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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTCATTACAACCTTTATTTAAGCATGTGGAGCAAGGATCAGAGATTCGTGAGAAGATTATTTGTTTTCTTCGAGACAAGgtacatagctgaatgtagggattacatgttctgttgatgataatttgtagtgtgctagatcaagaatgtggttgtgtgtttttttggattcag

Basic information

species Zea mays
transcript GRMZM2G059039_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G059039_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os02g20930.1 (Oryza sativa), 5'ss of exon 5
ATTCATTACAACCTTTATTTAAGCATGTGGAGCAAGGATCAGAGATTCGTGAGAAGATTATTTGTTTTCTTCGAGACAAGgtacatagctgaatgtagggattacatgttctgttgatgataatttgtagtgtgctagatcaagaatgtggttgtgtgtttttttggattcag
 ||| || || |||||||||||||||||||||   ||||||||||||||||| ||  |||||||||| |||  ||| |||||| |||| |  |  |||| |||||  |   ||| |            | ||| |||    || |   |   ||    |||||   |      
GTTCCTTGCAGCCTTTATTTAAGCATGTGGAGTCGGGATCAGAGATTCGTGAAAAAGTTATTTGTTTCCTTAAAGATAAGgtaaatagttacacataggaattactcgagttgtaggcatgggcaatcactgttctaccagaaaataataactgatcttttttccag------
















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|211179438|gb|FL364366.1|FL364366
EST:     GCAAGGATCAGAGATTCGTGAGAAGATTTATT-GTTTTCTTCGAGACAAG                         GTCTTTCCTCTTAAAGCAGAGCTGCTGNAACCTCA-GCAGAAATGGAGAGA
genomic: GCAAGGATCAGAGATTCGTGAGAAGATT-ATTTGTTTTCTTCGAGACAAGgtacatagct ... ttggattcagGTCTTTCCTCTTAAAGCAGAGCTGCTGAAACCTCAAGCAGAAATGGAGAGA
EST: gi|148969036|gb|EE019749.2|EE019749
EST:     AGCAAGGATCAGAGATTCGTGAGAAGATTATTTGTTTTCTTCGAGACAAG                         GTCTTTCCTCTTAAAGCAGAGCTGCTGAAACCTCAAGCAGAAATGGAGAGA
genomic: AGCAAGGATCAGAGATTCGTGAGAAGATTATTTGTTTTCTTCGAGACAAGgtacatagct ... ttggattcagGTCTTTCCTCTTAAAGCAGAGCTGCTGAAACCTCAAGCAGAAATGGAGAGA
EST: gi|71766575|gb|DR964512.1|DR964512
EST:     AGCAAGGATCAGAGATTCGTGAGAAGATTATTTGTTTTCTTCGAGACAAG                         GTCTTTCCTCTTAAAGCAGAGCTGCTGAAACCTCAAGCAGAAATGGAGAGA
genomic: AGCAAGGATCAGAGATTCGTGAGAAGATTATTTGTTTTCTTCGAGACAAGgtacatagct ... ttggattcagGTCTTTCCTCTTAAAGCAGAGCTGCTGAAACCTCAAGCAGAAATGGAGAGA
EST: gi|60338080|gb|DN205053.1|DN205053
EST:     AGCAAGGATCAGAGATTCGTGAGAAGATTATTTGTTTTCTTCGAGACAAG                         GTCTTTCCTCTTAAAGCAGAGCTGCTGAAACCTCAAGCAGAAATGGAGAGA
genomic: AGCAAGGATCAGAGATTCGTGAGAAGATTATTTGTTTTCTTCGAGACAAGgtacatagct ... ttggattcagGTCTTTCCTCTTAAAGCAGAGCTGCTGAAACCTCAAGCAGAAATGGAGAGA
EST: gi|211433492|gb|FL365020.1|FL365020
EST:     AGCAAGGATCAGAGATTCGTGAGAAGATTATTTGTTTTCTTCGAGACAAG                         GTCTTTCCTCTTAAAGCAGAGCTGCTGAAACCCTCA-GCAGAAATGG
genomic: AGCAAGGATCAGAGATTCGTGAGAAGATTATTTGTTTTCTTCGAGACAAGgtacatagct ... ttggattcagGTCTTTCCTCTTAAAGCAGAGCTGCTGAAACC-TCAAGCAGAAATGG
EST: gi|148943964|gb|EC889044.2|EC889044
EST:     AGCAAGGATCAGAGATTCGTGAGAAGATTATTTGTTTTCTTCGAGACAAG                         GTCTTTCCTCTTAAAGCAGAGCTGCTGAAACCTCAAGCAGAAATGGAGAGA
genomic: AGCAAGGATCAGAGATTCGTGAGAAGATTATTTGTTTTCTTCGAGACAAGgtacatagct ... ttggattcagGTCTTTCCTCTTAAAGCAGAGCTGCTGAAACCTCAAGCAGAAATGGAGAGA
EST: gi|211314239|gb|FL336753.1|FL336753
EST:     AGCAAGGATCAGAGATTCGTGAGAAGATTATTTGTTTTCTTCGAGACAAG                         GTCTTTCCTCTTCAAGCAGAGCTGCTGAAACCTCAAGCAGAAATGGAGAGA
genomic: AGCAAGGATCAGAGATTCGTGAGAAGATTATTTGTTTTCTTCGAGACAAGgtacatagct ... ttggattcagGTCTTTCCTCTTAAAGCAGAGCTGCTGAAACCTCAAGCAGAAATGGAGAGA
EST: gi|76014976|gb|DT942146.1|DT942146
EST:     AGCAAGGATCAGAGATTCGTGAGAAGATTATTTGTTTTCTTCGAGACAAG                         GTCTTTCCTCTTAAAGCAGAGCTGCTGAAACCTCAAGCAGAAATGGAGAGA
genomic: AGCAAGGATCAGAGATTCGTGAGAAGATTATTTGTTTTCTTCGAGACAAGgtacatagct ... ttggattcagGTCTTTCCTCTTAAAGCAGAGCTGCTGAAACCTCAAGCAGAAATGGAGAGA
EST: gi|32164953|gb|CD670271.1|CD670271
EST:     AGCAAGGATCAGAGATTCGTGAGAAGATTATTTGTTTTCTTCGAGACAAG                         GTCTTTCCTCTTAAAGCAGAGCTGCTGAAACCTCAAGCAGAAATGGAGAGA
genomic: AGCAAGGATCAGAGATTCGTGAGAAGATTATTTGTTTTCTTCGAGACAAGgtacatagct ... ttggattcagGTCTTTCCTCTTAAAGCAGAGCTGCTGAAACCTCAAGCAGAAATGGAGAGA
EST: gi|211306674|gb|FL363564.1|FL363564
EST:     AGCAAGGATCAGAGATTCGTGAGAAGATTATTTGTTTTCTTCGAGACAAG                         GTCTTTCCTCTTAAAGCAGAGCTGCTGAAACCTCAAGCAGAAATGGAGAGA
genomic: AGCAAGGATCAGAGATTCGTGAGAAGATTATTTGTTTTCTTCGAGACAAGgtacatagct ... ttggattcagGTCTTTCCTCTTAAAGCAGAGCTGCTGAAACCTCAAGCAGAAATGGAGAGA
EST: gi|108824166|gb|EC278174.1|EC278174
EST:     AGCAAGGATCAGAGATTCGTGAGAAGATTATTTGTTTTCTTCGAGACAAG                         GTCTTTCCTCTTAAAGCAGAGCTGCTGGAAACCTCAAGCAGAAATGGAGAG
genomic: AGCAAGGATCAGAGATTCGTGAGAAGATTATTTGTTTTCTTCGAGACAAGgtacatagct ... ttggattcagGTCTTTCCTCTTAAAGCAGAGCTGCTG-AAACCTCAAGCAGAAATGGAGAG
EST: gi|31356580|gb|CD440937.1|CD440937
EST:     AGCAAGGATCAGAGATTCGTGAGAAGATTATTTGTTTTCTTCGAGACAAG                         GTCTTTCCTCTTAAAGCAGAGCTGCTGAAACCTCAAGCAGAAATGGAGAGA
genomic: AGCAAGGATCAGAGATTCGTGAGAAGATTATTTGTTTTCTTCGAGACAAGgtacatagct ... ttggattcagGTCTTTCCTCTTAAAGCAGAGCTGCTGAAACCTCAAGCAGAAATGGAGAGA
EST: gi|211050490|gb|FL366022.1|FL366022
EST:     AGCAAGGATCAGAGATTCGTGAGAAGATTATTTGTTTTCTTCGAGACAAG                         GTCTTTCCTCTTAAAGCAGAGCTGCTGA
genomic: AGCAAGGATCAGAGATTCGTGAGAAGATTATTTGTTTTCTTCGAGACAAGgtacatagct ... ttggattcagGTCTTTCCTCTTAAAGCAGAGCTGCTGA
EST: gi|89761569|gb|DY689527.1|DY689527
EST:     AGCAAGGATCAGAGATTCGTGAGAAGATTATTTGTTTTCTTCGAGACAAG                         GTCTTTCCTCTTAAAGCAGAGCTGCTGAAACCTCAAGCAGAAATGGAGAGA
genomic: AGCAAGGATCAGAGATTCGTGAGAAGATTATTTGTTTTCTTCGAGACAAGgtacatagct ... ttggattcagGTCTTTCCTCTTAAAGCAGAGCTGCTGAAACCTCAAGCAGAAATGGAGAGA
EST: gi|149105666|gb|EE291222.2|EE291222
EST:     AGCAAGGATCAGAGATTCGTGAGAAGATTATTTGTTTTCTTCGAGACAAG                         GTCTTTCCTCTTAAAGCAGAGCTGCTGAAACCTCAAGCAGAAATGGAGAGA
genomic: AGCAAGGATCAGAGATTCGTGAGAAGATTATTTGTTTTCTTCGAGACAAGgtacatagct ... ttggattcagGTCTTTCCTCTTAAAGCAGAGCTGCTGAAACCTCAAGCAGAAATGGAGAGA
EST: gi|50326790|gb|CO521916.1|CO521916
EST:     AGCAAGGATCAGAGATTCGTGAGAAGATTATTTGTTTTCTTCGAGACAAG                         GTCTTTCCTCTTAAAGCAGAGCTGCTNGAA-CCTCAAGCAGAAATGGAGAG
genomic: AGCAAGGATCAGAGATTCGTGAGAAGATTATTTGTTTTCTTCGAGACAAGgtacatagct ... ttggattcagGTCTTTCCTCTTAAAGCAGAGCTGCT-GAAACCTCAAGCAGAAATGGAGAG
EST: gi|31358588|gb|CD442945.1|CD442945
EST:     AGCAAGGATCAGAGATTCGTGAGAAGATTATTTGTTTTCTTCGAGACAAG                         GTCTTTCCTCTTAAAGCAGAGCTGCTGAAACCTCAAGCAGAAATGGAGAGA
genomic: AGCAAGGATCAGAGATTCGTGAGAAGATTATTTGTTTTCTTCGAGACAAGgtacatagct ... ttggattcagGTCTTTCCTCTTAAAGCAGAGCTGCTGAAACCTCAAGCAGAAATGGAGAGA

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: 48 (upstream exon), 47 (downstream exon)
Score: 417

ATTCATTACAACCTTTATTTAAGCATGTGGAGCAAGGATCAGAGATTCGTGAGAAGATTATTTGTTTTCTTCGAGACAAGgtacatagct ... ttggattcagGTCTTTCCTCTTAAAGCAGAGCTGCTGAAACCTCAAGCAGAAATGGAGAGATTTATAACGGATTTGATAAAGAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 124

ATTCATTACAACCTTTATTTAAGCATGTGGAGCAAGGATCAGAGATTCGTGAGAAGATTATTTGTTTTCTTCGAGACAAGgtacatagct ... ttggattcagGTCTTTCCTCTTAAAGCAGAGCTGCTGAAACCTCAAGCAGAAATGGAGAGATTTATAACGGATTTGATAAAGAAA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 148

ATTCATTACAACCTTTATTTAAGCATGTGGAGCAAGGATCAGAGATTCGTGAGAAGATTATTTGTTTTCTTCGAGACAAGgtacatagct ... ttggattcagGTCTTTCCTCTTAAAGCAGAGCTGCTGAAACCTCAAGCAGAAATGGAGAGATTTATAACGGATTTGATAAAGAAA


Block sizes: 48 (upstream exon), 44 (downstream exon)
Score: 165

ATTCATTACAACCTTTATTTAAGCATGTGGAGCAAGGATCAGAGATTCGTGAGAAGATTATTTGTTTTCTTCGAGACAAGgtacatagct ... ttggattcagGTCTTTCCTCTTAAAGCAGAGCTGCTGAAACCTCAAGCAGAAATGGAGAGATTTATAACGGATTTGATAAAGAAA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTCATTACAACCTTTATTTAAGCATGTGGAGCAAGGATCAGAGATTCGTGAGAAGATTATTTGTTTTCTTCGAGACAAGgtacatagctgaatgtagggattacatgttctgttgatgataatttgtagtgtgctagatcaagaatgtggttgtgtgtttttttggattcag

- - - - - - - - - - - - - - - AGCAAG