCAG                         GTGTTTGACATATCATCACTGCAAATATTTTCTCCTCAAGAACTTGATTAT
genomic: AGACCGGCATAATGCGGCAAGTAGAGGCATTTAAGGCAGGATTCAATCAGgtcttctttc ... ctcacttcagGTGTTTGACATATCATCACTGCAAATATTTTCTCCTCAAGAACTTGATTAT
EST: gi|18659233|gb|BM500228.1|BM500228
EST:     AGACCGGCATAATGCGGCAAGTAGAGGCATTTAAGGCAGGATTCAATCAG                         GTGTTTGACATATCATCACTGCAAATATTTTCTCCTCAAGAACTTGATTAT
genomic: AGACCGGCATAATGCGGCAAGTAGAGGCATTTAAGGCAGGATTCAATCAGgtcttctttc ... ctcacttcagGTGTTTGACATATCATCACTGCAAATATTTTCTCCTCAAGAACTTGATTAT
EST: gi|211174646|gb|FL281696.1|FL281696
EST:     AGACCGGCATAATGCGGCAAGTANAGGCATTTAAGGCAGGATTCAATCAG                         GTGTTTGACATATCATCACTGCAAATATTTTCTCCTCAAGAACTTGATTAT
genomic: AGACCGGCATAATGCGGCAAGTAGAGGCATTTAAGGCAGGATTCAATCAGgtcttctttc ... ctcacttcagGTGTTTGACATATCATCACTGCAAATATTTTCTCCTCAAGAACTTGATTAT
EST: gi|211176315|gb|FL281701.1|FL281701
EST:     AGACCGGCATAATGCGGCAAGTAGAGGCATTTAAGGCAGGATTCAATCAG                         GTGTTTGACATATCATCACTGCAAATATTTTCTCCTCAAGAACTTGATTAT
genomic: AGACCGGCATAATGCGGCAAGTAGAGGCATTTAAGGCAGGATTCAATCAGgtcttctttc ... ctcacttcagGTGTTTGACATATCATCACTGCAAATATTTTCTCCTCAAGAACTTGATTAT
EST: gi|166580162|gb|EG274088.1|EG274088
EST:     AGACCGGCATAATGCGGCAAGTAGAGGCATTTAAGGCAGGATTCAATCAG                         GTGTTTGACATATCATCACTGCAAATAT
genomic: AGACCGGCATAATGCGGCAAGTAGAGGCATTTAAGGCAGGATTCAATCAGgtcttctttc ... ctcacttcagGTGTTTGACATATCATCACTGCAAATAT
EST: gi|211176317|gb|FL281703.1|FL281703
EST:     AGACCGGCATAATGCGGCAAGTAGAGGCATTTAAGGCAGGATTCAATCAG                         GTGTTTGACATATCATCACTGCAAATATTTTCTCCTCAAGAACTTGATTAT
genomic: AGACCGGCATAATGCGGCAAGTAGAGGCATTTAAGGCAGGATTCAATCAGgtcttctttc ... ctcacttcagGTGTTTGACATATCATCACTGCAAATATTTTCTCCTCAAGAACTTGATTAT
EST: gi|20301115|gb|BQ164058.1|BQ164058
EST:     AGACCGGCATAATGCGGCAAGTAGAGGCATTTAAGGCAGGATTCAATCAG                         GTGTTTGACATATCATCACTGCAAATATTTTCTCCTCAAGAACTTGATTAT
genomic: AGACCGGCATAATGCGGCAAGTAGAGGCATTTAAGGCAGGATTCAATCAGgtcttctttc ... ctcacttcagGTGTTTGACATATCATCACTGCAAATATTTTCTCCTCAAGAACTTGATTAT
EST: gi|67039619|gb|CO465874.1|CO465874
EST:     AGACCGGCATAATGCGGCAAGTAGAGGCATTTAAGGCAGGATTCAATCAG                         GTGTTTGACATATCATCACTGCAAATATTTTCTCCTCAAGAACTTGATTAT
genomic: AGACCGGCATAATGCGGCAAGTAGAGGCATTTAAGGCAGGATTCAATCAGgtcttctttc ... ctcacttcagGTGTTTGACATATCATCACTGCAAATATTTTCTCCTCAAGAACTTGATTAT
EST: gi|20299937|gb|BQ162880.1|BQ162880
EST:     AGACCGGCATAATGCGGCAAGTAGAGGCATTTAAGGCAGGATTCAATCAG                         GTGTTTGACATATCATCACTGCAAATATTTTCTCCTCAAGAACTTGATTAT
genomic: AGACCGGCATAATGCGGCAAGTAGAGGCATTTAAGGCAGGATTCAATCAGgtcttctttc ... ctcacttcagGTGTTTGACATATCATCACTGCAAATATTTTCTCCTCAAGAACTTGATTAT
EST: gi|67021475|gb|CO450224.1|CO450224
EST:     AGACCGGCATAATGCGGCAAGTAGAGGCATTTAAGGCATGATTCAATCAG                         GTGTTTGACATATCATCACTGCAAATATTTTCTCCTCAAGAACTTGATTAT
genomic: AGACCGGCATAATGCGGCAAGTAGAGGCATTTAAGGCAGGATTCAATCAGgtcttctttc ... ctcacttcagGTGTTTGACATATCATCACTGCAAATATTTTCTCCTCAAGAACTTGATTAT
EST: gi|211176314|gb|FL281700.1|FL281700
EST:     AGACCGGCATAATGCGGCAAGTAGAGGCATTTAAGGCAGGATTCAATCAG                         GTGTTTGACATATCATCACTGCAAATATTTTCTCCTCAAGAACTTGATTAT
genomic: AGACCGGCATAATGCGGCAAGTAGAGGCATTTAAGGCAGGATTCAATCAGgtcttctttc ... ctcacttcagGTGTTTGACATATCATCACTGCAAATATTTTCTCCTCAAGAACTTGATTAT
EST: gi|211174647|gb|FL281697.1|FL281697
EST:     AGACCGGCATAATGCGGCAAGTAGAGGCATTTAAGGCAGGATTCAATCAG                         GTGTTTGACATATCATCACTGCAAATATTTTCTCCTCAAGAACTTGATTAT
genomic: AGACCGGCATAATGCGGCAAGTAGAGGCATTTAAGGCAGGATTCAATCAGgtcttctttc ... ctcacttcagGTGTTTGACATATCATCACTGCAAATATTTTCTCCTCAAGAACTTGATTAT

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: 120

CATTTGTAACTTAGAAGAGTATATTTCTTTGGTTGTGGATGCTACTGTTAAGACCGGCATAATGCGGCAAGTAGAGGCATTTAAGGCAGGATTCAATCAGgtcttctttc ... ctcacttcagGTGTTTGACATATCATCACTGCAAATATTTTCTCCTCAAGAACTTGATTATCTGATTTGTGGTCGCTGTGAACTTTGGGAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 51

CATTTGTAACTTAGAAGAGTATATTTCTTTGGTTGTGGATGCTACTGTTAAGACCGGCATAATGCGGCAAGTAGAGGCATTTAAGGCAGGATTCAATCAGgtcttctttc ... ctcacttcagGTGTTTGACATATCATCACTGCAAATATTTTCTCCTCAAGAACTTGATTATCTGATTTGTGGTCGCTGTGAACTTTGGGAG


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

CATTTGTAACTTAGAAGAGTATATTTCTTTGGTTGTGGATGCTACTGTTAAGACCGGCATAATGCGGCAAGTAGAGGCATTTAAGGCAGGATTCAATCAGgtcttctttc ... ctcacttcagGTGTTTGACATATCATCACTGCAAATATTTTCTCCTCAAGAACTTGATTATCTGATTTGTGGTCGCTGTGAACTTTGGGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 110

CATTTGTAACTTAGAAGAGTATATTTCTTTGGTTGTGGATGCTACTGTTAAGACCGGCATAATGCGGCAAGTAGAGGCATTTAAGGCAGGATTCAATCAGgtcttctttc ... ctcacttcagGTGTTTGACATATCATCACTGCAAATATTTTCTCCTCAAGAACTTGATTATCTGATTTGTGGTCGCTGTGAACTTTGGGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcacatttatttatttattcagaaaaaaatactcattgtatatttctcacttcagGTGTTTGACATATCATCACTGCAAATATTTTCTCCTCAAGAACTTGATTATCTGATTTGTGGTCGCTGTGAACTTTGGGAG
                                           ttctcac  putative branch site (score: 110)
                                          tttctcacttc  CT-rich tract
     tttatttatttattca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcttctttcttattttgtgatttgtgggcaatttctattaataattgatcctagaactaactagcacatttatttatttattcagaaaaaaatactcattgtatatttctcacttcagGTGTTTGACATATCATCACTGCAAATATTTTCTCCTCAAGAACTTGATTATCTGATTTGTGGTCGCTGTGAACTTTGGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC