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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTAAGTTTGAGAGAACCCATCCGTACTGGTGTTGATGACGCTGGACTGAAGGAGATAATTGGTGCCGCGgtatgtaaataaatttaccaagttactatgtaggaagtatggcatgctctttttttttcactttttaggattaggacttgtttgcctttttttctgctat...

Basic information

species Zea mays
transcript GRMZM2G135816_T01
intron # 5
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|5058882|gb|AI737358.1|AI737358
EST:     TCCGTTCTGGTGTTGATGACGCTGGACTGAAGGAGATAATTGGTGCCGCG                         GTTAAAAGGAAGAAAGCTAAACATGCCGGGATGTTTGATATTGCCAAGACA
genomic: TCCGTACTGGTGTTGATGACGCTGGACTGAAGGAGATAATTGGTGCCGCGgtatgtaaat ... ctatgttcagGTTAAAAGGAAGAAAGCTAAACATGCCGGGATGTTTGATATTGCCAAGACA
EST: gi|6020607|gb|AW065640.1|AW065640
EST:     TCCGTACTGGTGTTGATGACGCTGGACTGAAGGAGATAATTGGTGCCGCG                         GTGAAAAGGAAGAAAGCTAAACATGCTGGGATGTTTGATATTGCCAAGACA
genomic: TCCGTACTGGTGTTGATGACGCTGGACTGAAGGAGATAATTGGTGCCGCGgtatgtaaat ... ctatgttcagGTTAAAAGGAAGAAAGCTAAACATGCCGGGATGTTTGATATTGCCAAGACA
EST: gi|211275416|gb|FL065995.1|FL065995
EST:     CTGAAGGAGATAATTGGTGCCGCG                         GTTAAAAGGAAGAAAGCTAAACATGCCGGGATGTTTGATATTGCMAAGACA
genomic: CTGAAGGAGATAATTGGTGCCGCGgtatgtaaat ... ctatgttcagGTTAAAAGGAAGAAAGCTAAACATGCCGGGATGTTTGATATTGCCAAGACA
EST: gi|211275417|gb|FL065996.1|FL065996
EST:     CTGAAGGAGATAATTGGTGCCGCG                         GTTAAAAGGAAGAAAGCTAAACATGCCGGGATGTTTGATATTGCCAAGACA
genomic: CTGAAGGAGATAATTGGTGCCGCGgtatgtaaat ... ctatgttcagGTTAAAAGGAAGAAAGCTAAACATGCCGGGATGTTTGATATTGCCAAGACA
EST: gi|6194756|gb|AW146860.1|AW146860
EST:     TCCGTACTGGTGTTGATGACGCTGGACTGAAGGAGATAATTGGTGCCGCG                         GTGAAAAGGAAGAAAGCTAAACATGCTGGGATGTTTGATATTGCCAAGACA
genomic: TCCGTACTGGTGTTGATGACGCTGGACTGAAGGAGATAATTGGTGCCGCGgtatgtaaat ... ctatgttcagGTTAAAAGGAAGAAAGCTAAACATGCCGGGATGTTTGATATTGCCAAGACA
EST: gi|78090417|gb|DV518791.1|DV518791
EST:     TCCGTACTGGTGTTGATGACGCTGGACTGAAGGAGATAATTGGTGCCGCG                         GTTAAAAGGAAGAAAGCTAAACATGCCGGGATGTTTGATATTGCCAAGACA
genomic: TCCGTACTGGTGTTGATGACGCTGGACTGAAGGAGATAATTGGTGCCGCGgtatgtaaat ... ctatgttcagGTTAAAAGGAAGAAAGCTAAACATGCCGGGATGTTTGATATTGCCAAGACA
EST: gi|149048405|gb|EE048313.2|EE048313
EST:     TCCGTACTGGTGTTGATGACGCTGGACTGAAGGAGATAATTGGTGCCGCG                         GTTAAAAGGAAGAAAGCTAAACATGCCGGGATGTTTGATATTGCCAAGACA
genomic: TCCGTACTGGTGTTGATGACGCTGGACTGAAGGAGATAATTGGTGCCGCGgtatgtaaat ... ctatgttcagGTTAAAAGGAAGAAAGCTAAACATGCCGGGATGTTTGATATTGCCAAGACA
EST: gi|91054281|gb|EB164699.1|EB164699
EST:     TCCGTACTGGTGTTGATGACGCTGGACTGAAGGAGATAATTGGTGCCGCG                         GTTAAAAGGAAGAAAGCTAAACATGCCGGGATGTTTGATATTGCCAAGACA
genomic: TCCGTACTGGTGTTGATGACGCTGGACTGAAGGAGATAATTGGTGCCGCGgtatgtaaat ... ctatgttcagGTTAAAAGGAAGAAAGCTAAACATGCCGGGATGTTTGATATTGCCAAGACA
EST: gi|16378519|gb|BI992468.1|BI992468
EST:     TCCGTACTGGTGTTGATGACGCTGGACTGAAGGAGATAATTGGTGCCGCG                         GTTAAAAGGAAGAAAGCTAAACATGCCGGGATGTTTGATATTGCCAAGACA
genomic: TCCGTACTGGTGTTGATGACGCTGGACTGAAGGAGATAATTGGTGCCGCGgtatgtaaat ... ctatgttcagGTTAAAAGGAAGAAAGCTAAACATGCCGGGATGTTTGATATTGCCAAGACA
EST: gi|13249841|gb|BG360746.1|BG360746
EST:     TCCGTACTGGTGTTGATGACGCTGGACTGAAGGAGATAATTGGTGCCGCG                         GTTAAAAGGAAGAAAGCTAAACATGCCGGGATGTTTGATATTGCCAAGACA
genomic: TCCGTACTGGTGTTGATGACGCTGGACTGAAGGAGATAATTGGTGCCGCGgtatgtaaat ... ctatgttcagGTTAAAAGGAAGAAAGCTAAACATGCCGGGATGTTTGATATTGCCAAGACA
EST: gi|91874219|gb|EB404176.1|EB404176
EST:     TCCGTACTGGTGTTGATGACGCTGGACTGAAGGAGATAATTGGTGCCGCG                         GTTAAAAGGAAGAAAGCTAAACATGCCGGGATGTTTGATATTGCCAAGACA
genomic: TCCGTACTGGTGTTGATGACGCTGGACTGAAGGAGATAATTGGTGCCGCGgtatgtaaat ... ctatgttcagGTTAAAAGGAAGAAAGCTAAACATGCCGGGATGTTTGATATTGCCAAGACA
EST: gi|32859387|gb|CD999068.1|CD999068
EST:     TCCGTACTGGTGTTGATGACGCTGGACTGAAGGAGATAATTGGTGCCGCG                         GTTAAAAGGAAGAAAGCTAAACATGCCGGGATGTTTGATATTGCCAAGACA
genomic: TCCGTACTGGTGTTGATGACGCTGGACTGAAGGAGATAATTGGTGCCGCGgtatgtaaat ... ctatgttcagGTTAAAAGGAAGAAAGCTAAACATGCCGGGATGTTTGATATTGCCAAGACA
EST: gi|211246367|gb|FL451965.1|FL451965
EST:     TCCGTACTGGTGTTGATGACGCTGGACTGAAGGAGATAATTGGTGCCGCG                         GTTAAAAGGAAGAAAGCTAAACATGCCGGGATGTTTGATATTGCCAAGACA
genomic: TCCGTACTGGTGTTGATGACGCTGGACTGAAGGAGATAATTGGTGCCGCGgtatgtaaat ... ctatgttcagGTTAAAAGGAAGAAAGCTAAACATGCCGGGATGTTTGATATTGCCAAGACA
EST: gi|211121393|gb|FL463011.1|FL463011
EST:     CTGAAGGAGATAATTGGTGCCGCG                         GTTAAAAGGAAGAAAGCTAAACATGCCGGGATGTTTGATATTGCCAAGACW
genomic: CTGAAGGAGATAATTGGTGCCGCGgtatgtaaat ... ctatgttcagGTTAAAAGGAAGAAAGCTAAACATGCCGGGATGTTTGATATTGCCAAGACA
EST: gi|211275415|gb|FL065994.1|FL065994
EST:     CTGAAGGAGATAATTGGTGCCGCG                         GTTAAAAGGAAGAAAGCTAAACATGCCGGGATGTTTGATATTGCCAAGACA
genomic: CTGAAGGAGATAATTGGTGCCGCGgtatgtaaat ... ctatgttcagGTTAAAAGGAAGAAAGCTAAACATGCCGGGATGTTTGATATTGCCAAGACA
EST: gi|148946521|gb|EC891833.2|EC891833
EST:     TCCGTACTGGTGTTGATGACGCTGGACTGAAGGAGATAATTGGTGCCGCG                         GTTAAAAGGAAGAAAGCTAAACATGCCGGGATGTTTGATATTGCCAAGACA
genomic: TCCGTACTGGTGTTGATGACGCTGGACTGAAGGAGATAATTGGTGCCGCGgtatgtaaat ... ctatgttcagGTTAAAAGGAAGAAAGCTAAACATGCCGGGATGTTTGATATTGCCAAGACA
EST: gi|13249840|gb|BG360745.1|BG360745
EST:     TCCGTACTGGTGTTGATGACGCTGGACTGAAGGAGATAATTGGTGCCCCG                         GTTAAAAGGAAGAAAGCTAAACATGCCGGGATGTTTGATATTGCCAAGACA
genomic: TCCGTACTGGTGTTGATGACGCTGGACTGAAGGAGATAATTGGTGCCGCGgtatgtaaat ... ctatgttcagGTTAAAAGGAAGAAAGCTAAACATGCCGGGATGTTTGATATTGCCAAGACA
EST: gi|148928476|gb|EE285290.2|EE285290
EST:     TCCGTACTGGTGTTGATGACGCTGGACTGAAGGAGATAATTGGTGCCGCG                         GTTAAAAGGAAGAAAGCTAAACATGCCGGGATGTTTGATATTGCCAAGACA
genomic: TCCGTACTGGTGTTGATGACGCTGGACTGAAGGAGATAATTGGTGCCGCGgtatgtaaat ... ctatgttcagGTTAAAAGGAAGAAAGCTAAACATGCCGGGATGTTTGATATTGCCAAGACA

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 4 RNA-Seq libraries.


Block sizes: 30 (upstream exon), 40 (downstream exon)
Score: 10

GTAAGTTTGAGAGAACCCATCCGTACTGGTGTTGATGACGCTGGACTGAAGGAGATAATTGGTGCCGCGgtatgtaaat ... ctatgttcagGTTAAAAGGAAGAAAGCTAAACATGCCGGGATGTTTGATATTGCCAAGACAGCAAATAGACCCATGATACATATAGGTGGCTGAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 163

GTAAGTTTGAGAGAACCCATCCGTACTGGTGTTGATGACGCTGGACTGAAGGAGATAATTGGTGCCGCGgtatgtaaat ... ctatgttcagGTTAAAAGGAAGAAAGCTAAACATGCCGGGATGTTTGATATTGCCAAGACAGCAAATAGACCCATGATACATATAGGTGGCTGAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 168

GTAAGTTTGAGAGAACCCATCCGTACTGGTGTTGATGACGCTGGACTGAAGGAGATAATTGGTGCCGCGgtatgtaaat ... ctatgttcagGTTAAAAGGAAGAAAGCTAAACATGCCGGGATGTTTGATATTGCCAAGACAGCAAATAGACCCATGATACATATAGGTGGCTGAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 48

GTAAGTTTGAGAGAACCCATCCGTACTGGTGTTGATGACGCTGGACTGAAGGAGATAATTGGTGCCGCGgtatgtaaat ... ctatgttcagGTTAAAAGGAAGAAAGCTAAACATGCCGGGATGTTTGATATTGCCAAGACAGCAAATAGACCCATGATACATATAGGTGGCTGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTAAGTTTGAGAGAACCCATCCGTACTGGTGTTGATGACGCTGGACTGAAGGAGATAATTGGTGCCGCGgtatgtaaataaatttaccaagttactatgtaggaagtatggcatgctctttttttttcactttttaggattaggacttgtttgcctttttttctgctat

- - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT