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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTAACCGCACCCACCTTTCGCGACTGGGATTTTTCTCGAGATCGATCGATCGCTTTCCATCAGAGAGCAGCATCACCTTCTTGCCTTGCCCACGCCCCAGgtaaagctcaatctcagctcgctggttttccaatcgcttcttggttctatcggtcgatccgattcttggggcttgtcctctcccgtgccttgccgcgtac...

Basic information

species Zea mays
transcript GRMZM2G416677_T01
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|37417646|gb|CF646477.1|CF646477
EST:     CGCTTTCCATCAGAGAGCAGCATCACCTTCTTGCCTTGCCCACGCCCCAG                         TTGTGACTGCCTGCCGGTTGCGAATCGAAGCGTAAACATGACGACGCTGTC
genomic: CGCTTTCCATCAGAGAGCAGCATCACCTTCTTGCCTTGCCCACGCCCCAGgtaaagctca ... cctgaactagTTGTGACTGCCTGCCGGTTGCGAATCGAAGCGTAAACATGACGACGCTGTC
EST: gi|76923594|gb|DV169564.1|DV169564
EST:     CGCTTTCCATCAGAGAGCAGCATCACCTTCTTGCCTTGCCCACGCCCCAG                         TTGTGACTGCCTGCCGGTTGCGAATCGAAGCGTAAACATGACGACGCTGTC
genomic: CGCTTTCCATCAGAGAGCAGCATCACCTTCTTGCCTTGCCCACGCCCCAGgtaaagctca ... cctgaactagTTGTGACTGCCTGCCGGTTGCGAATCGAAGCGTAAACATGACGACGCTGTC
EST: gi|74239661|gb|DT647575.1|DT647575
EST:     CGCTTTCCATCAGAGAGCAGCATCACCTTCTTGCCTTGCCCACGCCCCAG                         TTGTGACTGCCTGCCGGTTGCGAATCGAAGCGTAAACATGACGACGCTGTC
genomic: CGCTTTCCATCAGAGAGCAGCATCACCTTCTTGCCTTGCCCACGCCCCAGgtaaagctca ... cctgaactagTTGTGACTGCCTGCCGGTTGCGAATCGAAGCGTAAACATGACGACGCTGTC
EST: gi|94475168|gb|EB704126.1|EB704126
EST:     CGCTTTCCATCAGAGAGCAGCATCGCCTTCTTGCCTTGCCCACGCCCCGG                         TTGTGACTGCCTGCCGGTTGCGAATCGAAGCGTAAACATGACGACGCTGTC
genomic: CGCTTTCCATCAGAGAGCAGCATCACCTTCTTGCCTTGCCCACGCCCCAGgtaaagctca ... cctgaactagTTGTGACTGCCTGCCGGTTGCGAATCGAAGCGTAAACATGACGACGCTGTC
EST: gi|211053286|gb|FL359905.1|FL359905
EST:     CGCTTTCCATCAGAGAGCAGCATCACCTTCTTGCCTTGCCCACGCCCCAG                         TTGTGACTGCCTGCCGGTTGCGAATCGAAGCGTAAACATGACGACGCTGTC
genomic: CGCTTTCCATCAGAGAGCAGCATCACCTTCTTGCCTTGCCCACGCCCCAGgtaaagctca ... cctgaactagTTGTGACTGCCTGCCGGTTGCGAATCGAAGCGTAAACATGACGACGCTGTC
EST: gi|50333389|gb|CO528515.1|CO528515
EST:     CGCTTTCCATCAGAGAGCAGCATCACCTTCTTGCCTTGCCCACGCCCCAG                         TTGTGACTGCCTGCCGGTTGCGAATCGAAGCGTAAACATGACGACGCTGTC
genomic: CGCTTTCCATCAGAGAGCAGCATCACCTTCTTGCCTTGCCCACGCCCCAGgtaaagctca ... cctgaactagTTGTGACTGCCTGCCGGTTGCGAATCGAAGCGTAAACATGACGACGCTGTC
EST: gi|211467891|gb|FL343078.1|FL343078
EST:     CGCTTTCCATCAGAGAGCAGCATCACCTTCTTGCCTTGCCCACGCCCCAG                         TTGTGACTGCCTGCCGGTTGCGAATCGAAGCGTAAACATGACGACGCTGTC
genomic: CGCTTTCCATCAGAGAGCAGCATCACCTTCTTGCCTTGCCCACGCCCCAGgtaaagctca ... cctgaactagTTGTGACTGCCTGCCGGTTGCGAATCGAAGCGTAAACATGACGACGCTGTC
EST: gi|148983120|gb|EE029047.2|EE029047
EST:     CGCTTTCCATCAGAGAGCAGCATCACCTTCTTGCCTTGCCCACGCCCCAG                         TTGTGACTGCCTGCCGGTTGCGAATCGAAGCGTAAACATGACGACGCTGTC
genomic: CGCTTTCCATCAGAGAGCAGCATCACCTTCTTGCCTTGCCCACGCCCCAGgtaaagctca ... cctgaactagTTGTGACTGCCTGCCGGTTGCGAATCGAAGCGTAAACATGACGACGCTGTC
EST: gi|74238856|gb|DT646770.1|DT646770
EST:     CGCTTTCCATCAGAGAGCAGCATCACCTTCTTGCCTTGCCCACGCCCCAG                         TTGTGACTGCCTGCCGGTTGCGAATCGAAGCGTAAACATGACGACGCTGTC
genomic: CGCTTTCCATCAGAGAGCAGCATCACCTTCTTGCCTTGCCCACGCCCCAGgtaaagctca ... cctgaactagTTGTGACTGCCTGCCGGTTGCGAATCGAAGCGTAAACATGACGACGCTGTC
EST: gi|87157269|gb|DY402058.1|DY402058
EST:     CGCTTTCCATCAGAGAGCAGCATCACCTTCTTGCCTTGCCCACGCCCCAG                         TTGTGACTGCCTGCCGGTTGCGATTCGAAGCGTAAACATGACGACGCTGTC
genomic: CGCTTTCCATCAGAGAGCAGCATCACCTTCTTGCCTTGCCCACGCCCCAGgtaaagctca ... cctgaactagTTGTGACTGCCTGCCGGTTGCGAATCGAAGCGTAAACATGACGACGCTGTC
EST: gi|148936478|gb|EC880586.2|EC880586
EST:     CGCTTTCCATCAGAGAGCAGCATCACCTTCTTGCCTTGCCCACGCCCCAG                         TTGTGACTGCCTGCCGGTTGCGAATCGAAGCGTAAACATGACGACGCTGTC
genomic: CGCTTTCCATCAGAGAGCAGCATCACCTTCTTGCCTTGCCCACGCCCCAGgtaaagctca ... cctgaactagTTGTGACTGCCTGCCGGTTGCGAATCGAAGCGTAAACATGACGACGCTGTC
EST: gi|149087003|gb|EE176545.2|EE176545
EST:     CGCTTTCCATCAGAGAGCAGCATCACCTTCTTGCCTTGCCCACGCCCCAG                         TTGTGACTGCCTGCCGGTTGCGAATCGAAGCGTAAACATGACGACGCTGTC
genomic: CGCTTTCCATCAGAGAGCAGCATCACCTTCTTGCCTTGCCCACGCCCCAGgtaaagctca ... cctgaactagTTGTGACTGCCTGCCGGTTGCGAATCGAAGCGTAAACATGACGACGCTGTC
EST: gi|78110686|gb|DV529086.1|DV529086
EST:     CGCTTTCCATCAGAGAGCAGCATCACCTTCTTGCCTTGCCCACGCCCCAG                         TTGTGACTGCCTGCCGGTTGCGAATCGAAGCGTAAACATGACGACGCTGTC
genomic: CGCTTTCCATCAGAGAGCAGCATCACCTTCTTGCCTTGCCCACGCCCCAGgtaaagctca ... cctgaactagTTGTGACTGCCTGCCGGTTGCGAATCGAAGCGTAAACATGACGACGCTGTC
EST: gi|74233018|gb|DT640932.1|DT640932
EST:     CGCTTTCCATCAGAGAGCAGCATCACCTTCTTGCCTTGCCCACGCCCCAG                         TTGTGACTGCCTGCCGGTTGCGAATCGAAGCGTAAACATGACGACGCTGTC
genomic: CGCTTTCCATCAGAGAGCAGCATCACCTTCTTGCCTTGCCCACGCCCCAGgtaaagctca ... cctgaactagTTGTGACTGCCTGCCGGTTGCGAATCGAAGCGTAAACATGACGACGCTGTC
EST: gi|71302801|gb|DR787511.1|DR787511
EST:     ACCTTCTTGCCTTGCCCACGCCCCAG                         TTGTGACTGCCTGCCGGTTGCGAATCGAAGCGTAAACATGACGACGCTGTC
genomic: ACCTTCTTGCCTTGCCCACGCCCCAGgtaaagctca ... cctgaactagTTGTGACTGCCTGCCGGTTGCGAATCGAAGCGTAAACATGACGACGCTGTC
EST: gi|22542183|gb|BU092621.1|BU092621
EST:     CGCTTTCCATCAGAGAGCAGCATCACCTTCTTGCCTTGCCCACGCCCCAG                         TTGTGACTGCCTGCCGGTTGCGATTCGAAGCGTAAACATGACGACGCTGTC
genomic: CGCTTTCCATCAGAGAGCAGCATCACCTTCTTGCCTTGCCCACGCCCCAGgtaaagctca ... cctgaactagTTGTGACTGCCTGCCGGTTGCGAATCGAAGCGTAAACATGACGACGCTGTC
EST: gi|87155623|gb|DY400412.1|DY400412
EST:     CGCTTTCCATCAGAGAGCAGCATCACCTTCTTGCCTTGCCCACGCCCCAG                         TTGTGACTGCCTGCCGGTTGCGATTCGAAGCGTAAACATGACGACGCTGTC
genomic: CGCTTTCCATCAGAGAGCAGCATCACCTTCTTGCCTTGCCCACGCCCCAGgtaaagctca ... cctgaactagTTGTGACTGCCTGCCGGTTGCGAATCGAAGCGTAAACATGACGACGCTGTC
EST: gi|89756095|gb|DY686263.1|DY686263
EST:     CGCTTTCCATCAGAGAGCAGCATCACCTTCTTGCCTTGCCCACGCCCCAG                         TTGTGACTGCCTGCCGGTTGCGAATCGAAGCGTAAACATGACGACGCTGTC
genomic: CGCTTTCCATCAGAGAGCAGCATCACCTTCTTGCCTTGCCCACGCCCCAGgtaaagctca ... cctgaactagTTGTGACTGCCTGCCGGTTGCGAATCGAAGCGTAAACATGACGACGCTGTC
EST: gi|74243259|gb|DT651173.1|DT651173
EST:     CGCTTTCCATCAGAGAGCAGCATCACCTTCTTGCCTTGCCCACGCCCCAG                         TTGTGACTGCCTGCCGGTTGCGAATCGAAGCGTAAACATGACGACGCTGTC
genomic: CGCTTTCCATCAGAGAGCAGCATCACCTTCTTGCCTTGCCCACGCCCCAGgtaaagctca ... cctgaactagTTGTGACTGCCTGCCGGTTGCGAATCGAAGCGTAAACATGACGACGCTGTC
EST: gi|211523315|gb|FL357636.1|FL357636
EST:     CGCTTTCCATCAGAGAGCAGCATCACCTTCTTGCCTTGCCCACGCCCCAG                         TTGTGACTGCCTGCCGGTTGCGAATCGAAGCGTAAACATGACGACGCTGTC
genomic: CGCTTTCCATCAGAGAGCAGCATCACCTTCTTGCCTTGCCCACGCCCCAGgtaaagctca ... cctgaactagTTGTGACTGCCTGCCGGTTGCGAATCGAAGCGTAAACATGACGACGCTGTC
EST: gi|149111656|gb|EE190800.2|EE190800
EST:     CGCTTTCCATCAGAGAGCAGCATCACCTTCTTGCCTTGCCCACGCCCCAG                         TTGTGACTGCCTGCCGGTTGCGAATCGAAGCGTAAACATGACGACGCTGTC
genomic: CGCTTTCCATCAGAGAGCAGCATCACCTTCTTGCCTTGCCCACGCCCCAGgtaaagctca ... cctgaactagTTGTGACTGCCTGCCGGTTGCGAATCGAAGCGTAAACATGACGACGCTGTC
EST: gi|211291616|gb|FL348662.1|FL348662
EST:     CGCTTTCCATCAGAGAGCAGCATCACCTTCTTGCCTTGCCCACGCCCCAG                         TTGTGACTGCCTGCCGGTTGCGAATCGAAGCGTAAACATGACGACGCTGTC
genomic: CGCTTTCCATCAGAGAGCAGCATCACCTTCTTGCCTTGCCCACGCCCCAGgtaaagctca ... cctgaactagTTGTGACTGCCTGCCGGTTGCGAATCGAAGCGTAAACATGACGACGCTGTC
EST: gi|149102754|gb|EE288101.2|EE288101
EST:     CGCTTTCCATCAGAGAGCAGCATCACCTTCTTGCCTTGCCCACGCCCCAG                         TTGTGACTGCCTGCCGGTTGCGAATCGAAGCGTAAACATGACGACGCTGTC
genomic: CGCTTTCCATCAGAGAGCAGCATCACCTTCTTGCCTTGCCCACGCCCCAGgtaaagctca ... cctgaactagTTGTGACTGCCTGCCGGTTGCGAATCGAAGCGTAAACATGACGACGCTGTC
EST: gi|91052357|gb|EB162775.1|EB162775
EST:     CGCTTTCCATCAGAGAGCAGCATCACCTTCTTGCCTTGCCCACGCCCCAG                         TTGTGACTGCCTGCCGGTTGCGAATCGAAGCGTAAACATGACGACGCTGTC
genomic: CGCTTTCCATCAGAGAGCAGCATCACCTTCTTGCCTTGCCCACGCCCCAGgtaaagctca ... cctgaactagTTGTGACTGCCTGCCGGTTGCGAATCGAAGCGTAAACATGACGACGCTGTC
EST: gi|71449587|gb|DR830637.1|DR830637
EST:     CGCTTTCCATCAGAGAGCAGCATCACCTTCTTGCCTTGCCCACGCCCCAG                         TTGTGACTGCCTGCCGGTTGCGAATCGAAGCGTAAACATGACGACGCTGTC
genomic: CGCTTTCCATCAGAGAGCAGCATCACCTTCTTGCCTTGCCCACGCCCCAGgtaaagctca ... cctgaactagTTGTGACTGCCTGCCGGTTGCGAATCGAAGCGTAAACATGACGACGCTGTC
EST: gi|22546095|gb|BU098416.1|BU098416
EST:     CGCTTTCCATCAGAGAGCAGCATCACCTTCTTGCCTTGCCCACGCCCCAG                         TTGTGACTGCCTGCCGGTTGCGATTCGAAGCGTAAACATGACGACGCTGTC
genomic: CGCTTTCCATCAGAGAGCAGCATCACCTTCTTGCCTTGCCCACGCCCCAGgtaaagctca ... cctgaactagTTGTGACTGCCTGCCGGTTGCGAATCGAAGCGTAAACATGACGACGCTGTC
EST: gi|211098833|gb|FL340513.1|FL340513
EST:     CGCTTTCCATCAGAGAGCAGCATCACCTTCTTGCCTTGCCCACGCCCCAG                         TTGTGACTGCCTGCCGGTTGCGAATCGAAGCGTAAACATGACGACGCTGTC
genomic: CGCTTTCCATCAGAGAGCAGCATCACCTTCTTGCCTTGCCCACGCCCCAGgtaaagctca ... cctgaactagTTGTGACTGCCTGCCGGTTGCGAATCGAAGCGTAAACATGACGACGCTGTC
EST: gi|71773341|gb|DR971245.1|DR971245
EST:     CGCTTTCCATCAGAGAGCAGCATCACCTTCTTGCCTTGCCCACGCCCCAG                         TTGTGACTGCCTGCCGGTTGCGAATCGAAGCGTAAACATGACGACGCTGTC
genomic: CGCTTTCCATCAGAGAGCAGCATCACCTTCTTGCCTTGCCCACGCCCCAGgtaaagctca ... cctgaactagTTGTGACTGCCTGCCGGTTGCGAATCGAAGCGTAAACATGACGACGCTGTC
EST: gi|26559170|gb|CA831405.1|CA831405
EST:     CGCTTTCCATCAGAGAGCAGCATCACCTTCTTGCCTTGCCCACGCCCCAG                         TTGTGACTGCCTGCCGGTTGCGATTCGAAGCGTAAACATGACGACGCTGTC
genomic: CGCTTTCCATCAGAGAGCAGCATCACCTTCTTGCCTTGCCCACGCCCCAGgtaaagctca ... cctgaactagTTGTGACTGCCTGCCGGTTGCGAATCGAAGCGTAAACATGACGACGCTGTC
EST: gi|50322834|gb|CO517960.1|CO517960
EST:     CGCTTTCCATCAGAGAGCAGCATCACCTTCTTGCCTTGCCCACGCCCCAG                         TTGTGACTGCCTGCCGGTTGCGAATCGAAGCGTAAACATGACGACGCTGTC
genomic: CGCTTTCCATCAGAGAGCAGCATCACCTTCTTGCCTTGCCCACGCCCCAGgtaaagctca ... cctgaactagTTGTGACTGCCTGCCGGTTGCGAATCGAAGCGTAAACATGACGACGCTGTC

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 3 RNA-Seq libraries.


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 47

TTAACCGCACCCACCTTTCGCGACTGGGATTTTTCTCGAGATCGATCGATCGCTTTCCATCAGAGAGCAGCATCACCTTCTTGCCTTGCCCACGCCCCAGgtaaagctca ... cctgaactagTTGTGACTGCCTGCCGGTTGCGAATCGAAGCGTAAACATGACGACGCTGTCGTCCGGCGTCCTCCTGAAGCTCCTGGACGGCATGAAGAGCGGCGCCGCC


Block sizes: 37 (upstream exon), 13 (downstream exon)
Score: 2

TTAACCGCACCCACCTTTCGCGACTGGGATTTTTCTCGAGATCGATCGATCGCTTTCCATCAGAGAGCAGCATCACCTTCTTGCCTTGCCCACGCCCCAGgtaaagctca ... cctgaactagTTGTGACTGCCTGCCGGTTGCGAATCGAAGCGTAAACATGACGACGCTGTCGTCCGGCGTCCTCCTGAAGCTCCTGGACGGCATGAAGAGCGGCGCCGCC


Block sizes: 40 (upstream exon), 40 (downstream exon)
Score: 4

TTAACCGCACCCACCTTTCGCGACTGGGATTTTTCTCGAGATCGATCGATCGCTTTCCATCAGAGAGCAGCATCACCTTCTTGCCTTGCCCACGCCCCAGgtaaagctca ... cctgaactagTTGTGACTGCCTGCCGGTTGCGAATCGAAGCGTAAACATGACGACGCTGTCGTCCGGCGTCCTCCTGAAGCTCCTGGACGGCATGAAGAGCGGCGCCGCC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTAACCGCACCCACCTTTCGCGACTGGGATTTTTCTCGAGATCGATCGATCGCTTTCCATCAGAGAGCAGCATCACCTTCTTGCCTTGCCCACGCCCCAGgtaaagctcaatctcagctcgctggttttccaatcgcttcttggttctatcggtcgatccgattcttggggcttgtcctctcccgtgccttgccgcgtac

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctctccc