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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcccatggatttttactgctgtttaagatatcgttttggaatctggtgatcaaatgtgttcagcattcaattcacgtgcatctctcttatttggaatcagGTGTGCAGAATTTCCTCATGTCGAATATGAGCCAATAAAATGGATTTGCCAACTGCTGGGTTGCTGCCTGGTTTTACCTGAACGACCATGAAAAAGTTCT

Basic information

species Zea mays
transcript GRMZM2G135816_T01
intron # 6
splice site 3'
intron type U12 (go to U12 genes for details)

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|5058882|gb|AI737358.1|AI737358
EST:     TGATATTGCCAAGACAGCAAATAGACCCATGATACATATAGGTGGCTGAG                         GTGTGCAGAATTTCCTCATGTCGAATATGAGCCAATAAAATGGATTTGGCA
genomic: TGATATTGCCAAGACAGCAAATAGACCCATGATACATATAGGTGGCTGAGgtatcctctt ... ttggaatcagGTGTGCAGAATTTCCTCATGTCGAATATGAGCCAATAAAATGGATTTGCCA
EST: gi|6020607|gb|AW065640.1|AW065640
EST:     TGATATTGCCAAGACAGCAAATAGACCCATGATACATATAGGTGGCTGAG                         GTGTGCAGAATTTCCTCATGTCGAATATGAGC
genomic: TGATATTGCCAAGACAGCAAATAGACCCATGATACATATAGGTGGCTGAGgtatcctctt ... ttggaatcagGTGTGCAGAATTTCCTCATGTCGAATATGAGC
EST: gi|211275416|gb|FL065995.1|FL065995
EST:     TGATATTGCMAAGACAGCAAATAGACCCATGATACATATAGGTGGCTGAG                         GTGTGCAGAATTTCCTCATGTCGAATATGAGCCAATAAAATGGATTTGCCA
genomic: TGATATTGCCAAGACAGCAAATAGACCCATGATACATATAGGTGGCTGAGgtatcctctt ... ttggaatcagGTGTGCAGAATTTCCTCATGTCGAATATGAGCCAATAAAATGGATTTGCCA
EST: gi|211275417|gb|FL065996.1|FL065996
EST:     TGATATTGCCAAGACAGCAAATAGACCCATGATACATATAGGTGGCTGAG                         GTGTGCAGAATTTCCTCATGTCGAATATGAGCCAATAAAATGGATTTGCCA
genomic: TGATATTGCCAAGACAGCAAATAGACCCATGATACATATAGGTGGCTGAGgtatcctctt ... ttggaatcagGTGTGCAGAATTTCCTCATGTCGAATATGAGCCAATAAAATGGATTTGCCA
EST: gi|6194756|gb|AW146860.1|AW146860
EST:     TGATATTGCCAAGACAGCAAATAGACCCATGATACATATAGGTGGCTGAG                         GTGTGCAGAATTTCCT
genomic: TGATATTGCCAAGACAGCAAATAGACCCATGATACATATAGGTGGCTGAGgtatcctctt ... ttggaatcagGTGTGCAGAATTTCCT
EST: gi|78090417|gb|DV518791.1|DV518791
EST:     TGATATTGCCAAGACAGCAAATAGACCCATGATACATATAGGTGGCTGAG                         GTGTGCAGAATTTCCTCATGTCGAATATGAGCCAATAAAATGGATTTGCCA
genomic: TGATATTGCCAAGACAGCAAATAGACCCATGATACATATAGGTGGCTGAGgtatcctctt ... ttggaatcagGTGTGCAGAATTTCCTCATGTCGAATATGAGCCAATAAAATGGATTTGCCA
EST: gi|149048405|gb|EE048313.2|EE048313
EST:     TGATATTGCCAAGACAGCAAATAGACCCATGATACATATAGGTGGCTGAG                         GTGGGCAGAATTTCCTCATGTCGAATATGAGCCAATAAAATGGATTTGCCA
genomic: TGATATTGCCAAGACAGCAAATAGACCCATGATACATATAGGTGGCTGAGgtatcctctt ... ttggaatcagGTGTGCAGAATTTCCTCATGTCGAATATGAGCCAATAAAATGGATTTGCCA
EST: gi|91054281|gb|EB164699.1|EB164699
EST:     TGATATTGCCAAGACAGCAAATAGACCCATGATACATATAGGTGGCTGAG                         GTGTGCAGAATTTCCTCATGTCGAATATGAGCCAATAAAATGGATTTGCCA
genomic: TGATATTGCCAAGACAGCAAATAGACCCATGATACATATAGGTGGCTGAGgtatcctctt ... ttggaatcagGTGTGCAGAATTTCCTCATGTCGAATATGAGCCAATAAAATGGATTTGCCA
EST: gi|16378519|gb|BI992468.1|BI992468
EST:     TGATATTGCCAAGACAGCAAATAGACCCATGATACATATAGGTGGCTGAG                         GTGTGCAGAATTTCCTCATGTCGAATATGAGCCAATAAAATGGATTTGCCA
genomic: TGATATTGCCAAGACAGCAAATAGACCCATGATACATATAGGTGGCTGAGgtatcctctt ... ttggaatcagGTGTGCAGAATTTCCTCATGTCGAATATGAGCCAATAAAATGGATTTGCCA
EST: gi|13249841|gb|BG360746.1|BG360746
EST:     TGATATTGCCAAGACAGCAAATAGACCCATGATACATATAGGTGGCTGAG                         GTGTGCAGAATTTCCTCATGTCGAATATGAGCCAATAAAATGGATTTGCCA
genomic: TGATATTGCCAAGACAGCAAATAGACCCATGATACATATAGGTGGCTGAGgtatcctctt ... ttggaatcagGTGTGCAGAATTTCCTCATGTCGAATATGAGCCAATAAAATGGATTTGCCA
EST: gi|91874219|gb|EB404176.1|EB404176
EST:     TGATATTGCCAAGACAGCAAATAGACCCCTGATACATATAGGTGGGTGAG                         GTGTGCAGAATTTCCTCATGTCGAATATGAGCCAATAAAAAGGATTTGCCA
genomic: TGATATTGCCAAGACAGCAAATAGACCCATGATACATATAGGTGGCTGAGgtatcctctt ... ttggaatcagGTGTGCAGAATTTCCTCATGTCGAATATGAGCCAATAAAATGGATTTGCCA
EST: gi|32859387|gb|CD999068.1|CD999068
EST:     TGATATTGCCAAGACAGCAAATAGACCCATGATACATATAGGTGGCTGAG                         GTGTGCAGAATTTCCTCATGTCGAATATGAGCCAATAAAATGGATTTGCCA
genomic: TGATATTGCCAAGACAGCAAATAGACCCATGATACATATAGGTGGCTGAGgtatcctctt ... ttggaatcagGTGTGCAGAATTTCCTCATGTCGAATATGAGCCAATAAAATGGATTTGCCA
EST: gi|211246367|gb|FL451965.1|FL451965
EST:     TGATATTGCCAAGACAGCAAATAGACCCATGATACATATAGGTGGCTGAG                         GTGTGCAGAATTTCCTCATGTCGAATATGAGCCAATAAAATGGATTTGCCA
genomic: TGATATTGCCAAGACAGCAAATAGACCCATGATACATATAGGTGGCTGAGgtatcctctt ... ttggaatcagGTGTGCAGAATTTCCTCATGTCGAATATGAGCCAATAAAATGGATTTGCCA
EST: gi|161590185|gb|EY959342.1|EY959342
EST:     GATATTGCCAAGACAGCAAAATAGACCCATGATACATATAGGTGGCTGAG                         GTGTGCAGAATTTCCTCATGTCGAATA
genomic: GATATTGCCAAGACAGC-AAATAGACCCATGATACATATAGGTGGCTGAGgtatcctctt ... ttggaatcagGTGTGCAGAATTTCCTCATGTCGAATA
EST: gi|211121393|gb|FL463011.1|FL463011
EST:     TGATATTGCCAAGACWGCAAATAGACCCATGATACATATAGGTGGCTGAG                         GTGTGCAGAATTTCCTCATGTCGAATATGAGCCAATAAAATGGATTTGCCA
genomic: TGATATTGCCAAGACAGCAAATAGACCCATGATACATATAGGTGGCTGAGgtatcctctt ... ttggaatcagGTGTGCAGAATTTCCTCATGTCGAATATGAGCCAATAAAATGGATTTGCCA
EST: gi|211275415|gb|FL065994.1|FL065994
EST:     TGATATTGCCAAGACAGCAAATAGACCCATGATACATATAGGTGGCTGAG                         GTGTGCAGAATTTCCTCATGTCGAATATGAGCCAATAAAATGGATTTGCCA
genomic: TGATATTGCCAAGACAGCAAATAGACCCATGATACATATAGGTGGCTGAGgtatcctctt ... ttggaatcagGTGTGCAGAATTTCCTCATGTCGAATATGAGCCAATAAAATGGATTTGCCA
EST: gi|148946521|gb|EC891833.2|EC891833
EST:     TGATATTGCCAAGACAGCAAATAGACCCATGATACATATAGGTGGCTGAG                         GTGTGCAGAATTTCCTCATGTCGAATATGAGCCAATAAAATGGATTTGCCA
genomic: TGATATTGCCAAGACAGCAAATAGACCCATGATACATATAGGTGGCTGAGgtatcctctt ... ttggaatcagGTGTGCAGAATTTCCTCATGTCGAATATGAGCCAATAAAATGGATTTGCCA
EST: gi|13249840|gb|BG360745.1|BG360745
EST:     GATATTGCCAAGACAGCAAATAGANCCCATGATACATATAGGTGGCTGAG                         GTGTGCAGAATTTCCTCATGTCGAATATGAGCCAATAAAATGGATTTGCCA
genomic: GATATTGCCAAGACAGCAAATAGA-CCCATGATACATATAGGTGGCTGAGgtatcctctt ... ttggaatcagGTGTGCAGAATTTCCTCATGTCGAATATGAGCCAATAAAATGGATTTGCCA
EST: gi|148928476|gb|EE285290.2|EE285290
EST:     TGATATTGCCAAGACAGCAAATAGACCCATGATACATATAGGTGGCTGAG                         GTGTGCAGAATTTCCTCATGTCGAATATGAGCCAATAAAATGGATTTGCCA
genomic: TGATATTGCCAAGACAGCAAATAGACCCATGATACATATAGGTGGCTGAGgtatcctctt ... ttggaatcagGTGTGCAGAATTTCCTCATGTCGAATATGAGCCAATAAAATGGATTTGCCA
EST: gi|24764636|gb|CA399800.1|CA399800
EST:     TGATATTGCCAAGACAGCAAATAGACCCATGATACATATAGGTGGCTGAG                         GTGTGCAGAATTTCCTCATGTCGAATATGAGCCAATAAAATGGATTTGCCA
genomic: TGATATTGCCAAGACAGCAAATAGACCCATGATACATATAGGTGGCTGAGgtatcctctt ... ttggaatcagGTGTGCAGAATTTCCTCATGTCGAATATGAGCCAATAAAATGGATTTGCCA

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: 46 (upstream exon), 48 (downstream exon)
Score: 24

GTTAAAAGGAAGAAAGCTAAACATGCCGGGATGTTTGATATTGCCAAGACAGCAAATAGACCCATGATACATATAGGTGGCTGAGgtatcctctt ... ttggaatcagGTGTGCAGAATTTCCTCATGTCGAATATGAGCCAATAAAATGGATTTGCCAACTGCTGGGTTGCTGCCTGGTTTTACCTGAACGACCATGAAAAAGTTCT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 114

GTTAAAAGGAAGAAAGCTAAACATGCCGGGATGTTTGATATTGCCAAGACAGCAAATAGACCCATGATACATATAGGTGGCTGAGgtatcctctt ... ttggaatcagGTGTGCAGAATTTCCTCATGTCGAATATGAGCCAATAAAATGGATTTGCCAACTGCTGGGTTGCTGCCTGGTTTTACCTGAACGACCATGAAAAAGTTCT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 78

GTTAAAAGGAAGAAAGCTAAACATGCCGGGATGTTTGATATTGCCAAGACAGCAAATAGACCCATGATACATATAGGTGGCTGAGgtatcctctt ... ttggaatcagGTGTGCAGAATTTCCTCATGTCGAATATGAGCCAATAAAATGGATTTGCCAACTGCTGGGTTGCTGCCTGGTTTTACCTGAACGACCATGAAAAAGTTCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 71

GTTAAAAGGAAGAAAGCTAAACATGCCGGGATGTTTGATATTGCCAAGACAGCAAATAGACCCATGATACATATAGGTGGCTGAGgtatcctctt ... ttggaatcagGTGTGCAGAATTTCCTCATGTCGAATATGAGCCAATAAAATGGATTTGCCAACTGCTGGGTTGCTGCCTGGTTTTACCTGAACGACCATGAAAAAGTTCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgatcaaatgtgttcagcattcaattcacgtgcatctctcttatttggaatcagGTGTGCAGAATTTCCTCATGTCGAATATGAGCCAATAAAATGGATTTGCCAACTGCTGGGTTGCTGCCTGGTTTTACCTGAACGACCATGAAAAAGTTCT
                                     tctcttatt  putative branch site 
                                 catctctcttattt  CT-rich tract
                   attcaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcccatggatttttactgctgtttaagatatcgttttggaatctggtgatcaaatgtgttcagcattcaattcacgtgcatctctcttatttggaatcagGTGTGCAGAATTTCCTCATGTCGAATATGAGCCAATAAAATGGATTTGCCAACTGCTGGGTTGCTGCCTGGTTTTACCTGAACGACCATGAAAAAGTTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC