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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagcagcctcctcctactcgatctcccagatccgcactatctctgatgctacctgcttctttattactagctgtatcgatcgatcgatccagcgttgtttagctgacgagtcctgtttaattctgcgtgtttagCTGCAAGCAGTGTGACCAAAAGCAGGCCTGACGGCGATCCTCGGCTCTCTAGCCAGGCAGCAGGAGATGGAGCACGACGTGCACCACCAGCACCAGCAGG

Basic information

species Zea mays
transcript GRMZM5G898290_T02
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|78085883|gb|DV514276.1|DV514276
EST:     CCCATATCCCTCCGGCATAAACCCAAAAAG                         CTGCAAGCAGTGTGACCAAAAGCAGGCCTGACGGCGATCCTCGGCTCTCTA
genomic: CCCATATCCCTCCGGCATAAACCCAAAAAGgttagcagcc ... gcgtgtttagCTGCAAGCAGTGTGACCAAAAGCAGGCCTGACGGCGATCCTCGGCTCTCTA
EST: gi|71317486|gb|DR795459.1|DR795459
EST:     CCCATATCCCTCCGGCATAAACCCAAAAAG                         CTGCAAGCAGTGTGACCAAAAGCAGGCCTGACGGCGATCCTCGGCTCTCTA
genomic: CCCATATCCCTCCGGCATAAACCCAAAAAGgttagcagcc ... gcgtgtttagCTGCAAGCAGTGTGACCAAAAGCAGGCCTGACGGCGATCCTCGGCTCTCTA
EST: gi|149080827|gb|EE169898.2|EE169898
EST:     CCCATATCCCTCCGGCATAAACCCAAAAAG                         CTGCAAGCAGTGTGACCAAAAGCAGGCCTGACGGCGATCCTCGGCTCTCTA
genomic: CCCATATCCCTCCGGCATAAACCCAAAAAGgttagcagcc ... gcgtgtttagCTGCAAGCAGTGTGACCAAAAGCAGGCCTGACGGCGATCCTCGGCTCTCTA
EST: gi|78075643|gb|DV504077.1|DV504077
EST:     CCCATATCCCTCCGGCATAAACCCAAAAAG                         CTGCAAGCAGTGTGACCAAAAGCAGGCCTGACGGCGATCCTCGGCTCTCTA
genomic: CCCATATCCCTCCGGCATAAACCCAAAAAGgttagcagcc ... gcgtgtttagCTGCAAGCAGTGTGACCAAAAGCAGGCCTGACGGCGATCCTCGGCTCTCTA
EST: gi|149108650|gb|EE292890.2|EE292890
EST:     CCCATATCCCTCCGGCATAAACCCAAAAAG                         CTGCAAGCAGTGTGACCAAAAGCAGGCCTGACGGCGATCCTCGGCTCTCTA
genomic: CCCATATCCCTCCGGCATAAACCCAAAAAGgttagcagcc ... gcgtgtttagCTGCAAGCAGTGTGACCAAAAGCAGGCCTGACGGCGATCCTCGGCTCTCTA
EST: gi|149071005|gb|EE159410.2|EE159410
EST:     AAAAACCCATATCCCTCCGGCATAAACCCAAAAAG                         CTGCAAGCAGTGTGACCAAAAGCAGGCCTGACGGCGATCCTCGGCTCTCTA
genomic: AAAAACCCATATCCCTCCGGCATAAACCCAAAAAGgttagcagcc ... gcgtgtttagCTGCAAGCAGTGTGACCAAAAGCAGGCCTGACGGCGATCCTCGGCTCTCTA
EST: gi|89759018|gb|DY687976.1|DY687976
EST:     ACCCATATCCCTCCGGCATAAACCCAAAAAG                         CTGCAAGCAGTGTGACCAAAAGCAGGCCTGACGGCGATCCTCGGCTCTCTA
genomic: ACCCATATCCCTCCGGCATAAACCCAAAAAGgttagcagcc ... gcgtgtttagCTGCAAGCAGTGTGACCAAAAGCAGGCCTGACGGCGATCCTCGGCTCTCTA
EST: gi|74232934|gb|DT640848.1|DT640848
EST:     CCCATATCCCTCCGGCATAAACCCAAAAAG                         CTGCAAGCAGTGTGACCAAAAGCAGGCCTGACGGCGATCCTCGGCTCTCTA
genomic: CCCATATCCCTCCGGCATAAACCCAAAAAGgttagcagcc ... gcgtgtttagCTGCAAGCAGTGTGACCAAAAGCAGGCCTGACGGCGATCCTCGGCTCTCTA
EST: gi|149088337|gb|EE177434.2|EE177434
EST:     CCCATATCCCTCCGGCATAAACCCAAAAAG                         CTGCAAGCAGTGTGACCAAAAGCAGGCCTGACGGCGATCCTCGGCTCTCTA
genomic: CCCATATCCCTCCGGCATAAACCCAAAAAGgttagcagcc ... gcgtgtttagCTGCAAGCAGTGTGACCAAAAGCAGGCCTGACGGCGATCCTCGGCTCTCTA
EST: gi|74243340|gb|DT651254.1|DT651254
EST:     CCCATATCCCTCCGGCATAAACCCAAAAAG                         CTGCAAGCAGTGTGACCAAAAGCAGGCCTGACGGCGATCCTCGGCTCTCTA
genomic: CCCATATCCCTCCGGCATAAACCCAAAAAGgttagcagcc ... gcgtgtttagCTGCAAGCAGTGTGACCAAAAGCAGGCCTGACGGCGATCCTCGGCTCTCTA
EST: gi|78080430|gb|DV508842.1|DV508842
EST:     CCCATATCCCTCCGGCATAAACCCAAAAAG                         CTGCAAGCAGTGTGACCAAAAGCAGGCCTGACGGCGATCCTCGGCTCTCTA
genomic: CCCATATCCCTCCGGCATAAACCCAAAAAGgttagcagcc ... gcgtgtttagCTGCAAGCAGTGTGACCAAAAGCAGGCCTGACGGCGATCCTCGGCTCTCTA

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: 49 (upstream exon), 43 (downstream exon)
Score: 8

CTTAACAACTCCACTCCCGCGGAAAAAAAACCCATATCCCTCCGGCATAAACCCAAAAAGgttagcagcc ... gcgtgtttagCTGCAAGCAGTGTGACCAAAAGCAGGCCTGACGGCGATCCTCGGCTCTCTAGCCAGGCAGCAGGAGATGGAGCACGACGTGCACCACCAGCACCAGCAGG


Block sizes: 47 (upstream exon), 43 (downstream exon)
Score: 148

CTTAACAACTCCACTCCCGCGGAAAAAAAACCCATATCCCTCCGGCATAAACCCAAAAAGgttagcagcc ... gcgtgtttagCTGCAAGCAGTGTGACCAAAAGCAGGCCTGACGGCGATCCTCGGCTCTCTAGCCAGGCAGCAGGAGATGGAGCACGACGTGCACCACCAGCACCAGCAGG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 197

CTTAACAACTCCACTCCCGCGGAAAAAAAACCCATATCCCTCCGGCATAAACCCAAAAAGgttagcagcc ... gcgtgtttagCTGCAAGCAGTGTGACCAAAAGCAGGCCTGACGGCGATCCTCGGCTCTCTAGCCAGGCAGCAGGAGATGGAGCACGACGTGCACCACCAGCACCAGCAGG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 29

CTTAACAACTCCACTCCCGCGGAAAAAAAACCCATATCCCTCCGGCATAAACCCAAAAAGgttagcagcc ... gcgtgtttagCTGCAAGCAGTGTGACCAAAAGCAGGCCTGACGGCGATCCTCGGCTCTCTAGCCAGGCAGCAGGAGATGGAGCACGACGTGCACCACCAGCACCAGCAGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgatcgatccagcgttgtttagctgacgagtcctgtttaattctgcgtgtttagCTGCAAGCAGTGTGACCAAAAGCAGGCCTGACGGCGATCCTCGGCTCTCTAGCCAGGCAGCAGGAGATGGAGCACGACGTGCACCACCAGCACCAGCAGG
                                  tgtttaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagcagcctcctcctactcgatctcccagatccgcactatctctgatgctacctgcttctttattactagctgtatcgatcgatcgatccagcgttgtttagctgacgagtcctgtttaattctgcgtgtttagCTGCAAGCAGTGTGACCAAAAGCAGGCCTGACGGCGATCCTCGGCTCTCTAGCCAGGCAGCAGGAGATGGAGCACGACGTGCACCACCAGCACCAGCAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA