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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgctctccgttttgattaccccagtattctcctcttctatagtgtttactagtccagtttgtcggaggatttctctcgatgtttctacctattctcgatttaatattcattcctcctttgttacagTGCCGTCGCAACCCGCAGATCAGCACGCGACCCTCATGTCCCGGTTGG

Basic information

species Zea mays
transcript GRMZM2G056078_T01
intron # 1
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|32797500|gb|CD949736.1|CD949736
EST:     CCCTCTGATCAAGTTCCCCAAGCGGAATCTGAAAGCCCCATCCGCGCCAG                         TGCCGTCGCAACCCGCAGATCAGCACGCGACCCTCATGTCCCGGTTGG
genomic: CCCTCTGATCAAGTTCCCCAAGCGGAATCTGAAAGCCCCATCCGCGCCAGgtgctctccg ... tttgttacagTGCCGTCGCAACCCGCAGATCAGCACGCGACCCTCATGTCCCGGTTGG
EST: gi|211523857|gb|FL149373.1|FL149373
EST:     CCCTCTGATCAAGTTCCCCAAGCGGAATCTGAAAGCCCCATCCGCGCCAG                         TGCCGTCGCAACCCGCAGATCAGCACGCGACCCTCATGTCCCGGTTGG
genomic: CCCTCTGATCAAGTTCCCCAAGCGGAATCTGAAAGCCCCATCCGCGCCAGgtgctctccg ... tttgttacagTGCCGTCGCAACCCGCAGATCAGCACGCGACCCTCATGTCCCGGTTGG
EST: gi|211523863|gb|FL149379.1|FL149379
EST:     CCCTCTGATCAAGTTCCCCAAGCGGAATCTGAAAGCCCCATCCGCGCCAG                         TGCCGTCGCAACCCGCAGATCAGCACGCGACCCTCATGTCCCGGTTGG
genomic: CCCTCTGATCAAGTTCCCCAAGCGGAATCTGAAAGCCCCATCCGCGCCAGgtgctctccg ... tttgttacagTGCCGTCGCAACCCGCAGATCAGCACGCGACCCTCATGTCCCGGTTGG
EST: gi|116820025|gb|EC863204.1|EC863204
EST:     CCTCTNGATC-AG-TCCCCAAGCGGAATCTGAAAGCCCCATCCGCGCCAG                         TGCCGTCGCAACCCGCAGATCAGCACGCGACCCTCATGTCCCGGTTGG
genomic: CCTCT-GATCAAGTTCCCCAAGCGGAATCTGAAAGCCCCATCCGCGCCAGgtgctctccg ... tttgttacagTGCCGTCGCAACCCGCAGATCAGCACGCGACCCTCATGTCCCGGTTGG
EST: gi|44681853|gb|CK786901.1|CK786901
EST:     CCCTCTGATCAAGTTCCCCAAGCGGAATCTGAAAGCCCCATCCGCGCCAG                         TGCCGTCGCAACCCGCAGATCAGCACGCGACCCTCATGTCCCGGTTGG
genomic: CCCTCTGATCAAGTTCCCCAAGCGGAATCTGAAAGCCCCATCCGCGCCAGgtgctctccg ... tttgttacagTGCCGTCGCAACCCGCAGATCAGCACGCGACCCTCATGTCCCGGTTGG
EST: gi|32802862|gb|CD955098.1|CD955098
EST:     CCCTCTGATCAAGTTCCCCAAGCGGAATCTGAAAGCCCCATCCGCGCCAG                         TGCCGTCGCAACCCGCAGATCAGCACGCGACCCTCATGTCCCGGTTGG
genomic: CCCTCTGATCAAGTTCCCCAAGCGGAATCTGAAAGCCCCATCCGCGCCAGgtgctctccg ... tttgttacagTGCCGTCGCAACCCGCAGATCAGCACGCGACCCTCATGTCCCGGTTGG
EST: gi|211523849|gb|FL149365.1|FL149365
EST:     CCCTCTGATCAAGTTCCCCAAGCGGAATCTGAAAGCCCCATCCGCGCCAG                         TGCCGTCGCAACCCGCAGATCAGCACGCGACCCTCATGTCCCGGTTGG
genomic: CCCTCTGATCAAGTTCCCCAAGCGGAATCTGAAAGCCCCATCCGCGCCAGgtgctctccg ... tttgttacagTGCCGTCGCAACCCGCAGATCAGCACGCGACCCTCATGTCCCGGTTGG
EST: gi|211526858|gb|FL149380.1|FL149380
EST:     CCCTCTGATCAAGTTCCCCAAGCGGAATCTGAAAGCCCCATCCGCGCCAG                         TGCCGTCGCAACCCGCAGATCAGCACGCGACCCTCATGTCCCGGTTGG
genomic: CCCTCTGATCAAGTTCCCCAAGCGGAATCTGAAAGCCCCATCCGCGCCAGgtgctctccg ... tttgttacagTGCCGTCGCAACCCGCAGATCAGCACGCGACCCTCATGTCCCGGTTGG
EST: gi|211523854|gb|FL149370.1|FL149370
EST:     CCCTCTGATCAAGTTCCCCAAGCGGAATCTGAAAGCCCCATCCGCGCCAS                         TSCCSTCGCAACCCGCAGATCAGCACGCGACCCTCATGTCCCGGTTGG
genomic: CCCTCTGATCAAGTTCCCCAAGCGGAATCTGAAAGCCCCATCCGCGCCAGgtgctctccg ... tttgttacagTGCCGTCGCAACCCGCAGATCAGCACGCGACCCTCATGTCCCGGTTGG
EST: gi|5499310|gb|AI855177.1|AI855177
EST:     CCCTCTGATCAAGTTCCCCAAGCGGAATCTGAAAGCCCCATCCGCGCCAG                         TGCCGTCGCAACCCGCAGATCAGCACGCGACCCTCATGTCCCGGTTGG
genomic: CCCTCTGATCAAGTTCCCCAAGCGGAATCTGAAAGCCCCATCCGCGCCAGgtgctctccg ... tttgttacagTGCCGTCGCAACCCGCAGATCAGCACGCGACCCTCATGTCCCGGTTGG

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: 180

GAAGTCAGTAAATTCTGTCGCTCCAATCCGGACGAGGAGATGCCGCGGATCCCTCTGATCAAGTTCCCCAAGCGGAATCTGAAAGCCCCATCCGCGCCAGgtgctctccg ... tttgttacagTGCCGTCGCAACCCGCAGATCAGCACGCGACCCTCATGTCCCGGTTGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 185

GAAGTCAGTAAATTCTGTCGCTCCAATCCGGACGAGGAGATGCCGCGGATCCCTCTGATCAAGTTCCCCAAGCGGAATCTGAAAGCCCCATCCGCGCCAGgtgctctccg ... tttgttacagTGCCGTCGCAACCCGCAGATCAGCACGCGACCCTCATGTCCCGGTTGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 241

GAAGTCAGTAAATTCTGTCGCTCCAATCCGGACGAGGAGATGCCGCGGATCCCTCTGATCAAGTTCCCCAAGCGGAATCTGAAAGCCCCATCCGCGCCAGgtgctctccg ... tttgttacagTGCCGTCGCAACCCGCAGATCAGCACGCGACCCTCATGTCCCGGTTGG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 229

GAAGTCAGTAAATTCTGTCGCTCCAATCCGGACGAGGAGATGCCGCGGATCCCTCTGATCAAGTTCCCCAAGCGGAATCTGAAAGCCCCATCCGCGCCAGgtgctctccg ... tttgttacagTGCCGTCGCAACCCGCAGATCAGCACGCGACCCTCATGTCCCGGTTGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctctcgatgtttctacctattctcgatttaatattcattcctcctttgttacagTGCCGTCGCAACCCGCAGATCAGCACGCGACCCTCATGTCCCGGTTGG
                          atttaat  putative branch site (score: 229)
                                  ttcattcctcctttgt  CT-rich tract
                          atttaatattcatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgctctccgttttgattaccccagtattctcctcttctatagtgtttactagtccagtttgtcggaggatttctctcgatgtttctacctattctcgatttaatattcattcctcctttgttacagTGCCGTCGCAACCCGCAGATCAGCACGCGACCCTCATGTCCCGGTTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA