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 5'  3'   		2  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcttgctttccagcagtatctaaccgaatcagagcctgacatttctttttgtatctcgtgcttgcttgctgtaacaaacaaacgaacgaacgaccaaaagGTCGCGGAGCTGATGGTGACGCGGTGCATCCGCGAGGCGGTGGCGCTGGCGTGGGTGGTGCTTTGGGCGCTGAGCACGCGGGCGGGCACGCTGCTGCTGT

Basic information

species Zea mays
transcript GRMZM2G143883_T06
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G143883_T06 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os10g33550.1 (Oryza sativa), 3'ss of exon 1
---gcttgctt--tccagcagtatctaaccgaatcagagcctgacatttctt-tttgta-tctcgtgcttgcttg---ctgtaacaaacaaacgaacgaacgaccaaaagGTCGCGGAGCTGATGGTGACGCGGTGCATCCGCGAGGCGGTGGCGCTGGCGTGGGTGGTGCTTTGGGCGCTGAGCACGCGGGCGGGCACGCTGCTGCTGT
   | | | |   || | | ||     |||  ||  | ||  |   |||||| ||| || ||||     ||   |   | |   | | |        |   | |    |||| ||||||||| |||||||||| |||||  | ||||||||||||||| ||||||||||||| |||||||||||||||||||||||||||||||||||||
gtcggtcggtcggtcgatcggtcgaacaccccatgcgcgcgagttctttcttgtttataatctctaatctggcggcggccgcggcgaccgcggcgtggcgtggcgtgcagGTGGCGGAGCTGCTGGTGACGCGTTGCATATGGGAGGCGGTGGCGCTGACGTGGGTGGTGCTGTGGGCGCTGAGCACGCGGGCGGGCACGCTGCTGCTGT
















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|148948203|gb|EC893719.2|EC893719
EST:     TCGAGCGCTTCTACCTCGCCTCCGCGGCCGACTCCACCATCCCCGACGAG                         GTCGCGGAGCTGATGGTGACGCGGTGCATCCGCGAGGCGGTGGCGCTGGCG
genomic: TCGAGCGCTTCTACCTCGCCTCCGCGGCCGACTCCACCATCCCCGACGAGgtgagcagcg ... cgaccaaaagGTCGCGGAGCTGATGGTGACGCGGTGCATCCGCGAGGCGGTGGCGCTGGCG
EST: gi|148973859|gb|EE025001.2|EE025001
EST:     TCGAGCGCTTCTACCTCGCCTCCGCGGCCGACTCCACCATCCCCGACGAG                         GTCGCGGAGCTGATGGTGACGCGGTGCATCCGCGAGGCGGTGGCGCTGGCG
genomic: TCGAGCGCTTCTACCTCGCCTCCGCGGCCGACTCCACCATCCCCGACGAGgtgagcagcg ... cgaccaaaagGTCGCGGAGCTGATGGTGACGCGGTGCATCCGCGAGGCGGTGGCGCTGGCG
EST: gi|93283239|gb|EB675503.1|EB675503
EST:     TCGAGCGCTTCTACCTCGCCTCCGCGGCCGACTCCACCATCCCCGACGAG                         GTCGCGGAGCTGATGGTGACGCGGTGCATCCGCGAGGCGGTGGCGCTGGCG
genomic: TCGAGCGCTTCTACCTCGCCTCCGCGGCCGACTCCACCATCCCCGACGAGgtgagcagcg ... cgaccaaaagGTCGCGGAGCTGATGGTGACGCGGTGCATCCGCGAGGCGGTGGCGCTGGCG
EST: gi|211316715|gb|FL359694.1|FL359694
EST:     TCGAGCGCTTCTACCTCGCCTCCGCGGCCGACTCCACCATCCCCGACGAG                         GTCGCGGAGCTGATGGTGACGCGGTGCATCCGCGAGGGCG-TGGCGCTGGC
genomic: TCGAGCGCTTCTACCTCGCCTCCGCGGCCGACTCCACCATCCCCGACGAGgtgagcagcg ... cgaccaaaagGTCGCGGAGCTGATGGTGACGCGGTGCATCCGCGAGG-CGGTGGCGCTGGC
EST: gi|71328928|gb|DR801150.1|DR801150
EST:     TCGAGCGCTTCTACCTCGCCTCCGCGGCCGACTCCACCATCCCCGACGAG                         GTCGCGGAGCTGATGGTGACGCGGTGCATCCGCGAGGCGGTGGCGCTGGCG
genomic: TCGAGCGCTTCTACCTCGCCTCCGCGGCCGACTCCACCATCCCCGACGAGgtgagcagcg ... cgaccaaaagGTCGCGGAGCTGATGGTGACGCGGTGCATCCGCGAGGCGGTGGCGCTGGCG
EST: gi|148951656|gb|EC897401.2|EC897401
EST:     TCGAGCGCTTCTACCTCGCCTCCGCGGCCGACTCCACCATCCCCGACGAG                         GTCGCGGAGCTGATGGTGACGCGGTGCATCCGCGAGGCGGTGGCGCTGGCG
genomic: TCGAGCGCTTCTACCTCGCCTCCGCGGCCGACTCCACCATCCCCGACGAGgtgagcagcg ... cgaccaaaagGTCGCGGAGCTGATGGTGACGCGGTGCATCCGCGAGGCGGTGGCGCTGGCG
EST: gi|149069600|gb|EE157980.2|EE157980
EST:     TCGAGCGCTTCTACCTCGCCTCCGCGGCCGACTCCACCATCCCCGACGAG                         GTCGCGGAGCTGATGGTGACGCGGTGCATCCGCGAGGCGGTGGCGCTGGCG
genomic: TCGAGCGCTTCTACCTCGCCTCCGCGGCCGACTCCACCATCCCCGACGAGgtgagcagcg ... cgaccaaaagGTCGCGGAGCTGATGGTGACGCGGTGCATCCGCGAGGCGGTGGCGCTGGCG
EST: gi|211047107|gb|FL348892.1|FL348892
EST:     TCGAGCGCTTCTACCTCGCCTCCGCGGCCGACTCCACCATCCCCGACGAG                         GTCGCGGAGCTGATGGTGACGCGGTGCATCCGCGAGGCGGTGGCGCTTGGC
genomic: TCGAGCGCTTCTACCTCGCCTCCGCGGCCGACTCCACCATCCCCGACGAGgtgagcagcg ... cgaccaaaagGTCGCGGAGCTGATGGTGACGCGGTGCATCCGCGAGGCGGTGGCGCT-GGC
EST: gi|211278199|gb|FL349954.1|FL349954
EST:     TCGAGCGCTTCTACCTCGCCTCCGCGGCCGACTCCACCATCCCCGACGAG                         GTCGCGGAGCTGATGGTGACGCGGTGCATCCGCGAGGCGGTGGCGCTGGCG
genomic: TCGAGCGCTTCTACCTCGCCTCCGCGGCCGACTCCACCATCCCCGACGAGgtgagcagcg ... cgaccaaaagGTCGCGGAGCTGATGGTGACGCGGTGCATCCGCGAGGCGGTGGCGCTGGCG
EST: gi|211040402|gb|FL319771.1|FL319771
EST:     TCGAGCGCTTCTACCTCGCCTCCGCGGCCGACTCCACCATCCCCGACGAG                         GTCGCGGAGCTGATGGTGACGCGGTGCATCCGCGAAGCGGTGGCGCTGGCG
genomic: TCGAGCGCTTCTACCTCGCCTCCGCGGCCGACTCCACCATCCCCGACGAGgtgagcagcg ... cgaccaaaagGTCGCGGAGCTGATGGTGACGCGGTGCATCCGCGAGGCGGTGGCGCTGGCG
EST: gi|76281721|gb|DV021289.1|DV021289
EST:     TCGAGCGCTTCTACCTCGCCTCCGCGGCCGACTCCACCATCCCCGACGAG                         GTCGCGGAGCTGATGGTGACGCGGTGCATCCGCGAGGCGGTGGCGCTGGCG
genomic: TCGAGCGCTTCTACCTCGCCTCCGCGGCCGACTCCACCATCCCCGACGAGgtgagcagcg ... cgaccaaaagGTCGCGGAGCTGATGGTGACGCGGTGCATCCGCGAGGCGGTGGCGCTGGCG
EST: gi|149109316|gb|EE190135.2|EE190135
EST:     TCGAGCGCTTCTACCTCGCCTCCGCGGCCGACTCCACCATCCCCGACGAG                         GTCGCGGAGCTGATGGTGACGCGGTGCATCCGCGAGGCGGTGGCGCTGGCG
genomic: TCGAGCGCTTCTACCTCGCCTCCGCGGCCGACTCCACCATCCCCGACGAGgtgagcagcg ... cgaccaaaagGTCGCGGAGCTGATGGTGACGCGGTGCATCCGCGAGGCGGTGGCGCTGGCG
EST: gi|211086223|gb|FL328937.1|FL328937
EST:     TCGAGCGCTTCTACCTCGCCTCCGCGGCCGACTCCACCATCCCCGACGAG                         GTCGCGGAGCTGATGGTGACGCGGTGCATCCGCGAGGCGGGTGGCGCTGGC
genomic: TCGAGCGCTTCTACCTCGCCTCCGCGGCCGACTCCACCATCCCCGACGAGgtgagcagcg ... cgaccaaaagGTCGCGGAGCTGATGGTGACGCGGTGCATCCGCGAGGCGG-TGGCGCTGGC
EST: gi|211208169|gb|FL329118.1|FL329118
EST:     TCGAGCGCTTCTACCTCGCCTCCGCGGCCGACTCCACCATCCCCGACGAG                         GTCGCGGAGCTGATGGTGACGCGGTGCATCCGCGAGGCGGTGGCGCTGGCG
genomic: TCGAGCGCTTCTACCTCGCCTCCGCGGCCGACTCCACCATCCCCGACGAGgtgagcagcg ... cgaccaaaagGTCGCGGAGCTGATGGTGACGCGGTGCATCCGCGAGGCGGTGGCGCTGGCG
EST: gi|149069635|gb|EE158020.2|EE158020
EST:     TCGAGCGCTTCTACCTCGCCTCCGCGGCCGACTCCACCATCCCCGACGAG                         GTCGCGGAGCTGATGGTGACGCGGTGCATCCGCGAGGCGGTGGCGCTGGCG
genomic: TCGAGCGCTTCTACCTCGCCTCCGCGGCCGACTCCACCATCCCCGACGAGgtgagcagcg ... cgaccaaaagGTCGCGGAGCTGATGGTGACGCGGTGCATCCGCGAGGCGGTGGCGCTGGCG
EST: gi|211049235|gb|FL320171.1|FL320171
EST:     TCGAGCGCTTCTACCTCGCCTCCGCGGCCGACTCCACCATCCCCGACGAG                         GTCGCGGAGCTGATGGTGACGCGGTGCATCCGCGAGGCGGTGGCGCTGGCG
genomic: TCGAGCGCTTCTACCTCGCCTCCGCGGCCGACTCCACCATCCCCGACGAGgtgagcagcg ... cgaccaaaagGTCGCGGAGCTGATGGTGACGCGGTGCATCCGCGAGGCGGTGGCGCTGGCG
EST: gi|211537824|gb|FL337840.1|FL337840
EST:     TCGAGCGCTTCTACCTCGCCTCCGCGGCCGACTCCACCATCCCCGACGAG                         GTCGCGGAGCTGATGGTGACGCGGTGCATCCGCGAGGCGGTGGCGCTGGCG
genomic: TCGAGCGCTTCTACCTCGCCTCCGCGGCCGACTCCACCATCCCCGACGAGgtgagcagcg ... cgaccaaaagGTCGCGGAGCTGATGGTGACGCGGTGCATCCGCGAGGCGGTGGCGCTGGCG
EST: gi|211312214|gb|FL336744.1|FL336744
EST:     TCGAGCGCTTCTACCTCGCCTCCGCGGCCGACTCCACCATCCCCGACGAG                         GTCGCGGAGCTGATGGTGACGCGGTGCATCCGCGAGGCGGTGGCGCTGGCG
genomic: TCGAGCGCTTCTACCTCGCCTCCGCGGCCGACTCCACCATCCCCGACGAGgtgagcagcg ... cgaccaaaagGTCGCGGAGCTGATGGTGACGCGGTGCATCCGCGAGGCGGTGGCGCTGGCG
EST: gi|211137928|gb|FL319378.1|FL319378
EST:     TCGAGCGCTTCTACCTCGCCTCCGCGGCCGACTCCACCATCCCCGACGAG                         GTCGCGGAGCTGATGGTGACGCGGTGCATCCGCGAGGCGGTGGCGCTGGCG
genomic: TCGAGCGCTTCTACCTCGCCTCCGCGGCCGACTCCACCATCCCCGACGAGgtgagcagcg ... cgaccaaaagGTCGCGGAGCTGATGGTGACGCGGTGCATCCGCGAGGCGGTGGCGCTGGCG
EST: gi|93014896|gb|EB640416.1|EB640416
EST:     TCGAGCGCTTCTACCTCGCCTCCGCGGCCGACTCCACCATCCCCGACGAG                         GTCGCGGAGCTGATGGTGACGCGGTGCATCCGCGAGGCGGTGGCGCTGGCG
genomic: TCGAGCGCTTCTACCTCGCCTCCGCGGCCGACTCCACCATCCCCGACGAGgtgagcagcg ... cgaccaaaagGTCGCGGAGCTGATGGTGACGCGGTGCATCCGCGAGGCGGTGGCGCTGGCG
EST: gi|211382845|gb|FL310396.1|FL310396
EST:     TCGAGCGCTTCTACCTCGCCTCCGCGGCCGACTCCACCATCCCCGACGAG                         GTCGCGGAGCTGATGGGGACGCGGTGCATCCGCGAGGCGGTGGCCCTGGCG
genomic: TCGAGCGCTTCTACCTCGCCTCCGCGGCCGACTCCACCATCCCCGACGAGgtgagcagcg ... cgaccaaaagGTCGCGGAGCTGATGGTGACGCGGTGCATCCGCGAGGCGGTGGCGCTGGCG
EST: gi|149020921|gb|EE045762.2|EE045762
EST:     TCGAGCGCTTCTACCTCGCCTCCGCGGCCGACTCCACCATCCCCGACGAG                         GTCGCGGAGCTGATGGTGACGCGGTGCATCCGCGAGGCGGTGGCGCTGGCG
genomic: TCGAGCGCTTCTACCTCGCCTCCGCGGCCGACTCCACCATCCCCGACGAGgtgagcagcg ... cgaccaaaagGTCGCGGAGCTGATGGTGACGCGGTGCATCCGCGAGGCGGTGGCGCTGGCG
EST: gi|149085834|gb|EE175357.2|EE175357
EST:     TCGAGCGCTTCTACCTCGCCTCCGCGGCCGACTCCACCATCCCCGACGAG                         GTCGCGGAGCTGATGGTGACGCGGTGCATCCGCGAGGCGGTGGCGCTGGCG
genomic: TCGAGCGCTTCTACCTCGCCTCCGCGGCCGACTCCACCATCCCCGACGAGgtgagcagcg ... cgaccaaaagGTCGCGGAGCTGATGGTGACGCGGTGCATCCGCGAGGCGGTGGCGCTGGCG
EST: gi|211341854|gb|FL306858.1|FL306858
EST:     TCGAGCGCTTCTACCTCGCCTCCGCGGCCGACTCCACCATCCCCGACGAG                         GTCGCGGAGCTGATGGTGACGCGGTGCA
genomic: TCGAGCGCTTCTACCTCGCCTCCGCGGCCGACTCCACCATCCCCGACGAGgtgagcagcg ... cgaccaaaagGTCGCGGAGCTGATGGTGACGCGGTGCA
EST: gi|148938919|gb|EC883278.2|EC883278
EST:     TCGAGCGCTTCTACCTCGCCTCCGCGGCCGACTCCACCATCCCCGACGAG                         GTCGCGGAGCTGATGGTGACGCGGTGCATCCGCGAGGCGGTGGCGCTGGCG
genomic: TCGAGCGCTTCTACCTCGCCTCCGCGGCCGACTCCACCATCCCCGACGAGgtgagcagcg ... cgaccaaaagGTCGCGGAGCTGATGGTGACGCGGTGCATCCGCGAGGCGGTGGCGCTGGCG
EST: gi|78075545|gb|DV503979.1|DV503979
EST:     TCGAGCGCTTCTACCTCGCCTCCGCGGCCGACTCCACCATCCCCGACGAG                         GTCGCGGAGCTGATGGTGACGCGGTGCATCCGCGAGGCGGTGGCGCTGGCG
genomic: TCGAGCGCTTCTACCTCGCCTCCGCGGCCGACTCCACCATCCCCGACGAGgtgagcagcg ... cgaccaaaagGTCGCGGAGCTGATGGTGACGCGGTGCATCCGCGAGGCGGTGGCGCTGGCG
EST: gi|149084377|gb|EE173826.2|EE173826
EST:     CTCCACCATCCCCGACGAG                         GTCGCGGAGCTGATGGTGACGCGGTGCATCCGCGAGGCGGTGGCGCTGGCG
genomic: CTCCACCATCCCCGACGAGgtgagcagcg ... cgaccaaaagGTCGCGGAGCTGATGGTGACGCGGTGCATCCGCGAGGCGGTGGCGCTGGCG
EST: gi|89249377|gb|DY621163.1|DY621163
EST:     TCGAGCGCTTCTACCTCGCCTCCGCGGCCGACTCCACCATCCCCGACGAG                         GTCGCGGAGCTGATGGTGACGCGGTGCATCCGCGAGGCGGTGGCGCTGGCG
genomic: TCGAGCGCTTCTACCTCGCCTCCGCGGCCGACTCCACCATCCCCGACGAGgtgagcagcg ... cgaccaaaagGTCGCGGAGCTGATGGTGACGCGGTGCATCCGCGAGGCGGTGGCGCTGGCG
EST: gi|78087753|gb|DV516146.1|DV516146
EST:     TCGAGCGCTTCTACCTCGCCTCCGCGGCCGACTCCACCATCCCCGACGAG                         GTCGCGGAGCTGATGGTGACGCGGTGCATCCGCGAGGCGGTGGCGCTGGCG
genomic: TCGAGCGCTTCTACCTCGCCTCCGCGGCCGACTCCACCATCCCCGACGAGgtgagcagcg ... cgaccaaaagGTCGCGGAGCTGATGGTGACGCGGTGCATCCGCGAGGCGGTGGCGCTGGCG
EST: gi|149086895|gb|EE176439.2|EE176439
EST:     TCGAGCGCTTCTACCTCGCCTCCGCGGCCGACTCCACCATCCCCGACGAG                         GTCGCGGAGCTGATGGTGACGCGGTGCATCCGCGAGGCGGTGGCGCTGGCG
genomic: TCGAGCGCTTCTACCTCGCCTCCGCGGCCGACTCCACCATCCCCGACGAGgtgagcagcg ... cgaccaaaagGTCGCGGAGCTGATGGTGACGCGGTGCATCCGCGAGGCGGTGGCGCTGGCG
EST: gi|148931643|gb|EC874791.2|EC874791
EST:     TCGAGCGCTTCTACCTCGCCTCCGCAGCCGACTCCACCATCCCCGACGAG                         GTCGCGGAGCTGATGGTGACGCGGTGCATCCGCGAGGCGGTGGCGCTGGCG
genomic: TCGAGCGCTTCTACCTCGCCTCCGCGGCCGACTCCACCATCCCCGACGAGgtgagcagcg ... cgaccaaaagGTCGCGGAGCTGATGGTGACGCGGTGCATCCGCGAGGCGGTGGCGCTGGCG
EST: gi|71769980|gb|DR967917.1|DR967917
EST:     TCGAGCGCTTCTACCTCGCCTCCGCGGCCGACTCCACCATCCCCGACGAG                         GTCGCGGAGCTGATGGTGACGCGGTGCATCCGCGAGGCGGTGGCGCTGGCG
genomic: TCGAGCGCTTCTACCTCGCCTCCGCGGCCGACTCCACCATCCCCGACGAGgtgagcagcg ... cgaccaaaagGTCGCGGAGCTGATGGTGACGCGGTGCATCCGCGAGGCGGTGGCGCTGGCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttgtatctcgtgcttgcttgctgtaacaaacaaacgaacgaacgaccaaaagGTCGCGGAGCTGATGGTGACGCGGTGCATCCGCGAGGCGGTGGCGCTGGCGTGGGTGGTGCTTTGGGCGCTGAGCACGCGGGCGGGCACGCTGCTGCTGT
                       ctgtaac  putative branch site (score: 3)
                          taacaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcttgctttccagcagtatctaaccgaatcagagcctgacatttctttttgtatctcgtgcttgcttgctgtaacaaacaaacgaacgaacgaccaaaagGTCGCGGAGCTGATGGTGACGCGGTGCATCCGCGAGGCGGTGGCGCTGGCGTGGGTGGTGCTTTGGGCGCTGAGCACGCGGGCGGGCACGCTGCTGCTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT