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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCGAGAAAATGCTCATTAGCATGGTGGAAACTGAACTGGAGAAGAGAAAGGCAGAGGGGAGATACTCTGCACATTTCAGAGGGCAAGCTCATTTCTTTGGgtaagcattaatttttgcattttgtgaactgagcaataatttggttggtagtttcccactgaggaggccacccctgagaattggtttcagggagtttcct...

Basic information

species Zea mays
transcript GRMZM2G059151_T01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G059151_T01 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os06g13810.1 (Oryza sativa), 5'ss of exon 11
CCGAGAAAATGCTCATTAGCATGGTGGAAACTGAACTGGAGAAGAGAAAGGCAGAGGGGAGATACTCTGCACATTTCAGAGGGCAAGCTCATTTCTTTGGgtaagcattaatttttgcattttgtgaactgagcaataatttggttggtagt-ttcccactgaggaggccacccctgagaattggtttcagggagtttcct
| ||||||||||| ||| |||||| || |||||| ||||||||||||| || ||||||| ||| | |||||||||||||| ||| |||| ||||||||||| | || |||| ||||||||| || ||||||| | || | | ||| | | |
CAGAGAAAATGCTTATTGCCATGGTTGAGACTGAATTGGAGAAGAGAAAAGCTGAGGGGAAGTACCCCGCACATTTCAGAGGCCAATCTCACTTCTTTGGgtatgtatgaattgttgcattttccaaa----aaaataattccatctctaatgctgttgctgtgtaattttgcag--------------------------
















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|67015202|gb|CO443951.1|CO443951
EST:     GCAGAGGGGAGATACTCTGCACATTTCAGAGGGCAAGCTCATTTCTTTGG                         GTACGAAGGAAGATGCGGCCTTCCTACTAATTTTGATTCTAATTATTGCTA
genomic: GCAGAGGGGAGATACTCTGCACATTTCAGAGGGCAAGCTCATTTCTTTGGgtaagcatta ... ctatttgcagGTACGAAGGAAGATGCGGCCTTCCTACTAATTTTGATTCTAACTATTGCTA
EST: gi|32826654|gb|CD966332.1|CD966332
EST:     GCAGAGGGGAGATACTCTGCACATTTCAGAGGGCAAGCTCATTTCTTTGG                         ATATGAAGGAAGATGCGGCCTTCCTACTAATTTTGATTCTAACTATTGCTA
genomic: GCAGAGGGGAGATACTCTGCACATTTCAGAGGGCAAGCTCATTTCTTTGGgtaagcatta ... ctatttgcagGTACGAAGGAAGATGCGGCCTTCCTACTAATTTTGATTCTAACTATTGCTA
EST: gi|67014773|gb|CO443522.1|CO443522
EST:     GCAGAGGGGAGATACTCTGCACATTTCAGAGGGCAAGCTCATTTCTTTGG                         GTACGAAGGAAGATGCGGCCTTCCTACTAATTTTGATTCTAATTATTGCTA
genomic: GCAGAGGGGAGATACTCTGCACATTTCAGAGGGCAAGCTCATTTCTTTGGgtaagcatta ... ctatttgcagGTACGAAGGAAGATGCGGCCTTCCTACTAATTTTGATTCTAACTATTGCTA
EST: gi|67014279|gb|CO443028.1|CO443028
EST:     GCAGAGGGGAGATACTCTGCACATTTCAGAGGGCAAGCTCATTTCTTTGG                         GTACGAAGGAAGATGCGGCCTTCCTACTAATTTTGATTCTAATTATTGCTA
genomic: GCAGAGGGGAGATACTCTGCACATTTCAGAGGGCAAGCTCATTTCTTTGGgtaagcatta ... ctatttgcagGTACGAAGGAAGATGCGGCCTTCCTACTAATTTTGATTCTAACTATTGCTA
EST: gi|32801608|gb|CD953844.1|CD953844
EST:     GCAGAGGGGAGATACTCTGCACATTTCAGAGGGCAAGCTCATTTCTTTGG                         ATATGAAGGAAGATGCGGCCTTCCTACTAATTTTGATTCTAACTATTGCTA
genomic: GCAGAGGGGAGATACTCTGCACATTTCAGAGGGCAAGCTCATTTCTTTGGgtaagcatta ... ctatttgcagGTACGAAGGAAGATGCGGCCTTCCTACTAATTTTGATTCTAACTATTGCTA
EST: gi|6021533|gb|AW066461.1|AW066461
EST:     GCAGAGGGGAGATACTCTGCACATTTCAGAGGGCAAGCTCATTTCTTTGG                         GTACGAAGGAA
genomic: GCAGAGGGGAGATACTCTGCACATTTCAGAGGGCAAGCTCATTTCTTTGGgtaagcatta ... ctatttgcagGTACGAAGGAA
EST: gi|32831581|gb|CD971259.1|CD971259
EST:     GCAGAGAAGAGATACTCTGCACATTTCAGAGGGCAAGCTCATTTCTTTGG                         ATATGAAGGAAGATGCGGCCTTCCTACTAATTTTGATTCTAACTATTGCTA
genomic: GCAGAGGGGAGATACTCTGCACATTTCAGAGGGCAAGCTCATTTCTTTGGgtaagcatta ... ctatttgcagGTACGAAGGAAGATGCGGCCTTCCTACTAATTTTGATTCTAACTATTGCTA
EST: gi|32804076|gb|CD956312.1|CD956312
EST:     GCAGAGGGGAGATACTCTGCACATTTCAGAGGGCAAGCTCATTTCTTTGG                         ATATGAAGGAAGATGCGGCCTTCCTACTAATTTTGATTCTAACTATTGCTA
genomic: GCAGAGGGGAGATACTCTGCACATTTCAGAGGGCAAGCTCATTTCTTTGGgtaagcatta ... ctatttgcagGTACGAAGGAAGATGCGGCCTTCCTACTAATTTTGATTCTAACTATTGCTA
EST: gi|32795214|gb|CD947450.1|CD947450
EST:     GCAGAGGGGAGATACTCTGCACATTTCAGAGGGCAAGCTCATTTCTTTGG                         GTACGAAGGAAGATGCGGCCTTCCTACTAATTTTGATTCTAACTATTGCTA
genomic: GCAGAGGGGAGATACTCTGCACATTTCAGAGGGCAAGCTCATTTCTTTGGgtaagcatta ... ctatttgcagGTACGAAGGAAGATGCGGCCTTCCTACTAATTTTGATTCTAACTATTGCTA
EST: gi|211286470|gb|FL080391.1|FL080391
EST:     GCAGAGGGGAGATACTCTGCACATTTCAGAGGGCAAGCTCATTTCTTTGG                         GTACGAAGGAAGATGCGGCCTTCCTACTAATTTTGATTCTAACTATTGCTA
genomic: GCAGAGGGGAGATACTCTGCACATTTCAGAGGGCAAGCTCATTTCTTTGGgtaagcatta ... ctatttgcagGTACGAAGGAAGATGCGGCCTTCCTACTAATTTTGATTCTAACTATTGCTA
EST: gi|211286474|gb|FL080395.1|FL080395
EST:     GCAGAGGGGAGATACTCTGCACATTTCAGAGGGCAAGCTCATTTCTTTGG                         GTACGAAGGAAGATGCGGCCTTCCTACTAATTTTGATTCTAACTATTGCTA
genomic: GCAGAGGGGAGATACTCTGCACATTTCAGAGGGCAAGCTCATTTCTTTGGgtaagcatta ... ctatttgcagGTACGAAGGAAGATGCGGCCTTCCTACTAATTTTGATTCTAACTATTGCTA
EST: gi|31353849|gb|CD438206.1|CD438206
EST:     GCAGAGGGGAGATACTCTGCACATTTCAGAGGGCAAGCTCATTTCTTTGG                         GTACGAAGGAAGATGCGGCCTTCCTACTAATTTTGATTCTAACTATTGCTA
genomic: GCAGAGGGGAGATACTCTGCACATTTCAGAGGGCAAGCTCATTTCTTTGGgtaagcatta ... ctatttgcagGTACGAAGGAAGATGCGGCCTTCCTACTAATTTTGATTCTAACTATTGCTA
EST: gi|32804299|gb|CD956535.1|CD956535
EST:     GCAGAGGGGAGATACTCTGCACATTTCAGAGGGCAAGCTCATTTCTTTGG                         ATATGAAGGAAGATGCGGCCTTCCTACTAATTTTGATTCTAACTATTGCTA
genomic: GCAGAGGGGAGATACTCTGCACATTTCAGAGGGCAAGCTCATTTCTTTGGgtaagcatta ... ctatttgcagGTACGAAGGAAGATGCGGCCTTCCTACTAATTTTGATTCTAACTATTGCTA
EST: gi|149083928|gb|EE173305.2|EE173305
EST:     GGCAAGCTCATTTCTTTGG                         GTACGAAGGAAGATGCGGCCTTCCTACTAATTTTGATTTTAACTATTGCTA
genomic: GGCAAGCTCATTTCTTTGGgtaagcatta ... ctatttgcagGTACGAAGGAAGATGCGGCCTTCCTACTAATTTTGATTCTAACTATTGCTA
EST: gi|32801889|gb|CD954125.1|CD954125
EST:     GCAGAGGGGAGATACTCTGCACATTTCAGAGGGCAAGCTCATTTCTTTGG                         ATATGAAGGAAGATGCGGCCTTCCTACTAATTTTGATTCTAACTATTGCTA
genomic: GCAGAGGGGAGATACTCTGCACATTTCAGAGGGCAAGCTCATTTCTTTGGgtaagcatta ... ctatttgcagGTACGAAGGAAGATGCGGCCTTCCTACTAATTTTGATTCTAACTATTGCTA
EST: gi|32908579|gb|CF013392.1|CF013392
EST:     GCAGAGGGGAGATACTCTGCACATTTCAGAGGGCAAGCTCATTTCTTTGG                         ATATGAAGGAAGATGCGGCCTTCCTACTAATTTTGATTCTAACCATTGCTA
genomic: GCAGAGGGGAGATACTCTGCACATTTCAGAGGGCAAGCTCATTTCTTTGGgtaagcatta ... ctatttgcagGTACGAAGGAAGATGCGGCCTTCCTACTAATTTTGATTCTAACTATTGCTA

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), 49 (downstream exon)
Score: 392

CCGAGAAAATGCTCATTAGCATGGTGGAAACTGAACTGGAGAAGAGAAAGGCAGAGGGGAGATACTCTGCACATTTCAGAGGGCAAGCTCATTTCTTTGGgtaagcatta ... ctatttgcagGTACGAAGGAAGATGCGGCCTTCCTACTAATTTTGATTCTAACTATTGCTATGCATTAGGCTATGGCGCTGGTGCCCTTCTCCAAAGTGGGAAGACAGGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 489

CCGAGAAAATGCTCATTAGCATGGTGGAAACTGAACTGGAGAAGAGAAAGGCAGAGGGGAGATACTCTGCACATTTCAGAGGGCAAGCTCATTTCTTTGGgtaagcatta ... ctatttgcagGTACGAAGGAAGATGCGGCCTTCCTACTAATTTTGATTCTAACTATTGCTATGCATTAGGCTATGGCGCTGGTGCCCTTCTCCAAAGTGGGAAGACAGGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 304

CCGAGAAAATGCTCATTAGCATGGTGGAAACTGAACTGGAGAAGAGAAAGGCAGAGGGGAGATACTCTGCACATTTCAGAGGGCAAGCTCATTTCTTTGGgtaagcatta ... ctatttgcagGTACGAAGGAAGATGCGGCCTTCCTACTAATTTTGATTCTAACTATTGCTATGCATTAGGCTATGGCGCTGGTGCCCTTCTCCAAAGTGGGAAGACAGGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 586

CCGAGAAAATGCTCATTAGCATGGTGGAAACTGAACTGGAGAAGAGAAAGGCAGAGGGGAGATACTCTGCACATTTCAGAGGGCAAGCTCATTTCTTTGGgtaagcatta ... ctatttgcagGTACGAAGGAAGATGCGGCCTTCCTACTAATTTTGATTCTAACTATTGCTATGCATTAGGCTATGGCGCTGGTGCCCTTCTCCAAAGTGGGAAGACAGGA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCGAGAAAATGCTCATTAGCATGGTGGAAACTGAACTGGAGAAGAGAAAGGCAGAGGGGAGATACTCTGCACATTTCAGAGGGCAAGCTCATTTCTTTGGgtaagcattaatttttgcattttgtgaactgagcaataatttggttggtagtttcccactgaggaggccacccctgagaattggtttcagggagtttcct

- - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccacccc