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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGCATGCTGTTTGATGTACCGTGGCGACGTTGTTCCAAAAGATGTGAATGCTGCTGTCCATTCAATCAAGACCAAGAGAGCAGTGCAGTTTGTTGATTGgtatatgctcacaactcttaccaagttatatcagattatagattgtaatcttccactgaaaagatagctgcgcgagacatgaatgtctttctctgctgtctcatgcacag

Basic information

species Zea mays
transcript GRMZM2G051782_T01
intron # 4
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|32844161|gb|CD983842.1|CD983842
EST:     GCTGCTGTCCATTCAATCAAGACCAAGAGAGCAGTGCAGTTTGTTGATTG                         GTGCCCTACTGGTTTCAAGTGTGGGATAAACTACCAACCACCAACTGTAGT
genomic: GCTGCTGTCCATTCAATCAAGACCAAGAGAGCAGTGCAGTTTGTTGATTGgtatatgctc ... tcatgcacagGTGCCCTACTGGTTTCAAGTGTGGGATAAACTACCAACCACCAACTGTAGT
EST: gi|88750800|gb|DY534941.1|DY534941
EST:     GCTGCTGTCCATTCAATCAAGACCAAGAGAGCAGTGCAGTTTGTTGATTG                         GTGCCCTACTGGTTTCAAGTGTGGGATAAACTACCAACCACCAACTGTAGT
genomic: GCTGCTGTCCATTCAATCAAGACCAAGAGAGCAGTGCAGTTTGTTGATTGgtatatgctc ... tcatgcacagGTGCCCTACTGGTTTCAAGTGTGGGATAAACTACCAACCACCAACTGTAGT
EST: gi|16380124|gb|BI993333.1|BI993333
EST:     AGTTTGTTGATTG                         GTGCCCTACTGGTTTCAAGTGTGGGATAAACTACCAACCACCAACTGTAGT
genomic: AGTTTGTTGATTGgtatatgctc ... tcatgcacagGTGCCCTACTGGTTTCAAGTGTGGGATAAACTACCAACCACCAACTGTAGT
EST: gi|6760492|gb|AW324651.1|AW324651
EST:     GCTGCTGTCCATTCAATCAAGACCAAGAGAGCGGTGCAGTTTGTTGATTG                         GTGCCCTACTGGTTTCAAGTGTGGGATAAACTACCAACCACCAACTGTAGT
genomic: GCTGCTGTCCATTCAATCAAGACCAAGAGAGCAGTGCAGTTTGTTGATTGgtatatgctc ... tcatgcacagGTGCCCTACTGGTTTCAAGTGTGGGATAAACTACCAACCACCAACTGTAGT
EST: gi|33104189|gb|CF064149.1|CF064149
EST:     GCTGCTGTCCATTCAATCAAGACCAAGAGAGCAGTGCAGTTTGTTGATTG                         GTGCCCTACTGGTTTCAAGTGTGGGATAAATTACCAACCACCAACTGTAGT
genomic: GCTGCTGTCCATTCAATCAAGACCAAGAGAGCAGTGCAGTTTGTTGATTGgtatatgctc ... tcatgcacagGTGCCCTACTGGTTTCAAGTGTGGGATAAACTACCAACCACCAACTGTAGT
EST: gi|32845637|gb|CD985318.1|CD985318
EST:     GCTGCTGTCCATTCAATCAAGACCAAGAGAGCAGTGCAGTTTGTTGATTG                         GTGCCCTACTGGTTTCAAGTGTGGGATAAACTACCAACCACCAACTGTAGT
genomic: GCTGCTGTCCATTCAATCAAGACCAAGAGAGCAGTGCAGTTTGTTGATTGgtatatgctc ... tcatgcacagGTGCCCTACTGGTTTCAAGTGTGGGATAAACTACCAACCACCAACTGTAGT
EST: gi|33103375|gb|CF063335.1|CF063335
EST:     GCTGCTGTCCATTCAATCAAGACCAAGAGAGCAGTGCAGTTTGTTGATTG                         GTGCCCTACTGGTTTCAAGTGTGGGATAAATTACCAACCACCAACTGTGGT
genomic: GCTGCTGTCCATTCAATCAAGACCAAGAGAGCAGTGCAGTTTGTTGATTGgtatatgctc ... tcatgcacagGTGCCCTACTGGTTTCAAGTGTGGGATAAACTACCAACCACCAACTGTAGT
EST: gi|32843933|gb|CD983614.1|CD983614
EST:     GCTGCTGTCCATTCAATCAAGACCAAGAGAGCAGTGCAGTTTGTTGATTG                         GTGCCCTACTGGTTTCAAGTGTGGGATAAACTACCAACCACCAACTGTAGT
genomic: GCTGCTGTCCATTCAATCAAGACCAAGAGAGCAGTGCAGTTTGTTGATTGgtatatgctc ... tcatgcacagGTGCCCTACTGGTTTCAAGTGTGGGATAAACTACCAACCACCAACTGTAGT
EST: gi|13558368|gb|BG549724.1|BG549724
EST:     GCTGCTGTCCATTCAATCAAGACCAAGAGAGCAGTGCAGTTTGTTGATTG                         GTGCCCTACTGGTTTCAAGTGTGGGATAAGCTACCAACCACCAACTGTAGT
genomic: GCTGCTGTCCATTCAATCAAGACCAAGAGAGCAGTGCAGTTTGTTGATTGgtatatgctc ... tcatgcacagGTGCCCTACTGGTTTCAAGTGTGGGATAAACTACCAACCACCAACTGTAGT
EST: gi|211453319|gb|FL456387.1|FL456387
EST:     GCTGCTGTCCATTCAATCAAGACCAAGAGAGCAGTGCAGTTTGTTGATTG                         GTGCCCTACTGGTTTCAAGTGTGGGATAAACTACCAACCACCAACTGTAGT
genomic: GCTGCTGTCCATTCAATCAAGACCAAGAGAGCAGTGCAGTTTGTTGATTGgtatatgctc ... tcatgcacagGTGCCCTACTGGTTTCAAGTGTGGGATAAACTACCAACCACCAACTGTAGT
EST: gi|32844121|gb|CD983802.1|CD983802
EST:     GCTGCTGTCCATTCAATCAAGACCAAGAGAGCAGTGCAGTTTGTTGATTG                         GTGCCCTACTGGTTTCAAGTGTGGGATAAACTACCAACCACCAACTGTAGT
genomic: GCTGCTGTCCATTCAATCAAGACCAAGAGAGCAGTGCAGTTTGTTGATTGgtatatgctc ... tcatgcacagGTGCCCTACTGGTTTCAAGTGTGGGATAAACTACCAACCACCAACTGTAGT
EST: gi|32845237|gb|CD984918.1|CD984918
EST:     GCTGCTGTCCATTCAATCAAGACCAAGAGAGCAGTGCAGTTTGTTGATTG                         GTGCCCTACTGGTTTCAAGTGTGGGATAAACTACCAACCACCAACTGTAGT
genomic: GCTGCTGTCCATTCAATCAAGACCAAGAGAGCAGTGCAGTTTGTTGATTGgtatatgctc ... tcatgcacagGTGCCCTACTGGTTTCAAGTGTGGGATAAACTACCAACCACCAACTGTAGT
EST: gi|116814638|gb|EC857236.1|EC857236
EST:     GCTGCTGTCCATTCAATCAAGAACAAGAGAGCAGTGCAGTTTGTTGATTG                         GTGCCCTACTGGTTTCAAGTGTGGGATAAACTACCAACCACCAACTGTAGT
genomic: GCTGCTGTCCATTCAATCAAGACCAAGAGAGCAGTGCAGTTTGTTGATTGgtatatgctc ... tcatgcacagGTGCCCTACTGGTTTCAAGTGTGGGATAAACTACCAACCACCAACTGTAGT
EST: gi|32844213|gb|CD983894.1|CD983894
EST:     GCTGCTGTCCATTCAATCAAGACCAAGAGAGCAGTGCAGTTTGTTGATTG                         GTGCCCTACTGGTTTCAAGTGTGGGATAAACTACCAACCACCAACTGTAGT
genomic: GCTGCTGTCCATTCAATCAAGACCAAGAGAGCAGTGCAGTTTGTTGATTGgtatatgctc ... tcatgcacagGTGCCCTACTGGTTTCAAGTGTGGGATAAACTACCAACCACCAACTGTAGT
EST: gi|32845568|gb|CD985249.1|CD985249
EST:     GCTGCTGTCCATTCAATCAAGACCAAGAGAGCAGTGCAGTTTGTTGATTG                         GTGCCCTACTGGTTTCAAGTGTGGGATAAACTACCAACCACCAACTGTAGT
genomic: GCTGCTGTCCATTCAATCAAGACCAAGAGAGCAGTGCAGTTTGTTGATTGgtatatgctc ... tcatgcacagGTGCCCTACTGGTTTCAAGTGTGGGATAAACTACCAACCACCAACTGTAGT
EST: gi|32844979|gb|CD984660.1|CD984660
EST:     GCTGCTGTCCATTCAATCAAGACCAAGAGAGCAGTGCAGTTTGTTGATTG                         GTGCCCTACTGGTTTCAAGTGTGGGATAAACTACCAACCACCAACTGTAGT
genomic: GCTGCTGTCCATTCAATCAAGACCAAGAGAGCAGTGCAGTTTGTTGATTGgtatatgctc ... tcatgcacagGTGCCCTACTGGTTTCAAGTGTGGGATAAACTACCAACCACCAACTGTAGT

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), 24 (downstream exon)
Score: 4

TGGCATGCTGTTTGATGTACCGTGGCGACGTTGTTCCAAAAGATGTGAATGCTGCTGTCCATTCAATCAAGACCAAGAGAGCAGTGCAGTTTGTTGATTGgtatatgctc ... tcatgcacagGTGCCCTACTGGTTTCAAGTGTGGGATAAACTACCAACCACCAACTGTAGTCCCTGGAGGGGACCTGGCCAAGGTGCAACGAGCAGTCTGCATGATCAGC


Block sizes: 49 (upstream exon), 42 (downstream exon)
Score: 79

TGGCATGCTGTTTGATGTACCGTGGCGACGTTGTTCCAAAAGATGTGAATGCTGCTGTCCATTCAATCAAGACCAAGAGAGCAGTGCAGTTTGTTGATTGgtatatgctc ... tcatgcacagGTGCCCTACTGGTTTCAAGTGTGGGATAAACTACCAACCACCAACTGTAGTCCCTGGAGGGGACCTGGCCAAGGTGCAACGAGCAGTCTGCATGATCAGC


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 134

TGGCATGCTGTTTGATGTACCGTGGCGACGTTGTTCCAAAAGATGTGAATGCTGCTGTCCATTCAATCAAGACCAAGAGAGCAGTGCAGTTTGTTGATTGgtatatgctc ... tcatgcacagGTGCCCTACTGGTTTCAAGTGTGGGATAAACTACCAACCACCAACTGTAGTCCCTGGAGGGGACCTGGCCAAGGTGCAACGAGCAGTCTGCATGATCAGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 54

TGGCATGCTGTTTGATGTACCGTGGCGACGTTGTTCCAAAAGATGTGAATGCTGCTGTCCATTCAATCAAGACCAAGAGAGCAGTGCAGTTTGTTGATTGgtatatgctc ... tcatgcacagGTGCCCTACTGGTTTCAAGTGTGGGATAAACTACCAACCACCAACTGTAGTCCCTGGAGGGGACCTGGCCAAGGTGCAACGAGCAGTCTGCATGATCAGC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGCATGCTGTTTGATGTACCGTGGCGACGTTGTTCCAAAAGATGTGAATGCTGCTGTCCATTCAATCAAGACCAAGAGAGCAGTGCAGTTTGTTGATTGgtatatgctcacaactcttaccaagttatatcagattatagattgtaatcttccactgaaaagatagctgcgcgagacatgaatgtctttctctgctgtctcatgcacag

- - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG