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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCAACAGTGACCTCCCTGGGCCTACCAGCAGCCTCAACGGCCTGCTCAACGCTTTCTCCAACAAGGGTTTGAGCAGCACCGACATGGTTGCCCTCTCAGgtacacacatgtgctactacgcgtctccttttcccgcttcatgcattgcaatgcatgcatgccgccgtagattcgcagcagcagcaccggcaggtggcac...

Basic information

species Zea mays
transcript GRMZM2G020523_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G020523_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os03g32050.1 (Oryza sativa), 5'ss of exon 3
GCCAACAGTGACCTCCCTGGGCCTACCAGCAGCCTCAACGGCCTGCTCAACGCTTTCTCCAACAAGGGTTTGAGCAGCACCGACATGGTTGCCCTCTCAGgtaca-cacatgtgctactacgcgtctccttttcccgcttcatgc-attgcaatgcatgca-tgccgccgtagattcgcagcagcagcaccggcaggtggcac
|||||||| |||||||| | |||  ||  || ||||  |   || |||  ||||||||||||||||||  | | || |||||||||||||| |||||| ||||||  ||| || |   ||    | | ||  |      ||   | ||  |  ||  |  | |    |   |   ||  || |     | | ||| ||  |  
GCCAACAGCGACCTCCCCGCGCCGTCCTCCACCCTCGCCACTCTCCTCGCCGCTTTCTCCAACAAGGGACTCACCACCACCGACATGGTTGTCCTCTCGGgtacagtacacgtacgcttaattatatgctaattaatgatcgcacgatctctttgtctaaactaatccaacactatcctagaaatta-atcagcacgtacc--
















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|17932143|gb|BM269103.1|BM269103
EST:     CGCTTTCTCCAACAAGGGTTTGAGCAGCACCGACATGGTTGCCCTCTCAG                         GTGCCCACACCGTCGGCCGGGCGCAGTGCAAGAACTGCCGGGCCCGGATCT
genomic: CGCTTTCTCCAACAAGGGTTTGAGCAGCACCGACATGGTTGCCCTCTCAGgtacacacat ... tgcaatgcagGTGCCCACACCGTCGGCCGGGCGCAGTGCAAGAACTGCCGGGCCCGGATCT
EST: gi|78110954|gb|DV529352.1|DV529352
EST:     CGCTTTCTCCAACAAGGGTTTGAGCAGCACCGACATGGTTGCCCTCTCAG                         GTGCCCACACCGTCGGCCGGGCGCAGTGCAAGAACTGCCGGGCCCGGATCT
genomic: CGCTTTCTCCAACAAGGGTTTGAGCAGCACCGACATGGTTGCCCTCTCAGgtacacacat ... tgcaatgcagGTGCCCACACCGTCGGCCGGGCGCAGTGCAAGAACTGCCGGGCCCGGATCT
EST: gi|149090376|gb|EE179684.2|EE179684
EST:     CGCTTTCTCCAACAAGGGTTTGAGCAGCACCGACATGGTTGCCCTCTCAG                         GTGCCCACACCGTCGGCCGGGCGCAGTGCAAGAACTGCCGGGCCCCGATCT
genomic: CGCTTTCTCCAACAAGGGTTTGAGCAGCACCGACATGGTTGCCCTCTCAGgtacacacat ... tgcaatgcagGTGCCCACACCGTCGGCCGGGCGCAGTGCAAGAACTGCCGGGCCCGGATCT
EST: gi|211277208|gb|FL063663.1|FL063663
EST:     CGCTTTCTCCAACAAGGGTTTGAGCAGCACCGACATGGTTGCCCTCTCAG                         GTGCCCACACCGTCGGCCGGGCGCAGTGCAAGAACTGCCGGGCCCGGATCT
genomic: CGCTTTCTCCAACAAGGGTTTGAGCAGCACCGACATGGTTGCCCTCTCAGgtacacacat ... tgcaatgcagGTGCCCACACCGTCGGCCGGGCGCAGTGCAAGAACTGCCGGGCCCGGATCT
EST: gi|78084057|gb|DV512450.1|DV512450
EST:     CGCTTTCTCCAACAAGGGTTTGAGCAGCACCGACATGGTTGCCCTCTCAG                         GTGCCCACACCGTCGGCCGGGCGCAGTGCAAGAACTGCCGGGCCCGGATCT
genomic: CGCTTTCTCCAACAAGGGTTTGAGCAGCACCGACATGGTTGCCCTCTCAGgtacacacat ... tgcaatgcagGTGCCCACACCGTCGGCCGGGCGCAGTGCAAGAACTGCCGGGCCCGGATCT
EST: gi|76935157|gb|DV174204.1|DV174204
EST:     CGCTTTCTCCAACAAGGGTTTGAGCAGCACCGACATGGTTGCCCTCTCAG                         GTGCCCACACCGTCGGCCGGGCGCAGTGCAAGACCTGCCGGGGCCCGGATC
genomic: CGCTTTCTCCAACAAGGGTTTGAGCAGCACCGACATGGTTGCCCTCTCAGgtacacacat ... tgcaatgcagGTGCCCACACCGTCGGCCGGGCGCAGTGCAAGAACTGCCGGG-CCCGGATC
EST: gi|89758624|gb|DY687739.1|DY687739
EST:     CGCTTTCTCCAACAAGGGTTTGAGCAGCACCGACATGGTTGCCCTCTCAG                         GTGCCCACACCGTCGGCCGGGCGCAGTGCAAGAACTGCCGGGCCCGGGATC
genomic: CGCTTTCTCCAACAAGGGTTTGAGCAGCACCGACATGGTTGCCCTCTCAGgtacacacat ... tgcaatgcagGTGCCCACACCGTCGGCCGGGCGCAGTGCAAGAACTGCCGGGCCCGG-ATC
EST: gi|76289009|gb|DV028577.1|DV028577
EST:     CGCTTTCTCCAACAAGGGTTTGAGCAGCACCGACATGGTTGCCCTCTCAG                         GTGCCCACACCGTCGGCCGGGCGCAGTGCAAGAACTGCCGGGCCCGGATCT
genomic: CGCTTTCTCCAACAAGGGTTTGAGCAGCACCGACATGGTTGCCCTCTCAGgtacacacat ... tgcaatgcagGTGCCCACACCGTCGGCCGGGCGCAGTGCAAGAACTGCCGGGCCCGGATCT
EST: gi|91048790|gb|EB159208.1|EB159208
EST:     CGCTTTCTCCAACAAGGGTTTGAGCAGCACCGACATGGTTGCCCTCTCAG                         GTGCCCACACCGTCGGCCGGGCGCAGTGCAAGAACTGCCGGGCCCGGATCT
genomic: CGCTTTCTCCAACAAGGGTTTGAGCAGCACCGACATGGTTGCCCTCTCAGgtacacacat ... tgcaatgcagGTGCCCACACCGTCGGCCGGGCGCAGTGCAAGAACTGCCGGGCCCGGATCT
EST: gi|76280543|gb|DV020111.1|DV020111
EST:     CGCTTTCTCCAACAAGGGTTTGAGCAGCACCGACATGGTTGCCCTCTCAG                         GTGCCCACACCGTCGGCCGGGCGCAGTGCAAGAACTGCCGGGCCCGGATCT
genomic: CGCTTTCTCCAACAAGGGTTTGAGCAGCACCGACATGGTTGCCCTCTCAGgtacacacat ... tgcaatgcagGTGCCCACACCGTCGGCCGGGCGCAGTGCAAGAACTGCCGGGCCCGGATCT
EST: gi|76285538|gb|DV025106.1|DV025106
EST:     CGCTTTCTCCAACAAGGGTTTGAGCAGCACCGACATGGTTGCCCTCTCAG                         GTGCCCACACCGTCGGCCGGGCGCAGTGCAAGAACTGCCGGGCCCGGATCT
genomic: CGCTTTCTCCAACAAGGGTTTGAGCAGCACCGACATGGTTGCCCTCTCAGgtacacacat ... tgcaatgcagGTGCCCACACCGTCGGCCGGGCGCAGTGCAAGAACTGCCGGGCCCGGATCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCAACAGTGACCTCCCTGGGCCTACCAGCAGCCTCAACGGCCTGCTCAACGCTTTCTCCAACAAGGGTTTGAGCAGCACCGACATGGTTGCCCTCTCAGgtacacacatgtgctactacgcgtctccttttcccgcttcatgcattgcaatgcatgcatgccgccgtagattcgcagcagcagcaccggcaggtggcac

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG