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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACGCCGACGATTACATTTACACCAAGTGCCCAAGCCGTCTTCGACTACACCAGGTGCCAAGTTTTCTTCGCGTCCTTCACCCGCGACGAGCACCCACCAGgtatgcgcaccctctctcttccagtcttctgttcttgctatgcgaaaccgagcacacgaaccctaactttagctatctggctgtttatattcggatctga...

Basic information

species Zea mays
transcript GRMZM2G058498_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|37418983|gb|CF647165.1|CF647165
EST:     CGCGTCCTTCACCCGCGACGAGCACCCACCAG                         GCATAGAGAGAGATGGCAAGTCTAACCGGCCTCACCGCGAACCCTAATCCG
genomic: CGCGTCCTTCACCCGCGACGAGCACCCACCAGgtatgcgcac ... tctgccccagGCATAGAGAGAGATGGCAAGTCTAACCGGCCTCACCGCGAACCCTAATCCG
EST: gi|211052947|gb|FL232812.1|FL232812
EST:     CAGGTGCCAAGTTTTCTTCGCGTCCTTCACCCGCGACGAGCACCCACCAG                         GCATAGAGAGAGATGGCAAGTCTAACCGGCCTCACCGCGAACCCTAATCCG
genomic: CAGGTGCCAAGTTTTCTTCGCGTCCTTCACCCGCGACGAGCACCCACCAGgtatgcgcac ... tctgccccagGCATAGAGAGAGATGGCAAGTCTAACCGGCCTCACCGCGAACCCTAATCCG
EST: gi|71319015|gb|DR796255.1|DR796255
EST:     GTTTTCTTCGCGTCCTTCACCCGCGACGAGCACCCACCAG                         GCATAGAGAGAGATGGCAAGTCTAACCGGCCTCACCGCGAACCCTAATCCG
genomic: GTTTTCTTCGCGTCCTTCACCCGCGACGAGCACCCACCAGgtatgcgcac ... tctgccccagGCATAGAGAGAGATGGCAAGTCTAACCGGCCTCACCGCGAACCCTAATCCG
EST: gi|211049994|gb|FL232801.1|FL232801
EST:     CAGGTGCCAAGTTTTCTTCGCGTCCTTCNCCCGCGACGAGCACCCACCAG                         GCATAGAGAGAGATGGCAAGTCTAACCGGGCTCACCGCGAACCCTAATCCG
genomic: CAGGTGCCAAGTTTTCTTCGCGTCCTTCACCCGCGACGAGCACCCACCAGgtatgcgcac ... tctgccccagGCATAGAGAGAGATGGCAAGTCTAACCGGCCTCACCGCGAACCCTAATCCG
EST: gi|71435207|gb|DR816257.1|DR816257
EST:     CAGGTGCCAAGTTTTCTTCGCGTCCTTCACCCGCGACGAGCACCCACCAG                         GCATAGAGAGAGATGGCAAGTCTAACCGGCCTCACCGCGAACCCTAATCCG
genomic: CAGGTGCCAAGTTTTCTTCGCGTCCTTCACCCGCGACGAGCACCCACCAGgtatgcgcac ... tctgccccagGCATAGAGAGAGATGGCAAGTCTAACCGGCCTCACCGCGAACCCTAATCCG
EST: gi|211049997|gb|FL232804.1|FL232804
EST:     CAGGTGCCAAGTTTTCTTCGCGTCCTTCACCCGCGACGAGCACCCACCAG                         GCATAGAGAGAGATGGCAAGTCTAACCGGCCTCACCGCGAACCCTAATCCG
genomic: CAGGTGCCAAGTTTTCTTCGCGTCCTTCACCCGCGACGAGCACCCACCAGgtatgcgcac ... tctgccccagGCATAGAGAGAGATGGCAAGTCTAACCGGCCTCACCGCGAACCCTAATCCG
EST: gi|211052943|gb|FL232808.1|FL232808
EST:     CAGGTGCCAAGTTTTCTTCGCGTCCTTCACCCGCGACGAGCACCCACCAG                         GCATAGAGAGAGATGGCAAGTCTAACCGGCCTCACCGCGAACCCTAATCCG
genomic: CAGGTGCCAAGTTTTCTTCGCGTCCTTCACCCGCGACGAGCACCCACCAGgtatgcgcac ... tctgccccagGCATAGAGAGAGATGGCAAGTCTAACCGGCCTCACCGCGAACCCTAATCCG
EST: gi|211052951|gb|FL232816.1|FL232816
EST:     CAGGTGCCAAGTTTTCTTCGCGTCCTTCACCCGCGACGAGCACCCACCAG                         GCATTAGAGAGAGATGGCAAGTCTAACCGGCCTCACCGCGAACCCTAATCC
genomic: CAGGTGCCAAGTTTTCTTCGCGTCCTTCACCCGCGACGAGCACCCACCAGgtatgcgcac ... tctgccccagGCA-TAGAGAGAGATGGCAAGTCTAACCGGCCTCACCGCGAACCCTAATCC
EST: gi|31355022|gb|CD439379.1|CD439379
EST:     TTTTCTTCGCGTCCTTCACCCGCGACGAGCACCCACCCT                         TCATAGAGAGAGATGGCAAGTCTAACCGGCCTCACCGCGAACCCTAATCCG
genomic: TTTTCTTCGCGTCCTTCACCCGCGACGAGCACCCACCAGgtatgcgcac ... tctgccccagGCATAGAGAGAGATGGCAAGTCTAACCGGCCTCACCGCGAACCCTAATCCG
EST: gi|211050000|gb|FL232807.1|FL232807
EST:     TTTTCTTCGCGTCCTTCACCCGCGACGAGCACCCACCAG                         GCATAGAGAGAGATGGCAAGTCTAACCGGCCTCACCGCGAACCCTAATCCG
genomic: TTTTCTTCGCGTCCTTCACCCGCGACGAGCACCCACCAGgtatgcgcac ... tctgccccagGCATAGAGAGAGATGGCAAGTCTAACCGGCCTCACCGCGAACCCTAATCCG
EST: gi|32915973|gb|CF020785.1|CF020785
EST:     CAGGTGCCAAGTTTTCTTCGCGTCCTTCACCCGCGACGAGCACCCACCAG                         GCATAGAGAGAGATGGCAAGTCTAACCGGCCTCACCGCGAACCCTAATCCG
genomic: CAGGTGCCAAGTTTTCTTCGCGTCCTTCACCCGCGACGAGCACCCACCAGgtatgcgcac ... tctgccccagGCATAGAGAGAGATGGCAAGTCTAACCGGCCTCACCGCGAACCCTAATCCG
EST: gi|71427496|gb|DR808546.1|DR808546
EST:     GTTTTCTTCGCGTCCTTCACCCGCGACGAGCACCCACCAG                         GCATAGAGAGAGATGGCAAGTCTAACCGGCCTCACCGCGAACCCTAATCCG
genomic: GTTTTCTTCGCGTCCTTCACCCGCGACGAGCACCCACCAGgtatgcgcac ... tctgccccagGCATAGAGAGAGATGGCAAGTCTAACCGGCCTCACCGCGAACCCTAATCCG
EST: gi|211049999|gb|FL232806.1|FL232806
EST:     TTTCTTCGCGTCCTTCACCCGCGACGAGCACCCACCAG                         GCATAGAGAGAGATGGCAAGTYTAACCGGCCTCACCGCGAACCCTAATCCG
genomic: TTTCTTCGCGTCCTTCACCCGCGACGAGCACCCACCAGgtatgcgcac ... tctgccccagGCATAGAGAGAGATGGCAAGTCTAACCGGCCTCACCGCGAACCCTAATCCG
EST: gi|211052950|gb|FL232815.1|FL232815
EST:     CAGGTGCCAAGTTTTCTTCGCGTCCTTCACCCGCGACGAGCACCCACCAG                         GCATAGAGAGAGATGGCAAGTCTAACCGGCCTCACCGCGAACCCTAATCCG
genomic: CAGGTGCCAAGTTTTCTTCGCGTCCTTCACCCGCGACGAGCACCCACCAGgtatgcgcac ... tctgccccagGCATAGAGAGAGATGGCAAGTCTAACCGGCCTCACCGCGAACCCTAATCCG
EST: gi|211052945|gb|FL232810.1|FL232810
EST:     CAGGTGCCAAGTTTTCTTCGCGTCCTTCACCCGCGACGAGCACCCACCAG                         GCATAGAGAGAGATGGCAAGTCTAACCGGCCTCACCGCGAACCCTAATCCG
genomic: CAGGTGCCAAGTTTTCTTCGCGTCCTTCACCCGCGACGAGCACCCACCAGgtatgcgcac ... tctgccccagGCATAGAGAGAGATGGCAAGTCTAACCGGCCTCACCGCGAACCCTAATCCG
EST: gi|211052956|gb|FL232821.1|FL232821
EST:     CAGGTGCCAAGTTTTCTTCGCGTCCTTCACCCGCGACGAGCACCCACCAG                         GCATAGAGAGAGATGGCAAGTCTAACCGGCCTCACCGCGAACCCTAATCCG
genomic: CAGGTGCCAAGTTTTCTTCGCGTCCTTCACCCGCGACGAGCACCCACCAGgtatgcgcac ... tctgccccagGCATAGAGAGAGATGGCAAGTCTAACCGGCCTCACCGCGAACCCTAATCCG
EST: gi|78092605|gb|DV520979.1|DV520979
EST:     CGCGACGAGCACCCACCAG                         GCATAGAGAGAGATGGCAAGTCTAACCGGCCTCACCGCGAACCCTAATCCG
genomic: CGCGACGAGCACCCACCAGgtatgcgcac ... tctgccccagGCATAGAGAGAGATGGCAAGTCTAACCGGCCTCACCGCGAACCCTAATCCG
EST: gi|211052946|gb|FL232811.1|FL232811
EST:     CAGGTGCCAAGTTTTCTTCGCGTCCTTCACCCGCGACGAGCACCCACCAG                         GCATAGAGAGAGATGRCAAGTCTAACCGGCCTCACCGCGAACCCTAATCCG
genomic: CAGGTGCCAAGTTTTCTTCGCGTCCTTCACCCGCGACGAGCACCCACCAGgtatgcgcac ... tctgccccagGCATAGAGAGAGATGGCAAGTCTAACCGGCCTCACCGCGAACCCTAATCCG
EST: gi|211049992|gb|FL232799.1|FL232799
EST:     TTTTCTTCGCGTCCTTCACCCGCGACGAGCACCCACCAG                         GCATAGAGAGAGATGGCAAGTCTAACCGGCCTCACCGCGAACCCTAATCCG
genomic: TTTTCTTCGCGTCCTTCACCCGCGACGAGCACCCACCAGgtatgcgcac ... tctgccccagGCATAGAGAGAGATGGCAAGTCTAACCGGCCTCACCGCGAACCCTAATCCG
EST: gi|71765073|gb|DR963010.1|DR963010
EST:     GTTTTCTTCGCGTCCTTCACCCGCGACGAGCACCCACCAG                         GCATAGAGAGAGATGGCAAGTCTAACCGGCCTCACCGCGAACCCTAATCCG
genomic: GTTTTCTTCGCGTCCTTCACCCGCGACGAGCACCCACCAGgtatgcgcac ... tctgccccagGCATAGAGAGAGATGGCAAGTCTAACCGGCCTCACCGCGAACCCTAATCCG
EST: gi|211049998|gb|FL232805.1|FL232805
EST:     CAGGTGCCAAGTTTTCTTCGCGTCCTTCACCCGCGACGAGCACCCACCAG                         GCATAGAGAGAGATGGCAAGTCTAACCGGCCTCACCGCGAACCCTAATCCG
genomic: CAGGTGCCAAGTTTTCTTCGCGTCCTTCACCCGCGACGAGCACCCACCAGgtatgcgcac ... tctgccccagGCATAGAGAGAGATGGCAAGTCTAACCGGCCTCACCGCGAACCCTAATCCG
EST: gi|32868065|gb|CF007747.1|CF007747
EST:     CAGGTGCCAAGTTTTCTTCGCGTCCTTCACCCGCGACGAGCACCCACCAG                         GCATAGAGAGAGATGGCAAGTCTAACCGGCCTCACCGCGAACCCTAATCCG
genomic: CAGGTGCCAAGTTTTCTTCGCGTCCTTCACCCGCGACGAGCACCCACCAGgtatgcgcac ... tctgccccagGCATAGAGAGAGATGGCAAGTCTAACCGGCCTCACCGCGAACCCTAATCCG
EST: gi|62550552|gb|DN830972.1|DN830972
EST:     CAGGTGCCAAGTTTTCTTCGCGTCCTTCACCCGCGACGAGCACCCACCAG                         GCATAGAGAGAGATGGCAAGTCTAACCGGCCTCACCGCGAACCCTAATCCG
genomic: CAGGTGCCAAGTTTTCTTCGCGTCCTTCACCCGCGACGAGCACCCACCAGgtatgcgcac ... tctgccccagGCATAGAGAGAGATGGCAAGTCTAACCGGCCTCACCGCGAACCCTAATCCG
EST: gi|71310174|gb|DR791376.1|DR791376
EST:     GTTTTCTTCGCGTCCTTCACCCGCGACGAGCACCCACCAG                         GCATAGAGAGAGATGGCAAGTCTAACCGGCCTCACCGCGAACCCTAATCCG
genomic: GTTTTCTTCGCGTCCTTCACCCGCGACGAGCACCCACCAGgtatgcgcac ... tctgccccagGCATAGAGAGAGATGGCAAGTCTAACCGGCCTCACCGCGAACCCTAATCCG
EST: gi|211049995|gb|FL232802.1|FL232802
EST:     CAGGTGCCAAGTTTTCTTCGCGTCCTTCACCCGCGACGAGCACCCACCAG                         GCATAGAGAGAGATGGCAAGTCTAACCGGCCTCACCGCGAACCCTAATCCG
genomic: CAGGTGCCAAGTTTTCTTCGCGTCCTTCACCCGCGACGAGCACCCACCAGgtatgcgcac ... tctgccccagGCATAGAGAGAGATGGCAAGTCTAACCGGCCTCACCGCGAACCCTAATCCG
EST: gi|211052953|gb|FL232818.1|FL232818
EST:     CAGGTGCCAAGTTTTCTTCGCGTCCTTCACCCGCGACGAGCACCCACCAG                         GCATAGAGAGAGATGGCAAGTCTAACCGGCCTCACCGCGAACCCTAATCCG
genomic: CAGGTGCCAAGTTTTCTTCGCGTCCTTCACCCGCGACGAGCACCCACCAGgtatgcgcac ... tctgccccagGCATAGAGAGAGATGGCAAGTCTAACCGGCCTCACCGCGAACCCTAATCCG
EST: gi|211052952|gb|FL232817.1|FL232817
EST:     TTTCTTCGCGTCCTTCACCCGCGACGAGCACCCACCAG                         GCATAGAGAGAGATGGCAAGTCTAACCGGCCTCACCGCGAACCCTAATCCG
genomic: TTTCTTCGCGTCCTTCACCCGCGACGAGCACCCACCAGgtatgcgcac ... tctgccccagGCATAGAGAGAGATGGCAAGTCTAACCGGCCTCACCGCGAACCCTAATCCG
EST: gi|33102995|gb|CF062955.1|CF062955
EST:     CAGGTGCCAAGTTTTCTTCGCGTCCTTCACCCGCGACGAGCACCCACCAG                         GCATAGAGAGAGATGGCAAGTCTAACCGGCCTCACCGCGAACCCTAATCCG
genomic: CAGGTGCCAAGTTTTCTTCGCGTCCTTCACCCGCGACGAGCACCCACCAGgtatgcgcac ... tctgccccagGCATAGAGAGAGATGGCAAGTCTAACCGGCCTCACCGCGAACCCTAATCCG
EST: gi|211052949|gb|FL232814.1|FL232814
EST:     AGGTGCCAAGTTTTCTTCGCGTCCTTCACCCGCGACGAGCACCCACCAG                         GCATAGAGAGAGATGGCAAGTCTAACCGGCCTCACCGCGAACCCTAATCCG
genomic: AGGTGCCAAGTTTTCTTCGCGTCCTTCACCCGCGACGAGCACCCACCAGgtatgcgcac ... tctgccccagGCATAGAGAGAGATGGCAAGTCTAACCGGCCTCACCGCGAACCCTAATCCG
EST: gi|32943595|gb|CF048414.1|CF048414
EST:     CAGGTGCCAAGTTTTCTTCGCGTCCTTCACCCGCGACGAGCACCCACCAG                         GCATAGAGAGAGATGGCAAGTCTAACCGGCCTCACCGCGAACCCTAATCCG
genomic: CAGGTGCCAAGTTTTCTTCGCGTCCTTCACCCGCGACGAGCACCCACCAGgtatgcgcac ... tctgccccagGCATAGAGAGAGATGGCAAGTCTAACCGGCCTCACCGCGAACCCTAATCCG
EST: gi|67024188|gb|CO452937.1|CO452937
EST:     CAGGTGCCAAGTTTTCTTCGCGTCCTTCACCCGCGACGAGCACCCACCAG                         GCATAGAGAGAGATGGCAAGTCTAACCGGCCTCACCGCGAACCCTAATCCG
genomic: CAGGTGCCAAGTTTTCTTCGCGTCCTTCACCCGCGACGAGCACCCACCAGgtatgcgcac ... tctgccccagGCATAGAGAGAGATGGCAAGTCTAACCGGCCTCACCGCGAACCCTAATCCG

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: 208

ACGCCGACGATTACATTTACACCAAGTGCCCAAGCCGTCTTCGACTACACCAGGTGCCAAGTTTTCTTCGCGTCCTTCACCCGCGACGAGCACCCACCAGgtatgcgcac ... tctgccccagGCATAGAGAGAGATGGCAAGTCTAACCGGCCTCACCGCGAACCCTAATCCGAACAAGTCATTCGAG


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

ACGCCGACGATTACATTTACACCAAGTGCCCAAGCCGTCTTCGACTACACCAGGTGCCAAGTTTTCTTCGCGTCCTTCACCCGCGACGAGCACCCACCAGgtatgcgcac ... tctgccccagGCATAGAGAGAGATGGCAAGTCTAACCGGCCTCACCGCGAACCCTAATCCGAACAAGTCATTCGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 203

ACGCCGACGATTACATTTACACCAAGTGCCCAAGCCGTCTTCGACTACACCAGGTGCCAAGTTTTCTTCGCGTCCTTCACCCGCGACGAGCACCCACCAGgtatgcgcac ... tctgccccagGCATAGAGAGAGATGGCAAGTCTAACCGGCCTCACCGCGAACCCTAATCCGAACAAGTCATTCGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 86

ACGCCGACGATTACATTTACACCAAGTGCCCAAGCCGTCTTCGACTACACCAGGTGCCAAGTTTTCTTCGCGTCCTTCACCCGCGACGAGCACCCACCAGgtatgcgcac ... tctgccccagGCATAGAGAGAGATGGCAAGTCTAACCGGCCTCACCGCGAACCCTAATCCGAACAAGTCATTCGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACGCCGACGATTACATTTACACCAAGTGCCCAAGCCGTCTTCGACTACACCAGGTGCCAAGTTTTCTTCGCGTCCTTCACCCGCGACGAGCACCCACCAGgtatgcgcaccctctctcttccagtcttctgttcttgctatgcgaaaccgagcacacgaaccctaactttagctatctggctgtttatattcggatctga

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cgcaccc