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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGGAACCAGCTGTCATTGAGTCATACTATAACAAGCGGATAGTCGGTTGTCCTGGTGGCGAGGGTGgtaagtcggtattgtttatttttctaaaataaaaatagctggtgtcaacctagtgtgtaagaaattgcttggttttttaactagcctactttattggcag

Basic information

species Zea mays
transcript GRMZM2G134738_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G134738_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os01g42650.1 (Oryza sativa), 5'ss of exon 4
GAGGAACCAGCTGTCATTGAGTCATACTATAACAAGCGGATAGTCGGTTGTCCTGGTGGCGAGGGTGgtaagtcggtattgtttatttttctaaaataaaaatagctggtgtcaacctagtgtgtaagaaattgcttggttttttaactagcctactttattggcag
||||  |||||||||||||| || |||||||||||| ||||||| |||||||||||||| || || ||| |||| || |||   | ||  || |   |||| |      || |||  || | || || |      |     ||||   |  | |  || |||  |||
GAGGCCCCAGCTGTCATTGAATCCTACTATAACAAGAGGATAGTTGGTTGTCCTGGTGGTGAAGGAGgtcagtcagtgttg---acttggctcagcgaaaactctaaactgccaaa-tattatgcaatactggtatcaacatttt--ttcacttctttcatttacag
















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|60357675|gb|DN224648.1|DN224648
EST:     TGAGTCATACTATAACAAGCGGATAGTCGGTTGTCCTGGTGGCGAGGGTG                         AGGACGAACATGATGTTGTATGGTTCTGGTTGAAAAAAGACGAGCCGCATG
genomic: TGAGTCATACTATAACAAGCGGATAGTCGGTTGTCCTGGTGGCGAGGGTGgtaagtcggt ... ttattggcagAGGACGAACATGATGTTGTATGGTTCTGGTTGAAAAAAGACGAGCCGCATG
EST: gi|211038526|gb|FL455206.1|FL455206
EST:     TGAGTCATACTATAACAAGCGGATAGTCGGTTGTCCTGGTGGCGAGGGTG                         AGGACGAACATGATGTTGTATGGTTCTGGTTGAAAAAASMCGASCCGCATG
genomic: TGAGTCATACTATAACAAGCGGATAGTCGGTTGTCCTGGTGGCGAGGGTGgtaagtcggt ... ttattggcagAGGACGAACATGATGTTGTATGGTTCTGGTTGAAAAAAGACGAGCCGCATG
EST: gi|76288217|gb|DV027785.1|DV027785
EST:     TGAGTCATACTATAACAAGCGGATAGTCGGTTGTCCTGGTGGCGAGGGTG                         AGGACGAACATGATGTTGTATGGTTCTGGTTGAAAAAAGACGAGCCGCATG
genomic: TGAGTCATACTATAACAAGCGGATAGTCGGTTGTCCTGGTGGCGAGGGTGgtaagtcggt ... ttattggcagAGGACGAACATGATGTTGTATGGTTCTGGTTGAAAAAAGACGAGCCGCATG
EST: gi|28985245|gb|BQ538397.2|BQ538397
EST:     TGAGTCATACTATAACAAGCGGATAGTCGGTTGTCCTGGTGGCGAGGGTG                         AGGACGAACATGATGTTGTATGGTTCTGGTTGAAAAAAGACGAGCCGCATG
genomic: TGAGTCATACTATAACAAGCGGATAGTCGGTTGTCCTGGTGGCGAGGGTGgtaagtcggt ... ttattggcagAGGACGAACATGATGTTGTATGGTTCTGGTTGAAAAAAGACGAGCCGCATG
EST: gi|18173629|gb|BM349017.1|BM349017
EST:     TGAGTCATACTATAACAAGCGGATAGTCGGTTGTCCTGGTGGCGAGGGTG                         AGGACGAACATGATGTTGTATGGTTCTGGTTGAAAAAAGACGAGCCGCATG
genomic: TGAGTCATACTATAACAAGCGGATAGTCGGTTGTCCTGGTGGCGAGGGTGgtaagtcggt ... ttattggcagAGGACGAACATGATGTTGTATGGTTCTGGTTGAAAAAAGACGAGCCGCATG
EST: gi|18450528|gb|BM428806.1|BM428806
EST:     CTCAGAGGACAAGCCGGCGAGGGTGGAGGACGTCATGCCCATCGCCACGGGGCTCGAGCGGGAGGAGCTAGAGGCCGAGCTCCAG
genomic: CTCAGAGGACAAGCCGGCGAGGGTGGAGGACGTCATGCCCATCGCCACGGGGCTCGAGCGGGAGGAGCTAGAGGCCGAGCTCCAG
EST: gi|37382992|gb|CF628470.1|CF628470
EST:     CTCAGAGGACAAGCCGGCGAGGGTGGAGGACGTCATGCCCATCGCCACGGGGCTCGAGCGGGAGGAGCTAGAGGCCGAGCTCCAG
genomic: CTCAGAGGACAAGCCGGCGAGGGTGGAGGACGTCATGCCCATCGCCACGGGGCTCGAGCGGGAGGAGCTAGAGGCCGAGCTCCAG
EST: gi|18649503|gb|BM498322.1|BM498322
EST:     CTCAGAGGACAAGCCGGCGAGGGTGGAGGACGTCATGCCCATCGCCACGGGGCTCGAGCGGGAGGAGCTAGAGGCCGAGCTCCAG
genomic: CTCAGAGGACAAGCCGGCGAGGGTGGAGGACGTCATGCCCATCGCCACGGGGCTCGAGCGGGAGGAGCTAGAGGCCGAGCTCCAG
EST: gi|29130310|gb|CB381014.1|CB381014
EST:     TGAGTCATACTATAACAAGCGGATAGTCGGTTGTCCTGGTGGCGAGGGTG                         AGGACGAACATGATG
genomic: TGAGTCATACTATAACAAGCGGATAGTCGGTTGTCCTGGTGGCGAGGGTGgtaagtcggt ... ttattggcagAGGACGAACATGATG
EST: gi|18450555|gb|BM428833.1|BM428833
EST:     CTCAGAGGACAAGCCGGCGAGGGTGGAGGACGTCATGCCCATCGCCACGGGGCTCGAGCGGGAGGAGCTAGAGGCCGAGCTCCCAG
genomic: CTCAGAGGACAAGCCGGCGAGGGTGGAGGACGTCATGCCCATCGCCACGGGGCTCGAGCGGGAGGAGCTAGAGGCCGAGCT-CCAG
EST: gi|161588036|gb|EY962533.1|EY962533
EST:     TGAGTCATACTATAACAAGCGGATAGTCGGTTGTCCTGGTGGCGAGGGTG                         AGGACGAACATGA
genomic: TGAGTCATACTATAACAAGCGGATAGTCGGTTGTCCTGGTGGCGAGGGTGgtaagtcggt ... ttattggcagAGGACGAACATGA
EST: gi|60352341|gb|DN219314.1|DN219314
EST:     CAGAGGACAAGCCGGCGAGGGTGGAGGACGTCATGCCCATCGCCACGGGGCTCGAGCGGGAGGAGCTAGAGGCCGAGCTCCAG
genomic: CAGAGGACAAGCCGGCGAGGGTGGAGGACGTCATGCCCATCGCCACGGGGCTCGAGCGGGAGGAGCTAGAGGCCGAGCTCCAG
EST: gi|60340144|gb|DN207117.1|DN207117
EST:     TGAGTCATACTATAACAAGCGGATAGTCGGTTGTCCTGGTGGCGAGGGTG                         AGGACGAACATGATGTTGTATGGTTCTGGTTGAAAAAAGACGAGCCGCATG
genomic: TGAGTCATACTATAACAAGCGGATAGTCGGTTGTCCTGGTGGCGAGGGTGgtaagtcggt ... ttattggcagAGGACGAACATGATGTTGTATGGTTCTGGTTGAAAAAAGACGAGCCGCATG
EST: gi|24770192|gb|CA405321.1|CA405321
EST:     TGAGTCATACTATAACAAGCGGATAGTCGGTTGTCCTGGTGGCGAGGGTG                         AGGACGAACATGATGTTGTATGGTTCTGGTTGAAAAAAGACGAGCCGCATG
genomic: TGAGTCATACTATAACAAGCGGATAGTCGGTTGTCCTGGTGGCGAGGGTGgtaagtcggt ... ttattggcagAGGACGAACATGATGTTGTATGGTTCTGGTTGAAAAAAGACGAGCCGCATG
EST: gi|76288216|gb|DV027784.1|DV027784
EST:     TGAGTCATACTATAACAAGCGGATAGTCGGTTGTCCTGGTGGGGAGGGTG                         AGGACGAACATGATGTTGTATGGTTCTGGTTGAAAAAAGACGAGCCGCATG
genomic: TGAGTCATACTATAACAAGCGGATAGTCGGTTGTCCTGGTGGCGAGGGTGgtaagtcggt ... ttattggcagAGGACGAACATGATGTTGTATGGTTCTGGTTGAAAAAAGACGAGCCGCATG
EST: gi|60348157|gb|DN215130.1|DN215130
EST:     TGAGTCATACTATAACAAGCGGATAGTCGGTTGTCCTGGTGGCGAGGGTG                         AGGACGAACATGATGTTGTATGGTTCTGGTTGAAAAAAGACGAGCCGCATG
genomic: TGAGTCATACTATAACAAGCGGATAGTCGGTTGTCCTGGTGGCGAGGGTGgtaagtcggt ... ttattggcagAGGACGAACATGATGTTGTATGGTTCTGGTTGAAAAAAGACGAGCCGCATG
EST: gi|31354094|gb|CD438451.1|CD438451
EST:     CTCAGAGGACAAGCCGGCGAGGGTGGAGGACGTCATGCCCATCGCCACGGGGCTCGAGCGGGAGGAGCTAGAGGCCGAGCTCCAG
genomic: CTCAGAGGACAAGCCGGCGAGGGTGGAGGACGTCATGCCCATCGCCACGGGGCTCGAGCGGGAGGAGCTAGAGGCCGAGCTCCAG
EST: gi|21759837|gb|BQ635378.1|BQ635378
EST:     CGGATAGTCGGTTGTCCTGGTGGCGAGGGTG                         AGGACGAACATGATGTTGTATGGTTCTGGTTGAAAAAAGACGAGCCGCATG
genomic: CGGATAGTCGGTTGTCCTGGTGGCGAGGGTGgtaagtcggt ... ttattggcagAGGACGAACATGATGTTGTATGGTTCTGGTTGAAAAAAGACGAGCCGCATG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGGAACCAGCTGTCATTGAGTCATACTATAACAAGCGGATAGTCGGTTGTCCTGGTGGCGAGGGTGgtaagtcggtattgtttatttttctaaaataaaaatagctggtgtcaacctagtgtgtaagaaattgcttggttttttaactagcctactttattggcag

- - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG