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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcttctccatgcgctgttgccattatatttgacttctctccctcaattctgtaagtggtaatactggtatatgcttaattggcatgatttttccatgtagTTTTACGGGGGATATGCTTACCATGGCAACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAG

Basic information

species Zea mays
transcript GRMZM2G114220_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G114220_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os04g48770.1 (Oryza sativa), 3'ss of exon 2
tcttctccatgcgctgttgccattatatttgacttctctccctcaattctgtaagtggtaatactggtatatgcttaattgg---catgatttttccat--gtagTTTTACGGGGGATATGCTTACCATGGCAACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAG
   || | |     | ||  |  | | | |||    | ||  |  |   || |    |||||  ||| ||| |||||| |       | |||||| | |  | ||||||| |  |||||||  |||||||| |     |||||||||||||||||||||||||||||||| || ||||| |||
-aatcactacttattctt--ctgtgtgtgtgatgcttgtcttttcaggttgcactatgtaat--tggcataagcttaactaatccttttatttttgcttctgcagTTTTATGCAGGATATGGCTACCATGGGAGTAACTTTGAGCAAACATACCGTTGTTATCCAGCATCTTTCTTTGACAAG
















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|76909136|gb|DV163240.1|DV163240
EST:     GTTGAGGGAAGTTGAAGCAAAAGTCTAAGCAAAAATG                         TTTTACGGGGGATATGCTTACCATGGCAACTCGTTTGAGCAAACATACCGT
genomic: GTTGAGGGAAGTTGAAGCAAAAGTCTAAGCAAAAATGgtattcataa ... ttccatgtagTTTTACGGGGGATATGCTTACCATGGCAACTCGTTTGAGCAAACATACCGT
EST: gi|211392498|gb|FL156787.1|FL156787
EST:     GGTTGAGGGAAGTTGAAGCAAAAGTCTAAGCAAAAATG                         TTTTACGGGGGATATGCTTACCATGGCAACTCGTTTGAGCAAACATACCGT
genomic: G-TTGAGGGAAGTTGAAGCAAAAGTCTAAGCAAAAATGgtattcataa ... ttccatgtagTTTTACGGGGGATATGCTTACCATGGCAACTCGTTTGAGCAAACATACCGT
EST: gi|211392504|gb|FL156793.1|FL156793
EST:     GTTGAGGGAAGTTGAAGCAAAAGTCTAAGCAAAAATG                         TTTTACGGGGGATATGCTTACCATGGCAACTCGTTTGAGCAAACATACCGT
genomic: GTTGAGGGAAGTTGAAGCAAAAGTCTAAGCAAAAATGgtattcataa ... ttccatgtagTTTTACGGGGGATATGCTTACCATGGCAACTCGTTTGAGCAAACATACCGT
EST: gi|211395124|gb|FL156801.1|FL156801
EST:     GTTGAGGGAAGTTGAAGCAAAAGTCTAAGCAAAAATG                         TTTTACGGGGGATATGCTTACCATGGCAACTCGTTTGAGCAAACATACCGT
genomic: GTTGAGGGAAGTTGAAGCAAAAGTCTAAGCAAAAATGgtattcataa ... ttccatgtagTTTTACGGGGGATATGCTTACCATGGCAACTCGTTTGAGCAAACATACCGT
EST: gi|211389877|gb|FL156782.1|FL156782
EST:     GGTTGAGGGAAGTTGAAGCAAAAGTCTAAGCAAAAATG                         TTTTACGGGGGATATGCTTACCATGGCAACTCGTTTGAGCAAACATACCGT
genomic: G-TTGAGGGAAGTTGAAGCAAAAGTCTAAGCAAAAATGgtattcataa ... ttccatgtagTTTTACGGGGGATATGCTTACCATGGCAACTCGTTTGAGCAAACATACCGT
EST: gi|211392507|gb|FL156796.1|FL156796
EST:     GTTGAGGGAAGTTGAAGCAAAAGTCTAAGCAAAAATG                         TTTTACGGGGGATATGCTTACCATGGCAACTCGTTTGAGCAAACATACCGT
genomic: GTTGAGGGAAGTTGAAGCAAAAGTCTAAGCAAAAATGgtattcataa ... ttccatgtagTTTTACGGGGGATATGCTTACCATGGCAACTCGTTTGAGCAAACATACCGT
EST: gi|91873355|gb|EB403312.1|EB403312
EST:     GTTGAGGGAAGTTGAAGCAAAAGTCTAAGCAAAAATG                         TTTTACGGGGGATATGCTTACCATGGCAACTCGTTTGAGCAAACATACCGT
genomic: GTTGAGGGAAGTTGAAGCAAAAGTCTAAGCAAAAATGgtattcataa ... ttccatgtagTTTTACGGGGGATATGCTTACCATGGCAACTCGTTTGAGCAAACATACCGT
EST: gi|14242735|gb|BG840580.2|BG840580
EST:     GTTGAGGGAAGTTGAAGCAAAAGTCTAAGCAAAAATG                         TTTTACGGGGGATATGCTTACCATGGCAACTCGTTTGAGCAAACATACCGT
genomic: GTTGAGGGAAGTTGAAGCAAAAGTCTAAGCAAAAATGgtattcataa ... ttccatgtagTTTTACGGGGGATATGCTTACCATGGCAACTCGTTTGAGCAAACATACCGT
EST: gi|211392505|gb|FL156794.1|FL156794
EST:     GTTGAGGGAAGTTGAAGCAAAAGTCTAAGCAAAAATG                         TTTTACGGGGGATATGCTTACCATGGCAACTCGTTTGAGCAAACATACCGT
genomic: GTTGAGGGAAGTTGAAGCAAAAGTCTAAGCAAAAATGgtattcataa ... ttccatgtagTTTTACGGGGGATATGCTTACCATGGCAACTCGTTTGAGCAAACATACCGT
EST: gi|71417924|gb|DR804257.1|DR804257
EST:     GTTGAGGGAAGTTGAAGCAAAAGTCTAAGCAAAAATG                         TTTTACGGGGGATATGCTTACCATGGCAACTCGTCTGAGCAAACATACCGT
genomic: GTTGAGGGAAGTTGAAGCAAAAGTCTAAGCAAAAATGgtattcataa ... ttccatgtagTTTTACGGGGGATATGCTTACCATGGCAACTCGTTTGAGCAAACATACCGT
EST: gi|50338446|gb|CO533572.1|CO533572
EST:     GTTGAGGGAAGTTGAAGCAAAAGTCTAAGCAAAAATG                         TTTTACGGGGGATATGCTTACCATGGCAACTCGTTTGAGCAAACATACCGT
genomic: GTTGAGGGAAGTTGAAGCAAAAGTCTAAGCAAAAATGgtattcataa ... ttccatgtagTTTTACGGGGGATATGCTTACCATGGCAACTCGTTTGAGCAAACATACCGT
EST: gi|211392501|gb|FL156790.1|FL156790
EST:     GTTGAGGGAAGTTGAAGCAAAAGTCTAAGCAAAAATG                         TTTTACGGGGGATATGCTTACCATGGCAACTCGTTTGAGCAAACATACCGT
genomic: GTTGAGGGAAGTTGAAGCAAAAGTCTAAGCAAAAATGgtattcataa ... ttccatgtagTTTTACGGGGGATATGCTTACCATGGCAACTCGTTTGAGCAAACATACCGT
EST: gi|211389876|gb|FL156781.1|FL156781
EST:     GTTGAGGGAAGTTGAAGCAAAAGTCTAAGCAAAAATG                         TTTTACGGGGGATATGCTTACCATGGCAACTCGTTTGAGCAAACATACCGT
genomic: GTTGAGGGAAGTTGAAGCAAAAGTCTAAGCAAAAATGgtattcataa ... ttccatgtagTTTTACGGGGGATATGCTTACCATGGCAACTCGTTTGAGCAAACATACCGT
EST: gi|211392496|gb|FL156785.1|FL156785
EST:     GTTGAGGGAAGTTGAAGCAAAAGTCTAAGCAAAAATG                         TTTTACGGGGGATATGCTTACCATGGCAACTCGTTTGAGCAAACATACCGT
genomic: GTTGAGGGAAGTTGAAGCAAAAGTCTAAGCAAAAATGgtattcataa ... ttccatgtagTTTTACGGGGGATATGCTTACCATGGCAACTCGTTTGAGCAAACATACCGT
EST: gi|93015584|gb|EB641104.1|EB641104
EST:     GTTGAGGGAAGTTGAAGCAAAAGTCTAAGCAAAAATG                         TTTTACGGGGGATATGCTTACCATGGCAACTCGTTTGAGCAAACATACCGT
genomic: GTTGAGGGAAGTTGAAGCAAAAGTCTAAGCAAAAATGgtattcataa ... ttccatgtagTTTTACGGGGGATATGCTTACCATGGCAACTCGTTTGAGCAAACATACCGT
EST: gi|211389879|gb|FL156784.1|FL156784
EST:     GGTTGAGGGAAGTTGAAGCAAAAGTCTAAGCAAAAATG                         TTTTACGGGGGATATGCTTACCATGGCAACTCGTTTGAGCAAACATACCGT
genomic: G-TTGAGGGAAGTTGAAGCAAAAGTCTAAGCAAAAATGgtattcataa ... ttccatgtagTTTTACGGGGGATATGCTTACCATGGCAACTCGTTTGAGCAAACATACCGT
EST: gi|32862738|gb|CF002420.1|CF002420
EST:     GTTGAGGGAAGTTGAAGCAAAAGTCTAAGCAAAAATG                         TTTTACGGGGGATATGCTTACCATGGCAACTCGTTTGAGCAAACATACCGT
genomic: GTTGAGGGAAGTTGAAGCAAAAGTCTAAGCAAAAATGgtattcataa ... ttccatgtagTTTTACGGGGGATATGCTTACCATGGCAACTCGTTTGAGCAAACATACCGT
EST: gi|211392502|gb|FL156791.1|FL156791
EST:     GTTGAGGGAAGTTGAAGCAAAAGTCTAAGCAAAAATG                         TTTTACGGGGGATATGCTTACCATGGCAACTCGTTTGAGCAAACATACCGT
genomic: GTTGAGGGAAGTTGAAGCAAAAGTCTAAGCAAAAATGgtattcataa ... ttccatgtagTTTTACGGGGGATATGCTTACCATGGCAACTCGTTTGAGCAAACATACCGT
EST: gi|91049005|gb|EB159423.1|EB159423
EST:     GTTGAGGGAAGTTGAAGCAAAAGTCTAAGCAAAAATG                         TTTTACGGGGGATATGCTTACCATGGCAACTCGTTTGAGCAAACATACCGT
genomic: GTTGAGGGAAGTTGAAGCAAAAGTCTAAGCAAAAATGgtattcataa ... ttccatgtagTTTTACGGGGGATATGCTTACCATGGCAACTCGTTTGAGCAAACATACCGT
EST: gi|6637070|gb|AW261342.1|AW261342
EST:     GTTGAGGGAAGTTGAAGCAAAAGTCTAACCAAAAATG                         TTTTACGGGGGATATGCTTACCATGGCAACTCGTTTGAGCAAACATACCGT
genomic: GTTGAGGGAAGTTGAAGCAAAAGTCTAAGCAAAAATGgtattcataa ... ttccatgtagTTTTACGGGGGATATGCTTACCATGGCAACTCGTTTGAGCAAACATACCGT
EST: gi|211395123|gb|FL156800.1|FL156800
EST:     GTTGAGGGAAGTTGAAGCAAAAGTCTAAGCAAAAATG                         TTTTACGGGGGATATGCTTACCATGGCAACTCGTTTGAGCAAACATACCGT
genomic: GTTGAGGGAAGTTGAAGCAAAAGTCTAAGCAAAAATGgtattcataa ... ttccatgtagTTTTACGGGGGATATGCTTACCATGGCAACTCGTTTGAGCAAACATACCGT
EST: gi|211392503|gb|FL156792.1|FL156792
EST:     GTTGAGGGAAGTTGAAGCAAAAGTCTAAGCAAAAATG                         TTTTACGGGGGATATGCTTACCATGGCAACTCGTTTGAGCAAACATACCGT
genomic: GTTGAGGGAAGTTGAAGCAAAAGTCTAAGCAAAAATGgtattcataa ... ttccatgtagTTTTACGGGGGATATGCTTACCATGGCAACTCGTTTGAGCAAACATACCGT
EST: gi|211392499|gb|FL156788.1|FL156788
EST:     GTTGAGGGAAGTTGAAGCAAAAGTCTAAGCAAAAATG                         TTTTACGGGGGATATGCTTACCATGGCAACTCGTTTGAGCAAACATACCGT
genomic: GTTGAGGGAAGTTGAAGCAAAAGTCTAAGCAAAAATGgtattcataa ... ttccatgtagTTTTACGGGGGATATGCTTACCATGGCAACTCGTTTGAGCAAACATACCGT
EST: gi|211392510|gb|FL156799.1|FL156799
EST:     GTTGAGGGAAGTTGAAGCAAAAGTCTAAGCAAAAATG                         TTTTACGGGGGATATGCTTACCATGGCAACTCGTTTGAGCAAACATACCGT
genomic: GTTGAGGGAAGTTGAAGCAAAAGTCTAAGCAAAAATGgtattcataa ... ttccatgtagTTTTACGGGGGATATGCTTACCATGGCAACTCGTTTGAGCAAACATACCGT
EST: gi|213183590|gb|FM196389.1|FM196389
EST:     GTTGAGGGAAGTTGAAGCAAAAGTCTAAGCAAAAATG                         TTTTACGGGGGATATGCTTACCATGGCAACTCGTTTGAGCAAACATACCGT
genomic: GTTGAGGGAAGTTGAAGCAAAAGTCTAAGCAAAAATGgtattcataa ... ttccatgtagTTTTACGGGGGATATGCTTACCATGGCAACTCGTTTGAGCAAACATACCGT
EST: gi|32859779|gb|CD999460.1|CD999460
EST:     GTTGAGGGAAGTTGAAGCAAAAGTCTAAGCAAAAATG                         TTTTACGGGGGATATGCTTACCATGGCAACTCGTTTGAGCAAACATACCGT
genomic: GTTGAGGGAAGTTGAAGCAAAAGTCTAAGCAAAAATGgtattcataa ... ttccatgtagTTTTACGGGGGATATGCTTACCATGGCAACTCGTTTGAGCAAACATACCGT
EST: gi|211392508|gb|FL156797.1|FL156797
EST:     GTTGAGGGAAGTTGAAGCAAAAGTCTAA-CAAAAAATG                         TTTTACGGGGGATATGCTTACCATGGCAACTCGTTTGAGCAAACATACCG
genomic: GTTGAGGGAAGTTGAAGCAAAAGTCTAAGCAAAAA-TGgtattcataa ... ttccatgtagTTTTACGGGGGATATGCTTACCATGGCAACTCGTTTGAGCAAACATACCG

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: 47 (upstream exon), 49 (downstream exon)
Score: 112

GTTGAGGGAAGTTGAAGCAAAAGTCTAAGCAAAAATGgtattcataa ... ttccatgtagTTTTACGGGGGATATGCTTACCATGGCAACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 121

GTTGAGGGAAGTTGAAGCAAAAGTCTAAGCAAAAATGgtattcataa ... ttccatgtagTTTTACGGGGGATATGCTTACCATGGCAACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 159

GTTGAGGGAAGTTGAAGCAAAAGTCTAAGCAAAAATGgtattcataa ... ttccatgtagTTTTACGGGGGATATGCTTACCATGGCAACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 129

GTTGAGGGAAGTTGAAGCAAAAGTCTAAGCAAAAATGgtattcataa ... ttccatgtagTTTTACGGGGGATATGCTTACCATGGCAACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attctgtaagtggtaatactggtatatgcttaattggcatgatttttccatgtagTTTTACGGGGGATATGCTTACCATGGCAACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAG
                           gcttaat  putative branch site (score: 129)
                                          tttttccat  putative PPT
                                      atgattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcttctccatgcgctgttgccattatatttgacttctctccctcaattctgtaagtggtaatactggtatatgcttaattggcatgatttttccatgtagTTTTACGGGGGATATGCTTACCATGGCAACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAG

- - -tccatgc
- - - - - - gctgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tactggt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcttaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgatt