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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGGATGACGACCTGTCGCACCGCGAACGCAGCCGCCGTCGTCCGTCTCCTGCTGCTGTGCTCTTTCTGCGCCGCCGCCGCCATTGCCTGCGACCCTCCTAgtacgtgattgcatccacgcgtcctacacttacacgtactgtgttcttcgtctgcggcagagcccgagacttgcattagttctcctgtaatctctctctgctactgctgtttccag

Basic information

species Zea mays
transcript GRMZM5G807267_T04
intron # 3
splice site 5'
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|74239799|gb|DT647713.1|DT647713
EST:     GCTGCTGTGCTCTTTCTGCGCCGCCGCCGCCATTGCCTGCGACCCTCCTA                         ATGGCGCCAAGTTCGGGTACACCGGCTCCGTCGGTCCCGACCACTGGGGCG
genomic: GCTGCTGTGCTCTTTCTGCGCCGCCGCCGCCATTGCCTGCGACCCTCCTAgtacgtgatt ... ctgtttccagATGGCGCCAAGTTCGGGTACACCGGCTCCGTCGGTCCCGACCACTGGGGCG
EST: gi|71417345|gb|DR804018.1|DR804018
EST:     GCTGCTGTGCTCTTTCTGCGCCGCCGCCGCCATTGCCTGCGACCCTCCTA                         ATGGCGCCAAGTTCGGGTACTCCGGCTCCGTCGGTCCCGACCACTGGGGCG
genomic: GCTGCTGTGCTCTTTCTGCGCCGCCGCCGCCATTGCCTGCGACCCTCCTAgtacgtgatt ... ctgtttccagATGGCGCCAAGTTCGGGTACACCGGCTCCGTCGGTCCCGACCACTGGGGCG
EST: gi|78112701|gb|DV531095.1|DV531095
EST:     GCTGCTGTGCTCTTTCTGCGCCGCCGCCGCCATTGCCTGCGACCCTCCTA                         ATGGCGCCAAGTTCGGGTACACCGGCTCCGTCGGTCCCGACCACTGGGGCG
genomic: GCTGCTGTGCTCTTTCTGCGCCGCCGCCGCCATTGCCTGCGACCCTCCTAgtacgtgatt ... ctgtttccagATGGCGCCAAGTTCGGGTACACCGGCTCCGTCGGTCCCGACCACTGGGGCG
EST: gi|148933555|gb|EC877415.2|EC877415
EST:     GCTGCTGTGCTCTTTCTGCGCCGCCGCCGCCATTGCCTGCGACCCTCCTA                         ATGGCGCCAAGTTCGGGTACACCGGCTCCGTCGGTCCCGACCACTGGGGCG
genomic: GCTGCTGTGCTCTTTCTGCGCCGCCGCCGCCATTGCCTGCGACCCTCCTAgtacgtgatt ... ctgtttccagATGGCGCCAAGTTCGGGTACACCGGCTCCGTCGGTCCCGACCACTGGGGCG
EST: gi|76014111|gb|DT941281.1|DT941281
EST:     GCTGCTGTGCTCTTTCTGCGCCGCCGCCGCCATTGCCTGCGACCCTCCTA                         ATGGCGCCAAGTTCGGGTACACCGGCTCCGTCGGTCCCGACCACTGGGGCG
genomic: GCTGCTGTGCTCTTTCTGCGCCGCCGCCGCCATTGCCTGCGACCCTCCTAgtacgtgatt ... ctgtttccagATGGCGCCAAGTTCGGGTACACCGGCTCCGTCGGTCCCGACCACTGGGGCG
EST: gi|76288688|gb|DV028256.1|DV028256
EST:     GCTGCTGTGCTCTTTCTGCGCCGCCGCCGCCATTGCCTGCGACCCTCCTA                         ATGGCGCCAAGTTCGGGTACACCGGCTCCGTCGGTCCCGACCACTGGGGCG
genomic: GCTGCTGTGCTCTTTCTGCGCCGCCGCCGCCATTGCCTGCGACCCTCCTAgtacgtgatt ... ctgtttccagATGGCGCCAAGTTCGGGTACACCGGCTCCGTCGGTCCCGACCACTGGGGCG
EST: gi|91871059|gb|EB401220.1|EB401220
EST:     GCTGCTGTGCTCTTTCTGCGCCGCCGCCGCCATTGCCTGCGACCCTCCTA                         ATGGCGCCAAGTTCGGGTACACCGGCTCCGTCGGTCCCGACCACTGGGGCG
genomic: GCTGCTGTGCTCTTTCTGCGCCGCCGCCGCCATTGCCTGCGACCCTCCTAgtacgtgatt ... ctgtttccagATGGCGCCAAGTTCGGGTACACCGGCTCCGTCGGTCCCGACCACTGGGGCG
EST: gi|71316204|gb|DR794778.1|DR794778
EST:     GCTGCTGTGCTCTTTCTGCGCCGCCGCCGCCATTGCCTGCGACCCTCCTA                         ATGGCGCCAAGTTCGGGTACACCGGCTCCGTCGGTCCCGACCACTGGGGCG
genomic: GCTGCTGTGCTCTTTCTGCGCCGCCGCCGCCATTGCCTGCGACCCTCCTAgtacgtgatt ... ctgtttccagATGGCGCCAAGTTCGGGTACACCGGCTCCGTCGGTCCCGACCACTGGGGCG
EST: gi|50324602|gb|CO519728.1|CO519728
EST:     GCTGCTGTGCTCTTTCTGCGCCGCCGCCGCCATTGCCTGCGACCCTCCTA                         ATGGCGCCAAGTTCGGGTACACCGGCTCCGTCGGTCCCGACCACTGGGGCG
genomic: GCTGCTGTGCTCTTTCTGCGCCGCCGCCGCCATTGCCTGCGACCCTCCTAgtacgtgatt ... ctgtttccagATGGCGCCAAGTTCGGGTACACCGGCTCCGTCGGTCCCGACCACTGGGGCG
EST: gi|89758326|gb|DY687544.1|DY687544
EST:     GCTGCTGTGCTCTTTCTGCGCCGCCGCCGCCATTGCCTGCGACCCTCCTA                         ATGGCGCCAAGTTCGGGTACACCGGCTCCGTCGGTCCCGACCACTGGGGCG
genomic: GCTGCTGTGCTCTTTCTGCGCCGCCGCCGCCATTGCCTGCGACCCTCCTAgtacgtgatt ... ctgtttccagATGGCGCCAAGTTCGGGTACACCGGCTCCGTCGGTCCCGACCACTGGGGCG
EST: gi|74244873|gb|DT652787.1|DT652787
EST:     GCTGCTGTGCTCTTTCTGCGCCGCCGCCGCCATTGCCTGCGACCCTCCTA                         ATGGCGCCAAGTTCGGGTACACCGGCTCCGTCGGTCCCGACCACTGGGGCG
genomic: GCTGCTGTGCTCTTTCTGCGCCGCCGCCGCCATTGCCTGCGACCCTCCTAgtacgtgatt ... ctgtttccagATGGCGCCAAGTTCGGGTACACCGGCTCCGTCGGTCCCGACCACTGGGGCG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 3 RNA-Seq libraries.


Block sizes: 10 (upstream exon), 40 (downstream exon)
Score: 1

CGGATGACGACCTGTCGCACCGCGAACGCAGCCGCCGTCGTCCGTCTCCTGCTGCTGTGCTCTTTCTGCGCCGCCGCCGCCATTGCCTGCGACCCTCCTAgtacgtgatt ... ctgtttccagATGGCGCCAAGTTCGGGTACACCGGCTCCGTCGGTCCCGACCACTGGGGCGCACTGAGCCCCAGCTTCAGGCAGTGCGCGACAGGGACGAAGCAGTCCCC


Block sizes: 28 (upstream exon), 22 (downstream exon)
Score: 1

CGGATGACGACCTGTCGCACCGCGAACGCAGCCGCCGTCGTCCGTCTCCTGCTGCTGTGCTCTTTCTGCGCCGCCGCCGCCATTGCCTGCGACCCTCCTAgtacgtgatt ... ctgtttccagATGGCGCCAAGTTCGGGTACACCGGCTCCGTCGGTCCCGACCACTGGGGCGCACTGAGCCCCAGCTTCAGGCAGTGCGCGACAGGGACGAAGCAGTCCCC


Block sizes: 28 (upstream exon), 42 (downstream exon)
Score: 5

CGGATGACGACCTGTCGCACCGCGAACGCAGCCGCCGTCGTCCGTCTCCTGCTGCTGTGCTCTTTCTGCGCCGCCGCCGCCATTGCCTGCGACCCTCCTAgtacgtgatt ... ctgtttccagATGGCGCCAAGTTCGGGTACACCGGCTCCGTCGGTCCCGACCACTGGGGCGCACTGAGCCCCAGCTTCAGGCAGTGCGCGACAGGGACGAAGCAGTCCCC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGGATGACGACCTGTCGCACCGCGAACGCAGCCGCCGTCGTCCGTCTCCTGCTGCTGTGCTCTTTCTGCGCCGCCGCCGCCATTGCCTGCGACCCTCCTAgtacgtgattgcatccacgcgtcctacacttacacgtactgtgttcttcgtctgcggcagagcccgagacttgcattagttctcctgtaatctctctctgctactgctgtttccag

- - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT