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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtcgaagtgtgaaccactcagattccagtacctatagagagcagcaggacctgatatgtctaaccctgttttcccgctcctactcgattgcttttacagATGGTCGGTGGAATCCGGCATGCCTGGGGCCAGGGCAACAGTGGTAAGTTCTTGAATCGTCTCCCCTTTTGCAGGGTCAGGAAAAGCCACACTGGCCTGC

Basic information

species Zea mays
transcript GRMZM5G848945_T02
intron # 3
splice site 3'
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|31350229|gb|CD434586.1|CD434586
EST:     GATCCTACAGAGCTAGCCGCGACTACCCTTATATCTTCCCACCTTGAGAG                         ATGGTCGGTGGAATCCGGCATGCCTGGGGCCAGGGCAACAGTGGTAAGTTC
genomic: GATCCTACAGAGCTAGCCGCGACTACCCTTATATCTTCCCACCTTGAGAGgtgatacttc ... gcttttacagATGGTCGGTGGAATCCGGCATGCCTGGGGCCAGGGCAACAGTGGTAAGTTC
EST: gi|12973198|gb|BG268361.1|BG268361
EST:     GATCCTACAGAGCTAGCCGCGACTACCCTTATATCTTCCCACCTTGAGAG                         ATGGTCGGTGGAATCCGGCATGCCTGGGGCCAGGGCAACAGTGGTAAGTTC
genomic: GATCCTACAGAGCTAGCCGCGACTACCCTTATATCTTCCCACCTTGAGAGgtgatacttc ... gcttttacagATGGTCGGTGGAATCCGGCATGCCTGGGGCCAGGGCAACAGTGGTAAGTTC
EST: gi|5030693|gb|AI714887.1|AI714887
EST:     GATCCTACAGAGCTAGCCGCGACTACCCTTATATCTTCCCNCCTTGAGAG                         ATGGTCGGTGGAATCCGGCATGCCTGGGGCCAGGGCAACAGTGGTAAGTTC
genomic: GATCCTACAGAGCTAGCCGCGACTACCCTTATATCTTCCCACCTTGAGAGgtgatacttc ... gcttttacagATGGTCGGTGGAATCCGGCATGCCTGGGGCCAGGGCAACAGTGGTAAGTTC
EST: gi|7137961|gb|AW499359.1|AW499359
EST:     GATCCTACAGAGCTAGCCGCGACTACCCTTATATCTTCCCACCTTGAGAG                         ATGGTCGGTGGAATCCGGCATGCCTGGGGCCAGGGCAACAGTGGTAAGTTC
genomic: GATCCTACAGAGCTAGCCGCGACTACCCTTATATCTTCCCACCTTGAGAGgtgatacttc ... gcttttacagATGGTCGGTGGAATCCGGCATGCCTGGGGCCAGGGCAACAGTGGTAAGTTC
EST: gi|211002097|gb|FL461207.1|FL461207
EST:     GATCCTACAGAGCTAGCCGCGACTACCCTTATATCTTCCCMCCTTGARAR                         ATGGTCGGTGGAATCCGGCATGCCTGGGGCCAGGGCAACAGTGGTAAGTTC
genomic: GATCCTACAGAGCTAGCCGCGACTACCCTTATATCTTCCCACCTTGAGAGgtgatacttc ... gcttttacagATGGTCGGTGGAATCCGGCATGCCTGGGGCCAGGGCAACAGTGGTAAGTTC
EST: gi|32841538|gb|CD981219.1|CD981219
EST:     GATCCTACAGAGCTAGCCGCGACTACCCTTATATCTTCCCACCTTGAGAG                         ATGGTCGGTGGAATCCGGCATGCCTGGGGCCAGGGCAACAGTGGTAAGTTC
genomic: GATCCTACAGAGCTAGCCGCGACTACCCTTATATCTTCCCACCTTGAGAGgtgatacttc ... gcttttacagATGGTCGGTGGAATCCGGCATGCCTGGGGCCAGGGCAACAGTGGTAAGTTC
EST: gi|211131392|gb|FL432625.1|FL432625
EST:     GATCCTACAGAGCTAGCCGCGACTACCCTTATATCTTCCCACCTTGAGAG                         ATGGTCGGTGGAATCCGGCATGCCTGGGGCCAGGGCAACAGTGGTAAGTTC
genomic: GATCCTACAGAGCTAGCCGCGACTACCCTTATATCTTCCCACCTTGAGAGgtgatacttc ... gcttttacagATGGTCGGTGGAATCCGGCATGCCTGGGGCCAGGGCAACAGTGGTAAGTTC
EST: gi|32841219|gb|CD980900.1|CD980900
EST:     GATCCTACAGAGCTAGCCGCGACTACCCTTATATCTTCCCACCTTGAGAG                         ATGGTCGGTGGAATCCGGCATGCCTGGGGCCAGGGCAACAGTGGTAAGTTC
genomic: GATCCTACAGAGCTAGCCGCGACTACCCTTATATCTTCCCACCTTGAGAGgtgatacttc ... gcttttacagATGGTCGGTGGAATCCGGCATGCCTGGGGCCAGGGCAACAGTGGTAAGTTC
EST: gi|60349681|gb|DN216654.1|DN216654
EST:     GATCCTACAGAGCTAGCCGGGACTACCCTTATATCTTCCCACCTTGAGAG                         ATGGTCGGTGGAATCCGGCATGCCTGGGGCCAGGGCAACAGTGGTAAGTTC
genomic: GATCCTACAGAGCTAGCCGCGACTACCCTTATATCTTCCCACCTTGAGAGgtgatacttc ... gcttttacagATGGTCGGTGGAATCCGGCATGCCTGGGGCCAGGGCAACAGTGGTAAGTTC
EST: gi|211065840|gb|FL286062.1|FL286062
EST:     GATCCTACAGAGCTAGCCGCGACTACCCTTATATCTTCCCACCTTGAGAG                         ATGGTCGGTGGAATCCGGCATGCCTGGGGCCAGGGCAACAGGGGTAAGTTC
genomic: GATCCTACAGAGCTAGCCGCGACTACCCTTATATCTTCCCACCTTGAGAGgtgatacttc ... gcttttacagATGGTCGGTGGAATCCGGCATGCCTGGGGCCAGGGCAACAGTGGTAAGTTC
EST: gi|211065839|gb|FL286061.1|FL286061
EST:     GATCCTACAGAGCTAGCCGCGACTACCCTTATATCTTCCCACCTTGAGAG                         ATGGTCGGTGGAATCCGGCATGCCTGGGGCCAGGGCAACAGTGGTAAGTTC
genomic: GATCCTACAGAGCTAGCCGCGACTACCCTTATATCTTCCCACCTTGAGAGgtgatacttc ... gcttttacagATGGTCGGTGGAATCCGGCATGCCTGGGGCCAGGGCAACAGTGGTAAGTTC
EST: gi|15199096|gb|BI423654.1|BI423654
EST:     GATCCTACAGAGCTAGCCGCGACTACCCTTATATCTTCCCACCTTGAGAG                         ATGGTCGGTGGAATCCGGCATGCCTGGGGCCAGGGCAACAGTGGTAAGTTC
genomic: GATCCTACAGAGCTAGCCGCGACTACCCTTATATCTTCCCACCTTGAGAGgtgatacttc ... gcttttacagATGGTCGGTGGAATCCGGCATGCCTGGGGCCAGGGCAACAGTGGTAAGTTC
EST: gi|211065843|gb|FL286065.1|FL286065
EST:     TTCCCACCTTGAGAG                         ATGGTCGGTGGAATCCGGCATGCCTGGGGCCAGGGCAACAGTGGTAAGTTC
genomic: TTCCCACCTTGAGAGgtgatacttc ... gcttttacagATGGTCGGTGGAATCCGGCATGCCTGGGGCCAGGGCAACAGTGGTAAGTTC
EST: gi|60348563|gb|DN215536.1|DN215536
EST:     GATCCTACAGAGCTAGCCGCGACTACCCTTATATCTTCCCACCTTGAGAG                         ATGGTCGGTGGAATCCGGCATGCCTGGGGCCAGGGCAACAGTGGTAAGTTC
genomic: GATCCTACAGAGCTAGCCGCGACTACCCTTATATCTTCCCACCTTGAGAGgtgatacttc ... gcttttacagATGGTCGGTGGAATCCGGCATGCCTGGGGCCAGGGCAACAGTGGTAAGTTC
EST: gi|4730630|gb|AI649796.1|AI649796
EST:     GATCCTACAGAGCTAGCCGCGACTACCCTTATATCTTCCCACCTTGAGAG                         ATGGTCGGTGGAATCCGGCATGCCTGGGGCCAGGGCAACAGTGGTAAGTTC
genomic: GATCCTACAGAGCTAGCCGCGACTACCCTTATATCTTCCCACCTTGAGAGgtgatacttc ... gcttttacagATGGTCGGTGGAATCCGGCATGCCTGGGGCCAGGGCAACAGTGGTAAGTTC
EST: gi|24764653|gb|CA399817.1|CA399817
EST:     GATCCTACAGAGCTAGCCGCGACTACCCTTATATCTTCCCACCTTGAGAG                         ATGGTCGGTGGAATCCGGCATGCCTGGGGCCAGGGCAACAGTGGTAAGTTC
genomic: GATCCTACAGAGCTAGCCGCGACTACCCTTATATCTTCCCACCTTGAGAGgtgatacttc ... gcttttacagATGGTCGGTGGAATCCGGCATGCCTGGGGCCAGGGCAACAGTGGTAAGTTC
EST: gi|6564001|gb|AW231623.1|AW231623
EST:     GATCCTACAGAGCTAGCCGCGACTACCCTTATATCTTCCCACCTTGAGAG                         ATGGTCGGTGGAATCCGGCATGCCTGGGGCCAGGGCAACAGTGGTAAGTTC
genomic: GATCCTACAGAGCTAGCCGCGACTACCCTTATATCTTCCCACCTTGAGAGgtgatacttc ... gcttttacagATGGTCGGTGGAATCCGGCATGCCTGGGGCCAGGGCAACAGTGGTAAGTTC

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), 48 (downstream exon)
Score: 306

GTTTACCGCACAACTGCTGGAGCGAGGGATGATGCACCAAATTTTGTTAAGATCCTACAGAGCTAGCCGCGACTACCCTTATATCTTCCCACCTTGAGAGgtgatacttc ... gcttttacagATGGTCGGTGGAATCCGGCATGCCTGGGGCCAGGGCAACAGTGGTAAGTTCTTGAATCGTCTCCCCTTTTGCAGGGTCAGGAAAAGCCACACTGGCCTGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 184

GTTTACCGCACAACTGCTGGAGCGAGGGATGATGCACCAAATTTTGTTAAGATCCTACAGAGCTAGCCGCGACTACCCTTATATCTTCCCACCTTGAGAGgtgatacttc ... gcttttacagATGGTCGGTGGAATCCGGCATGCCTGGGGCCAGGGCAACAGTGGTAAGTTCTTGAATCGTCTCCCCTTTTGCAGGGTCAGGAAAAGCCACACTGGCCTGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 193

GTTTACCGCACAACTGCTGGAGCGAGGGATGATGCACCAAATTTTGTTAAGATCCTACAGAGCTAGCCGCGACTACCCTTATATCTTCCCACCTTGAGAGgtgatacttc ... gcttttacagATGGTCGGTGGAATCCGGCATGCCTGGGGCCAGGGCAACAGTGGTAAGTTCTTGAATCGTCTCCCCTTTTGCAGGGTCAGGAAAAGCCACACTGGCCTGC


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 99

GTTTACCGCACAACTGCTGGAGCGAGGGATGATGCACCAAATTTTGTTAAGATCCTACAGAGCTAGCCGCGACTACCCTTATATCTTCCCACCTTGAGAGgtgatacttc ... gcttttacagATGGTCGGTGGAATCCGGCATGCCTGGGGCCAGGGCAACAGTGGTAAGTTCTTGAATCGTCTCCCCTTTTGCAGGGTCAGGAAAAGCCACACTGGCCTGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caggacctgatatgtctaaccctgttttcccgctcctactcgattgcttttacagATGGTCGGTGGAATCCGGCATGCCTGGGGCCAGGGCAACAGTGGTAAGTTCTTGAATCGTCTCCCCTTTTGCAGGGTCAGGAAAAGCCACACTGGCCTGC
             gtctaac  putative branch site (score: 99)
                                           ttgctttt  putative PPT
                                               ttttaca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtcgaagtgtgaaccactcagattccagtacctatagagagcagcaggacctgatatgtctaaccctgttttcccgctcctactcgattgcttttacagATGGTCGGTGGAATCCGGCATGCCTGGGGCCAGGGCAACAGTGGTAAGTTCTTGAATCGTCTCCCCTTTTGCAGGGTCAGGAAAAGCCACACTGGCCTGC

- - - - - -gaaccac
- - - - - - - - - - - - - cagtacc
- - - - - - - - - - - - - - - - - - - - -gcagcag