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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCAGAGCCAGCTCCAAGGGAGCTTCCCAGGAATGAGGACCCGAGTTTGGTGAGAAGGAATAAGAGGATGCTGGGGCAGCTTCTTGTCGGTACATTAGAGgtaaagcaattctctgcacactgatgaatctgtacttctgcaagaatgcatatcaacctaatgtgatagttaatttctatttctgcctctagtattcctt...

Basic information

species Zea mays
transcript GRMZM2G102475_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G102475_T03 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os03g49520.1 (Oryza sativa), 5'ss of exon 5
GCCAGAGCCAGCTCCAAGGGAGCTTCCCAGGAATGAGGACCCGAGTTTGGTGAGAAGGAATAAGAGGATGCTGGGGCAGCTTCTTGTCGGTACATTAGAGgtaaagcaattctctgcacactgatgaatctgtacttc-tgcaagaatgcatatcaacctaatgtgatagttaatttctatttctgcctctagtattcctt--
|||||| ||    || |||||  |||||| | ||||||| |  ||  | ||||  ||||| ||||||||||||||| |||||||||||||||||||||||||||  | ||||  |  |||   |  ||     | | | ||    ||   |||  ||  ||     |   || | |  |   ||| |  ||  ||  |     
GCCAGAACCTCTCCCGAGGGAATTTCCCAAGGATGAGGATCAAAGCCTTGTGAAGAGGAACAAGAGGATGCTGGGGAAGCTTCTTGTCGGTACATTAGAGgtaac-cgattcaatagacat--acaaaggaacaatccatgggtcaagcgataataagatatcaacagttttcagtgtttcctctccaactgatacacacaaa
















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|94478087|gb|EB707045.1|EB707045
EST:     TGAGAAGGAATAAGAGGATGCTGGGGCAGCTTCTTGTCGGTACATTAGAG                         AAATTTCAACAAGAGGATAAAAAGCTATCCAACTCTGAGGCTTTTCTGCGC
genomic: TGAGAAGGAATAAGAGGATGCTGGGGCAGCTTCTTGTCGGTACATTAGAGgtaaagcaat ... tgcaatgcagAAATTTCAACAAGAGGATAAAAAGCTATCCAACTCTGAGGCTTTTCTGCGC
EST: gi|261490328|gb|GO359834.1|GO359834
EST:     TGAGGAGGAATAAGAGGATGCTGGGGCAGCTTCTTGTCGGTACATTAGAG                         AAA-TTCAACAAGAGGATAAAAAGCTATCCAACTCTGAGGCTTTTCTGCGC
genomic: TGAGAAGGAATAAGAGGATGCTGGGGCAGCTTCTTGTCGGTACATTAGAGgtaaagcaat ... tgcaatgcagAAATTTCAACAAGAGGATAAAAAGCTATCCAACTCTGAGGCTTTTCTGCGC
EST: gi|148953283|gb|EE152769.2|EE152769
EST:     TGAGAAGGAATAAGAGGATGCTGGGGCAGCTTCTTGTCGGTACATTAGAG                         AAATTTCAACAAGAGGATAAAAAGCTATCCAACTCTGAGGCTTTTCTGCGC
genomic: TGAGAAGGAATAAGAGGATGCTGGGGCAGCTTCTTGTCGGTACATTAGAGgtaaagcaat ... tgcaatgcagAAATTTCAACAAGAGGATAAAAAGCTATCCAACTCTGAGGCTTTTCTGCGC
EST: gi|149026687|gb|EE046096.2|EE046096
EST:     TGAGAAGGAATAAGAGGATGCTGGGGCAGCTTCTTGTCGGTACATTAGAG                         AAATTTCAACAAGAGGATAAAAAGCTATCCAACTCTGAGGCTTTTCTGCGC
genomic: TGAGAAGGAATAAGAGGATGCTGGGGCAGCTTCTTGTCGGTACATTAGAGgtaaagcaat ... tgcaatgcagAAATTTCAACAAGAGGATAAAAAGCTATCCAACTCTGAGGCTTTTCTGCGC
EST: gi|93013768|gb|EB639288.1|EB639288
EST:     TGAGAAGGAATAAGAGGATGCTGGGGCAGCTTCTTGTCGGTACATTAGAG                         AAATTTCAACAAGAGGATAAAAAGCTATCCAACTCTGAGGCTTTTCTGCGC
genomic: TGAGAAGGAATAAGAGGATGCTGGGGCAGCTTCTTGTCGGTACATTAGAGgtaaagcaat ... tgcaatgcagAAATTTCAACAAGAGGATAAAAAGCTATCCAACTCTGAGGCTTTTCTGCGC
EST: gi|149045935|gb|EE047933.2|EE047933
EST:     TGAGAAGGAATAAGAGGATGCTGGGGCAGCTTCTTGTCGGTACATTAGAG                         AAATTTCAACAAGAGGATAAAAAGCTATCCAACTCTGAGGCTTTTCTGCGC
genomic: TGAGAAGGAATAAGAGGATGCTGGGGCAGCTTCTTGTCGGTACATTAGAGgtaaagcaat ... tgcaatgcagAAATTTCAACAAGAGGATAAAAAGCTATCCAACTCTGAGGCTTTTCTGCGC

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: 663

GCCAGAGCCAGCTCCAAGGGAGCTTCCCAGGAATGAGGACCCGAGTTTGGTGAGAAGGAATAAGAGGATGCTGGGGCAGCTTCTTGTCGGTACATTAGAGgtaaagcaat ... tgcaatgcagAAATTTCAACAAGAGGATAAAAAGCTATCCAACTCTGAGGCTTTTCTGCGCAGATCAGAGACTCAGCGAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 275

GCCAGAGCCAGCTCCAAGGGAGCTTCCCAGGAATGAGGACCCGAGTTTGGTGAGAAGGAATAAGAGGATGCTGGGGCAGCTTCTTGTCGGTACATTAGAGgtaaagcaat ... tgcaatgcagAAATTTCAACAAGAGGATAAAAAGCTATCCAACTCTGAGGCTTTTCTGCGCAGATCAGAGACTCAGCGAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 298

GCCAGAGCCAGCTCCAAGGGAGCTTCCCAGGAATGAGGACCCGAGTTTGGTGAGAAGGAATAAGAGGATGCTGGGGCAGCTTCTTGTCGGTACATTAGAGgtaaagcaat ... tgcaatgcagAAATTTCAACAAGAGGATAAAAAGCTATCCAACTCTGAGGCTTTTCTGCGCAGATCAGAGACTCAGCGAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 259

GCCAGAGCCAGCTCCAAGGGAGCTTCCCAGGAATGAGGACCCGAGTTTGGTGAGAAGGAATAAGAGGATGCTGGGGCAGCTTCTTGTCGGTACATTAGAGgtaaagcaat ... tgcaatgcagAAATTTCAACAAGAGGATAAAAAGCTATCCAACTCTGAGGCTTTTCTGCGCAGATCAGAGACTCAGCGAAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCAGAGCCAGCTCCAAGGGAGCTTCCCAGGAATGAGGACCCGAGTTTGGTGAGAAGGAATAAGAGGATGCTGGGGCAGCTTCTTGTCGGTACATTAGAGgtaaagcaattctctgcacactgatgaatctgtacttctgcaagaatgcatatcaacctaatgtgatagttaatttctatttctgcctctagtattcctt

- - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT