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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCACAAAATAGTGATAGTTGAAGGGAACTATCTGTTACTGGAAGAAGATGTTTGGACCGAAATTAGAGACTTGTTTGATGAGAAATGgtgagtatgcagactccgcaactgtaatttgcagtaatacatactttttttaatgtcccttcatcatcttttcgactttggtgtgaaaatagtagtttctaatggccaaattactttcttag

Basic information

species Zea mays
transcript GRMZM2G035338_T02
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G035338_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os12g40880.2 (Oryza sativa), 5'ss of exon 8
-------------GCACAAAATAGTGATAGTTGAAGGGAACTATCTGTTACTGGAAGAAGATGTTTGGACCGAAATTAGAGACTTGTTTGATGAGAAATGgtgagtatgcagactccgcaactgtaa----tttgcagtaatacatactttttttaatgtcccttcatcatcttttcgactttggtgtgaaaatagtagtttctaatggccaaattactttcttag
              |||||||||||||| || ||||| || ||||| ||||||||||||||||  ||||  || ||||||| |||||||||||| ||||||||||||||| | ||   |||   |||    |||||||  ||| | | |  |  |    |       | |  ||    | ||||| |         ||  |                         
ATGATTTTGGCAGACACAAAATAGTGATTGTCGAAGGCAATTATCTATTACTGGAAGAAGATGCCTGGAGGGACATTAGAGCCTTGTTTGATGAAAAATGgtgagtatgctggctttacaatcataaataatttgcagcgatata-attgatcgtgccatgagccagtgag-ttccaaattttggagcttgttacttaactc------------------------

upper sequence: GRMZM2G035338_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os12g40880.1 (Oryza sativa), 5'ss of exon 9
GCACAAAATAGTGATAGTTGAAGGGAACTATCTGTTACTGGAAGAAGATGTTTGGACCGAAATTAGAGACTTGTTTGATGAGAAATGgtgagtatgcagactccgcaactgt----aatttgcagtaatacatactttttttaatgtcccttcatcatcttttcgactttggtgtgaaaatagtagtttctaatggccaaattactttcttag
 |||||||||||||| || ||||| || ||||| ||||||||||||||||  ||||  || ||||||| |||||||||||| ||||||||||||||| | ||   |||   |    |||||||||  ||| | | |  |  |    |       | |  ||    | ||||| |         ||  |                         
ACACAAAATAGTGATTGTCGAAGGCAATTATCTATTACTGGAAGAAGATGCCTGGAGGGACATTAGAGCCTTGTTTGATGAAAAATGgtgagtatgctggctttacaatcataaataatttgcagcgatata-attgatcgtgccatgagccagtgag-ttccaaattttggagcttgttacttaactc------------------------
















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|37389954|gb|CF632202.1|CF632202
EST:     CTGGAAGAAGATGTTTGGACCGAAATTAGAGACTTGTTTGATGAGAAATG                         GTTCATTGACATTGACATCGATATCTCCATGCAAAGAGTGCTCAAGAGACA
genomic: CTGGAAGAAGATGTTTGGACCGAAATTAGAGACTTGTTTGATGAGAAATGgtgagtatgc ... actttcttagGTTCATTGACATTGACATTGATATCTCCATGCAAAGAGTGCTCAAGAGACA
EST: gi|60350250|gb|DN217223.1|DN217223
EST:     CTGGAAGAAGATGTTTGGACCGAAATTAGAGACTTGTTTGATGAGAAATG                         GTTCATTGACATTGACATCGATATCTCCATGCAAAGAGTGCTCAAGAGACA
genomic: CTGGAAGAAGATGTTTGGACCGAAATTAGAGACTTGTTTGATGAGAAATGgtgagtatgc ... actttcttagGTTCATTGACATTGACATTGATATCTCCATGCAAAGAGTGCTCAAGAGACA
EST: gi|211338441|gb|FL481251.1|FL481251
EST:     GAAGAAGATGTTTGGACCGAAATTAGAGACTTGTTTGATGAGAAATG                         GTTCATTGACATTGACATCGATATCTCCATGCAAAGAGTGCTCAAGAGACA
genomic: GAAGAAGATGTTTGGACCGAAATTAGAGACTTGTTTGATGAGAAATGgtgagtatgc ... actttcttagGTTCATTGACATTGACATTGATATCTCCATGCAAAGAGTGCTCAAGAGACA
EST: gi|78179609|gb|DV549982.1|DV549982
EST:     CTGGAAGAAGATGTTTGGACCGAAATTAGAGACTTGTTTGATGAGAAATG                         GTTCATTGACATTGACATCGATATCTCCATGCAAAGAGTGCTCAAGAGACA
genomic: CTGGAAGAAGATGTTTGGACCGAAATTAGAGACTTGTTTGATGAGAAATGgtgagtatgc ... actttcttagGTTCATTGACATTGACATTGATATCTCCATGCAAAGAGTGCTCAAGAGACA
EST: gi|211102107|gb|FL031912.1|FL031912
EST:     CTGGAAGAAGATGTTTGGACCGAAATTAGAGACTTGTTTGATGAGAAATG                         GTTCATTGACATTGACATTGATATCTCCATGCAAAGAGTGCTCAAGAGACA
genomic: CTGGAAGAAGATGTTTGGACCGAAATTAGAGACTTGTTTGATGAGAAATGgtgagtatgc ... actttcttagGTTCATTGACATTGACATTGATATCTCCATGCAAAGAGTGCTCAAGAGACA
EST: gi|211102106|gb|FL031911.1|FL031911
EST:     CTGGAAGAAGATGTTTGGACCGAAATTAGAGACTTGTTTGATGAGAAATG                         GTTCATTGACATTGACATTGATATCTCCATGCAAAGAGTGCTCAAGAGACA
genomic: CTGGAAGAAGATGTTTGGACCGAAATTAGAGACTTGTTTGATGAGAAATGgtgagtatgc ... actttcttagGTTCATTGACATTGACATTGATATCTCCATGCAAAGAGTGCTCAAGAGACA
EST: gi|88751321|gb|DY535462.1|DY535462
EST:     CTGGAAGAAGATGTTTGGACCGAAATTAGAGACTTGTTTGATGAGAAATG                         GTTCATTGACATTGACATTGATATCTCCATGCAAAGAGTGCTCAAGAGACA
genomic: CTGGAAGAAGATGTTTGGACCGAAATTAGAGACTTGTTTGATGAGAAATGgtgagtatgc ... actttcttagGTTCATTGACATTGACATTGATATCTCCATGCAAAGAGTGCTCAAGAGACA
EST: gi|6952677|gb|AW424745.1|AW424745
EST:     CTGGAAGAAGATGTTTGGACCGAAATTAGAGACTTGTTTGATGAGAAATG                         GTTCATTGACATTGACATCGATATCTCCATGCAAAGAGTGCTCAAGAGACA
genomic: CTGGAAGAAGATGTTTGGACCGAAATTAGAGACTTGTTTGATGAGAAATGgtgagtatgc ... actttcttagGTTCATTGACATTGACATTGATATCTCCATGCAAAGAGTGCTCAAGAGACA
EST: gi|211532388|gb|FL468965.1|FL468965
EST:     CTGGAAGAAGATGTTTGGACCGAAATTAGAGACTTGTTTGATGAGAAATG                         GTTCATTGACATTGACATTGATATCTCCATGCAAAGAGTGCTCAAGAGACA
genomic: CTGGAAGAAGATGTTTGGACCGAAATTAGAGACTTGTTTGATGAGAAATGgtgagtatgc ... actttcttagGTTCATTGACATTGACATTGATATCTCCATGCAAAGAGTGCTCAAGAGACA
EST: gi|89249957|gb|DY621743.1|DY621743
EST:     CTGGAAGAAGATGTTTGGACCGAAATTAGAGACTTGTTTGATGAGAAATG                         GTTCATTGACATTGACATTGATATCTCCATGCAAAGAGTGCTCAAGAGACA
genomic: CTGGAAGAAGATGTTTGGACCGAAATTAGAGACTTGTTTGATGAGAAATGgtgagtatgc ... actttcttagGTTCATTGACATTGACATTGATATCTCCATGCAAAGAGTGCTCAAGAGACA
EST: gi|24765829|gb|CA400988.1|CA400988
EST:     CTGGAAGAAGATGTTTGGACCGAAATTAGAGACTTGTTTGATGAGAAATG                         GTTCATTGACATTGCCATTGATATCTCCATGCAAAGAGTGCTCAAGAGACA
genomic: CTGGAAGAAGATGTTTGGACCGAAATTAGAGACTTGTTTGATGAGAAATGgtgagtatgc ... actttcttagGTTCATTGACATTGACATTGATATCTCCATGCAAAGAGTGCTCAAGAGACA
EST: gi|149082265|gb|EE171450.2|EE171450
EST:     CTGGAAGAAGATGTTTGGACCGAAATTAGAGACTTGTTTGATGAGAAATG                         GTTCATTGACATTGACATTGATATCTCCATGCAAAGAGTGCTCAAGAGACA
genomic: CTGGAAGAAGATGTTTGGACCGAAATTAGAGACTTGTTTGATGAGAAATGgtgagtatgc ... actttcttagGTTCATTGACATTGACATTGATATCTCCATGCAAAGAGTGCTCAAGAGACA
EST: gi|94472538|gb|EB701496.1|EB701496
EST:     CTGGAAGAAGATGTTTGGACCGAAATTAGAGACTTGTTTGATGAGAAATG                         GTTCATTGACATTGACATTGATATCTCCATGCAAAGAGTGCTCAAGAGACA
genomic: CTGGAAGAAGATGTTTGGACCGAAATTAGAGACTTGTTTGATGAGAAATGgtgagtatgc ... actttcttagGTTCATTGACATTGACATTGATATCTCCATGCAAAGAGTGCTCAAGAGACA
EST: gi|71766668|gb|DR964605.1|DR964605
EST:     CTGGAAGAAGATGTTTGGACCGAAATTAGAGACTTGTTTGATGAGAAATG                         GTTCATTGACATTGACATTGATATCTCCATGCAAAGAGTGCTCAAGAGACA
genomic: CTGGAAGAAGATGTTTGGACCGAAATTAGAGACTTGTTTGATGAGAAATGgtgagtatgc ... actttcttagGTTCATTGACATTGACATTGATATCTCCATGCAAAGAGTGCTCAAGAGACA
EST: gi|86470370|gb|DY236740.1|DY236740
EST:     CTGGAAGAAGATGTTTGGACCGAAATTAGAGACTTGTTTGATGAGAAATG                         GTTCATTGACATTGCCATTGATATCTCCATGCAAAGAGTGCTCAAGAGACA
genomic: CTGGAAGAAGATGTTTGGACCGAAATTAGAGACTTGTTTGATGAGAAATGgtgagtatgc ... actttcttagGTTCATTGACATTGACATTGATATCTCCATGCAAAGAGTGCTCAAGAGACA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCACAAAATAGTGATAGTTGAAGGGAACTATCTGTTACTGGAAGAAGATGTTTGGACCGAAATTAGAGACTTGTTTGATGAGAAATGgtgagtatgcagactccgcaactgtaatttgcagtaatacatactttttttaatgtcccttcatcatcttttcgactttggtgtgaaaatagtagtttctaatggccaaattactttcttag

- - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - AAGATG