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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattgcatcggaaccgctgcgcccgcgcccttatgttctgctgaaatccgaatccgtcgcctcccgtccgcacgcgtgctcccgaaatcacatctccatgacctcttctcctagTGCCAAGAGCTCGCCGCGCTCGGCGCCACCGTCGGGGAGACGCCTGCCTCCGTCGTCTCCAAGTGCAGATACACCATCGCCATGCTCTCCGACCCCAGCG

Basic information

species Zea mays
transcript GRMZM2G153984_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|60350258|gb|DN217231.1|DN217231
EST:     TCCTCCGCCACGGCTTCCGCGTCACCGTCTGGAACAGGACCCTCGCCAAG                         TGCCAAGAGCTCGCCGCGCTCGGCGCCACCGTCGGGGAGACGCCTGCCTCC
genomic: TCCTCCGCCACGGCTTCCGCGTCACCGTCTGGAACAGGACCCTCGCCAAGgtattgcatc ... cttctcctagTGCCAAGAGCTCGCCGCGCTCGGCGCCACCGTCGGGGAGACGCCTGCCTCC
EST: gi|74244863|gb|DT652777.1|DT652777
EST:     TCCTCCGCCACGGCTTCCGCGTCACCGTCTGGAACAGGACCCTCGCCAAG                         TGCCAAGAGCTCGCCGCGCTCGGCGCCACCGTCGGGGAGACGCCTGCCTCC
genomic: TCCTCCGCCACGGCTTCCGCGTCACCGTCTGGAACAGGACCCTCGCCAAGgtattgcatc ... cttctcctagTGCCAAGAGCTCGCCGCGCTCGGCGCCACCGTCGGGGAGACGCCTGCCTCC
EST: gi|71328008|gb|DR800651.1|DR800651
EST:     TCCTCCGCCACGGCTTCCGCGTCACCGTCTGGAACAGGACCCTCGCCAAG                         TGCCAAGAGCTCGCCGCGCTCGGCGCCACCGTCGGGGAGACGCCTGCCTCC
genomic: TCCTCCGCCACGGCTTCCGCGTCACCGTCTGGAACAGGACCCTCGCCAAGgtattgcatc ... cttctcctagTGCCAAGAGCTCGCCGCGCTCGGCGCCACCGTCGGGGAGACGCCTGCCTCC
EST: gi|148969030|gb|EE019740.2|EE019740
EST:     TCCTCCGCCACGGCTTCCGCGTCACCGTCTGGAACAGGACCCTCGCCAAG                         TGCCAAGAGCTCGCCGCGCTCGGCGCCACCGTCGGGGAGACGCCTGCCTCC
genomic: TCCTCCGCCACGGCTTCCGCGTCACCGTCTGGAACAGGACCCTCGCCAAGgtattgcatc ... cttctcctagTGCCAAGAGCTCGCCGCGCTCGGCGCCACCGTCGGGGAGACGCCTGCCTCC
EST: gi|148969718|gb|EE020590.2|EE020590
EST:     TCCTCCGCCACGGCTTCCGCGTCACCGTCTGGAACAGGACCCTCGCCAAG                         TGCCAAGAGCTCGCCGCGCTCGGCGCCACCGTCGGGGAGACGCCTGCCTCC
genomic: TCCTCCGCCACGGCTTCCGCGTCACCGTCTGGAACAGGACCCTCGCCAAGgtattgcatc ... cttctcctagTGCCAAGAGCTCGCCGCGCTCGGCGCCACCGTCGGGGAGACGCCTGCCTCC
EST: gi|78084019|gb|DV512412.1|DV512412
EST:     TCCTCCGCCACGGCTTCCGCGTCACCGTCTGGAACAGGACCCTCGCCAAG                         TGCCAAGAGCTCGCCGCGCTCGGCGCCACCGTCGGGGAGACGCCTGCCTCC
genomic: TCCTCCGCCACGGCTTCCGCGTCACCGTCTGGAACAGGACCCTCGCCAAGgtattgcatc ... cttctcctagTGCCAAGAGCTCGCCGCGCTCGGCGCCACCGTCGGGGAGACGCCTGCCTCC
EST: gi|101382897|gb|EB813502.1|EB813502
EST:     TCCTCCGCCACGGCTTCCGCGTCACCGTCTGGAACAGGACCCTCGCCAAG                         TGCCAAGAGCTCGCCGCGCTCGGCGCCACCGTCGGGGAGACGCCTGCCTCC
genomic: TCCTCCGCCACGGCTTCCGCGTCACCGTCTGGAACAGGACCCTCGCCAAGgtattgcatc ... cttctcctagTGCCAAGAGCTCGCCGCGCTCGGCGCCACCGTCGGGGAGACGCCTGCCTCC
EST: gi|78119858|gb|DV538242.1|DV538242
EST:     TCCTCCGCCACGGCTTCCGCGTCACCGTCTGGAACAGGACCCTCGCCAAG                         TGCCAAGAGCTCGCCGCGCTCGGCGCCACCGTCGGGGAGACGCCTGCCTCC
genomic: TCCTCCGCCACGGCTTCCGCGTCACCGTCTGGAACAGGACCCTCGCCAAGgtattgcatc ... cttctcctagTGCCAAGAGCTCGCCGCGCTCGGCGCCACCGTCGGGGAGACGCCTGCCTCC
EST: gi|211111950|gb|FL269638.1|FL269638
EST:     TCCTCCGCCACGGCTTCCGCGTCACCGTCTGGAACAGGACCCTCGCCAAG                         TGCCAAGAGCTCGCCGCGCTCGGC-CCACCGTCGGGGAGACGCCTGCCTCC
genomic: TCCTCCGCCACGGCTTCCGCGTCACCGTCTGGAACAGGACCCTCGCCAAGgtattgcatc ... cttctcctagTGCCAAGAGCTCGCCGCGCTCGGCGCCACCGTCGGGGAGACGCCTGCCTCC
EST: gi|71439692|gb|DR820742.1|DR820742
EST:     TCCTCCGCCACGGCTTCCGCGTCACCGTCTGGAACAGGACCCTCGCCAAG                         TGCCAAGAGCTCGCCGCGCTCGGCGCCACCGTCGGGGAGACGCCTGCCTCC
genomic: TCCTCCGCCACGGCTTCCGCGTCACCGTCTGGAACAGGACCCTCGCCAAGgtattgcatc ... cttctcctagTGCCAAGAGCTCGCCGCGCTCGGCGCCACCGTCGGGGAGACGCCTGCCTCC
EST: gi|89764409|gb|DY691230.1|DY691230
EST:     TCCTCCGCCACGGCTTCCGCGTCACCGTCTGGAACAGGACCCTCGCCAAG                         TGCCAAGAGCTCGCCGCGCTCGGCGCCACCGTCGGGGAGACGCCTGCCTCC
genomic: TCCTCCGCCACGGCTTCCGCGTCACCGTCTGGAACAGGACCCTCGCCAAGgtattgcatc ... cttctcctagTGCCAAGAGCTCGCCGCGCTCGGCGCCACCGTCGGGGAGACGCCTGCCTCC
EST: gi|13198752|gb|BG354554.1|BG354554
EST:     TCCTCCGCCACGGCTTCCGCGTCACCGTCTGGAACAGGACCCTCGCCAAG                         TGCCAAGAGCTCGCCGCGCTCGGCGCCACCGTCGG
genomic: TCCTCCGCCACGGCTTCCGCGTCACCGTCTGGAACAGGACCCTCGCCAAGgtattgcatc ... cttctcctagTGCCAAGAGCTCGCCGCGCTCGGCGCCACCGTCGG
EST: gi|50326300|gb|CO521426.1|CO521426
EST:     TCCTCCGCCACGGCTTCCGCGTCACCGTCTGGAACAGGACCCTCGCCAAG                         TGCCAAGAGCTCGCCGCGCTCGGCGCCACCGTCGGGGAGACGCCTGCCTCC
genomic: TCCTCCGCCACGGCTTCCGCGTCACCGTCTGGAACAGGACCCTCGCCAAGgtattgcatc ... cttctcctagTGCCAAGAGCTCGCCGCGCTCGGCGCCACCGTCGGGGAGACGCCTGCCTCC
EST: gi|149051791|gb|EE155917.2|EE155917
EST:     TCCTCCGCCACGGCTTCCGCGTCACCGTCTGGAACAGGACCCTCGCCAAG                         TGCCAAGAGCTCGCCGCGCTCGGCGCCACCGTCGGGGAGACGCCTGCCTCC
genomic: TCCTCCGCCACGGCTTCCGCGTCACCGTCTGGAACAGGACCCTCGCCAAGgtattgcatc ... cttctcctagTGCCAAGAGCTCGCCGCGCTCGGCGCCACCGTCGGGGAGACGCCTGCCTCC
EST: gi|50334992|gb|CO530118.1|CO530118
EST:     TCCTCCGCCACGGCTTCCGCGTCACCGTCTGGAACAGGACCCTCGCCAAG                         TGCCAAGAGCTCGCCGCGCTCGGCGCCACCGTCGGGGAGACGCCTGCCTCC
genomic: TCCTCCGCCACGGCTTCCGCGTCACCGTCTGGAACAGGACCCTCGCCAAGgtattgcatc ... cttctcctagTGCCAAGAGCTCGCCGCGCTCGGCGCCACCGTCGGGGAGACGCCTGCCTCC
EST: gi|71448020|gb|DR829070.1|DR829070
EST:     TCCTCCGCCACGGCTTCCGCGTCACCGTCTGGAACAGGACCCTCGCCAAG                         TGCCAAGAGCTCGCCGCGCTCGGCGCCACCGTCGGGGAGACGCCTGCCTCC
genomic: TCCTCCGCCACGGCTTCCGCGTCACCGTCTGGAACAGGACCCTCGCCAAGgtattgcatc ... cttctcctagTGCCAAGAGCTCGCCGCGCTCGGCGCCACCGTCGGGGAGACGCCTGCCTCC
EST: gi|149075802|gb|EE164336.2|EE164336
EST:     TCCTCCGCCACGGCTTCCGCGTCACCGTCTGGAACAGGACCCTCGCCAAG                         TGCCAAGAGCTCGCCGCGCTCGGCGCCACCGTCGGGGAGACGCCTGCCTCC
genomic: TCCTCCGCCACGGCTTCCGCGTCACCGTCTGGAACAGGACCCTCGCCAAGgtattgcatc ... cttctcctagTGCCAAGAGCTCGCCGCGCTCGGCGCCACCGTCGGGGAGACGCCTGCCTCC
EST: gi|149081805|gb|EE170963.2|EE170963
EST:     TCCTCCGCCACGGCTTCCGCGTCACCGTCTGGAACAGGACCCTCGCCAAG                         TGCCAAGAGCTCGCCGCGCTCGGCGCCACCGTCGGGGAGACGCCTGCCTCC
genomic: TCCTCCGCCACGGCTTCCGCGTCACCGTCTGGAACAGGACCCTCGCCAAGgtattgcatc ... cttctcctagTGCCAAGAGCTCGCCGCGCTCGGCGCCACCGTCGGGGAGACGCCTGCCTCC
EST: gi|148954590|gb|EC900032.2|EC900032
EST:     TCCTCCGCCACGGCTTCCGCGTCACCGTCTGGAACAGGACCCTCGCCAAG                         TGCCAAGAGCTCGCCGCGCTCGGCGCCACCGTCGGGGAGACGCCTGCCTCC
genomic: TCCTCCGCCACGGCTTCCGCGTCACCGTCTGGAACAGGACCCTCGCCAAGgtattgcatc ... cttctcctagTGCCAAGAGCTCGCCGCGCTCGGCGCCACCGTCGGGGAGACGCCTGCCTCC
EST: gi|149079137|gb|EE168066.2|EE168066
EST:     TCCTCCGCCACGGCTTCCGCGTCACCGTCTGGAACAGGACCCTCGCCAAG                         TGCCAAGAGCTCGCCGCGCTCGGCGCCACCGTCGGGGAGACGCCTGCCTCC
genomic: TCCTCCGCCACGGCTTCCGCGTCACCGTCTGGAACAGGACCCTCGCCAAGgtattgcatc ... cttctcctagTGCCAAGAGCTCGCCGCGCTCGGCGCCACCGTCGGGGAGACGCCTGCCTCC
EST: gi|89762144|gb|DY689877.1|DY689877
EST:     TCCTCCGCCACGGCTTCCGCGTCACCGTCTGGAACAGGACCCTCGCCAAG                         TGCCAAGAGCTCGCCGCGCTCGGCGCCACCGTCGGGGAGACGCCTGCCTCC
genomic: TCCTCCGCCACGGCTTCCGCGTCACCGTCTGGAACAGGACCCTCGCCAAGgtattgcatc ... cttctcctagTGCCAAGAGCTCGCCGCGCTCGGCGCCACCGTCGGGGAGACGCCTGCCTCC
EST: gi|211111947|gb|FL269635.1|FL269635
EST:     TCCTCCGCCACGGCTTCCGCGTCACCGTCTGGAACAGGACCCTCGCCAAG                         TGCCAAGAGCTCGCCGCGCTCGGCGCCACCGTCGGGGAGACGCCTGCCTCC
genomic: TCCTCCGCCACGGCTTCCGCGTCACCGTCTGGAACAGGACCCTCGCCAAGgtattgcatc ... cttctcctagTGCCAAGAGCTCGCCGCGCTCGGCGCCACCGTCGGGGAGACGCCTGCCTCC
EST: gi|211111949|gb|FL269637.1|FL269637
EST:     TCCTCCGCCACGGCTTCCGCGTCACCGTCTGGAACAGGACCCTCGCCAAG                         TGCCAAGAGCTCGCCGCGCTCGGCGCCACCGTCGGGGAGACGCCTGCCTCC
genomic: TCCTCCGCCACGGCTTCCGCGTCACCGTCTGGAACAGGACCCTCGCCAAGgtattgcatc ... cttctcctagTGCCAAGAGCTCGCCGCGCTCGGCGCCACCGTCGGGGAGACGCCTGCCTCC
EST: gi|22133534|gb|BQ833766.1|BQ833766
EST:     TCCTCCGCCACGGCTTCCGCGTCACCGTCTGGAACAGGACCCTCGCCAAG                         TGCCAAGAGCTCGCCGCGCTCGGCGCCACCGTCGGGGAGACGCCTGCCTCC
genomic: TCCTCCGCCACGGCTTCCGCGTCACCGTCTGGAACAGGACCCTCGCCAAGgtattgcatc ... cttctcctagTGCCAAGAGCTCGCCGCGCTCGGCGCCACCGTCGGGGAGACGCCTGCCTCC
EST: gi|76917425|gb|DV166840.1|DV166840
EST:     TCCTCCGCCACGGCTTCCGCGTCACCGTCTGGAACAGGACCCTCGCCAAG                         TGCCAAGAGCTCGCCGCGCTCGGCGCCACCGTCGGGGAGACGCCTGCCTCC
genomic: TCCTCCGCCACGGCTTCCGCGTCACCGTCTGGAACAGGACCCTCGCCAAGgtattgcatc ... cttctcctagTGCCAAGAGCTCGCCGCGCTCGGCGCCACCGTCGGGGAGACGCCTGCCTCC
EST: gi|93013137|gb|EB638657.1|EB638657
EST:     TCCTCCGCCACGGCTTCCGCGTCACCGTCTGGAACAGGACCCTCGCCAAG                         TGCCAAGAGCTCGCCGCGCTCGGCGCCACCGTCGGGGAGACGCCTGCCTCC
genomic: TCCTCCGCCACGGCTTCCGCGTCACCGTCTGGAACAGGACCCTCGCCAAGgtattgcatc ... cttctcctagTGCCAAGAGCTCGCCGCGCTCGGCGCCACCGTCGGGGAGACGCCTGCCTCC
EST: gi|149112755|gb|EE295578.2|EE295578
EST:     CCTCCGCCACGGCTTCCGCGTCACCCGTCTGGAACAGGACCCTCGCCAAG                         TGCCAAGAGCTCGCCGCCGCTCGGCGCCACCGTCGGGGAGACGCCTGCCTC
genomic: CCTCCGCCACGGCTTCCGCGTCACC-GTCTGGAACAGGACCCTCGCCAAGgtattgcatc ... cttctcctagTGCCAAGAGCTCGCCGC-GCTCGGCGCCACCGTCGGGGAGACGCCTGCCTC
EST: gi|149073536|gb|EE161839.2|EE161839
EST:     TCCTCCGCCACGGCTTCCGCGTCACCGTCTGGAACAGGACCCTCGCCAAG                         TGCCAAGAGCTCGCCGCGCTCGGCGCCACCGTCGGGGAGACGCCTGCCTCC
genomic: TCCTCCGCCACGGCTTCCGCGTCACCGTCTGGAACAGGACCCTCGCCAAGgtattgcatc ... cttctcctagTGCCAAGAGCTCGCCGCGCTCGGCGCCACCGTCGGGGAGACGCCTGCCTCC
EST: gi|22819821|gb|BU499911.1|BU499911
EST:     TCCTCCGCCACGGCTTCCGCGTCACCGTCTGGAACAGGACCCTCGCCAAG                         TGCCAAGAGCTCGCCGCGCTCGGCGCCACCGTCGGGGAGACGCCTGCCTCC
genomic: TCCTCCGCCACGGCTTCCGCGTCACCGTCTGGAACAGGACCCTCGCCAAGgtattgcatc ... cttctcctagTGCCAAGAGCTCGCCGCGCTCGGCGCCACCGTCGGGGAGACGCCTGCCTCC
EST: gi|148967444|gb|EE018674.2|EE018674
EST:     TCCTCCGCCACGGCTTCCGCGTCACCGTCTGGAACAGGACCCTCGCCAAG                         TGCCAAGAGCTCGCCGCGCTCGGCGCCACCGTCGGGGAGACGCCTGCCTCC
genomic: TCCTCCGCCACGGCTTCCGCGTCACCGTCTGGAACAGGACCCTCGCCAAGgtattgcatc ... cttctcctagTGCCAAGAGCTCGCCGCGCTCGGCGCCACCGTCGGGGAGACGCCTGCCTCC
EST: gi|211111945|gb|FL269633.1|FL269633
EST:     TCCTCCGCCACGGCTTCCGCGTCACCGTCTGGAACAAGACCCTCGCCAAG                         TGCCAAGAGCTCGCCGCGCTCGGCGCCACCGGCGGGGAGACGCCTGCCTCC
genomic: TCCTCCGCCACGGCTTCCGCGTCACCGTCTGGAACAGGACCCTCGCCAAGgtattgcatc ... cttctcctagTGCCAAGAGCTCGCCGCGCTCGGCGCCACCGTCGGGGAGACGCCTGCCTCC

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: 157

GGTGGGGTTCTTGGGTCTGGGCATCATGGGCAAGGCAATGGCGACCAACCTCCTCCGCCACGGCTTCCGCGTCACCGTCTGGAACAGGACCCTCGCCAAGgtattgcatc ... cttctcctagTGCCAAGAGCTCGCCGCGCTCGGCGCCACCGTCGGGGAGACGCCTGCCTCCGTCGTCTCCAAGTGCAGATACACCATCGCCATGCTCTCCGACCCCAGCG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 136

GGTGGGGTTCTTGGGTCTGGGCATCATGGGCAAGGCAATGGCGACCAACCTCCTCCGCCACGGCTTCCGCGTCACCGTCTGGAACAGGACCCTCGCCAAGgtattgcatc ... cttctcctagTGCCAAGAGCTCGCCGCGCTCGGCGCCACCGTCGGGGAGACGCCTGCCTCCGTCGTCTCCAAGTGCAGATACACCATCGCCATGCTCTCCGACCCCAGCG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 80

GGTGGGGTTCTTGGGTCTGGGCATCATGGGCAAGGCAATGGCGACCAACCTCCTCCGCCACGGCTTCCGCGTCACCGTCTGGAACAGGACCCTCGCCAAGgtattgcatc ... cttctcctagTGCCAAGAGCTCGCCGCGCTCGGCGCCACCGTCGGGGAGACGCCTGCCTCCGTCGTCTCCAAGTGCAGATACACCATCGCCATGCTCTCCGACCCCAGCG


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 106

GGTGGGGTTCTTGGGTCTGGGCATCATGGGCAAGGCAATGGCGACCAACCTCCTCCGCCACGGCTTCCGCGTCACCGTCTGGAACAGGACCCTCGCCAAGgtattgcatc ... cttctcctagTGCCAAGAGCTCGCCGCGCTCGGCGCCACCGTCGGGGAGACGCCTGCCTCCGTCGTCTCCAAGTGCAGATACACCATCGCCATGCTCTCCGACCCCAGCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctcccgtccgcacgcgtgctcccgaaatcacatctccatgacctcttctcctagTGCCAAGAGCTCGCCGCGCTCGGCGCCACCGTCGGGGAGACGCCTGCCTCCGTCGTCTCCAAGTGCAGATACACCATCGCCATGCTCTCCGACCCCAGCG
                                       tgacctcttctcct  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattgcatcggaaccgctgcgcccgcgcccttatgttctgctgaaatccgaatccgtcgcctcccgtccgcacgcgtgctcccgaaatcacatctccatgacctcttctcctagTGCCAAGAGCTCGCCGCGCTCGGCGCCACCGTCGGGGAGACGCCTGCCTCCGTCGTCTCCAAGTGCAGATACACCATCGCCATGCTCTCCGACCCCAGCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT