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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTGATGTTTCACAAACGCGTGAGCGGCTCGCCCTCCTCTCCAGTCCCTCCTCCCTCCGGTCCGCACAGGGGAGCAGCCGGCAGCAGCTAGCTACCACAGgtacgcctgtctccggtccagtgcaatcttgtcttctttttggatttgtgatcgacgatgatgtagtatgtagcaaagtgtttgcttggcatgtgggctcaaggcgtaagtaaggatcagtctagaggtttggttgccaagttcagtgcactacgctgacactccctcctctccctgcgtgcactgctgctagtaccag

Basic information

species Zea mays
transcript GRMZM2G137868_T03
intron # 1
splice site 5'
intron type U2

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|149075108|gb|EE163598.2|EE163598
EST:     CTCCCTCCGGTCCGCACAGGGGAGCAGCCGGCAGCAGCTAGCTACCACAGTACCAG                    
genomic: CTCCCTCCGGTCCGCACAGGGGAGCAGCCGGCAGCAGCTAGCTA-C-C---A-CAGgtacgcctgt ... ctagt
EST: gi|71437747|gb|DR818797.1|DR818797
EST:     CTCCCTCCGGTCCGCACAGGGGAGCAGCCGGCAGCAGCTAGCTACCACAGTACCAG                    
genomic: CTCCCTCCGGTCCGCACAGGGGAGCAGCCGGCAGCAGCTAGCTA-C-C---A-CAGgtacgcctgt ... ctagt
EST: gi|76918900|gb|DV167499.1|DV167499
EST:     CTCCCTCCGGTCCGCACAGGGGAGCAGCCGGCAGCAGCTAGCTACCACAG                         CAGCAATAAGCTAATCAGCTACGATGGCGGACTACGTGTATGGCCCCGGGC
genomic: CTCCCTCCGGTCCGCACAGGGGAGCAGCCGGCAGCAGCTAGCTACCACAGgtacgcctgt ... ctagtaccagCAGCAATAAGCTAATCAGCTACGATGGCGGACTACGTGTATGGCCCCGGGC
EST: gi|148959061|gb|EE010556.2|EE010556
EST:     CTCCCTCCGGTCCGCACAGGGGAGCAGCCGGCAGCAGCTAGCTACCACAGTACCAG                    
genomic: CTCCCTCCGGTCCGCACAGGGGAGCAGCCGGCAGCAGCTAGCTA-C-C---A-CAGgtacgcctgt ... ctagt
EST: gi|74243688|gb|DT651602.1|DT651602
EST:     CTCCCTCCGGTCCGCACAGGGGAGCAGCCGGCAGCAGCTAGCTACCACAGTACCAG                    
genomic: CTCCCTCCGGTCCGCACAGGGGAGCAGCCGGCAGCAGCTAGCTA-C-C---A-CAGgtacgcctgt ... ctagt
EST: gi|78109038|gb|DV527455.1|DV527455
EST:     CTCCCTCCGGTCCGCACAGGGGAGCAGCCGGCAGCAGCTAGCTACCACAGTACCAG                    
genomic: CTCCCTCCGGTCCGCACAGGGGAGCAGCCGGCAGCAGCTAGCTA-C-C---A-CAGgtacgcctgt ... ctagt
EST: gi|149008924|gb|EE041144.2|EE041144
EST:     CTCCCTCCGGTCCGCACAGGGGAGCAGCCGGCAGCAGCTAGCTACCACAG                         CAGCAATAAGCTAATCAGCTACGATGGCGGACTACGTGTATGGCCCCGGGC
genomic: CTCCCTCCGGTCCGCACAGGGGAGCAGCCGGCAGCAGCTAGCTACCACAGgtacgcctgt ... ctagtaccagCAGCAATAAGCTAATCAGCTACGATGGCGGACTACGTGTATGGCCCCGGGC
EST: gi|211445898|gb|FL403745.1|FL403745
EST:     CTCCCTCCGGTCCGCACAGGGGAGCAGCCGGCAGCAGCTAGCTA-C-CA-                         CAGCAATAAGCTAATCAGCTACGATGGCGGACTACGTGTATGGCCCCGGGC
genomic: CTCCCTCCGGTCCGCACAGGGGAGCAGCCGGCAGCAGCTAGCTACCACAGgtacgcctgt ... ctagtaccagCAGCAATAAGCTAATCAGCTACGATGGCGGACTACGTGTATGGCCCCGGGC
EST: gi|211376270|gb|FL028048.1|FL028048
EST:     CTCCCTCCGGTCCGCACAGGGGAGCAGCCGGCAGCAGCTAGCTACCACAGTACCAG                    
genomic: CTCCCTCCGGTCCGCACAGGGGAGCAGCCGGCAGCAGCTAGCTA-C-C---A-CAGgtacgcctgt ... ctagt
EST: gi|211232280|gb|FL414442.1|FL414442
EST:     CTCCCTCCGGTCCGCACAGGGGAGCAGCCGGCAGCATCTAGCTA-C-CA-                         CAGCAAGAAGCTAATCAGCTACGATGGCGGACTACGTGTATGGCCCCGGGC
genomic: CTCCCTCCGGTCCGCACAGGGGAGCAGCCGGCAGCAGCTAGCTACCACAGgtacgcctgt ... ctagtaccagCAGCAATAAGCTAATCAGCTACGATGGCGGACTACGTGTATGGCCCCGGGC
EST: gi|148938194|gb|EC882479.2|EC882479
EST:     CTCCCTCCGGTCCGCACAGGGGAGCAGCCGGCAGCAGCTAGCTACCACAGTACCAG                    
genomic: CTCCCTCCGGTCCGCACAGGGGAGCAGCCGGCAGCAGCTAGCTA-C-C---A-CAGgtacgcctgt ... ctagt
EST: gi|33467631|gb|CF244680.1|CF244680
EST:     CTCCCTCCGGTCCGCACAGGGGAGCAGCCGGCAGCAGCTAGCTACCACAGTACCAG                    
genomic: CTCCCTCCGGTCCGCACAGGGGAGCAGCCGGCAGCAGCTAGCTA-C-C---A-CAGgtacgcctgt ... ctagt
EST: gi|148957248|gb|EC903268.2|EC903268
EST:     CTCCCTCCGGTCCGCACAGGGGAGCAGCCGGCAGCAGCTAGCTACCACAGTACCAG                    
genomic: CTCCCTCCGGTCCGCACAGGGGAGCAGCCGGCAGCAGCTAGCTA-C-C---A-CAGgtacgcctgt ... ctagt
EST: gi|76294078|gb|DV033646.1|DV033646
EST:     CTCCCTCCGGTCCGCACAGGGGAGCAGCCGGCAGCATCTAGCTACCACAGTACCAG                    
genomic: CTCCCTCCGGTCCGCACAGGGGAGCAGCCGGCAGCAGCTAGCTA-C-C---A-CAGgtacgcctgt ... ctagt
EST: gi|93014857|gb|EB640377.1|EB640377
EST:     CTCCCTCCGGTCCGCACAGGGGAGCAGCCGGCAGCAGCTAGCTACCACAGTACCAG                    
genomic: CTCCCTCCGGTCCGCACAGGGGAGCAGCCGGCAGCAGCTAGCTA-C-C---A-CAGgtacgcctgt ... ctagt

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 2 RNA-Seq libraries.


Block sizes: 37 (upstream exon), 39 (downstream exon)
Score: 23

TTTGATGTTTCACAAACGCGTGAGCGGCTCGCCCTCCTCTCCAGTCCCTCCTCCCTCCGGTCCGCACAGGGGAGCAGCCGGCAGCAGCTAGCTACCACAGgtacgcctgt ... ctagtaccagCAGCAATAAGCTAATCAGCTACGATGGCGGACTACGTGTATGGCCCCGGGCGGACCCACCTGTTCGTGCCGGGCCCCGTGAACATCCCGGACCCCGTGAT


Block sizes: 34 (upstream exon), 48 (downstream exon)
Score: 14

TTTGATGTTTCACAAACGCGTGAGCGGCTCGCCCTCCTCTCCAGTCCCTCCTCCCTCCGGTCCGCACAGGGGAGCAGCCGGCAGCAGCTAGCTACCACAGgtacgcctgt ... ctagtaccagCAGCAATAAGCTAATCAGCTACGATGGCGGACTACGTGTATGGCCCCGGGCGGACCCACCTGTTCGTGCCGGGCCCCGTGAACATCCCGGACCCCGTGAT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTGATGTTTCACAAACGCGTGAGCGGCTCGCCCTCCTCTCCAGTCCCTCCTCCCTCCGGTCCGCACAGGGGAGCAGCCGGCAGCAGCTAGCTACCACAGgtacgcctgtctccggtccagtgcaatcttgtcttctttttggatttgtgatcgacgatgatgtagtatgtagcaaagtgtttgcttggcatgtgggctcaaggcgtaagtaaggatcagtctagaggtttggttgccaagttcagtgcactacgctgacactccctcctctccctgcgtgcactgctgctagtaccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT