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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgacctttattactgcatataacttatttatcttagcaatagatagtttatgctctttcccccctttttctcaaaatgatcacacaattatgtgtgcagATTTATGTTCCTACAAACCCAAAAGGTGCTGAGAGACTTCCACCAGGCATTGTAGTGTCTGAAACAGATCTTTATCCCCGAAGACTATGGGGTGATCCTA

Basic information

species Zea mays
transcript GRMZM2G119725_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G119725_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os02g19510.1 (Oryza sativa), 3'ss of exon 4
--ttgaccttta--ttactgcatataacttatttatcttagcaatagatagtttatgctctttcccccctttttctcaaaatgatcacacaattatgtgtgcagATTTATGTTCCTACAAACCCAAAAGGTGCTGAGAGACTTCCACCAGGCATTGTAGTGTCTGAAACAGATCTTTATCCCCGAAGACTATGGGGTGATCCTA
  |  ||   ||  | |||| | |  | ||  |||   | |  |||||     | | || ||       || || | ||| | | ||  ||||| | | |||||||||||||||| |||||||| ||||||||||| || || |||||||||||||| || |||||||||||||||| ||| || ||| | |||||||||||||
tctcaactagtaattaactgaaaagtagttggttac--tggtcatagaccacatttcctattgtttattttgtttt-aaagtca-catgcaattctttctgcagATTTATGTTCCCACAAACCCTAAAGGTGCTGAAAGGCTCCCACCAGGCATTGTTGTTTCTGAAACAGATCTTTTTCCACGGAGATTGTGGGGTGATCCTA
















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|148930418|gb|EE284901.2|EE284901
EST:     ACAATCATAAAAAGAATAGTTCTGAATCTAACACTGATGAAATTCCCGAG                         ATTTATGTTCCTACAAACCCAAAAGGTGCTGAGAGACTTCCACCAGGCATT
genomic: ACAATCATAAAAAGAATAGTTCTGAATCTAACACTGATGAAATTCCCGAGgtacttcaac ... atgtgtgcagATTTATGTTCCTACAAACCCAAAAGGTGCTGAGAGACTTCCACCAGGCATT
EST: gi|149108358|gb|EE292696.2|EE292696
EST:     ACAATCATAAAAAGAATAGTTCTGAATCTAACACTGATGAAATTCCCGAG                         ATTTATGTTCCTACAAACCCAAAAGGTGCTGAGAGACTTCCACCAGGCATT
genomic: ACAATCATAAAAAGAATAGTTCTGAATCTAACACTGATGAAATTCCCGAGgtacttcaac ... atgtgtgcagATTTATGTTCCTACAAACCCAAAAGGTGCTGAGAGACTTCCACCAGGCATT
EST: gi|76930436|gb|DV172388.1|DV172388
EST:     ACAATCATAAAAAGAATAGTTCTGAATCTAACACTGATGAAATTCCCGAG                         ATTTATGTTCCTACAAACCCAAAAGGTGCTGAGAGACTTCCACCAGGCATT
genomic: ACAATCATAAAAAGAATAGTTCTGAATCTAACACTGATGAAATTCCCGAGgtacttcaac ... atgtgtgcagATTTATGTTCCTACAAACCCAAAAGGTGCTGAGAGACTTCCACCAGGCATT
EST: gi|148937093|gb|EC881269.2|EC881269
EST:     ACAATCATAAAAAGAATAGTTCTGAATCTAACACTGATGAAATTCCCGAG                         ATTTATGTTCCTACAAACCCAAAAGGTGCTGAGAGACTTCCACCAGGCATT
genomic: ACAATCATAAAAAGAATAGTTCTGAATCTAACACTGATGAAATTCCCGAGgtacttcaac ... atgtgtgcagATTTATGTTCCTACAAACCCAAAAGGTGCTGAGAGACTTCCACCAGGCATT
EST: gi|211445045|gb|FL132441.1|FL132441
EST:     TGAAATTCCCGAG                         ATTTATGTTCCTACAAACCCAAAAGGTGCTGAGAGACTTCCACCAGGCATT
genomic: TGAAATTCCCGAGgtacttcaac ... atgtgtgcagATTTATGTTCCTACAAACCCAAAAGGTGCTGAGAGACTTCCACCAGGCATT
EST: gi|211404454|gb|FL338957.1|FL338957
EST:     CAATCATNAAAAGAAATAGT-CTGAATCTAACACTGATGAAATCCCCGAG                         ATTTATGTTCCTACAAACCCAAAAAGTGCTGAGAGACTTCCAC-AGGCATT
genomic: CAATCATAAAAAGAA-TAGTTCTGAATCTAACACTGATGAAATTCCCGAGgtacttcaac ... atgtgtgcagATTTATGTTCCTACAAACCCAAAAGGTGCTGAGAGACTTCCACCAGGCATT
EST: gi|211220721|gb|FL343735.1|FL343735
EST:     ACAATCATAAAAAGAATAGTTCTGAATCTAACACTGATGAAATTCCCGAG                         ATTTATGTTCCTACAAACCCAAAAGGTGCTGAGAGACTTCCACCAGGCATT
genomic: ACAATCATAAAAAGAATAGTTCTGAATCTAACACTGATGAAATTCCCGAGgtacttcaac ... atgtgtgcagATTTATGTTCCTACAAACCCAAAAGGTGCTGAGAGACTTCCACCAGGCATT
EST: gi|148961302|gb|EE012027.2|EE012027
EST:     ACAATCATAAAAAGAATAGTTCTGAATCTAACACTGATGAAATTCCCGAG                         ATTTATGTTCCTACAAACCCAAAAGGTGCTGAGAGACTTCCACCAGGCATT
genomic: ACAATCATAAAAAGAATAGTTCTGAATCTAACACTGATGAAATTCCCGAGgtacttcaac ... atgtgtgcagATTTATGTTCCTACAAACCCAAAAGGTGCTGAGAGACTTCCACCAGGCATT
EST: gi|149104738|gb|EE290190.2|EE290190
EST:     ACAATCATAAAAAGAATAGTTCTGAATCTAACACTGATGAAATTCCCGAG                         ATTTATGTTCCTACAAACCCAAAAGGTGCTGAGAGACTTCCACCAGGCATT
genomic: ACAATCATAAAAAGAATAGTTCTGAATCTAACACTGATGAAATTCCCGAGgtacttcaac ... atgtgtgcagATTTATGTTCCTACAAACCCAAAAGGTGCTGAGAGACTTCCACCAGGCATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtttatgctctttcccccctttttctcaaaatgatcacacaattatgtgtgcagATTTATGTTCCTACAAACCCAAAAGGTGCTGAGAGACTTCCACCAGGCATTGTAGTGTCTGAAACAGATCTTTATCCCCGAAGACTATGGGGTGATCCTA
                            aaaatgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgacctttattactgcatataacttatttatcttagcaatagatagtttatgctctttcccccctttttctcaaaatgatcacacaattatgtgtgcagATTTATGTTCCTACAAACCCAAAAGGTGCTGAGAGACTTCCACCAGGCATTGTAGTGTCTGAAACAGATCTTTATCCCCGAAGACTATGGGGTGATCCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA