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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agcatgcttgtgaaaacaagcagcgccagtaattagtcattttcagcctgtattgggtgaactgatctgagtatctgaccttcttgcccttgtgttatagGAAAACACTGCTGAATTTCTCAGCTGGTGCCTAGTGGTGGGAAATAAAGCTAGGGACCCAGCATCCTTGTGATAGCAATCACATCATTGGTGTTGTTTTT

Basic information

species Zea mays
transcript GRMZM2G158069_T01
intron # 1
splice site 3'
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|71302358|gb|DR787297.1|DR787297
EST:     TGGTCCCGGGAGGTGTGGGTCAATGCATCCAAATAACGGCTCTTCCAGAG                         GAAAACACTGCTGAATTTCTCAGCTGGTGCCTAGTGGTGGGAAATAAAGCT
genomic: TGGTCCCGGGAGGTGTGGGTCAACGCATCCAAATAACGGCTCTTCCAGAGgtgcgctcac ... tgtgttatagGAAAACACTGCTGAATTTCTCAGCTGGTGCCTAGTGGTGGGAAATAAAGCT
EST: gi|78116007|gb|DV534395.1|DV534395
EST:     TGGTCCCGGGAGGTGTGGGTCAACGCATCCAAATAACGGCTCTTCCAGAG                         GAAAACACTGCTGAATTTCTCAGCTGGTGCCTAGTGGTGGGAAATAAAGCT
genomic: TGGTCCCGGGAGGTGTGGGTCAACGCATCCAAATAACGGCTCTTCCAGAGgtgcgctcac ... tgtgttatagGAAAACACTGCTGAATTTCTCAGCTGGTGCCTAGTGGTGGGAAATAAAGCT
EST: gi|78104712|gb|DV523130.1|DV523130
EST:     TGGTCCCGGGAGGTGTGGGTCAACGCATCCAAATAACGGCTCTTCCAGAG                         GAAAACACTGCTGAATTTCTCAGCTGGTGCCTAGTGGTGGGAAATAAAGCT
genomic: TGGTCCCGGGAGGTGTGGGTCAACGCATCCAAATAACGGCTCTTCCAGAGgtgcgctcac ... tgtgttatagGAAAACACTGCTGAATTTCTCAGCTGGTGCCTAGTGGTGGGAAATAAAGCT
EST: gi|33467121|gb|CF244170.1|CF244170
EST:     TGGTCCCGGGAGGTGTGGGTCAACGCATCCAAATAACGGCTCTTCCAGAG                         GAAAACACTGCTGAATTTCTCAGCTGGTGCCTAGTGGTGGGAAATAAAGCT
genomic: TGGTCCCGGGAGGTGTGGGTCAACGCATCCAAATAACGGCTCTTCCAGAGgtgcgctcac ... tgtgttatagGAAAACACTGCTGAATTTCTCAGCTGGTGCCTAGTGGTGGGAAATAAAGCT

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: 45 (upstream exon), 49 (downstream exon)
Score: 42

AAGCGACCTTCCGCCGGTCCAGTCTGTCCTTCTCGGCCTCCGCGACGCCGTGGTCCCGGGAGGTGTGGGTCAACGCATCCAAATAACGGCTCTTCCAGAGgtgcgctcac ... tgtgttatagGAAAACACTGCTGAATTTCTCAGCTGGTGCCTAGTGGTGGGAAATAAAGCTAGGGACCCAGCATCCTTGTGATAGCAATCACATCATTGGTGTTGTTTTT


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 66

AAGCGACCTTCCGCCGGTCCAGTCTGTCCTTCTCGGCCTCCGCGACGCCGTGGTCCCGGGAGGTGTGGGTCAACGCATCCAAATAACGGCTCTTCCAGAGgtgcgctcac ... tgtgttatagGAAAACACTGCTGAATTTCTCAGCTGGTGCCTAGTGGTGGGAAATAAAGCTAGGGACCCAGCATCCTTGTGATAGCAATCACATCATTGGTGTTGTTTTT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 66

AAGCGACCTTCCGCCGGTCCAGTCTGTCCTTCTCGGCCTCCGCGACGCCGTGGTCCCGGGAGGTGTGGGTCAACGCATCCAAATAACGGCTCTTCCAGAGgtgcgctcac ... tgtgttatagGAAAACACTGCTGAATTTCTCAGCTGGTGCCTAGTGGTGGGAAATAAAGCTAGGGACCCAGCATCCTTGTGATAGCAATCACATCATTGGTGTTGTTTTT


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 25

AAGCGACCTTCCGCCGGTCCAGTCTGTCCTTCTCGGCCTCCGCGACGCCGTGGTCCCGGGAGGTGTGGGTCAACGCATCCAAATAACGGCTCTTCCAGAGgtgcgctcac ... tgtgttatagGAAAACACTGCTGAATTTCTCAGCTGGTGCCTAGTGGTGGGAAATAAAGCTAGGGACCCAGCATCCTTGTGATAGCAATCACATCATTGGTGTTGTTTTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcctgtattgggtgaactgatctgagtatctgaccttcttgcccttgtgttatagGAAAACACTGCTGAATTTCTCAGCTGGTGCCTAGTGGTGGGAAATAAAGCTAGGGACCCAGCATCCTTGTGATAGCAATCACATCATTGGTGTTGTTTTT
                           atctgac  putative branch site (score: 25)
                                 ccttcttgcccttgt  CT-rich tract
                                               tgttata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agcatgcttgtgaaaacaagcagcgccagtaattagtcattttcagcctgtattgggtgaactgatctgagtatctgaccttcttgcccttgtgttatagGAAAACACTGCTGAATTTCTCAGCTGGTGCCTAGTGGTGGGAAATAAAGCTAGGGACCCAGCATCCTTGTGATAGCAATCACATCATTGGTGTTGTTTTT

agcatgc
- - - - - - - - -aagcagc
- - - - - - - - - - - - - - - - - - - - - - -gcctgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatctg