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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAGGTTGTCTACACATTACCTAGCTGCGGAGGTTCAGATGACTCTAGCGTATCATCTTTAGGAAGCCGGAGCTTCAAAGCAGCGTCTGACGATCTGATGgtgagactgtggcagctctcttctgatatgtatggaacttgtgattcacttataaattttcagttgtaactcttactgttgatcgtatctttggccgtacttttcag

Basic information

species Zea mays
transcript GRMZM2G171406_T01
intron # 6
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|94475041|gb|EB703999.1|EB703999
EST:     TATCATCTTTAGGAAGCCGGAGCTTCAAAGCAGCGTCTGACGATCTGATG                         ATGCTGAAGAATGCAAGCCTTGAAGAG
genomic: TATCATCTTTAGGAAGCCGGAGCTTCAAAGCAGCGTCTGACGATCTGATGgtgagactgt ... tacttttcagATGCTGAAGAATGCAAGCCTTGAAGAG
EST: gi|16919153|gb|BM074062.1|BM074062
EST:     TATCATCTTTAGGAAGCCGGAGCTTCAAAGCAGCGTCTGACGATCTGATG                         ATGCTGAAGAATGCAAGCCTTGAAGAG
genomic: TATCATCTTTAGGAAGCCGGAGCTTCAAAGCAGCGTCTGACGATCTGATGgtgagactgt ... tacttttcagATGCTGAAGAATGCAAGCCTTGAAGAG
EST: gi|60397188|gb|DN230004.1|DN230004
EST:     TATCATCTTTAGGAAGCCGGAGCTTCAAAGCAGCGTCTGACGATCTGATG                         ATGCTGAAGAATGCAAGCCTTGAAGAG
genomic: TATCATCTTTAGGAAGCCGGAGCTTCAAAGCAGCGTCTGACGATCTGATGgtgagactgt ... tacttttcagATGCTGAAGAATGCAAGCCTTGAAGAG
EST: gi|71429669|gb|DR810719.1|DR810719
EST:     TATCATCTTTAGGAAGCCGGAGCTTCAAAGCAGCGTCTGACGATCTGATG                         ATGCTGAAGAATGCAAGCCTTGAAGAG
genomic: TATCATCTTTAGGAAGCCGGAGCTTCAAAGCAGCGTCTGACGATCTGATGgtgagactgt ... tacttttcagATGCTGAAGAATGCAAGCCTTGAAGAG
EST: gi|71441217|gb|DR822267.1|DR822267
EST:     TATCATCTTTAGGAAGCCGGAGCTTCAAAGCAGCGTCTGACGATCTGATG                         ATGCTGAAGAATGCAAGCCTTGAAGAG
genomic: TATCATCTTTAGGAAGCCGGAGCTTCAAAGCAGCGTCTGACGATCTGATGgtgagactgt ... tacttttcagATGCTGAAGAATGCAAGCCTTGAAGAG
EST: gi|94475040|gb|EB703998.1|EB703998
EST:     TATCATCTTTAGGAAGCCGGAGCTTCAAAGCAGCGTCTGACGATCTGATG                         ATGCTGAAGAATGCAAGCCTTGAAGAG
genomic: TATCATCTTTAGGAAGCCGGAGCTTCAAAGCAGCGTCTGACGATCTGATGgtgagactgt ... tacttttcagATGCTGAAGAATGCAAGCCTTGAAGAG
EST: gi|91874947|gb|EB404904.1|EB404904
EST:     TATCATCTTTAGGAAGCCGGAGCTTCAAAGCAGCGTCTGACGATCTGATG                         ATGCTGAAGAATGCAAGCCTTGAAGAG
genomic: TATCATCTTTAGGAAGCCGGAGCTTCAAAGCAGCGTCTGACGATCTGATGgtgagactgt ... tacttttcagATGCTGAAGAATGCAAGCCTTGAAGAG
EST: gi|93012917|gb|EB638437.1|EB638437
EST:     TATCATCTTTAGGAAGCCGGAGCTTCAAAGCAGCGTCTGACGATCTGATG                         ATGCTGAAGAATGCAAGCCTTGAAGAG
genomic: TATCATCTTTAGGAAGCCGGAGCTTCAAAGCAGCGTCTGACGATCTGATGgtgagactgt ... tacttttcagATGCTGAAGAATGCAAGCCTTGAAGAG
EST: gi|89250482|gb|DY622268.1|DY622268
EST:     TATCATCTTTAGGAAGCCGGAGCTTCAAAGCAGCGTCTGACGATCTGATG                         ATGCTGAAGAATGCAAGCCTTGAAGAG
genomic: TATCATCTTTAGGAAGCCGGAGCTTCAAAGCAGCGTCTGACGATCTGATGgtgagactgt ... tacttttcagATGCTGAAGAATGCAAGCCTTGAAGAG
EST: gi|5069938|gb|AI737903.1|AI737903
EST:     AGCAGCGTCTGACGATCTGATG                         ATGCTGAAGAATGCAAGCCTTGAAGAG
genomic: AGCAGCGTCTGACGATCTGATGgtgagactgt ... tacttttcagATGCTGAAGAATGCAAGCCTTGAAGAG
EST: gi|89251407|gb|DY623193.1|DY623193
EST:     TATCATCTTTAGGAAGCCGGAGCTTCAAAGCAGCGTCTGACGATCTGATG                         ATGCTGAAGAATGCAAGCCTTGAAGAG
genomic: TATCATCTTTAGGAAGCCGGAGCTTCAAAGCAGCGTCTGACGATCTGATGgtgagactgt ... tacttttcagATGCTGAAGAATGCAAGCCTTGAAGAG

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: 49 (upstream exon), 47 (downstream exon)
Score: 291

CAAGGTTGTCTACACATTACCTAGCTGCGGAGGTTCAGATGACTCTAGCGTATCATCTTTAGGAAGCCGGAGCTTCAAAGCAGCGTCTGACGATCTGATGgtgagactgt ... tacttttcagATGCTGAAGAATGCAAGCCTTGAAGAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 117

CAAGGTTGTCTACACATTACCTAGCTGCGGAGGTTCAGATGACTCTAGCGTATCATCTTTAGGAAGCCGGAGCTTCAAAGCAGCGTCTGACGATCTGATGgtgagactgt ... tacttttcagATGCTGAAGAATGCAAGCCTTGAAGAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 129

CAAGGTTGTCTACACATTACCTAGCTGCGGAGGTTCAGATGACTCTAGCGTATCATCTTTAGGAAGCCGGAGCTTCAAAGCAGCGTCTGACGATCTGATGgtgagactgt ... tacttttcagATGCTGAAGAATGCAAGCCTTGAAGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 177

CAAGGTTGTCTACACATTACCTAGCTGCGGAGGTTCAGATGACTCTAGCGTATCATCTTTAGGAAGCCGGAGCTTCAAAGCAGCGTCTGACGATCTGATGgtgagactgt ... tacttttcagATGCTGAAGAATGCAAGCCTTGAAGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAAGGTTGTCTACACATTACCTAGCTGCGGAGGTTCAGATGACTCTAGCGTATCATCTTTAGGAAGCCGGAGCTTCAAAGCAGCGTCTGACGATCTGATGgtgagactgtggcagctctcttctgatatgtatggaacttgtgattcacttataaattttcagttgtaactcttactgttgatcgtatctttggccgtacttttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT