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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTCAACAAGATCAGACTATAGTCCAGCCTGgtaagttttcatttgaatcacgcaggcaccgataataggagataagcaactctgtttcgagtctccacaatgtttttcctcatatgagaggttcttgaga...

Basic information

species Zea mays
transcript GRMZM2G017089_T02
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G017089_T01 (Zea mays), 5'ss of exon 15
lower sequence: LOC_Os03g21990.1 (Oryza sativa), 5'ss of exon 17
GGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTCAACAAGATCAGACTATAGTCCAGCCTGgtaagttttcatttgaatcacgcaggcaccgataataggagataagcaact-ctgtttcgagtctccacaatg-tttttcctcatatgagaggttcttgaga
|||||||||| || || ||||||||||| ||||||||||| ||||||||||||||||||||||||||||| || |||||||||| || ||||| |||| | | |  | | || || |        |    ||   ||||   ||   | || | ||   ||  || | ||          
GGGATAATGGGAGTCTCTGGTTTTGGGATTGGAAGAGTGGCCATAACTTTCAACAAGATCAGACTATAGTACAACCTGgtaagtattgatttgcatcatgtatgggctgttattatgtttctttaagtcactaaatcgatcatcttgattgatcttatttccaattatag----------

upper sequence: GRMZM2G017089_T01 (Zea mays), 5'ss of exon 15
lower sequence: GLYMA15G15960.2 (Glycine max), 5'ss of exon 15
GGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTCAACAAGATCAGACTATAGTCCAGCCTGgtaagttttcatttgaatcacgcaggcaccgataataggagataagcaactctgtttcga-gtctccacaatgtttttcctcata-tgagaggttcttgaga------------------------
| || ||||| ||| ||||||| ||||| ||||||||||||||||| || || |||   || || || || ||||||||||   |   | ||      | |       ||| ||  |  ||  || |||  |||      |  ||  ||  ||       ||| | |   | | |                             
GTGACAATGGCAGCATGTGGTTCTGGGATTGGAAGAGTGGTCATAATTTCCAGCAATCCCAAACAATTGTACAGCCTGgta---tccaagtttggctgctc----ttagatgattagttatttgccacttagttctatcatacccgtaagattgactagtataattatttgctttcctctttcctcaacctccccctcttacag

upper sequence: GRMZM2G017089_T01 (Zea mays), 5'ss of exon 15
lower sequence: AT4G15900.1 (Arabidopsis thaliana), 5'ss of exon 16
GGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTCAACAAGATCAGACTATAGTCCAGCCTGgtaagttttcatttgaatcacgcaggcaccgataataggagataagcaactctgtttcgagtctccacaatgtttttcctcatatgagaggttcttgaga----
| |||||||||||  | ||||| |||||||||||||||||||| |  || |||||     | ||||| || |||||||||| ||   |||||  | |   || |  |   |  |              | || |   ||       | | |   |      ||   | ||  |  ||     
GTGATAATGGAAGTATATGGTTCTGGGACTGGAAGAGTGGTCACAGTTTCCAACAGTCAGAAACTATCGTACAGCCTGgtacgt--acatttatagctttcatggtcttttgctcctgatctccttgttatggt--aagatgtagaagtctcggtatgttcatacaacgtagtcaagtttga

upper sequence: GRMZM2G017089_T01 (Zea mays), 5'ss of exon 15
lower sequence: PP1S169_73V6.1 (Physcomitrella patens), 5'ss of exon 14
GGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTCAACAAGATCAGACTATAGTCCAGCCTGgtaagttttcatttgaatcacgcaggcaccgataataggagataagcaactctgtttcgagtctccacaatgtttttcctcatatgagaggttcttgaga
| |||||||||||  |||||||||||||||  |||||||| || || ||||| ||||  ||||| || || |||||||||| | |  |||||   |     |   |   |||     | |||  ||  |   |        | |     |  |||    ||         |||  | |
GTGATAATGGAAGTATGTGGTTTTGGGACTACAAGAGTGGGCACAATTTTCAGCAAGCGCAGACAATTGTGCAGCCTGgtatgctaccattttcctttgatatatatatatatatatacatatacatatacatgctttccgtgcgaggagacttttggaattgccccacatctgaata

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|211273977|gb|FL433139.1|FL433139
EST:     CTGGAAGAGTGGTCATAACTTTCAACAAGWTCAGACTATAGTCCAGCCTG                         GATCACTGGAGAGTGAGGCATGCATATATGCCCTCTCATATGACGTGAGCG
genomic: CTGGAAGAGTGGTCATAACTTTCAACAAGATCAGACTATAGTCCAGCCTGgtaagttttc ... ccattttcagGATCACTGGAGAGTGAGGCATGCATATATGCCCTCTCATATGACGTGAGCG
EST: gi|60342895|gb|DN209868.1|DN209868
EST:     CTGGAAGAGTGGTCATAACTTTCAACAAGATCAGACTATAGTCCAGCCTG                         GATCACTGGAGAGTGAGGCATGCATATATGCCCTCTCATATGACGTGAGCG
genomic: CTGGAAGAGTGGTCATAACTTTCAACAAGATCAGACTATAGTCCAGCCTGgtaagttttc ... ccattttcagGATCACTGGAGAGTGAGGCATGCATATATGCCCTCTCATATGACGTGAGCG
EST: gi|31909551|gb|CD650975.1|CD650975
EST:     CTGGAAGAGTGGTCATAACTTTCAACAAGATCAGACTATAGTCCAGCCTG                         GATCACTGGAGAGTGAGGCATGCATATATGCCCTCTCATATGACGTGAGCG
genomic: CTGGAAGAGTGGTCATAACTTTCAACAAGATCAGACTATAGTCCAGCCTGgtaagttttc ... ccattttcagGATCACTGGAGAGTGAGGCATGCATATATGCCCTCTCATATGACGTGAGCG
EST: gi|33091976|gb|CF051970.1|CF051970
EST:     CTGGAAGAGTGGTCATAACTTTCAACAAGATCAGACTATAGTCCAGCCTG                         GATCACTGGAGAGTGAGGCATGCATATATGCCCTCTCATATGACGTGAGCG
genomic: CTGGAAGAGTGGTCATAACTTTCAACAAGATCAGACTATAGTCCAGCCTGgtaagttttc ... ccattttcagGATCACTGGAGAGTGAGGCATGCATATATGCCCTCTCATATGACGTGAGCG
EST: gi|5871794|gb|AW018265.1|AW018265
EST:     TATAGTCCAGCCTG                         GATCACTGGAGAGTGAGGCATGCATATATGCCCTCTCATATGACGTGAGCG
genomic: TATAGTCCAGCCTGgtaagttttc ... ccattttcagGATCACTGGAGAGTGAGGCATGCATATATGCCCTCTCATATGACGTGAGCG
EST: gi|37376961|gb|CF625047.1|CF625047
EST:     CTGGAAGAGTGGTCATAACTTTCAACAAGATCAGACTATAGTCCAGCCTG                         GATCACTGGAGAGTGAGGCATGCATATATGCCCTCTCATATGACGTGAGCG
genomic: CTGGAAGAGTGGTCATAACTTTCAACAAGATCAGACTATAGTCCAGCCTGgtaagttttc ... ccattttcagGATCACTGGAGAGTGAGGCATGCATATATGCCCTCTCATATGACGTGAGCG
EST: gi|78023548|gb|DV491935.1|DV491935
EST:     CTGGAAGAGTGGTCATAACTTTCAACAAGATCAGACTATAGTCCAGCCTG                         GATCACTGGAGAGTGAGGCATGCATATATGCCCTCTCATATGACGTGAGCG
genomic: CTGGAAGAGTGGTCATAACTTTCAACAAGATCAGACTATAGTCCAGCCTGgtaagttttc ... ccattttcagGATCACTGGAGAGTGAGGCATGCATATATGCCCTCTCATATGACGTGAGCG
EST: gi|76013075|gb|DT940245.1|DT940245
EST:     CTGGAAGAGTGGTCATAACTTTCAACAAGATCAGACTATAGTCCAGCCTG                         GATCACTGGAGAGTGAGGCATGCATATATGCCCTCTCATATGACGTGAGCG
genomic: CTGGAAGAGTGGTCATAACTTTCAACAAGATCAGACTATAGTCCAGCCTGgtaagttttc ... ccattttcagGATCACTGGAGAGTGAGGCATGCATATATGCCCTCTCATATGACGTGAGCG
EST: gi|166473545|gb|EG130749.1|EG130749
EST:     CTGGAAGAGTGGTCATAACTTTCAACAAGATCAGACTATAGTCCAGCCTG                         GATCAACTGGAGAGTGAGGCATGCATATATGCCCTC
genomic: CTGGAAGAGTGGTCATAACTTTCAACAAGATCAGACTATAGTCCAGCCTGgtaagttttc ... ccattttcagGATCA-CTGGAGAGTGAGGCATGCATATATGCCCTC
EST: gi|4967045|gb|AI691809.1|AI691809
EST:     CTGGAAGAGTGGTCATAACTTTCAACAAGATCAGACTATAGTCCAGCCTG                         GATCACTGGAGAGTGAGGCATGCATATATGCCCTCTCATATGACGTGAGCG
genomic: CTGGAAGAGTGGTCATAACTTTCAACAAGATCAGACTATAGTCCAGCCTGgtaagttttc ... ccattttcagGATCACTGGAGAGTGAGGCATGCATATATGCCCTCTCATATGACGTGAGCG
EST: gi|6538870|gb|AW225009.1|AW225009
EST:     CTGGAAGAGTGGTCATAACTTTCAACAAGATCAGACTATAGTCCAGCCTG                         GATCACTGGAGAGTGAGGCATGCATATATGCCCTCTCATATGACGTGAGCG
genomic: CTGGAAGAGTGGTCATAACTTTCAACAAGATCAGACTATAGTCCAGCCTGgtaagttttc ... ccattttcagGATCACTGGAGAGTGAGGCATGCATATATGCCCTCTCATATGACGTGAGCG
EST: gi|31406178|gb|CD484910.1|CD484910
EST:     CTGGAAGAGTGGTCATAACTTTCAACAAGATCAGACTATAGTCCAGCCTG                         GATCACTGGAGAGTGAGGCATGCATATATGCCCTCTCATATGACGTGAGCG
genomic: CTGGAAGAGTGGTCATAACTTTCAACAAGATCAGACTATAGTCCAGCCTGgtaagttttc ... ccattttcagGATCACTGGAGAGTGAGGCATGCATATATGCCCTCTCATATGACGTGAGCG
EST: gi|71416740|gb|DR803804.1|DR803804
EST:     CTGGAAGAGTGGTCATAACTTTCAACAAGATCAGACTATAGTCCAGCCTG                         GATCACTGGAGAGTGAGGCATGCATATATGCCCTCTCATATGACGTGAGCG
genomic: CTGGAAGAGTGGTCATAACTTTCAACAAGATCAGACTATAGTCCAGCCTGgtaagttttc ... ccattttcagGATCACTGGAGAGTGAGGCATGCATATATGCCCTCTCATATGACGTGAGCG
EST: gi|33091625|gb|CF051619.1|CF051619
EST:     CTTTCAACAAGATCAGACTATAGTCCAGCCTG                         GATCACTGGAGAGTGAGGCATGCATATATGCCCTCTCATATGACGTGAGCG
genomic: CTTTCAACAAGATCAGACTATAGTCCAGCCTGgtaagttttc ... ccattttcagGATCACTGGAGAGTGAGGCATGCATATATGCCCTCTCATATGACGTGAGCG
EST: gi|6865096|gb|AW360446.1|AW360446
EST:     CTGGAAGAGTGGTCATAACTTTCAACAAGATCAGACTATAGTCCAGCCTG                         GATCCCTGGAGAGTGAGGCATGCATATATGCCCTCTCATATGACGTGAGCG
genomic: CTGGAAGAGTGGTCATAACTTTCAACAAGATCAGACTATAGTCCAGCCTGgtaagttttc ... ccattttcagGATCACTGGAGAGTGAGGCATGCATATATGCCCTCTCATATGACGTGAGCG
EST: gi|33091991|gb|CF051985.1|CF051985
EST:     CTGGAAGAGTGGTCATAACTTTCAACAAGATCAGACTATAGTCCAGCCTG                         GATCACTGGAGAGTGAGGCATGCATATATGCCCTCTCATATGACGTGAGCG
genomic: CTGGAAGAGTGGTCATAACTTTCAACAAGATCAGACTATAGTCCAGCCTGgtaagttttc ... ccattttcagGATCACTGGAGAGTGAGGCATGCATATATGCCCTCTCATATGACGTGAGCG
EST: gi|33093989|gb|CF053983.1|CF053983
EST:     CTGGAAGAGTGGTCATAACTTTCAACAAGATCAGACTATAGTCCAGCCTG                         GATCACTGGAGAGTGAGGCATGCATATATGCCCTCTCATATGACGTGAGCG
genomic: CTGGAAGAGTGGTCATAACTTTCAACAAGATCAGACTATAGTCCAGCCTGgtaagttttc ... ccattttcagGATCACTGGAGAGTGAGGCATGCATATATGCCCTCTCATATGACGTGAGCG
EST: gi|5055899|gb|AI734786.1|AI734786
EST:     CTGGAAGAGTGGTCATAACTTTCAACAAGATCAGACTATAGTCCAGCCTG                         GATCACTGGAGAGTGAGGCATGCATATATGCCCTCTCATATGACGTGAGCG
genomic: CTGGAAGAGTGGTCATAACTTTCAACAAGATCAGACTATAGTCCAGCCTGgtaagttttc ... ccattttcagGATCACTGGAGAGTGAGGCATGCATATATGCCCTCTCATATGACGTGAGCG
EST: gi|37382890|gb|CF628417.1|CF628417
EST:     CTGGAAGAGTGGTCATAACTTTCAACAAGATCAGACTATAGTCCAGCCTG                         GATCACTGGAGAGTGAGGCATGCATATATGCCCTCTCATATGACGTGAGCG
genomic: CTGGAAGAGTGGTCATAACTTTCAACAAGATCAGACTATAGTCCAGCCTGgtaagttttc ... ccattttcagGATCACTGGAGAGTGAGGCATGCATATATGCCCTCTCATATGACGTGAGCG
EST: gi|101383542|gb|EB813827.1|EB813827
EST:     CTGGAAGAGTGGTCATAACTTTCAACAAGATCAGACTATAGTCCAGCCTG                         GATCACTGGAGAGTGAGGCATGCATAT--GCCCTCTCATATGACGTGAGCG
genomic: CTGGAAGAGTGGTCATAACTTTCAACAAGATCAGACTATAGTCCAGCCTGgtaagttttc ... ccattttcagGATCACTGGAGAGTGAGGCATGCATATATGCCCTCTCATATGACGTGAGCG
EST: gi|32933315|gb|CF038127.1|CF038127
EST:     CTGGAAGAGTGGTCATAACTTTCAACAAGATCGGACTATAGTCCAGCCTG                         GATCACTGGAGAGTGAGGCATGCACATATGCCCTCTCATATGACGTGAGCG
genomic: CTGGAAGAGTGGTCATAACTTTCAACAAGATCAGACTATAGTCCAGCCTGgtaagttttc ... ccattttcagGATCACTGGAGAGTGAGGCATGCATATATGCCCTCTCATATGACGTGAGCG
EST: gi|94478033|gb|EB706991.1|EB706991
EST:     CGGGAAGAGTGGTCATAACTTTCAACAAGATCAGACTATAGTCCAGCCTG                         GATCACTGGAGAGTGAGGCATGCATATATGCCCTCTCATATGACGTGAGCG
genomic: CTGGAAGAGTGGTCATAACTTTCAACAAGATCAGACTATAGTCCAGCCTGgtaagttttc ... ccattttcagGATCACTGGAGAGTGAGGCATGCATATATGCCCTCTCATATGACGTGAGCG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTCAACAAGATCAGACTATAGTCCAGCCTGgtaagttttcatttgaatcacgcaggcaccgataataggagataagcaactctgtttcgagtctccacaatgtttttcctcatatgagaggttcttgaga

- - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA