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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAATACGGTCTTAATCAGCGCATCGGGCCAATATCACTTGCTACACTGTCAAATGGTGGGTTAGATGACTCTGGTGGTTCTCCATGGGGAAGAGATCAGgtttgcctcaaaacttctcgtgcaccttcaagaactattaagttgccatctgcaagcactgagctcaaacttggaacctaatggcag

Basic information

species Zea mays
transcript GRMZM2G163193_T02
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G163193_T03 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os02g43350.1 (Oryza sativa), 5'ss of exon 11
AGAATACGGTCTTAATCAGCGCATCGGGCCAATATCACTTGCTACACTGTCAAATGGTGGGTTAGATGACTCTGGTGGTTCTCCATGGGGAAGAGATCAGgtttgcctcaaaacttctcgtgcaccttca--agaactattaagttgccatctgcaagcact-----gagctcaaacttggaacctaatggcag-------
||| || ||||||||||||||||| || || |||||  | || ||| |||||||||||||| ||||||| || || || |||||||||||||| |||||||| || |||||||  || | | | |||| |   ||| | || | |||  || || |     |     |  ||     ||  ||| |  | | |        
AGAGTATGGTCTTAATCAGCGCATAGGTCCGATATCGGTGGCAACATTGTCAAATGGTGGGCTAGATGAATCCGGAGGCTCTCCATGGGGAAGGGATCAGgtctgtctcaaaatgtccc-tactcctttacttgaattttttatttggaatttggacattttcgcgggtacttttttttttaactttttagaaagtcaagt

upper sequence: GRMZM2G163193_T03 (Zea mays), 5'ss of exon 10
lower sequence: AT5G58870.1 (Arabidopsis thaliana), 5'ss of exon 11
AGAATACGGTCTTAATCAGCGCATCGGGCCAATATCACTTGCTACACTGTCAAATGGTGGGTTAGATGACTCTGGTGGTTCTCCATGGGGAAGAGATCAGgtttgcctcaaaacttctcgtgcaccttcaagaactattaagttgccatctgcaagcactgagctcaaacttggaacctaatggcag
 ||||| ||||| ||  ||   ||||| ||  | ||  | ||||| || ||   ||||||| | ||||||||||| || || ||||||||||||||||||||    ||| |  || |     |  |||   |  || ||            |||| |  | |  |   |    |||  ||  |    
TGAATATGGTCTCAACGAGAAAATCGGACCCGTCTCTGTGGCTACGCTTTCTGCTGGTGGGATTGATGACTCTGGGGGATCACCATGGGGAAGAGATCAGgt--aactctattctacctaaacttcttgttggtctttttcaaaatggaaagcaaac-ttaacatgtcatgctgaatttacag----
















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|67029785|gb|CO458534.1|CO458534
EST:     TGACTCTGGTGTTTCTCCATGGGNGAAGAGATCAG                         GGCCATCTAGTTGATCTCGTTCAGAGGGAAGTAATAGCGCTTTTACAGACG
genomic: TGACTCTGGTGGTTCTCCATGGG-GAAGAGATCAGgtttgcctca ... ctaatggcagGGCCATCTAGTTGATCTCGTTCAGAGGGAAGTAAAAGCGCTTTTACAGACG
EST: gi|78121515|gb|DV539899.1|DV539899
EST:     CAAATGGTGGGTTAGATGACTCTGGTGGTTCTCCATGGGGAAGAGATCAG                         GGCCATCTAGTTGATCTCGTTCAGAGGGAAGTAAAAGCGCTTTTACAGACG
genomic: CAAATGGTGGGTTAGATGACTCTGGTGGTTCTCCATGGGGAAGAGATCAGgtttgcctca ... ctaatggcagGGCCATCTAGTTGATCTCGTTCAGAGGGAAGTAAAAGCGCTTTTACAGACG
EST: gi|71449715|gb|DR830765.1|DR830765
EST:     CAAATGGTGGGTTAGATGACTCTGGTGGTTCTCCATGGGGAAGAGATCAG                         GGCCATCTAGTTGATCTCGTTCAGAGGGAAGTAAAAGCGCTTTTACAGACG
genomic: CAAATGGTGGGTTAGATGACTCTGGTGGTTCTCCATGGGGAAGAGATCAGgtttgcctca ... ctaatggcagGGCCATCTAGTTGATCTCGTTCAGAGGGAAGTAAAAGCGCTTTTACAGACG
EST: gi|67033989|gb|CO462738.1|CO462738
EST:     CAAATGGTGGGTTAGATGACTCTGGTGGTTCTCCATGGGGAAGAGATCAG                         GGCCATCTAGTTGATCTCGTTCAGAGGGAAGTAAAAGCGCTTTTACAGACG
genomic: CAAATGGTGGGTTAGATGACTCTGGTGGTTCTCCATGGGGAAGAGATCAGgtttgcctca ... ctaatggcagGGCCATCTAGTTGATCTCGTTCAGAGGGAAGTAAAAGCGCTTTTACAGACG
EST: gi|166505071|gb|EG317739.1|EG317739
EST:     TCTGGTGGTTCTCCATGGGGAAGAGATCAG                         GGCCATCTAGTTGATCTCGTTCAGAGGGAAGTAAAAGCGCTTTTACTTAGA
genomic: TCTGGTGGTTCTCCATGGGGAAGAGATCAGgtttgcctca ... ctaatggcagGGCCATCTAGTTGATCTCGTTCAGAGGGAAGTAAAAGCGCTTTTAC--AGA
EST: gi|71329683|gb|DR801566.1|DR801566
EST:     CAAATGGTGGGTTAGATGACTCTGGTGGTTCTCCATGGGGAAGAGATCAG                         GGCCATCTAGTTGATCTCGTTCAGAGGGAAGTAAAAGCGCTTTTACAGACG
genomic: CAAATGGTGGGTTAGATGACTCTGGTGGTTCTCCATGGGGAAGAGATCAGgtttgcctca ... ctaatggcagGGCCATCTAGTTGATCTCGTTCAGAGGGAAGTAAAAGCGCTTTTACAGACG
EST: gi|13558170|gb|BG549526.1|BG549526
EST:     TGGTTCTCCATGGGGAAGAGATCAG                         GGCCATCTAGTTGATCTCGTTCAGAGGGAAGTAAAAGCGCTTTTACAGACG
genomic: TGGTTCTCCATGGGGAAGAGATCAGgtttgcctca ... ctaatggcagGGCCATCTAGTTGATCTCGTTCAGAGGGAAGTAAAAGCGCTTTTACAGACG
EST: gi|211228739|gb|FL103757.1|FL103757
EST:     CAAATGGTGGGTTAGATGACTCTGGTGGCTCTCCATGGGGAAGAGATCAG                         GGCCATCTAGTTGATCTCGTTCAGAGGGAAGTAAAAGCGCTTTTACAGACG
genomic: CAAATGGTGGGTTAGATGACTCTGGTGGTTCTCCATGGGGAAGAGATCAGgtttgcctca ... ctaatggcagGGCCATCTAGTTGATCTCGTTCAGAGGGAAGTAAAAGCGCTTTTACAGACG
EST: gi|13558169|gb|BG549525.1|BG549525
EST:     GTGGTTCTCCATGGGGAAGAGATCAG                         GGCCATCTAGTTGATCTCGTTCAGAGGGAAGTAAAAGCGCTTTTACAGACG
genomic: GTGGTTCTCCATGGGGAAGAGATCAGgtttgcctca ... ctaatggcagGGCCATCTAGTTGATCTCGTTCAGAGGGAAGTAAAAGCGCTTTTACAGACG
EST: gi|101384111|gb|EB814110.1|EB814110
EST:     CCATGGGGAAGAGATCAG                         GGCCATCTAGTTGATCTCGTTCAGAGGGAAGTAAAAGCGCTTTTACAGACG
genomic: CCATGGGGAAGAGATCAGgtttgcctca ... ctaatggcagGGCCATCTAGTTGATCTCGTTCAGAGGGAAGTAAAAGCGCTTTTACAGACG

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: 119

AGAATACGGTCTTAATCAGCGCATCGGGCCAATATCACTTGCTACACTGTCAAATGGTGGGTTAGATGACTCTGGTGGTTCTCCATGGGGAAGAGATCAGgtttgcctca ... ctaatggcagGGCCATCTAGTTGATCTCGTTCAGAGGGAAGTAAAAGCGCTTTTACAGACGGCACTGGAAGTAGCTCTTTCAGTTATTCGTGCTAATCCTGCAGTTTTGG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 211

AGAATACGGTCTTAATCAGCGCATCGGGCCAATATCACTTGCTACACTGTCAAATGGTGGGTTAGATGACTCTGGTGGTTCTCCATGGGGAAGAGATCAGgtttgcctca ... ctaatggcagGGCCATCTAGTTGATCTCGTTCAGAGGGAAGTAAAAGCGCTTTTACAGACGGCACTGGAAGTAGCTCTTTCAGTTATTCGTGCTAATCCTGCAGTTTTGG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 246

AGAATACGGTCTTAATCAGCGCATCGGGCCAATATCACTTGCTACACTGTCAAATGGTGGGTTAGATGACTCTGGTGGTTCTCCATGGGGAAGAGATCAGgtttgcctca ... ctaatggcagGGCCATCTAGTTGATCTCGTTCAGAGGGAAGTAAAAGCGCTTTTACAGACGGCACTGGAAGTAGCTCTTTCAGTTATTCGTGCTAATCCTGCAGTTTTGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 188

AGAATACGGTCTTAATCAGCGCATCGGGCCAATATCACTTGCTACACTGTCAAATGGTGGGTTAGATGACTCTGGTGGTTCTCCATGGGGAAGAGATCAGgtttgcctca ... ctaatggcagGGCCATCTAGTTGATCTCGTTCAGAGGGAAGTAAAAGCGCTTTTACAGACGGCACTGGAAGTAGCTCTTTCAGTTATTCGTGCTAATCCTGCAGTTTTGG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAATACGGTCTTAATCAGCGCATCGGGCCAATATCACTTGCTACACTGTCAAATGGTGGGTTAGATGACTCTGGTGGTTCTCCATGGGGAAGAGATCAGgtttgcctcaaaacttctcgtgcaccttcaagaactattaagttgccatctgcaagcactgagctcaaacttggaacctaatggcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA