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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagattgggcacgaatgctaatacacaatgggtttgatttttggagcatccaagttttttttagtgtttctcctaacacgggtgaccactggtatcgcagGGTTGTAATCTCCACATCACATCAGTGGGGAGCAGAGCTCACGAAACTGAACGTGCCTGCCGACTGGAAAG

Basic information

species Zea mays
transcript GRMZM2G158489_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G158489_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os07g09000.1 (Oryza sativa), 3'ss of exon 8
tagattgggcacgaatgctaatacacaatgggtttgatttttggagcatcca-agttttttttagtgtttctcctaacacgggtgaccactggtatcgcagGGTTGTAATCTCCACATCACATCAGTGGGGAGCAGAGCTCACGAAACTGAACGTGCCTGCCGACTGGAAAG
|  |           |  ||| ||  ||||   |    || |  |   |||  ||  | | || || | | |  ||||| |  || |  ||| || |||||||  |||||||||||||| ||||| |||||||||||||| || || ||||| || ||||| ||||||||||
tgcaagaaatgtttctcttaaaactaaatgacctgtccttctccaatttccggagcatctctttgtttatgttataacatga-tgcctgctgataccgcagGGCCGTAATCTCCACATCGCATCAATGGGGAGCAGAGCTGACAAAGCTGAATGTCCCTGCTGACTGGAAAG
















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|149105792|gb|EE291382.2|EE291382
EST:     GTCCATCTTGGCTCCCCAGTCACCTCCATTGAATTTTGTCCTAGTGAAAG                         GGTTGTAATCTCCACATCACATCAGTGGGGAGCAGAGCTCACGAAACTGAA
genomic: GTCCATCTTGGCTCCCCAGTCACCTCCATTGAATTTTGTCCTAGTGAAAGgtaactacag ... ggtatcgcagGGTTGTAATCTCCACATCACATCAGTGGGGAGCAGAGCTCACGAAACTGAA
EST: gi|211501284|gb|FL248092.1|FL248092
EST:     GTCCATCTTGGCTCCCCAGTCACCTCCATTGAATTTTGTCCTACTGAAAG                         GGTTGTAATCTCCACATCACATCAGTGGGGAGCAGAGCTCACGAAACTGAA
genomic: GTCCATCTTGGCTCCCCAGTCACCTCCATTGAATTTTGTCCTAGTGAAAGgtaactacag ... ggtatcgcagGGTTGTAATCTCCACATCACATCAGTGGGGAGCAGAGCTCACGAAACTGAA
EST: gi|71308208|gb|DR790336.1|DR790336
EST:     GTCCATCTTGGCTCCCCAGTCACCTCCATTGAATTTTGTCCTAGTGAAAG                         GGTTGTAATCTCCACATCACATCAGTGGGGAGCAGAGCTCACGAAACTGAA
genomic: GTCCATCTTGGCTCCCCAGTCACCTCCATTGAATTTTGTCCTAGTGAAAGgtaactacag ... ggtatcgcagGGTTGTAATCTCCACATCACATCAGTGGGGAGCAGAGCTCACGAAACTGAA
EST: gi|32837118|gb|CD976796.1|CD976796
EST:     GTCCATCTTGGCTCCCCAGTCACCTCCATTGAATTTTGTCCTAGTGAAAG                         GGTTGTAATCTCCACATCACATCAGTGGGGAGCAGAGCTCACGAAACTGAA
genomic: GTCCATCTTGGCTCCCCAGTCACCTCCATTGAATTTTGTCCTAGTGAAAGgtaactacag ... ggtatcgcagGGTTGTAATCTCCACATCACATCAGTGGGGAGCAGAGCTCACGAAACTGAA
EST: gi|76010774|gb|DT937944.1|DT937944
EST:     GTCCATCTTGGCTCCCCAGTCACCTCCATTGAATTTTGTCCTAGTGAAAG                         GGTTGTAATCTCCACATCACATCAGTGGGGAGCAGAGCTCACGAAACTGAA
genomic: GTCCATCTTGGCTCCCCAGTCACCTCCATTGAATTTTGTCCTAGTGAAAGgtaactacag ... ggtatcgcagGGTTGTAATCTCCACATCACATCAGTGGGGAGCAGAGCTCACGAAACTGAA
EST: gi|89251668|gb|DY623454.1|DY623454
EST:     TCTTGGCTCCCCAGTCCCCTCCATTGAATTTTGTCCTAGTGAAAG                         GGTTGTAATTTCCCCATCCCATCAGTGGGGGGCGGAGCTCACGAAACTGAA
genomic: TCTTGGCTCCCCAGTCACCTCCATTGAATTTTGTCCTAGTGAAAGgtaactacag ... ggtatcgcagGGTTGTAATCTCCACATCACATCAGTGGGGAGCAGAGCTCACGAAACTGAA
EST: gi|89760375|gb|DY688809.1|DY688809
EST:     GTCCATCTTGGCTCCCCAGTCACCTCCATTGAATTTTGTCCTAGTGAAAG                         GGTTGTAATCTCCACATCACATCAGTGGGGAGCGGAGCTCACGAAACTGAA
genomic: GTCCATCTTGGCTCCCCAGTCACCTCCATTGAATTTTGTCCTAGTGAAAGgtaactacag ... ggtatcgcagGGTTGTAATCTCCACATCACATCAGTGGGGAGCAGAGCTCACGAAACTGAA
EST: gi|211501285|gb|FL248093.1|FL248093
EST:     GTCCATCTTGGCTCCCCAGTCACCTCCATTGAATTTTGTCCTAGTGAAAG                         GGTTGTAATCTCCACATCACATCAGTGGGGAGCAGAGCTCACGAAACTGAA
genomic: GTCCATCTTGGCTCCCCAGTCACCTCCATTGAATTTTGTCCTAGTGAAAGgtaactacag ... ggtatcgcagGGTTGTAATCTCCACATCACATCAGTGGGGAGCAGAGCTCACGAAACTGAA
EST: gi|78079988|gb|DV508400.1|DV508400
EST:     GTCCATCTTGGCTCCCCAGTCACCTCCATTGAATTTTGTCCTAGTGAAAG                         GGTTGTAATCTCCACATCACATCAGTGGGGAGCAGAGCTCACGAAACTGAA
genomic: GTCCATCTTGGCTCCCCAGTCACCTCCATTGAATTTTGTCCTAGTGAAAGgtaactacag ... ggtatcgcagGGTTGTAATCTCCACATCACATCAGTGGGGAGCAGAGCTCACGAAACTGAA
EST: gi|6021240|gb|AW066168.1|AW066168
EST:     GTCCATCTTGGCTCCCCAGTCACCTCCATTGAATTTTGTCCTAGTGAAAG                         GGTTGTAATCTCCACATCACATCAGTGGGGAGCAGAGCTCACGAAACTGAA
genomic: GTCCATCTTGGCTCCCCAGTCACCTCCATTGAATTTTGTCCTAGTGAAAGgtaactacag ... ggtatcgcagGGTTGTAATCTCCACATCACATCAGTGGGGAGCAGAGCTCACGAAACTGAA
EST: gi|211411697|gb|FL434955.1|FL434955
EST:     CTCCATTGAATTTTGTCCTACTGAAAG                         GGTTGTAATCTCCACATCACATCAGTGGGGAGCACAGCTCACGAAACTGAA
genomic: CTCCATTGAATTTTGTCCTAGTGAAAGgtaactacag ... ggtatcgcagGGTTGTAATCTCCACATCACATCAGTGGGGAGCAGAGCTCACGAAACTGAA
EST: gi|93017687|gb|EB643207.1|EB643207
EST:     GTCCATCTTGGCTCCCCAGTCACCTCCATTGAATTTTGTCCTAGTGAAAG                         GGTTGTAATCTCCACATCACATCAGTGGGGAGCAGAGCTCACGAAACTGAA
genomic: GTCCATCTTGGCTCCCCAGTCACCTCCATTGAATTTTGTCCTAGTGAAAGgtaactacag ... ggtatcgcagGGTTGTAATCTCCACATCACATCAGTGGGGAGCAGAGCTCACGAAACTGAA
EST: gi|86474634|gb|DY241004.1|DY241004
EST:     GTCCATCTTGGCTCCCCAGTCACCTCCATTGAATTTTGTCCTAGTGAAAG                         GGTTGTAATCTCCACATCACATCAGTGGGGAGCAGAGCTCACGAAACTGAA
genomic: GTCCATCTTGGCTCCCCAGTCACCTCCATTGAATTTTGTCCTAGTGAAAGgtaactacag ... ggtatcgcagGGTTGTAATCTCCACATCACATCAGTGGGGAGCAGAGCTCACGAAACTGAA
EST: gi|78115282|gb|DV533670.1|DV533670
EST:     GTCCATCTTGGCTCCCCAGTCACCTCCATTGAATTTTGTCCTAGTGAAAG                         GGTTGTAATCTCCACATCACATCAGTGGGGAGCAGAGCTCACGAAACTGAA
genomic: GTCCATCTTGGCTCCCCAGTCACCTCCATTGAATTTTGTCCTAGTGAAAGgtaactacag ... ggtatcgcagGGTTGTAATCTCCACATCACATCAGTGGGGAGCAGAGCTCACGAAACTGAA
EST: gi|76287602|gb|DV027170.1|DV027170
EST:     GTCCATCTTGGCTCCCCAGTCACCTCCATTGAATTTTGTCCTAGTGAAAG                         GGTTGTAATCTCCACATCACATCAGTGGGGAGCAGAGCTCACGAAACTGAA
genomic: GTCCATCTTGGCTCCCCAGTCACCTCCATTGAATTTTGTCCTAGTGAAAGgtaactacag ... ggtatcgcagGGTTGTAATCTCCACATCACATCAGTGGGGAGCAGAGCTCACGAAACTGAA
EST: gi|71596195|gb|DR906946.1|DR906946
EST:     GTCCATCTTGGCTCCCCAGTCACCTCCATTGAATTTTGTCCTAGTGAAAG                         GGTTGTAATCTCCACATCACATCAGTGGGGAGCAGAGCTCACGAAACTGAA
genomic: GTCCATCTTGGCTCCCCAGTCACCTCCATTGAATTTTGTCCTAGTGAAAGgtaactacag ... ggtatcgcagGGTTGTAATCTCCACATCACATCAGTGGGGAGCAGAGCTCACGAAACTGAA
EST: gi|16921161|gb|BM075014.1|BM075014
EST:     GTCCATCTTGGCTCCCCAGTCACCTCCATTGAATTTTGTCCTAGTGAAAG                         GGTTGTAATCTCCACATCACATCAGTGGGGAGCAGAGCTCACGAAACTGAA
genomic: GTCCATCTTGGCTCCCCAGTCACCTCCATTGAATTTTGTCCTAGTGAAAGgtaactacag ... ggtatcgcagGGTTGTAATCTCCACATCACATCAGTGGGGAGCAGAGCTCACGAAACTGAA
EST: gi|91053037|gb|EB163455.1|EB163455
EST:     GTCCATCTTGGCTCCCCAGTCACCTCCATTGAATTTTGTCTTAGTGAAAG                         GGTTGTAATCTCCACATCACATCAGTGGGGAGCAGAGCTCACGAAACTGAA
genomic: GTCCATCTTGGCTCCCCAGTCACCTCCATTGAATTTTGTCCTAGTGAAAGgtaactacag ... ggtatcgcagGGTTGTAATCTCCACATCACATCAGTGGGGAGCAGAGCTCACGAAACTGAA
EST: gi|74237401|gb|DT645315.1|DT645315
EST:     GTCCATCTTGGCTCCCCAGTCACCTCCATTGAATTTTGTCCTAGTGAAAG                         GGTTGTAATCTCCACATCACATCAGTGGGGAGCAGAGCTCACGAAACTGAA
genomic: GTCCATCTTGGCTCCCCAGTCACCTCCATTGAATTTTGTCCTAGTGAAAGgtaactacag ... ggtatcgcagGGTTGTAATCTCCACATCACATCAGTGGGGAGCAGAGCTCACGAAACTGAA
EST: gi|50329947|gb|CO525073.1|CO525073
EST:     GTCCATCTTGGCTCCCCAGTCACCTCCATTGAATTTTGTCCTAGTGAAAG                         GGTTGTAATCTCCACATCACATCAGTGGGGAGCAGAGCTCACGAAACTGAA
genomic: GTCCATCTTGGCTCCCCAGTCACCTCCATTGAATTTTGTCCTAGTGAAAGgtaactacag ... ggtatcgcagGGTTGTAATCTCCACATCACATCAGTGGGGAGCAGAGCTCACGAAACTGAA
EST: gi|86470686|gb|DY237056.1|DY237056
EST:     GTCCATCTTGGCTCCCCAGTCACCTCCATTGAATTTTGTCCTAGTGAAAG                         GGTTGTAATCTCCACATCACATCAGTGGGGAGCAGAGCTCACGAAACTGAA
genomic: GTCCATCTTGGCTCCCCAGTCACCTCCATTGAATTTTGTCCTAGTGAAAGgtaactacag ... ggtatcgcagGGTTGTAATCTCCACATCACATCAGTGGGGAGCAGAGCTCACGAAACTGAA
EST: gi|74236583|gb|DT644497.1|DT644497
EST:     GTCCATCTTGGCTCCCCAGTCACCTCCATTGAATTTTGTCCTAGTGAAAG                         GGTTGTAATCTCCACATCACATCAGTGGGGAGCAGAGCTCACGAAACTGAA
genomic: GTCCATCTTGGCTCCCCAGTCACCTCCATTGAATTTTGTCCTAGTGAAAGgtaactacag ... ggtatcgcagGGTTGTAATCTCCACATCACATCAGTGGGGAGCAGAGCTCACGAAACTGAA
EST: gi|211115136|gb|FL479369.1|FL479369
EST:     GTCCATCTTGGCTCCCCAGTCACCTCCATTGAATTTTGTCCTACTGAAAG                         GGTTGTAATCTCCACATCACATCAGTGGGGAGCAGAGCTCACGAAACTGAA
genomic: GTCCATCTTGGCTCCCCAGTCACCTCCATTGAATTTTGTCCTAGTGAAAGgtaactacag ... ggtatcgcagGGTTGTAATCTCCACATCACATCAGTGGGGAGCAGAGCTCACGAAACTGAA
EST: gi|88748364|gb|DY532505.1|DY532505
EST:     GTCCATCTTGGCTCCCCAGTCACCTCCATTGAATTTTGTCCTAGTGAAAG                         GGTTGTAATCTCCACATCACATCAGTGGGGAGCAGAGCTCACGAAACTGAA
genomic: GTCCATCTTGGCTCCCCAGTCACCTCCATTGAATTTTGTCCTAGTGAAAGgtaactacag ... ggtatcgcagGGTTGTAATCTCCACATCACATCAGTGGGGAGCAGAGCTCACGAAACTGAA
EST: gi|32938162|gb|CF042981.1|CF042981
EST:     GACCATCTTGGCTCCCCAGTCACCTCCATTGAATTTTGTCCTAGGGAAAG                         GGTTGTAATCTCCACATCACATCAGTGGGGAGCAGAGCTCACGAAACTGAA
genomic: GTCCATCTTGGCTCCCCAGTCACCTCCATTGAATTTTGTCCTAGTGAAAGgtaactacag ... ggtatcgcagGGTTGTAATCTCCACATCACATCAGTGGGGAGCAGAGCTCACGAAACTGAA
EST: gi|6445478|gb|AW179396.1|AW179396
EST:     GTCCATCTTGGCTCCCCAGTCACCTCCATTGAATTTTGTCCTAGTGAAAG                         GGTTGTAATCTCCACATCACATCAGTGGGGAGCAGAGCTCACGAAACTGAA
genomic: GTCCATCTTGGCTCCCCAGTCACCTCCATTGAATTTTGTCCTAGTGAAAGgtaactacag ... ggtatcgcagGGTTGTAATCTCCACATCACATCAGTGGGGAGCAGAGCTCACGAAACTGAA
EST: gi|76020754|gb|DT947924.1|DT947924
EST:     GTCCATCTTGGCTCCCCAGTCACCTCCATTGAATTTTGTCCTAGTGAAAG                         GGTTGTAATCTCCACATCACATCAGTGGGGAGCAGAGCTCACGAAACTGAA
genomic: GTCCATCTTGGCTCCCCAGTCACCTCCATTGAATTTTGTCCTAGTGAAAGgtaactacag ... ggtatcgcagGGTTGTAATCTCCACATCACATCAGTGGGGAGCAGAGCTCACGAAACTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcatccaagttttttttagtgtttctcctaacacgggtgaccactggtatcgcagGGTTGTAATCTCCACATCACATCAGTGGGGAGCAGAGCTCACGAAACTGAACGTGCCTGCCGACTGGAAAG
                         tcctaac  putative branch site (score: 1)
         ttttttttagtgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagattgggcacgaatgctaatacacaatgggtttgatttttggagcatccaagttttttttagtgtttctcctaacacgggtgaccactggtatcgcagGGTTGTAATCTCCACATCACATCAGTGGGGAGCAGAGCTCACGAAACTGAACGTGCCTGCCGACTGGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA