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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcttccctactagtactagtgcagtgtatctctctcactcacccatcccaggggattccgattcgtcccgtaaattcggaatccattccgtccttgcagAAACGTGCGGCGCCCGGTGACTCCTCGCCTCCTCGCGTCCTTCGCTCTCCTCGGATTCACTGG

Basic information

species Zea mays
transcript GRMZM2G134930_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|148963460|gb|EE014479.2|EE014479
EST:     GACCTCGTCGCGCTCGCGCTCCTCGCGCCCATCGCCTTCTTTCGCGAGAG                         AAACGTGCGGCGCCCCGGTGACTCCTCGCCTCCTCGCGTCCTTCGCTCTCC
genomic: GACCTCGTCGCGCTCGCGCTCCTCGCGCCCATCGCCTTCTTTCGCGAGAGgtctccccgc ... gtccttgcagAAACGTGCGGCGCCC-GGTGACTCCTCGCCTCCTCGCGTCCTTCGCTCTCC
EST: gi|71434594|gb|DR815644.1|DR815644
EST:     GACCTCGTCGCGCTCGCGCTCCTCGCGCCCATCGCCTTCTTTCGCGAGAG                         AAACGTGCGGCGCCCGGTGACTCCCTCGCCTCCTCGCGTCCTTCGCTCTCC
genomic: GACCTCGTCGCGCTCGCGCTCCTCGCGCCCATCGCCTTCTTTCGCGAGAGgtctccccgc ... gtccttgcagAAACGTGCGGCGCCCGGTGACTCC-TCGCCTCCTCGCGTCCTTCGCTCTCC
EST: gi|18384215|gb|BM417414.1|BM417414
EST:     GACCTCGTCGCGCTCGCGCTCCTCGCGCCCATCGCCTTCTTTCGCGAGAG                         AAACGTGCGGCGCCCGGTGACGCCTCGCCTCCTCGCGTCCTTCGCTCTCCT
genomic: GACCTCGTCGCGCTCGCGCTCCTCGCGCCCATCGCCTTCTTTCGCGAGAGgtctccccgc ... gtccttgcagAAACGTGCGGCGCCCGGTGACTCCTCGCCTCCTCGCGTCCTTCGCTCTCCT
EST: gi|94476183|gb|EB705141.1|EB705141
EST:     GACCTCGTCGCGCTCGCGCTCCTCGCGCCCATCGCCTTCTTTCGCGAGAG                         AAACGTGCGGCGCCCGGTGACTCCTCGCCTCCTCGCGTCCTTCGCTCTCCT
genomic: GACCTCGTCGCGCTCGCGCTCCTCGCGCCCATCGCCTTCTTTCGCGAGAGgtctccccgc ... gtccttgcagAAACGTGCGGCGCCCGGTGACTCCTCGCCTCCTCGCGTCCTTCGCTCTCCT
EST: gi|88758283|gb|DY542424.1|DY542424
EST:     GACCTCGTCGCGCTCGCGCTCCTCGCGCCCATCGCCTTCTTTCGCGAGAG                         AAACGTGCGGCGCCCGGTGACTCCTCGCCTCCTCGCGTCCTTCGCTCTCCT
genomic: GACCTCGTCGCGCTCGCGCTCCTCGCGCCCATCGCCTTCTTTCGCGAGAGgtctccccgc ... gtccttgcagAAACGTGCGGCGCCCGGTGACTCCTCGCCTCCTCGCGTCCTTCGCTCTCCT
EST: gi|148951696|gb|EC897448.2|EC897448
EST:     GACCTCGTCGCGCTCGCGCTCCTCGCGCCCATCGCCTTCTTTCGCGAGAG                         AAACGTGCGGCGCCCGGTGACTCCTCGCCTCCTCGCGTCCTTCGCTCTCCT
genomic: GACCTCGTCGCGCTCGCGCTCCTCGCGCCCATCGCCTTCTTTCGCGAGAGgtctccccgc ... gtccttgcagAAACGTGCGGCGCCCGGTGACTCCTCGCCTCCTCGCGTCCTTCGCTCTCCT
EST: gi|149058751|gb|EE156769.2|EE156769
EST:     GACCTCGTCGCGCTCGCGCTCCTCGCGCCCATCGCCTTCTTTCGCGAGAG                         AAACGTGCGGCGCCCGGTGACTCCTCGCCTCCTCGCGTCCTTCGCTCTCCT
genomic: GACCTCGTCGCGCTCGCGCTCCTCGCGCCCATCGCCTTCTTTCGCGAGAGgtctccccgc ... gtccttgcagAAACGTGCGGCGCCCGGTGACTCCTCGCCTCCTCGCGTCCTTCGCTCTCCT
EST: gi|78106564|gb|DV524982.1|DV524982
EST:     GACCTCGTCGCGCTCGCGCTCCTCGCGCCCATCGCCTTCTTTCGCGAGAG                         AAACGTGCGGCGCCCGGTGACTCCTCGCCTCCTCGCGTCCTTCGCTCTCCT
genomic: GACCTCGTCGCGCTCGCGCTCCTCGCGCCCATCGCCTTCTTTCGCGAGAGgtctccccgc ... gtccttgcagAAACGTGCGGCGCCCGGTGACTCCTCGCCTCCTCGCGTCCTTCGCTCTCCT
EST: gi|89762148|gb|DY689879.1|DY689879
EST:     GACCTCGTCGCGCTCGCGCTCCTCGCGCCCATCGCCTTCTTTCGCGAGAG                         AAACGTGCGGCGCCCGGTGACTCCTCGCCTCCTCGCGTCCTTCGCTCTCCT
genomic: GACCTCGTCGCGCTCGCGCTCCTCGCGCCCATCGCCTTCTTTCGCGAGAGgtctccccgc ... gtccttgcagAAACGTGCGGCGCCCGGTGACTCCTCGCCTCCTCGCGTCCTTCGCTCTCCT
EST: gi|148971932|gb|EE022716.2|EE022716
EST:     GACCTCGTCGCGCTCGCGCTCCTCGCGCCCATCGCCTTCTTTCGCGAGAG                         AAACGTGCGGCGCCCGGTGACTCCTCGCCTCCTCGCGTCCTTCGCTCTCCT
genomic: GACCTCGTCGCGCTCGCGCTCCTCGCGCCCATCGCCTTCTTTCGCGAGAGgtctccccgc ... gtccttgcagAAACGTGCGGCGCCCGGTGACTCCTCGCCTCCTCGCGTCCTTCGCTCTCCT
EST: gi|148966599|gb|EE017634.2|EE017634
EST:     GACCTCGTCGCGCTCGCGCTCCTCGCGCCCATCGCCTTCTTTCGCGAGAG                         AAACGTGCGGCGCCCGGTGACTCCTCGCCTCCTCGCGTCCTTCGCTCTCCT
genomic: GACCTCGTCGCGCTCGCGCTCCTCGCGCCCATCGCCTTCTTTCGCGAGAGgtctccccgc ... gtccttgcagAAACGTGCGGCGCCCGGTGACTCCTCGCCTCCTCGCGTCCTTCGCTCTCCT
EST: gi|78114582|gb|DV532970.1|DV532970
EST:     GACCTCGTCGCGCTCGCGCTCCTCGCGCCCATCGCCTTCTTTCGCGAGAG                         AAACGTGCGGCGCCCGGTGACTCCTCGCCTCCTCGCGTCCTTCGCTCTCCT
genomic: GACCTCGTCGCGCTCGCGCTCCTCGCGCCCATCGCCTTCTTTCGCGAGAGgtctccccgc ... gtccttgcagAAACGTGCGGCGCCCGGTGACTCCTCGCCTCCTCGCGTCCTTCGCTCTCCT
EST: gi|87153844|gb|DY398633.1|DY398633
EST:     GACCTCGTCGCGCTCGCGCTCCTCGCGCCCATCGCCTTCTTTCGCGAGAG                         AAACGTGCGGCGCCCGGTGACGCCTCGCCTCCTCGCGTCCTTCGCTCTCCT
genomic: GACCTCGTCGCGCTCGCGCTCCTCGCGCCCATCGCCTTCTTTCGCGAGAGgtctccccgc ... gtccttgcagAAACGTGCGGCGCCCGGTGACTCCTCGCCTCCTCGCGTCCTTCGCTCTCCT
EST: gi|149101866|gb|EE287429.2|EE287429
EST:     GACCTCGTCGCGCTCGCGCTCCTCGCGCCCATCGCCTTCTTTCGCGAGAG                         AAACGTGCGGCGCCCGGTGACTCCTCGCCTCCTCGCGTCCTTCGCTCTCCT
genomic: GACCTCGTCGCGCTCGCGCTCCTCGCGCCCATCGCCTTCTTTCGCGAGAGgtctccccgc ... gtccttgcagAAACGTGCGGCGCCCGGTGACTCCTCGCCTCCTCGCGTCCTTCGCTCTCCT

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: 47 (upstream exon), 37 (downstream exon)
Score: 42

AGTCCGTCCTCAACGTCGGCATGAACCAGATCGTCTTCTGCGTCTACCGCGACCTCGTCGCGCTCGCGCTCCTCGCGCCCATCGCCTTCTTTCGCGAGAGgtctccccgc ... gtccttgcagAAACGTGCGGCGCCCGGTGACTCCTCGCCTCCTCGCGTCCTTCGCTCTCCTCGGATTCACTGG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 249

AGTCCGTCCTCAACGTCGGCATGAACCAGATCGTCTTCTGCGTCTACCGCGACCTCGTCGCGCTCGCGCTCCTCGCGCCCATCGCCTTCTTTCGCGAGAGgtctccccgc ... gtccttgcagAAACGTGCGGCGCCCGGTGACTCCTCGCCTCCTCGCGTCCTTCGCTCTCCTCGGATTCACTGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 175

AGTCCGTCCTCAACGTCGGCATGAACCAGATCGTCTTCTGCGTCTACCGCGACCTCGTCGCGCTCGCGCTCCTCGCGCCCATCGCCTTCTTTCGCGAGAGgtctccccgc ... gtccttgcagAAACGTGCGGCGCCCGGTGACTCCTCGCCTCCTCGCGTCCTTCGCTCTCCTCGGATTCACTGG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 47

AGTCCGTCCTCAACGTCGGCATGAACCAGATCGTCTTCTGCGTCTACCGCGACCTCGTCGCGCTCGCGCTCCTCGCGCCCATCGCCTTCTTTCGCGAGAGgtctccccgc ... gtccttgcagAAACGTGCGGCGCCCGGTGACTCCTCGCCTCCTCGCGTCCTTCGCTCTCCTCGGATTCACTGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcccaggggattccgattcgtcccgtaaattcggaatccattccgtccttgcagAAACGTGCGGCGCCCGGTGACTCCTCGCCTCCTCGCGTCCTTCGCTCTCCTCGGATTCACTGG
                                     tccattccgtcctt  CT-rich tract
                          taaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttcttccctactagtactagtgcagtgtatctctctcactcacccatcccaggggattccgattcgtcccgtaaattcggaatccattccgtccttgcagAAACGTGCGGCGCCCGGTGACTCCTCGCCTCCTCGCGTCCTTCGCTCTCCTCGGATTCACTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - tgcagtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccattcc