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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcacataagttcgctgcattcatggttggatatatgctgcatcacataatatctgttgtgtctaactacgctgagattgcttttccaacatatctgcagGGCGCTGCTAGCATTGGAAGTGTATCAAACGCACAACCGTCTGGAAGAGTGCACCCATCTACTGAGAGCATCCCATCTTCCCATGTGCCATTGATCGTTC

Basic information

species Zea mays
transcript GRMZM2G348866_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|148969459|gb|EE020269.2|EE020269
EST:     CCGCTGTAGTCCTTGATACCCCTGATGAATCATTAATCAGTTACTTCAGT                         GGCGCTGCTAGCATTGGAAGTGTATCAAACGCACAACCGTCTGGAAGAGTG
genomic: CCGCTGTAGTCCTTGATACCCCTGATGAATCATTAATCAGTTACTTCAGTgtatgctcaa ... atatctgcagGGCGCTGCTAGCATTGGAAGTGTATCAAACGCACAACCGTCTGGAAGAGTG
EST: gi|76021487|gb|DT948657.1|DT948657
EST:     CCGCTGTAGTCCTTGATACCCCTGATGAATCATTAATCAGTTACTTCAGT                         GGCGCTGCTAGCATTGGAAGTGTATCAAACGCACAACCGTCTGGAAGAGTG
genomic: CCGCTGTAGTCCTTGATACCCCTGATGAATCATTAATCAGTTACTTCAGTgtatgctcaa ... atatctgcagGGCGCTGCTAGCATTGGAAGTGTATCAAACGCACAACCGTCTGGAAGAGTG
EST: gi|76932642|gb|DV173100.1|DV173100
EST:     CCGCTGTAGTCCTTGATACCCCTGATGAATCATTAATCAGTTACTTCAGT                         GGCGCTGCTAGCATTGGAAGTGTATCAAACGCACAACCGTCTGGAAGAGTG
genomic: CCGCTGTAGTCCTTGATACCCCTGATGAATCATTAATCAGTTACTTCAGTgtatgctcaa ... atatctgcagGGCGCTGCTAGCATTGGAAGTGTATCAAACGCACAACCGTCTGGAAGAGTG
EST: gi|76915823|gb|DV166138.1|DV166138
EST:     CCGCTGTAGTCCTTGATACCCCTGATGAATCATTAATCAGTTACTTCAGT                         GGCGCTGCTAGCATTGGAAGTGTATCAAACGCACAACCGTCTGGAAGAGTG
genomic: CCGCTGTAGTCCTTGATACCCCTGATGAATCATTAATCAGTTACTTCAGTgtatgctcaa ... atatctgcagGGCGCTGCTAGCATTGGAAGTGTATCAAACGCACAACCGTCTGGAAGAGTG
EST: gi|101402261|gb|EB822718.1|EB822718
EST:     CCGCTGTAGTCCTTGATACCCCTGATGAATCATTAATCAGTTACTTCAGT                         GGCGCTGCTAGCATTGGAAGTGTATCAAACGCACAACCGTCTGGGAGAGTG
genomic: CCGCTGTAGTCCTTGATACCCCTGATGAATCATTAATCAGTTACTTCAGTgtatgctcaa ... atatctgcagGGCGCTGCTAGCATTGGAAGTGTATCAAACGCACAACCGTCTGGAAGAGTG
EST: gi|78073578|gb|DV502012.1|DV502012
EST:     CCGCTGTAGTCCTTGATACCCCTGATGAATCATTAATCAGTTACTTCAGT                         GGCGCTGCTAGCATTGGAAGTGTATCAAACGCACAACCGTCTGGAAGAGTG
genomic: CCGCTGTAGTCCTTGATACCCCTGATGAATCATTAATCAGTTACTTCAGTgtatgctcaa ... atatctgcagGGCGCTGCTAGCATTGGAAGTGTATCAAACGCACAACCGTCTGGAAGAGTG
EST: gi|76286853|gb|DV026421.1|DV026421
EST:     CCGCTGTAGTCCTTGATACCCCTGATGAATCATTAATCAGTTACTTCAGT                         GGCGCTGCTAGCATTGGAAGTGTATCAAACGC
genomic: CCGCTGTAGTCCTTGATACCCCTGATGAATCATTAATCAGTTACTTCAGTgtatgctcaa ... atatctgcagGGCGCTGCTAGCATTGGAAGTGTATCAAACGC
EST: gi|78119406|gb|DV537790.1|DV537790
EST:     CCGCTGTAGTCCTTGACACCCCTGATGAATCATTAATCAGTTACTTCAGT                         GGCGCTGCTAGCATTGGAAGTGTATCAAACGCACACCCGTCTGGAAAGAGT
genomic: CCGCTGTAGTCCTTGATACCCCTGATGAATCATTAATCAGTTACTTCAGTgtatgctcaa ... atatctgcagGGCGCTGCTAGCATTGGAAGTGTATCAAACGCACAACCGTCTGGAA-GAGT
EST: gi|211286797|gb|FL325896.1|FL325896
EST:     CCGCTGTAGTCCTTGATACCCCTGATGAATCATTAATCAGTTACTTCAGT                         GGCTCTGCTAGCATTGGAAGTGTATCAAACGCACAACCGTCTGGAAGAGTG
genomic: CCGCTGTAGTCCTTGATACCCCTGATGAATCATTAATCAGTTACTTCAGTgtatgctcaa ... atatctgcagGGCGCTGCTAGCATTGGAAGTGTATCAAACGCACAACCGTCTGGAAGAGTG
EST: gi|211497313|gb|FL084183.1|FL084183
EST:     CCGCTGTAGTCCTTGATACCCCTGATGAATCATTAATCAGTTACTTCAGT                         GGCGCTGCTAGCCATTGGAAGTGTATCAAACGCACAACCGTTCTGGGAA-A
genomic: CCGCTGTAGTCCTTGATACCCCTGATGAATCATTAATCAGTTACTTCAGTgtatgctcaa ... atatctgcagGGCGCTGCTAGC-ATTGGAAGTGTATCAAACGCACAACCGT-CTGG-AAGA
EST: gi|71444517|gb|DR825567.1|DR825567
EST:     CCGCTGTAGTCCTTGATACCCCTGATGAATCATTAATCAGTTACTTCAGT                         GGCGCTGCTAGCATTGGAAGTGTATCAAACGCACAACCGTCTGGAAGAGTG
genomic: CCGCTGTAGTCCTTGATACCCCTGATGAATCATTAATCAGTTACTTCAGTgtatgctcaa ... atatctgcagGGCGCTGCTAGCATTGGAAGTGTATCAAACGCACAACCGTCTGGAAGAGTG
EST: gi|101396950|gb|EB820400.1|EB820400
EST:     CCGCTGTAGTCCTTGATACCCCTGATGAATCATTAATCAGTTACTTCAGT                         GGCGCTGCTAGCATTGGAAGTGTATCAAACGCACAACCGT
genomic: CCGCTGTAGTCCTTGATACCCCTGATGAATCATTAATCAGTTACTTCAGTgtatgctcaa ... atatctgcagGGCGCTGCTAGCATTGGAAGTGTATCAAACGCACAACCGT
EST: gi|71449627|gb|DR830677.1|DR830677
EST:     CCGCTGTAGTCCTTGATACCCCTGATGAATCATTAATCAGTTACTTCAGT                         GGCGCTGCTAGCATTGGAAGTGTATCAAACGCACAACCGTCTGGAAGAGTG
genomic: CCGCTGTAGTCCTTGATACCCCTGATGAATCATTAATCAGTTACTTCAGTgtatgctcaa ... atatctgcagGGCGCTGCTAGCATTGGAAGTGTATCAAACGCACAACCGTCTGGAAGAGTG
EST: gi|71447776|gb|DR828826.1|DR828826
EST:     CCGCTGTAGTCCTTGATACCCCTGATGAATCATTAATCAGTTACTTCAGT                         GGCGCTGCTAGCATTGGAAGTGTATCAAACGCACAACCGTCTGGAAGAGTG
genomic: CCGCTGTAGTCCTTGATACCCCTGATGAATCATTAATCAGTTACTTCAGTgtatgctcaa ... atatctgcagGGCGCTGCTAGCATTGGAAGTGTATCAAACGCACAACCGTCTGGAAGAGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cataatatctgttgtgtctaactacgctgagattgcttttccaacatatctgcagGGCGCTGCTAGCATTGGAAGTGTATCAAACGCACAACCGTCTGGAAGAGTGCACCCATCTACTGAGAGCATCCCATCTTCCCATGTGCCATTGATCGTTC
               gtctaac  putative branch site (score: 2)
                                          aacatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgcacataagttcgctgcattcatggttggatatatgctgcatcacataatatctgttgtgtctaactacgctgagattgcttttccaacatatctgcagGGCGCTGCTAGCATTGGAAGTGTATCAAACGCACAACCGTCTGGAAGAGTGCACCCATCTACTGAGAGCATCCCATCTTCCCATGTGCCATTGATCGTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
-gcacata
- - - - - - - -tgcattc
- - - - - - - - - - - atggttg
- - - - - - - - - - - - - - - - - atgctgc
- - - - - - - - - - - - - - - - - - - - - - - - - - -ctgttgt