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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCAACTGCTGCAGATCCAAAATTGCTTGTATATCTCAAGGCGTACCGAAATACAGTACCTGTCCCTAGGCACTGGTCTCAGAAGCGCAAGTTCTTGCAGgtttgtgactctcaactcatctatttaattttaaatatgggtgcttacatttgctgaaatcagttggtgtacatttacatatcgtgtttgcattctcttc...

Basic information

species Zea mays
transcript GRMZM2G132060_T01
intron # 4
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|211162502|gb|FL243921.1|FL243921
EST:     TACAGTACCTGGTCCCTAGGCACTGGTCTCAGAAGCGCAAGTTCTTGCAG                         GGGAAGGAGAGGTATTGAGAAACAGGCCTT-CCAGCTTCTTGAACT-CATT
genomic: TACAGTACCTG-TCCCTAGGCACTGGTCTCAGAAGCGCAAGTTCTTGCAGgtttgtgact ... gttgtttcagGGGAAG-AGAGGTATTGAGAAACAG-CCTTTCCAGCTTCCTGA-CTTCATT
EST: gi|211159306|gb|FL243892.1|FL243892
EST:     ATACAGTACCTGTCCCTAGGCACTGGTCTCAGAAGCGCAAGTTCTTGCAG                         GGGAAGAGAGGGTAT-GAGAAACAGCCTTTCCAGCTTCCTGACTTNCAT-G
genomic: ATACAGTACCTGTCCCTAGGCACTGGTCTCAGAAGCGCAAGTTCTTGCAGgtttgtgact ... gttgtttcagGGGAAGAGAGG-TATTGAGAAACAGCCTTTCCAGCTTCCTGACTT-CATTG
EST: gi|148930320|gb|EE284721.2|EE284721
EST:     ATACAGTACCTGTCCCTAGGCACTGGTCTCAGAAGCGCAAGTTCTTGCAG                         GGGAAGAGAGGTATTGAGAAACAGCCTTTC
genomic: ATACAGTACCTGTCCCTAGGCACTGGTCTCAGAAGCGCAAGTTCTTGCAGgtttgtgact ... gttgtttcagGGGAAGAGAGGTATTGAGAAACAGCCTTTC
EST: gi|148936928|gb|EC881083.2|EC881083
EST:     ATACAGTACCTGTCCCTAGGCACTGGTCTCAGAAGCGCAAGTTCTTGCAG                         GGGAAGAGAGGTATTGAGAAACAGCCTTTCCAGCTTCCTGACTTCATTGCT
genomic: ATACAGTACCTGTCCCTAGGCACTGGTCTCAGAAGCGCAAGTTCTTGCAGgtttgtgact ... gttgtttcagGGGAAGAGAGGTATTGAGAAACAGCCTTTCCAGCTTCCTGACTTCATTGCT
EST: gi|148974670|gb|EE025472.2|EE025472
EST:     ATACAGTACCTGTCCCTAGGCACTGGTCTCAGAAGCGCAAGTTCTTGCCG                         GGGAAGAGAGGTATTGAGAAACAGCCTTTTTCCAGCTTCCTGACTTCATTG
genomic: ATACAGTACCTGTCCCTAGGCACTGGTCTCAGAAGCGCAAGTTCTTGCAGgtttgtgact ... gttgtttcagGGGAAGAGAGGTATTGAGAAACAGCCTTT--CCAGCTTCCTGACTTCATTG
EST: gi|31359279|gb|CD443636.1|CD443636
EST:     ATACAGTACCTGTCCCTAGGCACTGGTCTCAGAAGCGCAAGTTCTTGCAG                         GGGAAGAGAGGTATTGAGAAACAGCCTTTCCAGCTTCCTGACTTCATTGCT
genomic: ATACAGTACCTGTCCCTAGGCACTGGTCTCAGAAGCGCAAGTTCTTGCAGgtttgtgact ... gttgtttcagGGGAAGAGAGGTATTGAGAAACAGCCTTTCCAGCTTCCTGACTTCATTGCT
EST: gi|211159299|gb|FL243885.1|FL243885
EST:     ATACAGTACCTGTCCCTAGGCACTGGTCTCAGAAGCGCAAGTTCTTGCAG                         GGGAAGAGGAG-TATTGAGAAAC
genomic: ATACAGTACCTGTCCCTAGGCACTGGTCTCAGAAGCGCAAGTTCTTGCAGgtttgtgact ... gttgtttcagGGGAAGAG-AGGTATTGAGAAAC
EST: gi|148944299|gb|EC889396.2|EC889396
EST:     ATACAGTACCTGTCCCTAGGCACTGGTCTCAGAAGCGCAAGTTCTTGCAG                         GGGAAGAGAGGTATTGAGAAACAGCCTTTCCAGCTTCCTGACTTCATTGCT
genomic: ATACAGTACCTGTCCCTAGGCACTGGTCTCAGAAGCGCAAGTTCTTGCAGgtttgtgact ... gttgtttcagGGGAAGAGAGGTATTGAGAAACAGCCTTTCCAGCTTCCTGACTTCATTGCT
EST: gi|148931686|gb|EC874876.2|EC874876
EST:     ATACAGTACCTGTCCCTAGGCACTGGTCTCAGAAGCGCAAGTTCTTGCAG                         GGGAAGAGAGGTATTGAGAAACAGCCTTTCCAGCTTCCTGACTTCATTGCT
genomic: ATACAGTACCTGTCCCTAGGCACTGGTCTCAGAAGCGCAAGTTCTTGCAGgtttgtgact ... gttgtttcagGGGAAGAGAGGTATTGAGAAACAGCCTTTCCAGCTTCCTGACTTCATTGCT
EST: gi|22521467|gb|BU080278.1|BU080278
EST:     ATACAGTACCTGTCCCTAGGCACTGGTCTCAGAAGCGCAAGTTCTTGCAG                         GGGAAGAGAGGTATTGAGAAACAGCCTTTCCAGCTTCCTGACTTCATTGCT
genomic: ATACAGTACCTGTCCCTAGGCACTGGTCTCAGAAGCGCAAGTTCTTGCAGgtttgtgact ... gttgtttcagGGGAAGAGAGGTATTGAGAAACAGCCTTTCCAGCTTCCTGACTTCATTGCT
EST: gi|91050200|gb|EB160618.1|EB160618
EST:     ATACAGTACCTGTCCCTAGGCACTGGTCTCAGAAGCGCAAGTTCTTGCAG                         GGGAAGAGAGGTATTGAGAAACAGCCTTTCCAGCTTCCTGACTTCATTGCT
genomic: ATACAGTACCTGTCCCTAGGCACTGGTCTCAGAAGCGCAAGTTCTTGCAGgtttgtgact ... gttgtttcagGGGAAGAGAGGTATTGAGAAACAGCCTTTCCAGCTTCCTGACTTCATTGCT
EST: gi|21843267|gb|BQ703848.1|BQ703848
EST:     ATACAGTACCTGTCCCTAGGCACTGGTCTCAGAAGCGCAAGTTCTTGCAG                         GGGAAGAGAGGTATTGAGAAACAGCCTTTCCAGCTTCCTGACTTCATTGCT
genomic: ATACAGTACCTGTCCCTAGGCACTGGTCTCAGAAGCGCAAGTTCTTGCAGgtttgtgact ... gttgtttcagGGGAAGAGAGGTATTGAGAAACAGCCTTTCCAGCTTCCTGACTTCATTGCT
EST: gi|148931684|gb|EC874873.2|EC874873
EST:     ATACAGTACCTGTCCCTAGGCACTGGTCTCAGAAGCGCAAGTTCTTGCAG                         GGGAAGAGAGGTATTGAGAAACAGCCTTTCCAGCTTCCTGACTTCATTGCT
genomic: ATACAGTACCTGTCCCTAGGCACTGGTCTCAGAAGCGCAAGTTCTTGCAGgtttgtgact ... gttgtttcagGGGAAGAGAGGTATTGAGAAACAGCCTTTCCAGCTTCCTGACTTCATTGCT
EST: gi|26557871|gb|CA830106.1|CA830106
EST:     ATACAGTACCTGTCCCTAGGCACTGGTCTCAGAAGCGCAAGTTCTTGCAG                         GGGCAAGAGAGGTATTGCAGAAACAGCCTTTCCAGCTTCCTGACTTCATTG
genomic: ATACAGTACCTGTCCCTAGGCACTGGTCTCAGAAGCGCAAGTTCTTGCAGgtttgtgact ... gttgtttcagGGG-AAGAGAGGTATTG-AGAAACAGCCTTTCCAGCTTCCTGACTTCATTG
EST: gi|148966452|gb|EE017460.2|EE017460
EST:     ATACAGTACCTGTCCCTAGGCACTGGTCTCAGAAGCGCAAGTTCTTGCAG                         GGGAAGAGAGGTATTGAGAAACAGCCTTTCCAGCTTCCTGACTTCATTGCT
genomic: ATACAGTACCTGTCCCTAGGCACTGGTCTCAGAAGCGCAAGTTCTTGCAGgtttgtgact ... gttgtttcagGGGAAGAGAGGTATTGAGAAACAGCCTTTCCAGCTTCCTGACTTCATTGCT
EST: gi|89761601|gb|DY689546.1|DY689546
EST:     ATACAGTACCTGTCCCTAGGCACTGGTCTCAGAAGCGCAAGTTCTTGCAG                         GGGAAGAGAGGTATTGAGAAACAGCCTTTCCAGCTTCCTGACTTCATTGCT
genomic: ATACAGTACCTGTCCCTAGGCACTGGTCTCAGAAGCGCAAGTTCTTGCAGgtttgtgact ... gttgtttcagGGGAAGAGAGGTATTGAGAAACAGCCTTTCCAGCTTCCTGACTTCATTGCT
EST: gi|21843287|gb|BQ703868.1|BQ703868
EST:     ATACAGTACCTGTCCCTAGGCACTGGTCTCAGAAGCGCAAGTTCTTGCAG                         GGGAAGAGAGGTATTGAGAAACAGCCTTTCCAGCTTCCTGACTTCATTGCT
genomic: ATACAGTACCTGTCCCTAGGCACTGGTCTCAGAAGCGCAAGTTCTTGCAGgtttgtgact ... gttgtttcagGGGAAGAGAGGTATTGAGAAACAGCCTTTCCAGCTTCCTGACTTCATTGCT

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: 43 (upstream exon), 49 (downstream exon)
Score: 418

TGCAACTGCTGCAGATCCAAAATTGCTTGTATATCTCAAGGCGTACCGAAATACAGTACCTGTCCCTAGGCACTGGTCTCAGAAGCGCAAGTTCTTGCAGgtttgtgact ... gttgtttcagGGGAAGAGAGGTATTGAGAAACAGCCTTTCCAGCTTCCTGACTTCATTGCTGCAACTGGAATAGAAAAGATAAGACAG


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 241

TGCAACTGCTGCAGATCCAAAATTGCTTGTATATCTCAAGGCGTACCGAAATACAGTACCTGTCCCTAGGCACTGGTCTCAGAAGCGCAAGTTCTTGCAGgtttgtgact ... gttgtttcagGGGAAGAGAGGTATTGAGAAACAGCCTTTCCAGCTTCCTGACTTCATTGCTGCAACTGGAATAGAAAAGATAAGACAG


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 381

TGCAACTGCTGCAGATCCAAAATTGCTTGTATATCTCAAGGCGTACCGAAATACAGTACCTGTCCCTAGGCACTGGTCTCAGAAGCGCAAGTTCTTGCAGgtttgtgact ... gttgtttcagGGGAAGAGAGGTATTGAGAAACAGCCTTTCCAGCTTCCTGACTTCATTGCTGCAACTGGAATAGAAAAGATAAGACAG


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 201

TGCAACTGCTGCAGATCCAAAATTGCTTGTATATCTCAAGGCGTACCGAAATACAGTACCTGTCCCTAGGCACTGGTCTCAGAAGCGCAAGTTCTTGCAGgtttgtgact ... gttgtttcagGGGAAGAGAGGTATTGAGAAACAGCCTTTCCAGCTTCCTGACTTCATTGCTGCAACTGGAATAGAAAAGATAAGACAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCAACTGCTGCAGATCCAAAATTGCTTGTATATCTCAAGGCGTACCGAAATACAGTACCTGTCCCTAGGCACTGGTCTCAGAAGCGCAAGTTCTTGCAGgtttgtgactctcaactcatctatttaattttaaatatgggtgcttacatttgctgaaatcagttggtgtacatttacatatcgtgtttgcattctcttc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC