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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atttaagatcttacaatgccctttggcatattttaaatggaaatcaaagcactctgtttctttgttatttatttgttgtataatttgcttccacttgcagAATTGGTCTTCTAGTGGTCTGCTTGAGAAAATGAAGAAACTTTCTGAAAGAAGGAAGCTTGAAGATTTAACAATTGGTCCAGTCCTTACA

Basic information

species Zea mays
transcript GRMZM2G090087_T03
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G090087_T03 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os05g45960.1 (Oryza sativa), 3'ss of exon 10
atttaagatcttacaatgccctttggcata-ttttaaatggaaatcaaagcactctgtttctttgt-tatttatttgttgtataatttgcttccacttgcagAATTGGTCTTCTAGTGGTCTGCTTGAGAAAATGAAGAAACTTTCTGAAAGAAGGAAGCTTGAAGATTTAACAATTGGTCCAGTCCTTACA
   ||  || |  |  |    |||     |  |||  | |  | |  |     | |   | ||  | | || || |||||| |||||| |||  |||||||||||||||| |||||||| || ||||| |||||||| |  |||||||||||||||||||||||||| || || ||||| ||||||||||| 
-aatacaatttgtctttcttttttatttgagctttggaagctagttgagcttgtgttacttttcatatcttaatctgttgtttaattttctta-acttgcagAATTGGTCGTCTAGTGGGCTTCTTGATAAAATGAAAAGTCTTTCTGAAAGAAGGAAGCTTGAAGACTTGACCATTGGCCCAGTCCTTACT
















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|211226663|gb|FL216925.1|FL216925
EST:     CTTGTAGCGGTCAGAAATGCTCTGCTCAATCTGTTCTATTCATGCACAAG                         AATTGGTCTTCTAGTGGTCTGCTTGAGAAAATGAAGAAACTTGTCTGAAAG
genomic: CTTGTAGCGGTCAGAAATGCTCTGCTCAGTCTGTTCTATTCATGCACAAGgtaaagactg ... ccacttgcagAATTGGTCTTCTAGTGGTCTGCTTGAGAAAATGAAGAAACTT-TCTGAAAG
EST: gi|211228708|gb|FL216926.1|FL216926
EST:     CTTGTAGCGGTCAGAAATGCTCTGCTCAATCTGTTCTATTCATGCACAAG                         AATTGGTCTTCTAGTGGTCTGCTTGAGAAAATGAAGAAACTTTCTGAAAGA
genomic: CTTGTAGCGGTCAGAAATGCTCTGCTCAGTCTGTTCTATTCATGCACAAGgtaaagactg ... ccacttgcagAATTGGTCTTCTAGTGGTCTGCTTGAGAAAATGAAGAAACTTTCTGAAAGA
EST: gi|67019711|gb|CO448460.1|CO448460
EST:     CTTGTAGCGGTCAGAAATGCTCTGCTCAATCTGTTCTATTCATGCACAAG                         AATTGGTCTTCTAGTGGTCTGCTTGAGAAAATGAAGAAACTTTCTGAAAGA
genomic: CTTGTAGCGGTCAGAAATGCTCTGCTCAGTCTGTTCTATTCATGCACAAGgtaaagactg ... ccacttgcagAATTGGTCTTCTAGTGGTCTGCTTGAGAAAATGAAGAAACTTTCTGAAAGA
EST: gi|33101148|gb|CF061108.1|CF061108
EST:     CTTGTAGCGGTCAGAAATGCTCTGCTCAATCTGTTCTATTCATGCACAAG                         AATTGGTCTTCTAGTGGTCTGCTTGAGAAAATGAAGAAACTTTCTGAAAGA
genomic: CTTGTAGCGGTCAGAAATGCTCTGCTCAGTCTGTTCTATTCATGCACAAGgtaaagactg ... ccacttgcagAATTGGTCTTCTAGTGGTCTGCTTGAGAAAATGAAGAAACTTTCTGAAAGA
EST: gi|67026280|gb|CO455029.1|CO455029
EST:     CTTGTAGCGGTCAGAAATGCTCTGCTCAATCTGTTCTATTCATGCACAAG                         AATTGGTCTTCTAGTGGTCTGCTTGAGAAA-TGAAGAA-CTTTCTGAAAGA
genomic: CTTGTAGCGGTCAGAAATGCTCTGCTCAGTCTGTTCTATTCATGCACAAGgtaaagactg ... ccacttgcagAATTGGTCTTCTAGTGGTCTGCTTGAGAAAATGAAGAAACTTTCTGAAAGA
EST: gi|67024223|gb|CO452972.1|CO452972
EST:     CTTGTAGCGGTCAGAAATGCTCTGCTCAATCTGTTCTATTCATGCACAAG                         AATTGGTCTTCTAGTGGTCTGCTTGAGAAAATGAAGAAACTTTCTGAAAGA
genomic: CTTGTAGCGGTCAGAAATGCTCTGCTCAGTCTGTTCTATTCATGCACAAGgtaaagactg ... ccacttgcagAATTGGTCTTCTAGTGGTCTGCTTGAGAAAATGAAGAAACTTTCTGAAAGA
EST: gi|211228710|gb|FL216928.1|FL216928
EST:     CTTGTAGCGGTCAGAAATGCTCTGCTCAATCTGTTCTATTCATGCACAAG                         AATTGGTCTTCTAGTGGTCTGCTTGAGAAAATGGAAGAAACTTTCTGAAAG
genomic: CTTGTAGCGGTCAGAAATGCTCTGCTCAGTCTGTTCTATTCATGCACAAGgtaaagactg ... ccacttgcagAATTGGTCTTCTAGTGGTCTGCTTGAGAAAATG-AAGAAACTTTCTGAAAG
EST: gi|24773212|gb|CA408466.1|CA408466
EST:     CTTGTAGCGGTCAGAAATGCTCTGCTCAGTCTGTTCTATTCATGCACAAG                         AATTGGTCTTCTAGTGGTCTGCTTGAGAAAATGAAGAAACTTTCTGAAAGA
genomic: CTTGTAGCGGTCAGAAATGCTCTGCTCAGTCTGTTCTATTCATGCACAAGgtaaagactg ... ccacttgcagAATTGGTCTTCTAGTGGTCTGCTTGAGAAAATGAAGAAACTTTCTGAAAGA
EST: gi|67023454|gb|CO452203.1|CO452203
EST:     CTTGTAGCGGTCAGAAATGCTCTGCTCAATCTGTTCTATTCATGCACAAG                         AATTGGTCTTCTAGTGGTCTGCTTGAGAAAATGAAGAAACTTTCTGAAAGA
genomic: CTTGTAGCGGTCAGAAATGCTCTGCTCAGTCTGTTCTATTCATGCACAAGgtaaagactg ... ccacttgcagAATTGGTCTTCTAGTGGTCTGCTTGAGAAAATGAAGAAACTTTCTGAAAGA
EST: gi|32846970|gb|CD986651.1|CD986651
EST:     CTTGTAGCGGTCAGAAATGCTCTGCTCAGTCTGTTCTATTCATGCACAAG                         AATTGGTCTTCTAGTGGTCTGCTTGAGAAAATGAAGAAACTTTCTGAAAGA
genomic: CTTGTAGCGGTCAGAAATGCTCTGCTCAGTCTGTTCTATTCATGCACAAGgtaaagactg ... ccacttgcagAATTGGTCTTCTAGTGGTCTGCTTGAGAAAATGAAGAAACTTTCTGAAAGA
EST: gi|211120258|gb|FL200679.1|FL200679
EST:     CTTGTAGCGGTCAGAAATGCTCTGCTCAATCTGTTCTATTCATGCACAAG                         AATTGGTCTTCTAGTGGTCTGCTTGAGAAAATGAAGAAACTTTCTGAAAGA
genomic: CTTGTAGCGGTCAGAAATGCTCTGCTCAGTCTGTTCTATTCATGCACAAGgtaaagactg ... ccacttgcagAATTGGTCTTCTAGTGGTCTGCTTGAGAAAATGAAGAAACTTTCTGAAAGA
EST: gi|32847832|gb|CD987513.1|CD987513
EST:     CTTGTAGCGGTCAGAAATGCTCTGCTCAGTCTGTTCTATTCATGCACAAG                         AATTGGTCTTCTAGTGGTCTGCTTGAGAAAATGAAGAAACTTTCTGAAAGA
genomic: CTTGTAGCGGTCAGAAATGCTCTGCTCAGTCTGTTCTATTCATGCACAAGgtaaagactg ... ccacttgcagAATTGGTCTTCTAGTGGTCTGCTTGAGAAAATGAAGAAACTTTCTGAAAGA
EST: gi|211228712|gb|FL216930.1|FL216930
EST:     CTTGTAGCGGTCAGAAATGCTCTGCTCAATCTGTTCTATTCATGCACAAG                         AATTGGTCTTCTAGTGGTCTGCTTGAGAAAATGAAGAAACTTTCTGAAAAG
genomic: CTTGTAGCGGTCAGAAATGCTCTGCTCAGTCTGTTCTATTCATGCACAAGgtaaagactg ... ccacttgcagAATTGGTCTTCTAGTGGTCTGCTTGAGAAAATGAAGAAACTTTCTGAAA-G

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), 49 (downstream exon)
Score: 543

GTTGATTATGTTGCATGGGTTTGCGATCAGGATGCTTATGCTTGTAGCGGTCAGAAATGCTCTGCTCAGTCTGTTCTATTCATGCACAAGgtaaagactg ... ccacttgcagAATTGGTCTTCTAGTGGTCTGCTTGAGAAAATGAAGAAACTTTCTGAAAGAAGGAAGCTTGAAGATTTAACAATTGGTCCAGTCCTTACA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 295

GTTGATTATGTTGCATGGGTTTGCGATCAGGATGCTTATGCTTGTAGCGGTCAGAAATGCTCTGCTCAGTCTGTTCTATTCATGCACAAGgtaaagactg ... ccacttgcagAATTGGTCTTCTAGTGGTCTGCTTGAGAAAATGAAGAAACTTTCTGAAAGAAGGAAGCTTGAAGATTTAACAATTGGTCCAGTCCTTACA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 158

GTTGATTATGTTGCATGGGTTTGCGATCAGGATGCTTATGCTTGTAGCGGTCAGAAATGCTCTGCTCAGTCTGTTCTATTCATGCACAAGgtaaagactg ... ccacttgcagAATTGGTCTTCTAGTGGTCTGCTTGAGAAAATGAAGAAACTTTCTGAAAGAAGGAAGCTTGAAGATTTAACAATTGGTCCAGTCCTTACA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 239

GTTGATTATGTTGCATGGGTTTGCGATCAGGATGCTTATGCTTGTAGCGGTCAGAAATGCTCTGCTCAGTCTGTTCTATTCATGCACAAGgtaaagactg ... ccacttgcagAATTGGTCTTCTAGTGGTCTGCTTGAGAAAATGAAGAAACTTTCTGAAAGAAGGAAGCTTGAAGATTTAACAATTGGTCCAGTCCTTACA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaagcactctgtttctttgttatttatttgttgtataatttgcttccacttgcagAATTGGTCTTCTAGTGGTCTGCTTGAGAAAATGAAGAAACTTTCTGAAAGAAGGAAGCTTGAAGATTTAACAATTGGTCCAGTCCTTACA
                                      tttgcttcc  CT-rich tract
           tttctttgttatttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atttaagatcttacaatgccctttggcatattttaaatggaaatcaaagcactctgtttctttgttatttatttgttgtataatttgcttccacttgcagAATTGGTCTTCTAGTGGTCTGCTTGAGAAAATGAAGAAACTTTCTGAAAGAAGGAAGCTTGAAGATTTAACAATTGGTCCAGTCCTTACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - tgccctt
- - - - - - - - - - - - - - - - - - - - -aatcaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tttgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tttgctt