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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttattttcatcttttctctatgctttctagctaatctcgacttttatgtgtctgtcttggctctgccttacagtttgtatttcatgctggtagGGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAGAACTCGGATAGGCACCTCAGGCTCTTTTAGAATGATCAGATGCAAAGAC

Basic information

species Zea mays
transcript GRMZM2G701689_T01
intron # 2
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|211366534|gb|FL297817.1|FL297817
EST:     TTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAG                         GGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAG
genomic: TTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAGgtttattttc ... atgctggtagGGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAG
EST: gi|87152637|gb|DY397426.1|DY397426
EST:     TTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAG                         GGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAG
genomic: TTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAGgtttattttc ... atgctggtagGGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAG
EST: gi|211513604|gb|FL043440.1|FL043440
EST:     TTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAG                         GGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTTAGCAGTGTCA
genomic: TTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAGgtttattttc ... atgctggtagGGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCT-AGCAGTGTCA
EST: gi|211366529|gb|FL297812.1|FL297812
EST:     TTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAG                         GGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAG
genomic: TTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAGgtttattttc ... atgctggtagGGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAG
EST: gi|19272496|gb|BM888752.1|BM888752
EST:     TTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAG                         GGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAG
genomic: TTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAGgtttattttc ... atgctggtagGGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAG
EST: gi|211366525|gb|FL297808.1|FL297808
EST:     TTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAG                         GGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAG
genomic: TTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAGgtttattttc ... atgctggtagGGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAG
EST: gi|87152122|gb|DY396911.1|DY396911
EST:     TTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAG                         GGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAG
genomic: TTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAGgtttattttc ... atgctggtagGGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAG
EST: gi|211366538|gb|FL297821.1|FL297821
EST:     TTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAG                         GGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAG
genomic: TTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAGgtttattttc ... atgctggtagGGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAG
EST: gi|19437165|gb|BM953575.1|BM953575
EST:     TTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAG                         GGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAG
genomic: TTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAGgtttattttc ... atgctggtagGGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAG
EST: gi|211366527|gb|FL297810.1|FL297810
EST:     TTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAG                         GGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAG
genomic: TTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAGgtttattttc ... atgctggtagGGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAG
EST: gi|211366530|gb|FL297813.1|FL297813
EST:     TTGCCTCACCACATGTTAATCCAACAAGGGGGAACTAAAGTTCTGATCAG                         GGACGAATCTGTTCAGCTTCCTCATGAATTGC-CTCCACCTAGCAGTGTCA
genomic: TTGCCTCACCACATGTTAATCCAACAAAGGG-AACTAAAGTTCTGATCAGgtttattttc ... atgctggtagGGACGAATCTGTTCAGCTTCCTCATGAATTGCACTC-ACCTAGCAGTGTCA
EST: gi|211366524|gb|FL297807.1|FL297807
EST:     TTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAG                         GGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAG
genomic: TTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAGgtttattttc ... atgctggtagGGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAG
EST: gi|71312702|gb|DR792875.1|DR792875
EST:     TTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAG                         GGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAG
genomic: TTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAGgtttattttc ... atgctggtagGGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAG
EST: gi|211366536|gb|FL297819.1|FL297819
EST:     TTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAG                         GGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAG
genomic: TTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAGgtttattttc ... atgctggtagGGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAG
EST: gi|211366537|gb|FL297820.1|FL297820
EST:     TTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAG                         GGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGGGTCAG
genomic: TTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAGgtttattttc ... atgctggtagGGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAG
EST: gi|211369184|gb|FL297822.1|FL297822
EST:     TTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAG                         GGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAG
genomic: TTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAGgtttattttc ... atgctggtagGGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAG
EST: gi|211363879|gb|FL297806.1|FL297806
EST:     TTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAG                         GGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAG
genomic: TTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAGgtttattttc ... atgctggtagGGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAG
EST: gi|211363877|gb|FL297804.1|FL297804
EST:     TTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAG                         GGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAG
genomic: TTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAGgtttattttc ... atgctggtagGGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAG
EST: gi|211404142|gb|FL328727.1|FL328727
EST:     TTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAG                         GGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAG
genomic: TTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAGgtttattttc ... atgctggtagGGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAG
EST: gi|211366531|gb|FL297814.1|FL297814
EST:     TTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAG                         GGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAG
genomic: TTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAGgtttattttc ... atgctggtagGGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAG
EST: gi|211366532|gb|FL297815.1|FL297815
EST:     TTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAG                         GGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAG
genomic: TTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAGgtttattttc ... atgctggtagGGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAG
EST: gi|211366526|gb|FL297809.1|FL297809
EST:     TTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAG                         GGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAG
genomic: TTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAGgtttattttc ... atgctggtagGGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAG
EST: gi|22491113|gb|BU051036.1|BU051036
EST:     TTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAG                         GGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAG
genomic: TTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAGgtttattttc ... atgctggtagGGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAG
EST: gi|22490856|gb|BU050779.1|BU050779
EST:     TTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAG                         GGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAG
genomic: TTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAGgtttattttc ... atgctggtagGGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAG

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), 48 (downstream exon)
Score: 980

ATAATGTGCAGCTATTCAAGTCATCAGATTTGGCACCTGTTTCTTCGATCTTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAGgtttattttc ... atgctggtagGGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAGAACTCGGATAGGCACCTCAGGCTCTTTTAGAATGATCAGATGCAAAGAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 467

ATAATGTGCAGCTATTCAAGTCATCAGATTTGGCACCTGTTTCTTCGATCTTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAGgtttattttc ... atgctggtagGGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAGAACTCGGATAGGCACCTCAGGCTCTTTTAGAATGATCAGATGCAAAGAC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 633

ATAATGTGCAGCTATTCAAGTCATCAGATTTGGCACCTGTTTCTTCGATCTTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAGgtttattttc ... atgctggtagGGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAGAACTCGGATAGGCACCTCAGGCTCTTTTAGAATGATCAGATGCAAAGAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 820

ATAATGTGCAGCTATTCAAGTCATCAGATTTGGCACCTGTTTCTTCGATCTTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAGgtttattttc ... atgctggtagGGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAGAACTCGGATAGGCACCTCAGGCTCTTTTAGAATGATCAGATGCAAAGAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gacttttatgtgtctgtcttggctctgccttacagtttgtatttcatgctggtagGGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAGAACTCGGATAGGCACCTCAGGCTCTTTTAGAATGATCAGATGCAAAGAC
                          gccttac  putative branch site (score: 820)
                                   tttgtattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttattttcatcttttctctatgctttctagctaatctcgacttttatgtgtctgtcttggctctgccttacagtttgtatttcatgctggtagGGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAGAACTCGGATAGGCACCTCAGGCTCTTTTAGAATGATCAGATGCAAAGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG