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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attgctggattggttcagtatgcataataaaatgtgttcgtttctttattggtccatatggcagctgactaatgtttcttcttcccttgtggcctcacagAGCATTAGAGCAATTATCTTGGAGTTGCAGATCTGTACCTGAAGATTCATATTGAAATCTGGAAGCTTCTGCTGTTGAGTACAGAGAAATATTTCTTGCC

Basic information

species Zea mays
transcript GRMZM2G089466_T01
intron # 1
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|211439060|gb|FL385009.1|FL385009
EST:     TACGGGAGGGCCACTGCTGCCATCGCGTCCACCGACGAATTTCCCCACAG                         AGCATTAGAGCAATTATCTTGGAGTTGCAGATCTGTACCTGAAGATTCATA
genomic: TACGGGAGGGCCACTGCTGCCATCGCGTCCACCGACGAATTTCCCCACAGgttcagctcc ... ggcctcacagAGCATTAGAGCAATTATCTTGGAGTTGCAGATCTGTACCTGAAGATTCATA
EST: gi|211024309|gb|FL368566.1|FL368566
EST:     TACGGGAGGGCCACTGCTGCCATCGCGTCCACCGACGAATTTCCCCACAG                         AGCATTAGAGCAATTATCTTGGAGTTGCAGATCTGTACCTGAAGATTCATA
genomic: TACGGGAGGGCCACTGCTGCCATCGCGTCCACCGACGAATTTCCCCACAGgttcagctcc ... ggcctcacagAGCATTAGAGCAATTATCTTGGAGTTGCAGATCTGTACCTGAAGATTCATA
EST: gi|211117708|gb|FL407754.1|FL407754
EST:     TACGGGAGGGCCACTGCTGCCATCGCGTCCACCGACGAATTTCCCCACAG                         AGCATTAGAGCAATTATCTTGGAGTTGCAGATCTGTACCTGAAGATTCATA
genomic: TACGGGAGGGCCACTGCTGCCATCGCGTCCACCGACGAATTTCCCCACAGgttcagctcc ... ggcctcacagAGCATTAGAGCAATTATCTTGGAGTTGCAGATCTGTACCTGAAGATTCATA
EST: gi|31353406|gb|CD437763.1|CD437763
EST:     TACGGGAGGGCCACTGCTGCCATCGCGTCCACCGACGAATTTCCCCACAG                         AGCATTAGAGCAATTATCTTGGAGTTGCAGATCTGCACCTGAAGATTCATA
genomic: TACGGGAGGGCCACTGCTGCCATCGCGTCCACCGACGAATTTCCCCACAGgttcagctcc ... ggcctcacagAGCATTAGAGCAATTATCTTGGAGTTGCAGATCTGTACCTGAAGATTCATA
EST: gi|148967335|gb|EE018546.2|EE018546
EST:     TACGGGAGGGCCACTGCTGCCATCGCGTCCACCGACGAATTTCCCCACAG                         AGCATTAGAGCAATTATCTTGGAGTTGCAGATCTGTACCTGAAGATTCATA
genomic: TACGGGAGGGCCACTGCTGCCATCGCGTCCACCGACGAATTTCCCCACAGgttcagctcc ... ggcctcacagAGCATTAGAGCAATTATCTTGGAGTTGCAGATCTGTACCTGAAGATTCATA
EST: gi|76288627|gb|DV028195.1|DV028195
EST:     TACGGGAGGGCCACTGCTGCCATCGCGTCCACCGACGAATTTCCCCACAG                         AGCATTAGAGCAATTATCTTGGAGTTGCAGATCTGTACCTGAAGATTCATA
genomic: TACGGGAGGGCCACTGCTGCCATCGCGTCCACCGACGAATTTCCCCACAGgttcagctcc ... ggcctcacagAGCATTAGAGCAATTATCTTGGAGTTGCAGATCTGTACCTGAAGATTCATA
EST: gi|78082447|gb|DV510859.1|DV510859
EST:     TACGGGAGGGCCACTGCTGCCATCGCGTCCACCGACGAATTTCCCCACAG                         AGCATTAGAGCAATTATCTTGGAGTTGCAGATCTGTACCTGAAGATTCATA
genomic: TACGGGAGGGCCACTGCTGCCATCGCGTCCACCGACGAATTTCCCCACAGgttcagctcc ... ggcctcacagAGCATTAGAGCAATTATCTTGGAGTTGCAGATCTGTACCTGAAGATTCATA
EST: gi|211340947|gb|FL378190.1|FL378190
EST:     TACGGGAGGGCCACTGCTGCCATCGCGTCCACCGACGAATTTCCCCACAG                         AGCATTAGAGCAATTATCTTGGAGTTGCAGATCTGTACCTGAAGATTCATA
genomic: TACGGGAGGGCCACTGCTGCCATCGCGTCCACCGACGAATTTCCCCACAGgttcagctcc ... ggcctcacagAGCATTAGAGCAATTATCTTGGAGTTGCAGATCTGTACCTGAAGATTCATA
EST: gi|211057626|gb|FL411731.1|FL411731
EST:     TACGGGAGGGCCACTGCTGCCATCGCGTCCACCGACGAATTTCCCCACAG                         AGCATTAGAGCAATTATCTTGGAGTTGCAGATCTGTACCTGAAGATTCATA
genomic: TACGGGAGGGCCACTGCTGCCATCGCGTCCACCGACGAATTTCCCCACAGgttcagctcc ... ggcctcacagAGCATTAGAGCAATTATCTTGGAGTTGCAGATCTGTACCTGAAGATTCATA
EST: gi|5566966|gb|AI881877.1|AI881877
EST:     TACGGGAGGGCCACTGCTGCCATCGCGTCCACCGACGAATTTCCCCACAG                         AGCATTAGAGCAATTATCTTGGAGTTGCAGATCTGTACCTGAAGATTCATA
genomic: TACGGGAGGGCCACTGCTGCCATCGCGTCCACCGACGAATTTCCCCACAGgttcagctcc ... ggcctcacagAGCATTAGAGCAATTATCTTGGAGTTGCAGATCTGTACCTGAAGATTCATA
EST: gi|71449706|gb|DR830756.1|DR830756
EST:     TACGGGAGGGCCACTGCTGCCATCGCGTCCACCGACGAATTTCCCCACAG                         AGCATTAGAGCAATTATCTTGGAGTTGCAGATCTGTACCTGAAGATTCATA
genomic: TACGGGAGGGCCACTGCTGCCATCGCGTCCACCGACGAATTTCCCCACAGgttcagctcc ... ggcctcacagAGCATTAGAGCAATTATCTTGGAGTTGCAGATCTGTACCTGAAGATTCATA
EST: gi|149111397|gb|EE294900.2|EE294900
EST:     TACGGGAGGGCCACTGCTGCCATCGCGTCCACCGACGAATTTCCCCACAG                         AGCATTAGAGCAATTATCTTGGAGTTGCAGATCTGTACCTGAAGATTCATA
genomic: TACGGGAGGGCCACTGCTGCCATCGCGTCCACCGACGAATTTCCCCACAGgttcagctcc ... ggcctcacagAGCATTAGAGCAATTATCTTGGAGTTGCAGATCTGTACCTGAAGATTCATA
EST: gi|148998320|gb|EE035991.2|EE035991
EST:     TACGGGAGGGCCACTGCTGCCATCGCGTCCACCGACGAATTTCCCCACAG                         AGCATTAGAGCAATTATCTTGGAGTTGCAGATCTGTACCTGAAGATTCATA
genomic: TACGGGAGGGCCACTGCTGCCATCGCGTCCACCGACGAATTTCCCCACAGgttcagctcc ... ggcctcacagAGCATTAGAGCAATTATCTTGGAGTTGCAGATCTGTACCTGAAGATTCATA
EST: gi|211037705|gb|FL424825.1|FL424825
EST:     TACGGGAGGGCCACTGCTGCCATCGCGTCCACCGACGAATTTCCCCACAG                         AGCATTAGAGCAATTATCTTGGAGTTGCAGATCTGTACCTGAAGATTCATA
genomic: TACGGGAGGGCCACTGCTGCCATCGCGTCCACCGACGAATTTCCCCACAGgttcagctcc ... ggcctcacagAGCATTAGAGCAATTATCTTGGAGTTGCAGATCTGTACCTGAAGATTCATA
EST: gi|93013214|gb|EB638734.1|EB638734
EST:     TACGGGAGGGCCACTGCTGCCATCGCGTCCACCGACGAATTTCCCCACAG                         AGCATTAGAGCAATTATCTTGGAGTTGCAGATCTGTACCTGAAGATTCATA
genomic: TACGGGAGGGCCACTGCTGCCATCGCGTCCACCGACGAATTTCCCCACAGgttcagctcc ... ggcctcacagAGCATTAGAGCAATTATCTTGGAGTTGCAGATCTGTACCTGAAGATTCATA
EST: gi|31349188|gb|CD433545.1|CD433545
EST:     TACGGGAGGGCCACTGCTGCCATCGCGTCCACCGACGAATTTCCCCACTT                         AGTATTAGAGCAATTATCTTGGAGTTGCAGATCTGCACCTGAAGATTCATA
genomic: TACGGGAGGGCCACTGCTGCCATCGCGTCCACCGACGAATTTCCCCACAGgttcagctcc ... ggcctcacagAGCATTAGAGCAATTATCTTGGAGTTGCAGATCTGTACCTGAAGATTCATA
EST: gi|211508912|gb|FL388477.1|FL388477
EST:     TACGGGAGGGCCACTGCTGCCATCGCGTCCACCGACGAATTTCCCCACAG                         AGCATTAGAGCAATTATCTTGGAGTTGCAGATCTGTACCTGAAGATTCATA
genomic: TACGGGAGGGCCACTGCTGCCATCGCGTCCACCGACGAATTTCCCCACAGgttcagctcc ... ggcctcacagAGCATTAGAGCAATTATCTTGGAGTTGCAGATCTGTACCTGAAGATTCATA
EST: gi|67029501|gb|CO458250.1|CO458250
EST:     TACGGGAGGGCCACTGCTGCCATCGCGTCCACCGACGAATTTCCCCACAG                         AGCATTAGAGCAATTATCTTGGAGTTGCAGATCTGCACCTGAAGATTCATA
genomic: TACGGGAGGGCCACTGCTGCCATCGCGTCCACCGACGAATTTCCCCACAGgttcagctcc ... ggcctcacagAGCATTAGAGCAATTATCTTGGAGTTGCAGATCTGTACCTGAAGATTCATA
EST: gi|211317787|gb|FL422357.1|FL422357
EST:     TACGGGAGGGCCACTGCTGCCATCGCGTCCACCGACGAATTTCCCCACAG                         AGCATTAGAGCAATTATCTTGGAGTTGCAGATCTGTACCTGAAGATTCATA
genomic: TACGGGAGGGCCACTGCTGCCATCGCGTCCACCGACGAATTTCCCCACAGgttcagctcc ... ggcctcacagAGCATTAGAGCAATTATCTTGGAGTTGCAGATCTGTACCTGAAGATTCATA
EST: gi|211445224|gb|FL373038.1|FL373038
EST:     TACGGGAGGGCCACTGCTGCCATCGCGTCCACCGACGAATTTCCCCACAG                         AGCATTAGAGCAATTATCTTGGAGTTGCAGATCTGTACCTGAAGATTCATA
genomic: TACGGGAGGGCCACTGCTGCCATCGCGTCCACCGACGAATTTCCCCACAGgttcagctcc ... ggcctcacagAGCATTAGAGCAATTATCTTGGAGTTGCAGATCTGTACCTGAAGATTCATA
EST: gi|78081436|gb|DV509848.1|DV509848
EST:     TACGGGAGGGCCACTGCTGCCATCGCGTCCACCGACGAATTTCCCCACAG                         AGCATTAGAGCAATTATCTTGGAGTTGCAGATCTGTACCTGAAGATTCATA
genomic: TACGGGAGGGCCACTGCTGCCATCGCGTCCACCGACGAATTTCCCCACAGgttcagctcc ... ggcctcacagAGCATTAGAGCAATTATCTTGGAGTTGCAGATCTGTACCTGAAGATTCATA
EST: gi|211352942|gb|FL378258.1|FL378258
EST:     TACGGGAGGGCCACTGCTGCCATCGCGTCCACCGACGAATTTCCCCACAG                         AGCATTAGAGCAATTATCTTGGAGTTGCAGATCTGTACCTGAAGATTCATA
genomic: TACGGGAGGGCCACTGCTGCCATCGCGTCCACCGACGAATTTCCCCACAGgttcagctcc ... ggcctcacagAGCATTAGAGCAATTATCTTGGAGTTGCAGATCTGTACCTGAAGATTCATA
EST: gi|149084661|gb|EE174145.2|EE174145
EST:     TACGGGAGGGCCACTGCTGCCATCGCGTCCACCGACGAATTTCCCCACAG                         AGCATTAGAGCAATTATCTTGGAGTTGCAGATCTGTACCTGAAGATTCATA
genomic: TACGGGAGGGCCACTGCTGCCATCGCGTCCACCGACGAATTTCCCCACAGgttcagctcc ... ggcctcacagAGCATTAGAGCAATTATCTTGGAGTTGCAGATCTGTACCTGAAGATTCATA
EST: gi|22490974|gb|BU050897.1|BU050897
EST:     TACGGGAGGGCCACTGCTGCCATCGCGTCCACCGACGAATTTCCCCACAG                         AGCATTAGAGCAATTATCTTGGAGTTGCAGATCTGTACCTGAAGATTCATA
genomic: TACGGGAGGGCCACTGCTGCCATCGCGTCCACCGACGAATTTCCCCACAGgttcagctcc ... ggcctcacagAGCATTAGAGCAATTATCTTGGAGTTGCAGATCTGTACCTGAAGATTCATA
EST: gi|149090590|gb|EE179903.2|EE179903
EST:     TACGGGAGGGCCACTGCTGCCATCGCGTCCACCGACGAATTTCCCCACAG                         AGCATTAGAGCAATTATCTTGGAGTTGCAGATCTGTACCTGAAGATTCATA
genomic: TACGGGAGGGCCACTGCTGCCATCGCGTCCACCGACGAATTTCCCCACAGgttcagctcc ... ggcctcacagAGCATTAGAGCAATTATCTTGGAGTTGCAGATCTGTACCTGAAGATTCATA
EST: gi|30088379|gb|CB886584.1|CB886584
EST:     TACGGGAGGGCCACTGCTGCCATCGCGTCCACCGACGAATTTCCCCACAG                         AGCATTAGAGCAATTATCTTGGAGTTGCAGATCTGTACCTGAAGATTCATA
genomic: TACGGGAGGGCCACTGCTGCCATCGCGTCCACCGACGAATTTCCCCACAGgttcagctcc ... ggcctcacagAGCATTAGAGCAATTATCTTGGAGTTGCAGATCTGTACCTGAAGATTCATA

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: 167

TCTCTCCATCCGTTGTGACTGCTTGCCGTCCCCCGCTTGCTTCGTCCTGCTACGGGAGGGCCACTGCTGCCATCGCGTCCACCGACGAATTTCCCCACAGgttcagctcc ... ggcctcacagAGCATTAGAGCAATTATCTTGGAGTTGCAGATCTGTACCTGAAGATTCATATTGAAATCTGGAAGCTTCTGCTGTTGAGTACAGAGAAATATTTCTTGCC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 224

TCTCTCCATCCGTTGTGACTGCTTGCCGTCCCCCGCTTGCTTCGTCCTGCTACGGGAGGGCCACTGCTGCCATCGCGTCCACCGACGAATTTCCCCACAGgttcagctcc ... ggcctcacagAGCATTAGAGCAATTATCTTGGAGTTGCAGATCTGTACCTGAAGATTCATATTGAAATCTGGAAGCTTCTGCTGTTGAGTACAGAGAAATATTTCTTGCC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 162

TCTCTCCATCCGTTGTGACTGCTTGCCGTCCCCCGCTTGCTTCGTCCTGCTACGGGAGGGCCACTGCTGCCATCGCGTCCACCGACGAATTTCCCCACAGgttcagctcc ... ggcctcacagAGCATTAGAGCAATTATCTTGGAGTTGCAGATCTGTACCTGAAGATTCATATTGAAATCTGGAAGCTTCTGCTGTTGAGTACAGAGAAATATTTCTTGCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 285

TCTCTCCATCCGTTGTGACTGCTTGCCGTCCCCCGCTTGCTTCGTCCTGCTACGGGAGGGCCACTGCTGCCATCGCGTCCACCGACGAATTTCCCCACAGgttcagctcc ... ggcctcacagAGCATTAGAGCAATTATCTTGGAGTTGCAGATCTGTACCTGAAGATTCATATTGAAATCTGGAAGCTTCTGCTGTTGAGTACAGAGAAATATTTCTTGCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttattggtccatatggcagctgactaatgtttcttcttcccttgtggcctcacagAGCATTAGAGCAATTATCTTGGAGTTGCAGATCTGTACCTGAAGATTCATATTGAAATCTGGAAGCTTCTGCTGTTGAGTACAGAGAAATATTTCTTGCC
                     gactaat  putative branch site (score: 285)
                             tttcttcttcccttgt  CT-rich tract
                        taatgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attgctggattggttcagtatgcataataaaatgtgttcgtttctttattggtccatatggcagctgactaatgtttcttcttcccttgtggcctcacagAGCATTAGAGCAATTATCTTGGAGTTGCAGATCTGTACCTGAAGATTCATATTGAAATCTGGAAGCTTCTGCTGTTGAGTACAGAGAAATATTTCTTGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
attgctg
- - - - - - - - -gtatgca
- - - - - - - - - - - - -aataaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - -ccatatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcagctg