Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagttatatgaacttcactgttcatttattcattgagaacagtattgcatgttctggtatcacatctggcttcacctgtattaacttgtgggttttttgttcagGCAATTTTCGGTCGAGAGGCAGAGGTGGGTTTGGTAACCGGGGCCATATGTCTGGATCAAATACCTTTCCTTTAGGAGGAAGAAGGCCATATTGATGTGT

Basic information

species Zea mays
transcript GRMZM2G362850_T02
intron # 9
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|78079678|gb|DV508090.1|DV508090
EST:     GAATCCTGCCTTAGAATCCATGTCCAGGTCTTCGAACTCAACGGGAGGAG                         GCAATTTTCGGTCGAGAGGCAGAGGTGGGTTTGGTAACCGGGGCCATATGT
genomic: GAATCCTGCCTTAGAATCCATGTCCAGGTCTTCGAACTCAACGGGAGGAGgtagttatat ... ttttgttcagGCAATTTTCGGTCGAGAGGCAGAGGTGGGTTTGGTAACCGGGGCCATATGT
EST: gi|211019779|gb|FL282427.1|FL282427
EST:     CCATGTCCAGGTCTTCGAACTCAACGGGAGGAG                         GCAATTTTCGGTCGAGAGGCAGAGGTGGGTTTGGTAACCGGGGCCATATGT
genomic: CCATGTCCAGGTCTTCGAACTCAACGGGAGGAGgtagttatat ... ttttgttcagGCAATTTTCGGTCGAGAGGCAGAGGTGGGTTTGGTAACCGGGGCCATATGT
EST: gi|91875331|gb|EB405288.1|EB405288
EST:     GAATCCTGCCTTAGAATCCATGTCCAGGTCTTCGAACTCAACGGGAGGAG                         GCAATTTTCGGTCGAGAGGCAGAGGTGGGTTTGGTAACCGGGGCCATATGT
genomic: GAATCCTGCCTTAGAATCCATGTCCAGGTCTTCGAACTCAACGGGAGGAGgtagttatat ... ttttgttcagGCAATTTTCGGTCGAGAGGCAGAGGTGGGTTTGGTAACCGGGGCCATATGT
EST: gi|211019778|gb|FL282426.1|FL282426
EST:     GAATCCTGCCTTAGAATCCATGTCCAGGTCTTCGAACTCAACGGGAGGAG                         GCAATTTCCGGTCGAGAGGCAGAGGTGGGTTTGGTAACCGGGGCCATATGT
genomic: GAATCCTGCCTTAGAATCCATGTCCAGGTCTTCGAACTCAACGGGAGGAGgtagttatat ... ttttgttcagGCAATTTTCGGTCGAGAGGCAGAGGTGGGTTTGGTAACCGGGGCCATATGT
EST: gi|78180630|gb|DV550958.1|DV550958
EST:     TCCATGTCCAGGTCTTCGAACTCAACGGGAGGAG                         GCAATTTTCGGTCGAGAGGCAGAGGTGGGTTTGGTAACCGGGGCCATATGT
genomic: TCCATGTCCAGGTCTTCGAACTCAACGGGAGGAGgtagttatat ... ttttgttcagGCAATTTTCGGTCGAGAGGCAGAGGTGGGTTTGGTAACCGGGGCCATATGT
EST: gi|84980833|gb|DW531182.1|DW531182
EST:     CTTCGAACTC-ACGGGAGGAG                         GCAATTTCCGGTCGAGAGGCAGAGGTGGGTTTGGTAACCGGGGCCATATGT
genomic: CTTCGAACTCAACGGGAGGAGgtagttatat ... ttttgttcagGCAATTTTCGGTCGAGAGGCAGAGGTGGGTTTGGTAACCGGGGCCATATGT
EST: gi|60346381|gb|DN213354.1|DN213354
EST:     GAATCCTGCCTTAGAATCCATGTCCAGGTCTTCGAACTCAACGGGAGGAG                         GCAATTTTCGGTCGAGAGGCAGAGGTGGGTTTGGTAACCGGGGCCATATGT
genomic: GAATCCTGCCTTAGAATCCATGTCCAGGTCTTCGAACTCAACGGGAGGAGgtagttatat ... ttttgttcagGCAATTTTCGGTCGAGAGGCAGAGGTGGGTTTGGTAACCGGGGCCATATGT
EST: gi|6654234|gb|AW267639.1|AW267639
EST:     GAATCCTGCCTTAGAATCCATGTCCAGGTCTTCGAACTCAACGGGAGGAG                         GCAATTTTCGGTCGAGAGGCAGAGGTGGGTTTGGTAACCGGGGCCATATGT
genomic: GAATCCTGCCTTAGAATCCATGTCCAGGTCTTCGAACTCAACGGGAGGAGgtagttatat ... ttttgttcagGCAATTTTCGGTCGAGAGGCAGAGGTGGGTTTGGTAACCGGGGCCATATGT
EST: gi|32832791|gb|CD972469.1|CD972469
EST:     GAATCCTGCCTTAGAATCCATGTCCAGGTCTTCGAACTCAACGGGAGGAG                         GCAATTTCCGGTCGAGAGGCAGAGGTGGGTTTGGTAACCGGGGCCATATGT
genomic: GAATCCTGCCTTAGAATCCATGTCCAGGTCTTCGAACTCAACGGGAGGAGgtagttatat ... ttttgttcagGCAATTTTCGGTCGAGAGGCAGAGGTGGGTTTGGTAACCGGGGCCATATGT
EST: gi|32833291|gb|CD972969.1|CD972969
EST:     GAATCCTGCCTTAGAATCCATGTCCAGGTCTTCGAACTCAACGGGAGGAG                         GCAATTTCCGGTCGAGAGGCAGAGGTGGGTTTGGTAACCGGGGCCATATGT
genomic: GAATCCTGCCTTAGAATCCATGTCCAGGTCTTCGAACTCAACGGGAGGAGgtagttatat ... ttttgttcagGCAATTTTCGGTCGAGAGGCAGAGGTGGGTTTGGTAACCGGGGCCATATGT
EST: gi|88757232|gb|DY541373.1|DY541373
EST:     GAATCCTGCCTTAGAATCCATGTCCAGGTCTTCGAACTCAACGGGAGGAG                         GCAATTTTCGGTCGAGAGGCAGAGGTGGGTTTGGTAACCGGGGCCATATGT
genomic: GAATCCTGCCTTAGAATCCATGTCCAGGTCTTCGAACTCAACGGGAGGAGgtagttatat ... ttttgttcagGCAATTTTCGGTCGAGAGGCAGAGGTGGGTTTGGTAACCGGGGCCATATGT
EST: gi|78079591|gb|DV508003.1|DV508003
EST:     GAATCCTGCCTTAGAATCCATGTCCAGGTCTTCGAACTCAACGGGAGGAG                         GCAATTTTCGGTCGAGAGGCAGAGGTGGGTTTGGTAACCGGGGCCATATGT
genomic: GAATCCTGCCTTAGAATCCATGTCCAGGTCTTCGAACTCAACGGGAGGAGgtagttatat ... ttttgttcagGCAATTTTCGGTCGAGAGGCAGAGGTGGGTTTGGTAACCGGGGCCATATGT
EST: gi|6760632|gb|AW324731.1|AW324731
EST:     CAACGGGAGGAG                         GCAATTTTCGGTCGAGAGGCAGAGGTGGGTTTGGTAACCGGGGCCATATGT
genomic: CAACGGGAGGAGgtagttatat ... ttttgttcagGCAATTTTCGGTCGAGAGGCAGAGGTGGGTTTGGTAACCGGGGCCATATGT
EST: gi|67022617|gb|CO451366.1|CO451366
EST:     GAATCCTGCCTTAGAATCCATGTCCAGGTCTTCGAACTCAACGGGAGGAG                         GCAATTTCCGGTCGAGAGGCAGAGGTGGGTTTGGTAACCGGGGCCATATGT
genomic: GAATCCTGCCTTAGAATCCATGTCCAGGTCTTCGAACTCAACGGGAGGAGgtagttatat ... ttttgttcagGCAATTTTCGGTCGAGAGGCAGAGGTGGGTTTGGTAACCGGGGCCATATGT
EST: gi|76291633|gb|DV031201.1|DV031201
EST:     GAATCCTGCCTTAGAATCCATGTCCAGGTCTTCGAACTCAACGGGAGGAG                         GCAATTTTCGGTCGAGAGGCAGAGGTGGGTTTGGTAACCGGGGCCATATGT
genomic: GAATCCTGCCTTAGAATCCATGTCCAGGTCTTCGAACTCAACGGGAGGAGgtagttatat ... ttttgttcagGCAATTTTCGGTCGAGAGGCAGAGGTGGGTTTGGTAACCGGGGCCATATGT
EST: gi|149060826|gb|EE157279.2|EE157279
EST:     GAATCCTGCCTTAGAATCCATGTCCAGGTCTTCGAACTCAACGGGAGGAG                         GCAATTTTCGGTCGAGAGGCAGAGGTGGGTTTGGTAACCGGGGCCATATGT
genomic: GAATCCTGCCTTAGAATCCATGTCCAGGTCTTCGAACTCAACGGGAGGAGgtagttatat ... ttttgttcagGCAATTTTCGGTCGAGAGGCAGAGGTGGGTTTGGTAACCGGGGCCATATGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttctggtatcacatctggcttcacctgtattaacttgtgggttttttgttcagGCAATTTTCGGTCGAGAGGCAGAGGTGGGTTTGGTAACCGGGGCCATATGTCTGGATCAAATACCTTTCCTTTAGGAGGAAGAAGGCCATATTGATGTGT
                             tattaac  putative branch site (score: 1)
                                           ttttttgttc  putative PPT
                             tattaactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagttatatgaacttcactgttcatttattcattgagaacagtattgcatgttctggtatcacatctggcttcacctgtattaacttgtgggttttttgttcagGCAATTTTCGGTCGAGAGGCAGAGGTGGGTTTGGTAACCGGGGCCATATGTCTGGATCAAATACCTTTCCTTTAGGAGGAAGAAGGCCATATTGATGTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG