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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGACATGATTGCCTTGTCATTTGTTCGGAAGGGTTCGGATCTTGTGGAGGTTAGGAAGGTACTTGGTGAGCATGCCAAGTCCATAATGCTGATGTCAAAGgtatggttctagcattttcttttgggtttcaaactagtagattttcaaattcaaggttataattgttttgaacatgcag

Basic information

species Zea mays
transcript GRMZM2G003883_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G003883_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os01g16960.1 (Oryza sativa), 5'ss of exon 2
TGACATGATTGCCTTGTCATTTGTTCGGAAGGGTTCGGATCTTGTGGAGGTTAGGAAGGTACTTGGTGAGCATGCCAAGTCCATAATGCTGATGTCAAAGgtatggttctagcattttcttttgggtttcaaactagtagattttcaaattcaaggttataattgttttgaacatgcag
||||||||||||  |||| |||||||| || || || || ||||| ||||| |||||||| |||||  ||||||| ||||| ||||||||||||||||||||||      | |||| ||||||| || |   |||  ||   |      | ||| | | | | | | |||||  | |||
TGACATGATTGCTCTGTCTTTTGTTCGTAAAGGCTCAGACCTTGTAGAGGTCAGGAAGGTGCTTGGGAAGCATGCAAAGTCAATAATGCTGATGTCAAAGgtat------aacattctcttttgagtattgcacttctaagctgcactttgcaaagattttaatctattgaattttcag
















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|211304788|gb|FL143337.1|FL143337
EST:     TTAGGAAGGTACTTGGTGAGCATGCCAAGTCCATAATGCTGATGTCAAAG                         GTTGAGAATCAAGAGGGAGTAGCTNACTTTGATGATATCCTGGCAAACTCT
genomic: TTAGGAAGGTACTTGGTGAGCATGCCAAGTCCATAATGCTGATGTCAAAGgtatggttct ... gaacatgcagGTTGAGAATCAAGAGGGAGTAGCTAACTTTGATGATATCCTGGCAAACTCT
EST: gi|18659675|gb|BM500464.1|BM500464
EST:     TTAGGAAGGTACTTGGTGAGCATGCCAAGTCCATAATGCTGATGTCAAAG                         GTTGAGAATCAAGAGGGAGTAGCTAACTTTGATGATATCCTGGCAAACTCT
genomic: TTAGGAAGGTACTTGGTGAGCATGCCAAGTCCATAATGCTGATGTCAAAGgtatggttct ... gaacatgcagGTTGAGAATCAAGAGGGAGTAGCTAACTTTGATGATATCCTGGCAAACTCT
EST: gi|30160512|gb|CB924241.1|CB924241
EST:     TTAGGAAGGTACTTGGTGAGCATGCCAAGTCCATAATACTGATGTCAAAG                         GTTGAGAATCAAGAGGGAGTAGCTAACTTTGATGATATCCTGGCAAACTCT
genomic: TTAGGAAGGTACTTGGTGAGCATGCCAAGTCCATAATGCTGATGTCAAAGgtatggttct ... gaacatgcagGTTGAGAATCAAGAGGGAGTAGCTAACTTTGATGATATCCTGGCAAACTCT
EST: gi|67020378|gb|CO449127.1|CO449127
EST:     TTAGGAAGGTACTTGGTGAGCATGCCAAGTCCATAATGCTGATGTCAAAG                         GTTGAGAATCAAGAGGGAGTAGCTAACTTTGATGATATCCTGGCAAACTCT
genomic: TTAGGAAGGTACTTGGTGAGCATGCCAAGTCCATAATGCTGATGTCAAAGgtatggttct ... gaacatgcagGTTGAGAATCAAGAGGGAGTAGCTAACTTTGATGATATCCTGGCAAACTCT
EST: gi|211304791|gb|FL143340.1|FL143340
EST:     TTAGGAAGGTACTTGGTGAGCATGCCAAGTCCATAATGCTGATGTCAAAG                         GTTGAGAATCAAGAGGGAGTAGCTTACTTTGATGATATCCTGGCAAACTCT
genomic: TTAGGAAGGTACTTGGTGAGCATGCCAAGTCCATAATGCTGATGTCAAAGgtatggttct ... gaacatgcagGTTGAGAATCAAGAGGGAGTAGCTAACTTTGATGATATCCTGGCAAACTCT
EST: gi|32919129|gb|CF023941.1|CF023941
EST:     TTAGGAAGGTACTTGGTGAGCATGCCAAGTCCATAATGCTGATGTCAAAG                         GTTGAGAATCAAGAGGGAGTAGCTAACTTTGATGATATCCTGGCAAACTCT
genomic: TTAGGAAGGTACTTGGTGAGCATGCCAAGTCCATAATGCTGATGTCAAAGgtatggttct ... gaacatgcagGTTGAGAATCAAGAGGGAGTAGCTAACTTTGATGATATCCTGGCAAACTCT
EST: gi|91055016|gb|EB165434.1|EB165434
EST:     TTAAGAAGGTACTTGGTGAGCATGCCAAGTCCATAATGCTGATGTCAAAG                         GGTGAGAATCAAGAGGGAGTAGCTAACTT
genomic: TTAGGAAGGTACTTGGTGAGCATGCCAAGTCCATAATGCTGATGTCAAAGgtatggttct ... gaacatgcagGTTGAGAATCAAGAGGGAGTAGCTAACTT
EST: gi|211304792|gb|FL143341.1|FL143341
EST:     TTAGGAAGGTACTTGGTGAGCATGCCAAGTCCATAATGCTGATGTCAAAG                         GTTGAGAATCAAGAGGGAGTAGCTAACTTTGATGATATCCTGGCAAACTCT
genomic: TTAGGAAGGTACTTGGTGAGCATGCCAAGTCCATAATGCTGATGTCAAAGgtatggttct ... gaacatgcagGTTGAGAATCAAGAGGGAGTAGCTAACTTTGATGATATCCTGGCAAACTCT
EST: gi|211304789|gb|FL143338.1|FL143338
EST:     TTAGGAAGGTACTTGGTGAGCATGCCAAGTCCATAATGCTGATGTCAAAG                         GTTGAGAATCAAGAGGGAGTAGCTAACTTTGATGATATCCTGGCAAACTCT
genomic: TTAGGAAGGTACTTGGTGAGCATGCCAAGTCCATAATGCTGATGTCAAAGgtatggttct ... gaacatgcagGTTGAGAATCAAGAGGGAGTAGCTAACTTTGATGATATCCTGGCAAACTCT
EST: gi|32849568|gb|CD989249.1|CD989249
EST:     ACTTGGTGAGCATGCCAAGTCCATAATGCTGATGTCAAAG                         GTTGAGAATCAAGAGGGAGTAGCTAACTTTGATGATATCCTGGCAAACTCT
genomic: ACTTGGTGAGCATGCCAAGTCCATAATGCTGATGTCAAAGgtatggttct ... gaacatgcagGTTGAGAATCAAGAGGGAGTAGCTAACTTTGATGATATCCTGGCAAACTCT
EST: gi|40334624|gb|CK368694.1|CK368694
EST:     TTAGGAAGGTACTTGGTGAGCATGCCAAGTCCATAATGCTGATGTCAAAG                         GTTGAGAATCAAGAGGGAGTAGCTAACTTTGATGATATCCTGGCAAACTCT
genomic: TTAGGAAGGTACTTGGTGAGCATGCCAAGTCCATAATGCTGATGTCAAAGgtatggttct ... gaacatgcagGTTGAGAATCAAGAGGGAGTAGCTAACTTTGATGATATCCTGGCAAACTCT
EST: gi|211304790|gb|FL143339.1|FL143339
EST:     TTAGGAAGGTACTTGGTGAGCATGCCAAGTCCATAATGCTGATGTCAAAG                         GTTNAGAATCAAGAGGGAGTAGCTAACTTTGAKGATATCCTGGCAAACTCT
genomic: TTAGGAAGGTACTTGGTGAGCATGCCAAGTCCATAATGCTGATGTCAAAGgtatggttct ... gaacatgcagGTTGAGAATCAAGAGGGAGTAGCTAACTTTGATGATATCCTGGCAAACTCT
EST: gi|86856108|gb|DY307119.1|DY307119
EST:     TTAGGAAGGTACTTGGTGAGCATGCCAAGTCCATAATGCTGATGTCAAAG                         GTTGAGAATCAAGAGGGAGTAGCTAACTTTGATGATATCCCTGGCAAACTC
genomic: TTAGGAAGGTACTTGGTGAGCATGCCAAGTCCATAATGCTGATGTCAAAGgtatggttct ... gaacatgcagGTTGAGAATCAAGAGGGAGTAGCTAACTTTGATGATATCC-TGGCAAACTC
EST: gi|32849773|gb|CD989454.1|CD989454
EST:     ACTTGGTGAGCATGCCAAGTCCATAATGCTGATGTCAAAG                         GTTGAGAATCAAGAGGGAGTAGCTAACTTTGATGATATCCTGGCAAACTCT
genomic: ACTTGGTGAGCATGCCAAGTCCATAATGCTGATGTCAAAGgtatggttct ... gaacatgcagGTTGAGAATCAAGAGGGAGTAGCTAACTTTGATGATATCCTGGCAAACTCT
EST: gi|148999358|gb|EE036297.2|EE036297
EST:     TAGGAAGGTACTTGGTGAGCATGCCAAGTCCCATA-TGCTGATGTCAAAG                         GTTGAGAATCAAGAGGGAGTAGCTAACTTTGATGATATCCTGGCAAACTCT
genomic: TAGGAAGGTACTTGGTGAGCATGCCAAGTCC-ATAATGCTGATGTCAAAGgtatggttct ... gaacatgcagGTTGAGAATCAAGAGGGAGTAGCTAACTTTGATGATATCCTGGCAAACTCT
EST: gi|101382630|gb|EB813369.1|EB813369
EST:     TTAGGAAGGTACTTGGTGAGCATGCCAAGTCCATAATGCTGATGTCAAAG                         GTTGAGAATCAGGAGGGAGTAGCTAACTTTGATGATATCCTGGCAAACTCT
genomic: TTAGGAAGGTACTTGGTGAGCATGCCAAGTCCATAATGCTGATGTCAAAGgtatggttct ... gaacatgcagGTTGAGAATCAAGAGGGAGTAGCTAACTTTGATGATATCCTGGCAAACTCT
EST: gi|31558339|gb|CD527551.1|CD527551
EST:     TTAGGAAGGTACTTGGTGAGCATGCCAAGTCCATAATGCTGATGTCAAAG                         GTTGAGAATCAAGAGGGAGTAGCTAACTTTGATGATATCCTGGCAAACTCT
genomic: TTAGGAAGGTACTTGGTGAGCATGCCAAGTCCATAATGCTGATGTCAAAGgtatggttct ... gaacatgcagGTTGAGAATCAAGAGGGAGTAGCTAACTTTGATGATATCCTGGCAAACTCT
EST: gi|32850195|gb|CD989876.1|CD989876
EST:     ACTTGGTGAGCATGCCAAGTCCATAATGCTGATGTCAAAG                         GTTGAGAATCAAGAGGGAGTAGCTAACTTTGATGATATCCTGGCAAACTCT
genomic: ACTTGGTGAGCATGCCAAGTCCATAATGCTGATGTCAAAGgtatggttct ... gaacatgcagGTTGAGAATCAAGAGGGAGTAGCTAACTTTGATGATATCCTGGCAAACTCT
EST: gi|32919187|gb|CF023999.1|CF023999
EST:     TTAGGAAGGTACTTGGTGAGCATGCCAAGTCCATAATGCTGATGTCAAAG                         GTTGAGAATCAAGAGGGAGTAGCTAACTTTGATGATATCCTGGCAAACTCT
genomic: TTAGGAAGGTACTTGGTGAGCATGCCAAGTCCATAATGCTGATGTCAAAGgtatggttct ... gaacatgcagGTTGAGAATCAAGAGGGAGTAGCTAACTTTGATGATATCCTGGCAAACTCT

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), 49 (downstream exon)
Score: 59

TGACATGATTGCCTTGTCATTTGTTCGGAAGGGTTCGGATCTTGTGGAGGTTAGGAAGGTACTTGGTGAGCATGCCAAGTCCATAATGCTGATGTCAAAGgtatggttct ... gaacatgcagGTTGAGAATCAAGAGGGAGTAGCTAACTTTGATGATATCCTGGCAAACTCTGATGCTTTTATGGTGGCAAGAGGTGATTTAGGAATGGAAATTCCTATAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 178

TGACATGATTGCCTTGTCATTTGTTCGGAAGGGTTCGGATCTTGTGGAGGTTAGGAAGGTACTTGGTGAGCATGCCAAGTCCATAATGCTGATGTCAAAGgtatggttct ... gaacatgcagGTTGAGAATCAAGAGGGAGTAGCTAACTTTGATGATATCCTGGCAAACTCTGATGCTTTTATGGTGGCAAGAGGTGATTTAGGAATGGAAATTCCTATAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 156

TGACATGATTGCCTTGTCATTTGTTCGGAAGGGTTCGGATCTTGTGGAGGTTAGGAAGGTACTTGGTGAGCATGCCAAGTCCATAATGCTGATGTCAAAGgtatggttct ... gaacatgcagGTTGAGAATCAAGAGGGAGTAGCTAACTTTGATGATATCCTGGCAAACTCTGATGCTTTTATGGTGGCAAGAGGTGATTTAGGAATGGAAATTCCTATAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 253

TGACATGATTGCCTTGTCATTTGTTCGGAAGGGTTCGGATCTTGTGGAGGTTAGGAAGGTACTTGGTGAGCATGCCAAGTCCATAATGCTGATGTCAAAGgtatggttct ... gaacatgcagGTTGAGAATCAAGAGGGAGTAGCTAACTTTGATGATATCCTGGCAAACTCTGATGCTTTTATGGTGGCAAGAGGTGATTTAGGAATGGAAATTCCTATAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGACATGATTGCCTTGTCATTTGTTCGGAAGGGTTCGGATCTTGTGGAGGTTAGGAAGGTACTTGGTGAGCATGCCAAGTCCATAATGCTGATGTCAAAGgtatggttctagcattttcttttgggtttcaaactagtagattttcaaattcaaggttataattgttttgaacatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT