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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgctacgtttcaccccccttgctttttatagtcgctaagaccattaaagcctgttagatgatatttggcattctgtacagGGTTTGGTTGCGAAGGACAAGTTTCATGTAAGTTACAGAGGTGGAAAACTAAACAGCTCCTTATCTCAG

Basic information

species Zea mays
transcript GRMZM5G825902_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G825902_T02 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os12g05650.1 (Oryza sativa), 3'ss of exon 8
gtatgctacgtttcaccccccttgctttttatagtcgctaagaccattaaagcct---gttagatgatatttggcattctgtacagGGTTTGGTTGCGAAGGACAAGTTTCATGTAAGTTACAGAGGTGGAAAACTAAACAGCTCCTTATCTCAG
|||||| | ||| |     | ||| || | | |  | ||    |  | ||  ||     |||  | |||| ||   || | | ||||| |||||||| |||||||| || ||||| ||||||||||||| |||| | |||||||| |||||||||
gtatgccatgttcctatttctttg-ttatgaaatccccttgttctgtcaactcccttccttacttcatatgtgatgttttattcagGGCTTGGTTGCAAAGGACAAATTCCATGTGAGTTACAGAGGTGCAAAATTGAACAGCTCATTATCTCAG
















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|32859294|gb|CD998975.1|CD998975
EST:     TCATCGCGGACACAAATATTGATGTGGAATCAGCTGAGATTGATACTGAA                         GGTTTGGTTGCGAAGGACAAGTTTCATGTAAGTTACAGAGGTGGAAAACTA
genomic: TCATCGCGGACACAAATATTGATGTGGAATCAGCTGAGATTGATACTGAAgtatgctacg ... ttctgtacagGGTTTGGTTGCGAAGGACAAGTTTCATGTAAGTTACAGAGGTGGAAAACTA
EST: gi|5846978|gb|AW000057.1|AW000057
EST:     TCATCGCGGACACAAATATTGATGTGGAATCAGCTGAGATTGATACTGAA                         GGTTTGGTTGCGAAGGACAAGTTTCATGTAAGTTACAGAGGTGGAAAACTA
genomic: TCATCGCGGACACAAATATTGATGTGGAATCAGCTGAGATTGATACTGAAgtatgctacg ... ttctgtacagGGTTTGGTTGCGAAGGACAAGTTTCATGTAAGTTACAGAGGTGGAAAACTA
EST: gi|211056798|gb|FL037810.1|FL037810
EST:     TCATTGCGGACACAAATATTGATGTGGAATCAGCTGAGATTGATACTGAA                         GGTTTGGTTGCGAAGGACAAGTTTCATGTAAGTTACAGAGGTGGAAAACTA
genomic: TCATCGCGGACACAAATATTGATGTGGAATCAGCTGAGATTGATACTGAAgtatgctacg ... ttctgtacagGGTTTGGTTGCGAAGGACAAGTTTCATGTAAGTTACAGAGGTGGAAAACTA
EST: gi|60394392|gb|DN227262.1|DN227262
EST:     TCATCGCGGACACAAATATTGATGTGGAATCAGCTGAGATTGATACTGAA                         GGTTTGGTTGCGAAGGACAAGTTTCATGTAAGTTACAGAGGTGGAAAACTA
genomic: TCATCGCGGACACAAATATTGATGTGGAATCAGCTGAGATTGATACTGAAgtatgctacg ... ttctgtacagGGTTTGGTTGCGAAGGACAAGTTTCATGTAAGTTACAGAGGTGGAAAACTA
EST: gi|211056797|gb|FL037809.1|FL037809
EST:     TGTGGAATCAGCTGAGATTGATACTGAA                         GGTTTGGTTGCGAAGGACAAGTTTCATGTAAGTTACAGAGGTGGAAAACTA
genomic: TGTGGAATCAGCTGAGATTGATACTGAAgtatgctacg ... ttctgtacagGGTTTGGTTGCGAAGGACAAGTTTCATGTAAGTTACAGAGGTGGAAAACTA
EST: gi|5762240|gb|AI967288.1|AI967288
EST:     TCATCGCGGACCCAAATATTGATGTGGAATCAGCTGAGATTGATACTGAA                         GGTTTGGTTGCGAAGGACAAGTTTCATGTAAGTTACAGAGGTGGAAAACTA
genomic: TCATCGCGGACACAAATATTGATGTGGAATCAGCTGAGATTGATACTGAAgtatgctacg ... ttctgtacagGGTTTGGTTGCGAAGGACAAGTTTCATGTAAGTTACAGAGGTGGAAAACTA
EST: gi|60354178|gb|DN221151.1|DN221151
EST:     TCATCGCGGACACAAATATTGATGTGGAATCAGCTGAGATTGATACTGAA                         GGTTTGGTTGCGAAGGACAAGTTTCATGTAAGTTACAGAGGTGGAAAACTA
genomic: TCATCGCGGACACAAATATTGATGTGGAATCAGCTGAGATTGATACTGAAgtatgctacg ... ttctgtacagGGTTTGGTTGCGAAGGACAAGTTTCATGTAAGTTACAGAGGTGGAAAACTA
EST: gi|60394317|gb|DN227187.1|DN227187
EST:     TCATCGCGGACACAAATATTGATGTGGAATCAGCTGAGATTGATACTGAA                         GGTTTGGTTGCGAAGGACAAGTTTCATGTAAGTTACAGAGGTGGAAAACTA
genomic: TCATCGCGGACACAAATATTGATGTGGAATCAGCTGAGATTGATACTGAAgtatgctacg ... ttctgtacagGGTTTGGTTGCGAAGGACAAGTTTCATGTAAGTTACAGAGGTGGAAAACTA
EST: gi|16922165|gb|BM075455.1|BM075455
EST:     TCATCGCGGACACAAATATTGATGTGGAATCAGCTGAGATTGATACTGAA                         GGTTTGGTTGCGAAGGACAAGTTTCATGTAAGTTACAGAGGTGGAAAACTA
genomic: TCATCGCGGACACAAATATTGATGTGGAATCAGCTGAGATTGATACTGAAgtatgctacg ... ttctgtacagGGTTTGGTTGCGAAGGACAAGTTTCATGTAAGTTACAGAGGTGGAAAACTA
EST: gi|71762075|gb|DR960012.1|DR960012
EST:     TCATCGCGGACACAAATATTGATGTGGAATCAGCTGAGATTGATACTGAA                         GGTTTGGTTGCGAAGGACAAGTTTCATGTAAGTTACAGAGGTGGAAAACTA
genomic: TCATCGCGGACACAAATATTGATGTGGAATCAGCTGAGATTGATACTGAAgtatgctacg ... ttctgtacagGGTTTGGTTGCGAAGGACAAGTTTCATGTAAGTTACAGAGGTGGAAAACTA
EST: gi|5871577|gb|AW018048.1|AW018048
EST:     TCATCGCGGACACAAATATTGATGTGGAATCAGCTGAGATTGATACTGAA                         GGTTTGGTTGCGAAGGACAAGTTTCATGTAAGTTACAGAGGTGGAAAACTA
genomic: TCATCGCGGACACAAATATTGATGTGGAATCAGCTGAGATTGATACTGAAgtatgctacg ... ttctgtacagGGTTTGGTTGCGAAGGACAAGTTTCATGTAAGTTACAGAGGTGGAAAACTA
EST: gi|6031251|gb|AW076258.1|AW076258
EST:     TCATCGCGGACACAAATATTGATGTGGAATCAGCTGAGATTGATACTGAA                         GGTTTGGTTGCGAAGGACAAGTTTCATGTAAGTTACAGAGGTGGAAAACTA
genomic: TCATCGCGGACACAAATATTGATGTGGAATCAGCTGAGATTGATACTGAAgtatgctacg ... ttctgtacagGGTTTGGTTGCGAAGGACAAGTTTCATGTAAGTTACAGAGGTGGAAAACTA
EST: gi|5597232|gb|AI891225.1|AI891225
EST:     ATTGATACTGAA                         GGTTTGGTTGCGAAGGCCAAGTTTCATGTAAGTTCCAGAGGTGGAAAACTA
genomic: ATTGATACTGAAgtatgctacg ... ttctgtacagGGTTTGGTTGCGAAGGACAAGTTTCATGTAAGTTACAGAGGTGGAAAACTA
EST: gi|5006113|gb|AI712175.1|AI712175
EST:     TCATCGCGGACNCAAATATTGATGTGGAATCAGCTGAGATTGATACTGAA                         GGTTTGGTTGCGAAGGACAAGTTTCATGTAAGTTACAGAGGTGGAAAACTA
genomic: TCATCGCGGACACAAATATTGATGTGGAATCAGCTGAGATTGATACTGAAgtatgctacg ... ttctgtacagGGTTTGGTTGCGAAGGACAAGTTTCATGTAAGTTACAGAGGTGGAAAACTA
EST: gi|24934311|gb|CA452529.1|CA452529
EST:     TCATCGCGGACACAAATATTGATGTGGAATCAGCTGAGATTGATACTGAA                         GGTTTGGTTGCGAAGGACAAGTTTCATGTAAGTTACAGAGGTGGAAAACTA
genomic: TCATCGCGGACACAAATATTGATGTGGAATCAGCTGAGATTGATACTGAAgtatgctacg ... ttctgtacagGGTTTGGTTGCGAAGGACAAGTTTCATGTAAGTTACAGAGGTGGAAAACTA
EST: gi|5915187|gb|AW052828.1|AW052828
EST:     TCATCGCGGACACAAATATTGATGTGGAATCAGCTGAGATTGATACTGAA                         GGTTTGGTTGCGAAGGACAAGTTTCATGTAAGTTACAGAGGTGGAAAACTA
genomic: TCATCGCGGACACAAATATTGATGTGGAATCAGCTGAGATTGATACTGAAgtatgctacg ... ttctgtacagGGTTTGGTTGCGAAGGACAAGTTTCATGTAAGTTACAGAGGTGGAAAACTA
EST: gi|31356321|gb|CD440678.1|CD440678
EST:     TCATCGCGGACACAAATATTGATGTGGAATCAGCTGAGATTGATACTGAA                         GGTTTGGTTGCGAAGGACAAGTTTCATGTAAGTTACAGAGGTGGAAAACTA
genomic: TCATCGCGGACACAAATATTGATGTGGAATCAGCTGAGATTGATACTGAAgtatgctacg ... ttctgtacagGGTTTGGTTGCGAAGGACAAGTTTCATGTAAGTTACAGAGGTGGAAAACTA
EST: gi|32859012|gb|CD998693.1|CD998693
EST:     TCATCGCGGACACAAATATTGATGTGGAATCAGCTGAGATTGATACTGAA                         GGTTTGGTTGCGAAGGACAAGTTTCATGTAAGTTACAGAGGTGGAAAACTA
genomic: TCATCGCGGACACAAATATTGATGTGGAATCAGCTGAGATTGATACTGAAgtatgctacg ... ttctgtacagGGTTTGGTTGCGAAGGACAAGTTTCATGTAAGTTACAGAGGTGGAAAACTA
EST: gi|6827302|gb|AW330945.1|AW330945
EST:     TCATCGCGGACACAAATATTGATGTGGAATCAGCTGAGATTGATACTGAA                         GGTTTGGTTGCGAAGGACAAGTTTCATGTAAGTTACAGAGGTGGAAAACTA
genomic: TCATCGCGGACACAAATATTGATGTGGAATCAGCTGAGATTGATACTGAAgtatgctacg ... ttctgtacagGGTTTGGTTGCGAAGGACAAGTTTCATGTAAGTTACAGAGGTGGAAAACTA
EST: gi|24767769|gb|CA402905.1|CA402905
EST:     TCATCGCGGACACAAATATTGATGTGGAATCAGCTGAGATTGATACTGAA                         GGTTTGGTTGCGAAGGACAAGTTTCATGTAAGTTACAGAGGTGGAAAACTA
genomic: TCATCGCGGACACAAATATTGATGTGGAATCAGCTGAGATTGATACTGAAgtatgctacg ... ttctgtacagGGTTTGGTTGCGAAGGACAAGTTTCATGTAAGTTACAGAGGTGGAAAACTA
EST: gi|31353042|gb|CD437399.1|CD437399
EST:     TCATCGCGGACACAAATATTGATGTGGAATCAGCTGAGATTGATACTGAA                         GGTTTGGTTGCGAAGGACAAGTTTCATGTAAGTTACAGAGGTGGAAAACTA
genomic: TCATCGCGGACACAAATATTGATGTGGAATCAGCTGAGATTGATACTGAAgtatgctacg ... ttctgtacagGGTTTGGTTGCGAAGGACAAGTTTCATGTAAGTTACAGAGGTGGAAAACTA
EST: gi|148950230|gb|EC895780.2|EC895780
EST:     TCATCGCGGACACAAATATTGATGTGGAATCAGCTGAGATTGATACTGAA                         GGTTTGGTTGCGAAGGACAAGTTTCATGTAAGTTACAGAGGTGGAAAACTA
genomic: TCATCGCGGACACAAATATTGATGTGGAATCAGCTGAGATTGATACTGAAgtatgctacg ... ttctgtacagGGTTTGGTTGCGAAGGACAAGTTTCATGTAAGTTACAGAGGTGGAAAACTA
EST: gi|6194493|gb|AW146597.1|AW146597
EST:     GCGGACACAAATATNTGATGTGGAATCAGCCTTGAGAAATTGATACTGAA                         GGTTTGGTTGCGAAGGACAAGTTTCATGTAAGTTACAGAGGTNNGGAAAAC
genomic: GCGGACACAAATAT-TGATGTGGAATCAGC-T-GAGA--TTGATACTGAAgtatgctacg ... ttctgtacagGGTTTGGTTGCGAAGGACAAGTTTCATGTAAGTTACAGAGGT--GGAAAAC
EST: gi|194716957|gb|FK934116.1|FK934116
EST:     TCATCGCGGACACAAATATTGATGTGGAATCAGCTGAGATTGATACTGAA                         GGTTTGGTTGCGAAGGACAAGTTTCATGTAAGTTACAGAGGTGGAAAACTA
genomic: TCATCGCGGACACAAATATTGATGTGGAATCAGCTGAGATTGATACTGAAgtatgctacg ... ttctgtacagGGTTTGGTTGCGAAGGACAAGTTTCATGTAAGTTACAGAGGTGGAAAACTA
EST: gi|5739701|gb|AI947277.1|AI947277
EST:     CAAATATTGATGTGGAATCAGCTGAGATT-ATA-TGAA                         GGTTTGGTTGCGAAGGACAAGTTTCATGTAAGTTACAGAGGTGGAAAACTA
genomic: CAAATATTGATGTGGAATCAGCTGAGATTGATACTGAAgtatgctacg ... ttctgtacagGGTTTGGTTGCGAAGGACAAGTTTCATGTAAGTTACAGAGGTGGAAAACTA
EST: gi|16927072|gb|BM080141.1|BM080141
EST:     TCATCGCGGACGCAAATATTAATGTGGAATCAGCTGAGATTAATACTGAA                         GGTTTGGTTGCGAAGGACAAGTTTCATGTAAGTTACAGAGGGGGAAAACTA
genomic: TCATCGCGGACACAAATATTGATGTGGAATCAGCTGAGATTGATACTGAAgtatgctacg ... ttctgtacagGGTTTGGTTGCGAAGGACAAGTTTCATGTAAGTTACAGAGGTGGAAAACTA
EST: gi|32859295|gb|CD998976.1|CD998976
EST:     TCATCGCGGACACAAATATTGATGTGGAATCAGCTGAGATTGATACTGAA                         GGTTTGGTTGCGAAGGACAAGTTTCATGTAAGTTACAGAGGTGGAAAACTA
genomic: TCATCGCGGACACAAATATTGATGTGGAATCAGCTGAGATTGATACTGAAgtatgctacg ... ttctgtacagGGTTTGGTTGCGAAGGACAAGTTTCATGTAAGTTACAGAGGTGGAAAACTA
EST: gi|211399224|gb|FL447437.1|FL447437
EST:     TCATTGCGGACACAAATATTGATGTGGAATCAGCTGAGATTGATACTGAA                         GGTTTGGTTGCGAAGGACAAGTTTCATGTAAGTTACAGAGGTGGAAAACTA
genomic: TCATCGCGGACACAAATATTGATGTGGAATCAGCTGAGATTGATACTGAAgtatgctacg ... ttctgtacagGGTTTGGTTGCGAAGGACAAGTTTCATGTAAGTTACAGAGGTGGAAAACTA
EST: gi|5871038|gb|AW017614.1|AW017614
EST:     TCATCGCGGACNCAAATA-TGATGTGGAATCAGCTGAGATTGATACTGAA                         GGTTTGGTTGCGAAGGNCAAGTTTCATGTAAGTTCCAGAGGTGGAAAACTA
genomic: TCATCGCGGACACAAATATTGATGTGGAATCAGCTGAGATTGATACTGAAgtatgctacg ... ttctgtacagGGTTTGGTTGCGAAGGACAAGTTTCATGTAAGTTACAGAGGTGGAAAACTA
EST: gi|31360452|gb|CD444809.1|CD444809
EST:     TCATCGCGGACACAAATATTGATGTGGAATCAGCTGAGATTGATACTGAA                         GGTTTGGTTGCGAAGGACAAGTTTCATGTAAGTTACAGAGGTGGAAAACTA
genomic: TCATCGCGGACACAAATATTGATGTGGAATCAGCTGAGATTGATACTGAAgtatgctacg ... ttctgtacagGGTTTGGTTGCGAAGGACAAGTTTCATGTAAGTTACAGAGGTGGAAAACTA
EST: gi|16927075|gb|BM080144.1|BM080144
EST:     TCATCGCGGACACAAATATTGATGTGGAATCAGCTGAGATTGATACTGAA                         GGTTTGGTTGCGAAGGACAAGTTTCATGTAAGTTACAGAGGTGGAAAACTA
genomic: TCATCGCGGACACAAATATTGATGTGGAATCAGCTGAGATTGATACTGAAgtatgctacg ... ttctgtacagGGTTTGGTTGCGAAGGACAAGTTTCATGTAAGTTACAGAGGTGGAAAACTA
EST: gi|4775819|gb|AI664824.1|AI664824
EST:     TCATCGCGGACACAAATATTGATGTGGAATCAGCTGAGATTGATACTGAA                         GGTTTGGTTGCGAAGGACAAGTTTCATGTAAGTTACAGAGGTGGAAAACTA
genomic: TCATCGCGGACACAAATATTGATGTGGAATCAGCTGAGATTGATACTGAAgtatgctacg ... ttctgtacagGGTTTGGTTGCGAAGGACAAGTTTCATGTAAGTTACAGAGGTGGAAAACTA
EST: gi|149074677|gb|EE163095.2|EE163095
EST:     TCATCGCGGACACAAATATTGATGTGGAATCAGCTGAGATTGATACTGAA                         GGTTTGGTTGCGAAGGACAAGTTTCATGTAAGTTACAGAGGTGGAAAACTA
genomic: TCATCGCGGACACAAATATTGATGTGGAATCAGCTGAGATTGATACTGAAgtatgctacg ... ttctgtacagGGTTTGGTTGCGAAGGACAAGTTTCATGTAAGTTACAGAGGTGGAAAACTA
EST: gi|32828950|gb|CD968628.1|CD968628
EST:     TCATCGCGGACACAAATATTGATGTGGAATCAGCTGAGATTGATACTGAA                         GGTTTGGTTGCGAAGGACAAGTTTCATGTAAGTTACAGAGGTGGAAAACTA
genomic: TCATCGCGGACACAAATATTGATGTGGAATCAGCTGAGATTGATACTGAAgtatgctacg ... ttctgtacagGGTTTGGTTGCGAAGGACAAGTTTCATGTAAGTTACAGAGGTGGAAAACTA
EST: gi|32828741|gb|CD968419.1|CD968419
EST:     TCATCGCGGACACAAATATTGATGTGGAATCAGCTGAGATTGATACTGAA                         GGTTTGGTTGCGAAGGACAAGTTTCATGTAAGTTACAGAGGTGGAAAACTA
genomic: TCATCGCGGACACAAATATTGATGTGGAATCAGCTGAGATTGATACTGAAgtatgctacg ... ttctgtacagGGTTTGGTTGCGAAGGACAAGTTTCATGTAAGTTACAGAGGTGGAAAACTA
EST: gi|6031249|gb|AW076256.1|AW076256
EST:     ATTGATGTGGAATCAGCTGAGATTGATACTGAA                         GGTTTGGTTGCGAAGGACCAAGTTTCCATGTAAGTTACAGAGGTGGAAAAC
genomic: ATTGATGTGGAATCAGCTGAGATTGATACTGAAgtatgctacg ... ttctgtacagGGTTTGGTTGCGAAGGA-CAAGTTT-CATGTAAGTTACAGAGGTGGAAAAC
EST: gi|8929966|gb|BE224730.1|BE224730
EST:     TCATCGCGGACCCAAATATTGATGTGGAATCAGCTGAGATTGATACTGAA                         GGTTTGGTTGCGAAGGACAAGTTTCATGTAAGTTACAGAGGTGGAAAACTA
genomic: TCATCGCGGACACAAATATTGATGTGGAATCAGCTGAGATTGATACTGAAgtatgctacg ... ttctgtacagGGTTTGGTTGCGAAGGACAAGTTTCATGTAAGTTACAGAGGTGGAAAACTA
EST: gi|6031454|gb|AW076356.1|AW076356
EST:     TCATCGCGGACACAAATATTGATGTGGAATCAGCTGAGATTGATACTGAA                         GGTTTGGTTGCGAAGGACAAGTTTCATGTAAGTTACAGAGGTGGAAAACTA
genomic: TCATCGCGGACACAAATATTGATGTGGAATCAGCTGAGATTGATACTGAAgtatgctacg ... ttctgtacagGGTTTGGTTGCGAAGGACAAGTTTCATGTAAGTTACAGAGGTGGAAAACTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatagtcgctaagaccattaaagcctgttagatgatatttggcattctgtacagGGTTTGGTTGCGAAGGACAAGTTTCATGTAAGTTACAGAGGTGGAAAACTAAACAGCTCCTTATCTCAG
                                atgatattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgctacgtttcaccccccttgctttttatagtcgctaagaccattaaagcctgttagatgatatttggcattctgtacagGGTTTGGTTGCGAAGGACAAGTTTCATGTAAGTTACAGAGGTGGAAAACTAAACAGCTCCTTATCTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC