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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTTTCAAAATAAAGGGTCAAAAGAAAGATGAGGCAGCAAGTGCTACTGGAAAGGCCCCTGTTAAGAAACAGTCTGCTGGGGAGCTCCGTCTTCATAAAGgtttgttgaattataggtgaaatatttcttgtatcaatctgctccttgtttttaatacacaacatgtatttatataatcccaaataactgaaaagttatc...

Basic information

species Zea mays
transcript GRMZM2G115939_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G115939_T03 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os10g11260.4 (Oryza sativa), 5'ss of exon 2
CTTTTCAAAATAAAGGGTCAAAAGAAAGATGAGGCAGCAAGTGCTACTGGAAAGGCCCCTGTTAAGAAACAGTCTGCTGGGGAGCTCCGTCTTCATAAAGgtttgttgaattataggtgaaatatttcttgtatcaatctgctccttgtttttaatacacaacatgtatttatata---atcccaaataactgaaaagttatc-----
||| |||||||||||| | ||||||||||  |||||||||||||| |||||||||| ||||| ||||| || |||||||| |||||||||||||| ||||||   |||| |||||| |||         |||    |  | ||  | ||  | || |||     | |    ||  |   | ||   | |    ||   |||||     
CTTATCAAAATAAAGGATAAAAAGAAAGAGCAGGCAGCAAGTGCTGCTGGAAAGGCTCCTGTGAAGAAGCAATCTGCTGGAGAGCTCCGTCTTCACAAAGgtgcattgagttatagatga--------ctgtcagcacttccttttggtcataaaaacatgttgtctggacattgacagagccttcacagtgcaatctttatctctaa
















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|211132803|gb|FL366559.1|FL366559
EST:     AAAGGCCCCTGTTAAGAAACAGTCTGCTGGGGAGCTCCGTCTTCATAAAG                         ATATTAGTGAGCTCAACCTGCCGAAGACCACATCAATTTCTTTTCCCAATG
genomic: AAAGGCCCCTGTTAAGAAACAGTCTGCTGGGGAGCTCCGTCTTCATAAAGgtttgttgaa ... aatgttccagATATTAGTGAGCTCAACCTGCCGAAGACCACATCAATTTCTTTTCCCAATG
EST: gi|211373002|gb|FL342998.1|FL342998
EST:     AAAGGCCCCTGTTAAGAAACAGTCTGCTGGGGAGCTCCGTCTTCATAAAG                         ATATTAGTGAGCTCAACCTGCCGAAGACCACATCAATTTCTTTTCCCAATG
genomic: AAAGGCCCCTGTTAAGAAACAGTCTGCTGGGGAGCTCCGTCTTCATAAAGgtttgttgaa ... aatgttccagATATTAGTGAGCTCAACCTGCCGAAGACCACATCAATTTCTTTTCCCAATG
EST: gi|32801453|gb|CD953689.1|CD953689
EST:     TAAGAAACAGTCTGCTGGGGAGCTCCGTCTTCATAAAG                         ATATTAGTGAGCTCAACCTGCCGAAGACCACATCAATTTCTTTTCCCAATG
genomic: TAAGAAACAGTCTGCTGGGGAGCTCCGTCTTCATAAAGgtttgttgaa ... aatgttccagATATTAGTGAGCTCAACCTGCCGAAGACCACATCAATTTCTTTTCCCAATG
EST: gi|9028438|gb|BE238583.1|BE238583
EST:     AAAGGCCCCTGTTAAGAAACAGTCTGCTGGGGAGCTCCGTCTTCATAAAG                         ATATTAGTGAGCTCAACCTGCCGAAGACCACATCAATTTCTTTTCCCAATG
genomic: AAAGGCCCCTGTTAAGAAACAGTCTGCTGGGGAGCTCCGTCTTCATAAAGgtttgttgaa ... aatgttccagATATTAGTGAGCTCAACCTGCCGAAGACCACATCAATTTCTTTTCCCAATG
EST: gi|211398788|gb|FL318386.1|FL318386
EST:     AAAGGCCCCTGTTAAGAAACAGTCTGCTGGGGAGCTCCGTCTTCATAAAG                         ATATTAGTGAGCTCAACCTGCCGAAGACCACATCAATTTCTTTTCCCAATG
genomic: AAAGGCCCCTGTTAAGAAACAGTCTGCTGGGGAGCTCCGTCTTCATAAAGgtttgttgaa ... aatgttccagATATTAGTGAGCTCAACCTGCCGAAGACCACATCAATTTCTTTTCCCAATG
EST: gi|32915063|gb|CF019875.1|CF019875
EST:     AAAGGCCCCTGTTAAGAAACAGTCTGCTGGGGAGCTCCGTCTTCATAAAG                         ATATTAGTGAGCTCAACCTGCCGAAGACCACATCAATTTCTTTTCCCAATG
genomic: AAAGGCCCCTGTTAAGAAACAGTCTGCTGGGGAGCTCCGTCTTCATAAAGgtttgttgaa ... aatgttccagATATTAGTGAGCTCAACCTGCCGAAGACCACATCAATTTCTTTTCCCAATG
EST: gi|211259767|gb|FL311710.1|FL311710
EST:     AAAGGCCCCTGTTAAGAAACAGTCTGCTGGGGAGCTCCGTCTTCATAAAG                         ATATTAGTGAGCTCAACCTGCCGAAGACCACATCAATTTCTTTTCCCAATG
genomic: AAAGGCCCCTGTTAAGAAACAGTCTGCTGGGGAGCTCCGTCTTCATAAAGgtttgttgaa ... aatgttccagATATTAGTGAGCTCAACCTGCCGAAGACCACATCAATTTCTTTTCCCAATG
EST: gi|211291785|gb|FL131028.1|FL131028
EST:     AAAGGCCCCTGTTAAGAAACAGTCTGCTGGGGAGCTCCGTCTTCATAAAG                         ATATTAGTGAGCTCAACCTGCCGAAGACCACATCAATTTCTTTTCCCAATG
genomic: AAAGGCCCCTGTTAAGAAACAGTCTGCTGGGGAGCTCCGTCTTCATAAAGgtttgttgaa ... aatgttccagATATTAGTGAGCTCAACCTGCCGAAGACCACATCAATTTCTTTTCCCAATG
EST: gi|78077789|gb|DV506218.1|DV506218
EST:     AAAGGCCCCTGTTAAGAAACAGTCTGCTGGGGAGCTCCGTCTTCATAAAG                         ATATTAGTGAGCTCAACCTGCCGAAGACCACATCAATTTCTTTTCCCAATG
genomic: AAAGGCCCCTGTTAAGAAACAGTCTGCTGGGGAGCTCCGTCTTCATAAAGgtttgttgaa ... aatgttccagATATTAGTGAGCTCAACCTGCCGAAGACCACATCAATTTCTTTTCCCAATG
EST: gi|24462527|gb|BM660058.1|BM660058
EST:     AAAGGCCCCTGTTAAGAAACAGTCTGCTGGGGAGCTCCGTCTTCATAAAG                         ATATTAGTGAGCTCAACCTGCCGAAGACNACATCAATTTCTTTTCCCAATG
genomic: AAAGGCCCCTGTTAAGAAACAGTCTGCTGGGGAGCTCCGTCTTCATAAAGgtttgttgaa ... aatgttccagATATTAGTGAGCTCAACCTGCCGAAGACCACATCAATTTCTTTTCCCAATG
EST: gi|211350032|gb|FL354315.1|FL354315
EST:     AAAGGCCCCTGTTAAGAAACAGTCTGCTGGGGAGCTCCGTCTTCATAAAG                         ATATTAGTGAGCTCAACCTGCCGAAGACCACATCAATTTCTTTTCCCAATG
genomic: AAAGGCCCCTGTTAAGAAACAGTCTGCTGGGGAGCTCCGTCTTCATAAAGgtttgttgaa ... aatgttccagATATTAGTGAGCTCAACCTGCCGAAGACCACATCAATTTCTTTTCCCAATG
EST: gi|211320075|gb|FL327296.1|FL327296
EST:     AAAGGCCCCTGTTAAGAAACAGTCTGCTGGGGAGCTCCGTCTTCATAAAG                         ATATTAGTGAGCTCAACCTGCCGAAGACCACATCAATTTCTTTTCCCAATG
genomic: AAAGGCCCCTGTTAAGAAACAGTCTGCTGGGGAGCTCCGTCTTCATAAAGgtttgttgaa ... aatgttccagATATTAGTGAGCTCAACCTGCCGAAGACCACATCAATTTCTTTTCCCAATG
EST: gi|211153912|gb|FL325451.1|FL325451
EST:     AAAGGCCCCTGTTAAGAAACAGTCTGCTGGGGAGCTCCGTCTTCATAAAG                         ATATTAGTGAGCTCAACCTGCCGAAGACCACATCAATTTCTTTTCCCAATG
genomic: AAAGGCCCCTGTTAAGAAACAGTCTGCTGGGGAGCTCCGTCTTCATAAAGgtttgttgaa ... aatgttccagATATTAGTGAGCTCAACCTGCCGAAGACCACATCAATTTCTTTTCCCAATG
EST: gi|50326390|gb|CO521516.1|CO521516
EST:     AAAGGCCCCTGTTAAGAAACAGTCTGCTGGGGAGCTCCGTCTTCATAAAG                         ATATTAGTGAGCTCAACCTGCCGAAGACCACATCAATTTCTTTTCCCAATG
genomic: AAAGGCCCCTGTTAAGAAACAGTCTGCTGGGGAGCTCCGTCTTCATAAAGgtttgttgaa ... aatgttccagATATTAGTGAGCTCAACCTGCCGAAGACCACATCAATTTCTTTTCCCAATG
EST: gi|211407585|gb|FL360124.1|FL360124
EST:     AAAGGCCCCTGTTAAGAAACAGTCTGCTGGGGAGCTCCGTCTTCATAAAG                         ATATTAGTGAGCTCAACCTGCCGAAGACCACATCAATTTCTTTTCCCAATG
genomic: AAAGGCCCCTGTTAAGAAACAGTCTGCTGGGGAGCTCCGTCTTCATAAAGgtttgttgaa ... aatgttccagATATTAGTGAGCTCAACCTGCCGAAGACCACATCAATTTCTTTTCCCAATG
EST: gi|211291786|gb|FL131029.1|FL131029
EST:     AAAGGCCCCTGTTAAGAAACAGTCTGCTGGGGAGCTCCGTCTTCATAAAG                         ATATTAGTGAGCTCAACCTGCCGAAGACCACATCAATTTCTTTTCCCAATG
genomic: AAAGGCCCCTGTTAAGAAACAGTCTGCTGGGGAGCTCCGTCTTCATAAAGgtttgttgaa ... aatgttccagATATTAGTGAGCTCAACCTGCCGAAGACCACATCAATTTCTTTTCCCAATG
EST: gi|91875000|gb|EB404957.1|EB404957
EST:     AAAGGCCCCTGTTAAGAAACAGTCTGCTGGGGAGCTCCGTCTTCATAAAG                         ATATTAGTGAGCTCAACCTGCCGAAGACCACATCAATTTCTTTTCCCAATG
genomic: AAAGGCCCCTGTTAAGAAACAGTCTGCTGGGGAGCTCCGTCTTCATAAAGgtttgttgaa ... aatgttccagATATTAGTGAGCTCAACCTGCCGAAGACCACATCAATTTCTTTTCCCAATG
EST: gi|211291784|gb|FL131027.1|FL131027
EST:     AAAGGCCCCTGTTAAGAAACAGTCTGCTGGGGAGCTCCGTCTTCATAAAG                         ATATTAGTGAGCTCAACCTGCCGAAGACCACATCAATTTCTTTTCCCAATG
genomic: AAAGGCCCCTGTTAAGAAACAGTCTGCTGGGGAGCTCCGTCTTCATAAAGgtttgttgaa ... aatgttccagATATTAGTGAGCTCAACCTGCCGAAGACCACATCAATTTCTTTTCCCAATG
EST: gi|19770077|gb|BQ034798.1|BQ034798
EST:     AAAGGCCCCTGTTAAGAAACAGTCTGCTGGGGAGCTCCGTCTTCATAAAG                         ATATTAGTGAGCTCAACCTGCCGAAGACCACATCAATTTCTTTTCCCAATG
genomic: AAAGGCCCCTGTTAAGAAACAGTCTGCTGGGGAGCTCCGTCTTCATAAAGgtttgttgaa ... aatgttccagATATTAGTGAGCTCAACCTGCCGAAGACCACATCAATTTCTTTTCCCAATG
EST: gi|211472923|gb|FL342170.1|FL342170
EST:     AAAGGCCCCTGTTAAGAAACAGTCTGCTGGGGAGCTCCGTCTTCATAAAG                         ATATTAGTGAGCTCAACCTGCCGAAGACCACATCAATTTCTTTTCCCAATG
genomic: AAAGGCCCCTGTTAAGAAACAGTCTGCTGGGGAGCTCCGTCTTCATAAAGgtttgttgaa ... aatgttccagATATTAGTGAGCTCAACCTGCCGAAGACCACATCAATTTCTTTTCCCAATG
EST: gi|211118985|gb|FL350356.1|FL350356
EST:     AAAGGCCCCTGTTAAGAAACAGTCTGCTGGGGAGCTCCGTCTTCATAAAG                         ATATTAGTGAGCTCAACCTGCCGAAGACCACATCAATTTCTTTTCCCAATG
genomic: AAAGGCCCCTGTTAAGAAACAGTCTGCTGGGGAGCTCCGTCTTCATAAAGgtttgttgaa ... aatgttccagATATTAGTGAGCTCAACCTGCCGAAGACCACATCAATTTCTTTTCCCAATG
EST: gi|71442439|gb|DR823489.1|DR823489
EST:     AAAGGCCCCTGTTAAGAAACAGTCTGCTGGGGAGCTCCGTCTTCATAAAG                         ATATTAGTGAGCTCAACCTGCCGAAGACCACATCAATTTCTTTTCCCAATG
genomic: AAAGGCCCCTGTTAAGAAACAGTCTGCTGGGGAGCTCCGTCTTCATAAAGgtttgttgaa ... aatgttccagATATTAGTGAGCTCAACCTGCCGAAGACCACATCAATTTCTTTTCCCAATG
EST: gi|211090799|gb|FL312054.1|FL312054
EST:     AAAGGCCCCTGTTAAGAAACAGTCTGCTGGGGAGCTCCGTCTTCATAAAG                         ATATTAGTGAGCTCAACCTGCCGAAGACCACATCAATTTCTTTTCCCAATG
genomic: AAAGGCCCCTGTTAAGAAACAGTCTGCTGGGGAGCTCCGTCTTCATAAAGgtttgttgaa ... aatgttccagATATTAGTGAGCTCAACCTGCCGAAGACCACATCAATTTCTTTTCCCAATG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTTTCAAAATAAAGGGTCAAAAGAAAGATGAGGCAGCAAGTGCTACTGGAAAGGCCCCTGTTAAGAAACAGTCTGCTGGGGAGCTCCGTCTTCATAAAGgtttgttgaattataggtgaaatatttcttgtatcaatctgctccttgtttttaatacacaacatgtatttatataatcccaaataactgaaaagttatc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caaataac