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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcgccctctaccttcctctggcgccgcgtagttgcctaattgcaattcgtgcagcgtagtgggctcgtggtgatcaattccgtcgcattgtgggtgactgggtggcccgcatacgagggtttctgacttctgcgtgcttttcaagTGATTAAGCTGTGGTCGGGCGGGAGTAGCTCCAATGGCAGCGCACCGATATGGAAGTACTGGGGCGTCAGCGTCACCAATACCATCGGGCCGACCATGGG

Basic information

species Zea mays
transcript GRMZM2G176029_T01
intron # 2
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|78118465|gb|DV536850.1|DV536850
EST:     GTTCCTCAACTTCGCGCAGAACGTCATCTGCTTCGTCTGGTCCTTCATAA                         TGATTAAGCTGTGGTCGGGCGGGAGTAGCTCCAATGGCAGCGCACCGATAT
genomic: GTTCCTCAACTTCGCGCAGAACGTCATCTGCTTCGTCTGGTCCTTCATAAgtgagcgccc ... gcttttcaagTGATTAAGCTGTGGTCGGGCGGGAGTAGCTCCAATGGCAGCGCACCGATAT
EST: gi|211352183|gb|FL343466.1|FL343466
EST:     GTTCCTCAACTTCGCGCAGAACGTCATCTGCTTCGTCTGGTCCTTCATAA                         TGATTAAGCTGTGGTCGGGCGGGAGTAGCTCCAATGGCAGCGCACCGATAT
genomic: GTTCCTCAACTTCGCGCAGAACGTCATCTGCTTCGTCTGGTCCTTCATAAgtgagcgccc ... gcttttcaagTGATTAAGCTGTGGTCGGGCGGGAGTAGCTCCAATGGCAGCGCACCGATAT
EST: gi|148931883|gb|EC877348.2|EC877348
EST:     GTTCCTCAACTTCGCGCAGAACGTCATCTGCTTCGTCTGGTCCTTCATAA                         TGATTAAGCTGTGGTCGGGCGGGAGTAGCTCCAATGGCAGCGCACCGATAT
genomic: GTTCCTCAACTTCGCGCAGAACGTCATCTGCTTCGTCTGGTCCTTCATAAgtgagcgccc ... gcttttcaagTGATTAAGCTGTGGTCGGGCGGGAGTAGCTCCAATGGCAGCGCACCGATAT
EST: gi|149005383|gb|EE039935.2|EE039935
EST:     GTTCCTCAACTTCGCGCAGAACGTCATCTGCTTCGTCTGGTCCTTCATAA                         TGATTAAGCTGTGGTCGGGCGGGAGTAGCTCCAATGGCAGCGCACCGATAT
genomic: GTTCCTCAACTTCGCGCAGAACGTCATCTGCTTCGTCTGGTCCTTCATAAgtgagcgccc ... gcttttcaagTGATTAAGCTGTGGTCGGGCGGGAGTAGCTCCAATGGCAGCGCACCGATAT
EST: gi|211432973|gb|FL347888.1|FL347888
EST:     GTTCCTCAACTTCGCGCAGAACGTCATCTGCTTCGTCTGGTCCTTCATAA                         TGATTAAGCTGTGGTCGGGCGGGAGTAGCTCCAATGGCAGCGCACCGATAT
genomic: GTTCCTCAACTTCGCGCAGAACGTCATCTGCTTCGTCTGGTCCTTCATAAgtgagcgccc ... gcttttcaagTGATTAAGCTGTGGTCGGGCGGGAGTAGCTCCAATGGCAGCGCACCGATAT
EST: gi|211053272|gb|FL359434.1|FL359434
EST:     GTTCCTCAACTTCGCGCAGAACGTCATCTGCTTCGTCTGGTCCTTCATAA                         TGATTAAGCTGTGGTCGGGCGGGAGTAGCTCCAATGGCAGCGCACCGATAT
genomic: GTTCCTCAACTTCGCGCAGAACGTCATCTGCTTCGTCTGGTCCTTCATAAgtgagcgccc ... gcttttcaagTGATTAAGCTGTGGTCGGGCGGGAGTAGCTCCAATGGCAGCGCACCGATAT
EST: gi|148977669|gb|EE026096.2|EE026096
EST:     GTTCCTCAACTTCGCGCAGAACGTCATCTGCTTCGTCTGGTCCTTCATAA                         TGATTAAGCTGTGGTCGGGCGGGAGTAGCTCCAATGGCAGCGCACCGATAT
genomic: GTTCCTCAACTTCGCGCAGAACGTCATCTGCTTCGTCTGGTCCTTCATAAgtgagcgccc ... gcttttcaagTGATTAAGCTGTGGTCGGGCGGGAGTAGCTCCAATGGCAGCGCACCGATAT
EST: gi|78080957|gb|DV509369.1|DV509369
EST:     GTTCCTCAACTTCGCGCAGAACGTCATCTGCTTCGTCTGGTCCTTCATAA                         TGATTAAGCTGTGGTCGGGCGGGAGTAGCTCCAATGGCAGCGCACCGATAT
genomic: GTTCCTCAACTTCGCGCAGAACGTCATCTGCTTCGTCTGGTCCTTCATAAgtgagcgccc ... gcttttcaagTGATTAAGCTGTGGTCGGGCGGGAGTAGCTCCAATGGCAGCGCACCGATAT
EST: gi|148985614|gb|EE029715.2|EE029715
EST:     GTTCCTCAACTTCGCGCAGAACGTCATCTGCTTCGTCTGGTCCTTCATAA                         TGATTAAGCTGTGGTCGGGCGGGAGTAGCTCCAATGGCAGCGCACCGATAT
genomic: GTTCCTCAACTTCGCGCAGAACGTCATCTGCTTCGTCTGGTCCTTCATAAgtgagcgccc ... gcttttcaagTGATTAAGCTGTGGTCGGGCGGGAGTAGCTCCAATGGCAGCGCACCGATAT
EST: gi|211537618|gb|FL330685.1|FL330685
EST:     GTTCCTCAACTTCGCGCAGAACGTCATCTGCTTCGTCTGGTCCTTCATAA                         TGATTAAGCTGTGGTCGGGCGGGAGTAGCTCCAATGGCAGCGCACCGATAT
genomic: GTTCCTCAACTTCGCGCAGAACGTCATCTGCTTCGTCTGGTCCTTCATAAgtgagcgccc ... gcttttcaagTGATTAAGCTGTGGTCGGGCGGGAGTAGCTCCAATGGCAGCGCACCGATAT
EST: gi|211335766|gb|FL352927.1|FL352927
EST:     GTTCCTCAACTTCGCGCAGAACGTCATCTGCTTCGTCTGGTCCTTCATAA                         TTGATTAAGCTGTGGTCGGGCGGGAGTAGCT
genomic: GTTCCTCAACTTCGCGCAGAACGTCATCTGCTTCGTCTGGTCCTTCATAAgtgagcgccc ... gcttttcaagT-GATTAAGCTGTGGTCGGGCGGGAGTAGCT
EST: gi|94479889|gb|EB708847.1|EB708847
EST:     GTTCCTCAACTTCGCGCAGAACGTCATCTGCTTCGTCTGGTCCTTCATAA                         TGATTAAGCTGTGGTCGGGCGGGAGTAGCTCCAATGGCAGCGCACCGATAT
genomic: GTTCCTCAACTTCGCGCAGAACGTCATCTGCTTCGTCTGGTCCTTCATAAgtgagcgccc ... gcttttcaagTGATTAAGCTGTGGTCGGGCGGGAGTAGCTCCAATGGCAGCGCACCGATAT
EST: gi|50324993|gb|CO520119.1|CO520119
EST:     GTTCCTCAACTTCGCGCAGAACGTCATCTGCTTCGTCTGGTCCTTCATAA                         TGATTAAGCTGTGGTCGGGCGGGAGTAGCTCCAATGGCAGCGCACCGATAT
genomic: GTTCCTCAACTTCGCGCAGAACGTCATCTGCTTCGTCTGGTCCTTCATAAgtgagcgccc ... gcttttcaagTGATTAAGCTGTGGTCGGGCGGGAGTAGCTCCAATGGCAGCGCACCGATAT
EST: gi|74234865|gb|DT642779.1|DT642779
EST:     GTTCCTCAACTTCGCGCAGAACGTCATCTGCTTCGTCTGGTCCTTCATAA                         TGATTAAGCTGTGGTCGGGCGGGAGTAGCTCCAATGGCAGCGCACCGATAT
genomic: GTTCCTCAACTTCGCGCAGAACGTCATCTGCTTCGTCTGGTCCTTCATAAgtgagcgccc ... gcttttcaagTGATTAAGCTGTGGTCGGGCGGGAGTAGCTCCAATGGCAGCGCACCGATAT
EST: gi|148953372|gb|EE152866.2|EE152866
EST:     GTTCCTCAACTTCGCGCAGAACGTCATCTGCTTCGTCTGGTCCTTCATAA                         TGATTAAGCTGTGGTCGGGCGGGAGTAGCTCCAATGGCAGCGCACCGATAT
genomic: GTTCCTCAACTTCGCGCAGAACGTCATCTGCTTCGTCTGGTCCTTCATAAgtgagcgccc ... gcttttcaagTGATTAAGCTGTGGTCGGGCGGGAGTAGCTCCAATGGCAGCGCACCGATAT
EST: gi|211189091|gb|FL366154.1|FL366154
EST:     GTTCCTCAACTTCGCGCAGAACGTCATCTGCTTCGTCTGGTCCTTCATAA                         TGATTAAGCTGTGGTCGGGCGGGAGTAGCTCCAATGGCAGCGCACCGATAT
genomic: GTTCCTCAACTTCGCGCAGAACGTCATCTGCTTCGTCTGGTCCTTCATAAgtgagcgccc ... gcttttcaagTGATTAAGCTGTGGTCGGGCGGGAGTAGCTCCAATGGCAGCGCACCGATAT
EST: gi|211523327|gb|FL357648.1|FL357648
EST:     GTTCCTCAACTTCGCGCAGAACGTCATCTGCTTCGTCTGGTCCTTCATAA                         TGATTAAGCTGTGGTCGGGCGGGAGTAGCTCCAATGGCAGCGCACCGATAT
genomic: GTTCCTCAACTTCGCGCAGAACGTCATCTGCTTCGTCTGGTCCTTCATAAgtgagcgccc ... gcttttcaagTGATTAAGCTGTGGTCGGGCGGGAGTAGCTCCAATGGCAGCGCACCGATAT
EST: gi|78107092|gb|DV525510.1|DV525510
EST:     GTTCCTCAACTTCGCGCAGAACGTCATCTGCTTCGTCTGGTCCTTCATAA                         TGATTAAGCTGTGGTCGGGCGGGAGTAGCTCCAATGGCAGCGCACCGATAT
genomic: GTTCCTCAACTTCGCGCAGAACGTCATCTGCTTCGTCTGGTCCTTCATAAgtgagcgccc ... gcttttcaagTGATTAAGCTGTGGTCGGGCGGGAGTAGCTCCAATGGCAGCGCACCGATAT
EST: gi|211190516|gb|FL321614.1|FL321614
EST:     GTTCCTCAACTTCGCGCAGAACGTCATCTGCTTCGTCTGGTCCTTCATAA                         TGATTAAGCTGTGGTCGGGCGGGAGTAGCTCCAATGGCAGCGCACCGATAT
genomic: GTTCCTCAACTTCGCGCAGAACGTCATCTGCTTCGTCTGGTCCTTCATAAgtgagcgccc ... gcttttcaagTGATTAAGCTGTGGTCGGGCGGGAGTAGCTCCAATGGCAGCGCACCGATAT
EST: gi|71318369|gb|DR795946.1|DR795946
EST:     GTTCCTCAACTTCGCGCAGAACGTCATCTGCTTCGTCTGGTCCTTCATAA                         TGATTAAGCTGTGGTCGGGCGGGAGTAGCTCCAATGGCAGCGCACCGATAT
genomic: GTTCCTCAACTTCGCGCAGAACGTCATCTGCTTCGTCTGGTCCTTCATAAgtgagcgccc ... gcttttcaagTGATTAAGCTGTGGTCGGGCGGGAGTAGCTCCAATGGCAGCGCACCGATAT
EST: gi|71440454|gb|DR821504.1|DR821504
EST:     GTTCCTCAACTTCGCGCAGAACGTCATCTGCTTCGTCTGGTCCTTCATAA                         TGATTAAGCTGTGGTCGGGCGGGAGTAGCTCCAATGGCAGCGCACCGATAT
genomic: GTTCCTCAACTTCGCGCAGAACGTCATCTGCTTCGTCTGGTCCTTCATAAgtgagcgccc ... gcttttcaagTGATTAAGCTGTGGTCGGGCGGGAGTAGCTCCAATGGCAGCGCACCGATAT
EST: gi|101390801|gb|EB817335.1|EB817335
EST:     TTCCTCAACTTCGCGCAGAACGTCCATCTGCTTCGTCTGGTCCTTCATAA                         TGATTAAGCTGTGGTCGGGCGGGAGTAGCTCCAATGGCAGCGCACCCGATA
genomic: TTCCTCAACTTCGCGCAGAACGTC-ATCTGCTTCGTCTGGTCCTTCATAAgtgagcgccc ... gcttttcaagTGATTAAGCTGTGGTCGGGCGGGAGTAGCTCCAATGGCAGCGCACC-GATA

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: 283

ATCGACGAAGCGGTTCGGGCCGGATGCGCGGCGGTTCGAGCACCTCGCGTTCCTCAACTTCGCGCAGAACGTCATCTGCTTCGTCTGGTCCTTCATAAgtgagcgccc ... gcttttcaagTGATTAAGCTGTGGTCGGGCGGGAGTAGCTCCAATGGCAGCGCACCGATATGGAAGTACTGGGGCGTCAGCGTCACCAATACCATCGGGCCGACCATGGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 232

ATCGACGAAGCGGTTCGGGCCGGATGCGCGGCGGTTCGAGCACCTCGCGTTCCTCAACTTCGCGCAGAACGTCATCTGCTTCGTCTGGTCCTTCATAAgtgagcgccc ... gcttttcaagTGATTAAGCTGTGGTCGGGCGGGAGTAGCTCCAATGGCAGCGCACCGATATGGAAGTACTGGGGCGTCAGCGTCACCAATACCATCGGGCCGACCATGGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 305

ATCGACGAAGCGGTTCGGGCCGGATGCGCGGCGGTTCGAGCACCTCGCGTTCCTCAACTTCGCGCAGAACGTCATCTGCTTCGTCTGGTCCTTCATAAgtgagcgccc ... gcttttcaagTGATTAAGCTGTGGTCGGGCGGGAGTAGCTCCAATGGCAGCGCACCGATATGGAAGTACTGGGGCGTCAGCGTCACCAATACCATCGGGCCGACCATGGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 883

ATCGACGAAGCGGTTCGGGCCGGATGCGCGGCGGTTCGAGCACCTCGCGTTCCTCAACTTCGCGCAGAACGTCATCTGCTTCGTCTGGTCCTTCATAAgtgagcgccc ... gcttttcaagTGATTAAGCTGTGGTCGGGCGGGAGTAGCTCCAATGGCAGCGCACCGATATGGAAGTACTGGGGCGTCAGCGTCACCAATACCATCGGGCCGACCATGGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgggtgactgggtggcccgcatacgagggtttctgacttctgcgtgcttttcaagTGATTAAGCTGTGGTCGGGCGGGAGTAGCTCCAATGGCAGCGCACCGATATGGAAGTACTGGGGCGTCAGCGTCACCAATACCATCGGGCCGACCATGGG
                              ttctgac  putative branch site (score: 883)
                                            tgcttttc  putative PPT
                                               ttttcaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagcgccctctaccttcctctggcgccgcgtagttgcctaattgcaattcgtgcagcgtagtgggctcgtggtgatcaattccgtcgcattgtgggtgactgggtggcccgcatacgagggtttctgacttctgcgtgcttttcaagTGATTAAGCTGTGGTCGGGCGGGAGTAGCTCCAATGGCAGCGCACCGATATGGAAGTACTGGGGCGTCAGCGTCACCAATACCATCGGGCCGACCATGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG