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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcatctcagctgatgtatgcacataagtttgctgcattacaaactatctgctgtgcctgtgtgtaactatgctgaggttgtttttccaacatatctgcagGTTGCTAGCAGCATTGGAAGCGAATCAAACGCGCCACTGTCTGGAAGAGTGCAGCTGGCTACTGAGAGCATCCCATCCTCCCATGTGCTGCTGATCATTC

Basic information

species Zea mays
transcript GRMZM2G011173_T02
intron # 6
splice site 3'
intron type U2

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|76013658|gb|DT940828.1|DT940828
EST:     TGCTGTAGTCCTTGATACCCCCGACGAACCATTGATCAACTACTTCAGT                         GTTGCTAGCAGCATTGGAAGCGAATCAAACGCGCCACTGTCTGGAAGAGTG
genomic: TGCTGTAGTCCTTGATACCCCCGACGAACCATTGATCAACTACTTCAGTgtatatgttc ... atatctgcagGTTGCTAGCAGCATTGGAAGCGAATCAAACGCGCCACTGTCTGGAAGAGTG
EST: gi|91050350|gb|EB160768.1|EB160768
EST:     CTGCTGTAGTCCTTGATACCCCCGACGAACCATTGATCAACTACTTCAGT                         GTTGCTAGCAGCATTGGAAGCGAATCAAACGCGCCACTGTCTGGAAGAGTG
genomic: CTGCTGTAGTCCTTGATACCCCCGACGAACCATTGATCAACTACTTCAGTgtatatgttc ... atatctgcagGTTGCTAGCAGCATTGGAAGCGAATCAAACGCGCCACTGTCTGGAAGAGTG
EST: gi|71762637|gb|DR960574.1|DR960574
EST:     CTGCTGTAGTCCTTGATACCCCCGACGAACCATTGATCAACTACTTCAGT                         GTTGCTAGCAGCATTGGAAGCGAATCAAACGCGCCACTGTCTGGAAGAGTG
genomic: CTGCTGTAGTCCTTGATACCCCCGACGAACCATTGATCAACTACTTCAGTgtatatgttc ... atatctgcagGTTGCTAGCAGCATTGGAAGCGAATCAAACGCGCCACTGTCTGGAAGAGTG
EST: gi|71419808|gb|DR804903.1|DR804903
EST:     CTGCTGTAGTCCTTGATACCCCCGACGAACCATTGATCAACTACTTCAGT                         GTTGCTAGCAGCATTGGAAGCGAATCAAACGCGCCACTGTCTGGAAGAGTG
genomic: CTGCTGTAGTCCTTGATACCCCCGACGAACCATTGATCAACTACTTCAGTgtatatgttc ... atatctgcagGTTGCTAGCAGCATTGGAAGCGAATCAAACGCGCCACTGTCTGGAAGAGTG
EST: gi|71435432|gb|DR816482.1|DR816482
EST:     CTGCTGTAGTCCTTGATACCCCCGACGAACCATTGATCAACTACTTCAGT                         GTTGCTAGCAGCATTGGAAGCGAATCAAACGCGCCACTGTCTGGGAGAGTG
genomic: CTGCTGTAGTCCTTGATACCCCCGACGAACCATTGATCAACTACTTCAGTgtatatgttc ... atatctgcagGTTGCTAGCAGCATTGGAAGCGAATCAAACGCGCCACTGTCTGGAAGAGTG
EST: gi|71320866|gb|DR797150.1|DR797150
EST:     CTGCTGTAGTCCTTGATACCCCCGACGAACCATTGATCAACTACTTCAGT                         GTTGCTAGCAGCATTGGAAGCGAATCAAACGCGCCACTGTCTGGAAGAGTG
genomic: CTGCTGTAGTCCTTGATACCCCCGACGAACCATTGATCAACTACTTCAGTgtatatgttc ... atatctgcagGTTGCTAGCAGCATTGGAAGCGAATCAAACGCGCCACTGTCTGGAAGAGTG
EST: gi|76013659|gb|DT940829.1|DT940829
EST:     CTGCTGTAGTCCTTGATACCCCCGACGAACCATTGATCAACTACTTCAGT                         GTTGCTAGCAGCATTGGAAGCGAATCAAACGCGCCACTGTCTGGAAGAGTG
genomic: CTGCTGTAGTCCTTGATACCCCCGACGAACCATTGATCAACTACTTCAGTgtatatgttc ... atatctgcagGTTGCTAGCAGCATTGGAAGCGAATCAAACGCGCCACTGTCTGGAAGAGTG
EST: gi|71313019|gb|DR793034.1|DR793034
EST:     CTGCTGTAGTCCTTGATACCCCCGACGAACCATTGATCAACTACTTCAGT                         GTTGCTAGCAGCATTGGAAGCGAATCAAACGCGCCACTGTCTGGAAGAGTG
genomic: CTGCTGTAGTCCTTGATACCCCCGACGAACCATTGATCAACTACTTCAGTgtatatgttc ... atatctgcagGTTGCTAGCAGCATTGGAAGCGAATCAAACGCGCCACTGTCTGGAAGAGTG
EST: gi|78091119|gb|DV519493.1|DV519493
EST:     CTGCTGTAGTCCTTGATACCCCCGACGAACCATTGATCAACTACTTCAGT                         GTTGCTAGCAGCATTGGAAGCGAATCAAACGCGCCACTGTCTGGAAGAGTG
genomic: CTGCTGTAGTCCTTGATACCCCCGACGAACCATTGATCAACTACTTCAGTgtatatgttc ... atatctgcagGTTGCTAGCAGCATTGGAAGCGAATCAAACGCGCCACTGTCTGGAAGAGTG
EST: gi|67034610|gb|CO463160.1|CO463160
EST:     CTGCTGTAGTCCTTGATACCCCCGACGAATCATTAATCAACTACTTCAGT                         GTTGCTAGCAGCATTGGAAGCGAATCAAACGCAACACTGTCTGGAAGAGTG
genomic: CTGCTGTAGTCCTTGATACCCCCGACGAACCATTGATCAACTACTTCAGTgtatatgttc ... atatctgcagGTTGCTAGCAGCATTGGAAGCGAATCAAACGCGCCACTGTCTGGAAGAGTG
EST: gi|78091120|gb|DV519494.1|DV519494
EST:     CTGCTGTAGTCCTTGATACCCCCGACGAACCATTGATCAACTACTTCAGT                         GTTGCTAGCAGCATTGGAAGCGAATCAAACGCGCCACTGTCTGGAAGAGTG
genomic: CTGCTGTAGTCCTTGATACCCCCGACGAACCATTGATCAACTACTTCAGTgtatatgttc ... atatctgcagGTTGCTAGCAGCATTGGAAGCGAATCAAACGCGCCACTGTCTGGAAGAGTG
EST: gi|74241849|gb|DT649763.1|DT649763
EST:     CTGCTGTAGTCCTTGATACCCCCGACGAACCATTGATCAACTACTTCAGT                         GTTGCTAGCAGCATTGGAAGCGAATCAAACGCGCCACTGTCTGGAAGAGTG
genomic: CTGCTGTAGTCCTTGATACCCCCGACGAACCATTGATCAACTACTTCAGTgtatatgttc ... atatctgcagGTTGCTAGCAGCATTGGAAGCGAATCAAACGCGCCACTGTCTGGAAGAGTG
EST: gi|93016793|gb|EB642313.1|EB642313
EST:     CTGCTGTAGTCCTTGATACCCCCGACGAACCATTGATCAACTACTTCAGT                         GTTGCTAGCAGCATTGGAAGCGAATCAAACGCGCCACTGTCTGGAAGAGTG
genomic: CTGCTGTAGTCCTTGATACCCCCGACGAACCATTGATCAACTACTTCAGTgtatatgttc ... atatctgcagGTTGCTAGCAGCATTGGAAGCGAATCAAACGCGCCACTGTCTGGAAGAGTG
EST: gi|71768256|gb|DR966193.1|DR966193
EST:     CTGCTGTAGTCCTTGATACCCCCGACGAACCATTGATCAACTACTTCAGT                         GTTGCTAGCAGCATTGGAAGCGAATCAAACGCGCCACTGTCTGGGAGAGTG
genomic: CTGCTGTAGTCCTTGATACCCCCGACGAACCATTGATCAACTACTTCAGTgtatatgttc ... atatctgcagGTTGCTAGCAGCATTGGAAGCGAATCAAACGCGCCACTGTCTGGAAGAGTG
EST: gi|94477701|gb|EB706659.1|EB706659
EST:     CTGCTGTAGTCCTTGATACCCCCGACGAACCATTGATCAACTACTTCAGT                         GTTGCTAGCAGCATTGGAAGCGAATCAAACGCGCCACTGTCTGGAAGAGTG
genomic: CTGCTGTAGTCCTTGATACCCCCGACGAACCATTGATCAACTACTTCAGTgtatatgttc ... atatctgcagGTTGCTAGCAGCATTGGAAGCGAATCAAACGCGCCACTGTCTGGAAGAGTG
EST: gi|101382184|gb|EB813148.1|EB813148
EST:     CTGCTGTAGTCCTTGATACCCCCGACGAACCATTGATCAACTACTTCAGT                         GTTGCTAGCAGCATTGGAAGCGAATCAAACGCGCCACTGTCTGGAAGAGTG
genomic: CTGCTGTAGTCCTTGATACCCCCGACGAACCATTGATCAACTACTTCAGTgtatatgttc ... atatctgcagGTTGCTAGCAGCATTGGAAGCGAATCAAACGCGCCACTGTCTGGAAGAGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atctgctgtgcctgtgtgtaactatgctgaggttgtttttccaacatatctgcagGTTGCTAGCAGCATTGGAAGCGAATCAAACGCGCCACTGTCTGGAAGAGTGCAGCTGGCTACTGAGAGCATCCCATCCTCCCATGTGCTGCTGATCATTC
               gtgtaac  putative branch site (score: 3)
                                ttgttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcatctcagctgatgtatgcacataagtttgctgcattacaaactatctgctgtgcctgtgtgtaactatgctgaggttgtttttccaacatatctgcagGTTGCTAGCAGCATTGGAAGCGAATCAAACGCGCCACTGTCTGGAAGAGTGCAGCTGGCTACTGAGAGCATCCCATCCTCCCATGTGCTGCTGATCATTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - gctgatg
- - - - - - - -tatgcac
- - - - - - - - - - - - - - ttgctgc
- - - - - - - - - - - - - - - - - - - - - - - tctgctg
- - - - - - - - - - - - - - - - - - - - - - - - - - -tgcctgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tatgctg