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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCCCCTTTTCCTCTCCCCCAGATCCACCCGCCGCGCCACCCCTCTCGGCTCCTCCCAGGCGGCGTCGGCCCTTTCCTCGCCCTCCTCCGTTTCTCTCCGgtaaaaaaagaaacatccttgcttgcctgatttgcgatacctctaaagccaaatctttgttggcatacaatttatttcggatttgtttgacgctcacactcccctgctag

Basic information

species Zea mays
transcript GRMZM2G034143_T01
intron # 1
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|211489871|gb|FL134685.1|FL134685
EST:     TCCTCCCAGGCGGCGTCGGCCCTTTCCTCGCCCTCCTCCGTTTCTCTCCG                         GCGTATATATTGGTTCGAAATCGGTAGATGAGGTGCTCGATGCCGCCGCCG
genomic: TCCTCCCAGGCGGCGTCGGCCCTTTCCTCGCCCTCCTCCGTTTCTCTCCGgtaaaaaaag ... cccctgctagGCGTATATATGGGTTCGAAATCGGTAGATGAGGTGCTCGATGCCGCCGCCG
EST: gi|78113249|gb|DV531643.1|DV531643
EST:     TCCTCCCAGGCGGCGTCGGCCCTTTCCTCGCCCTCCTCCGTTTCTCTCCG                         GCGTATATATGGGTTCGAAATCGGTAGATGAGGTGCTCGATGCCGCCGCCG
genomic: TCCTCCCAGGCGGCGTCGGCCCTTTCCTCGCCCTCCTCCGTTTCTCTCCGgtaaaaaaag ... cccctgctagGCGTATATATGGGTTCGAAATCGGTAGATGAGGTGCTCGATGCCGCCGCCG
EST: gi|211492747|gb|FL134690.1|FL134690
EST:     TCCTCCTAGGCGGCGTCGGCCCTTTCCTCGCCCTCCTCCGTTTCTCTCCG                         GCGTATATATTGGTTCGAAATCGGTAGATGAGGTGCTCGATGCCGCCGCCG
genomic: TCCTCCCAGGCGGCGTCGGCCCTTTCCTCGCCCTCCTCCGTTTCTCTCCGgtaaaaaaag ... cccctgctagGCGTATATATGGGTTCGAAATCGGTAGATGAGGTGCTCGATGCCGCCGCCG
EST: gi|211492748|gb|FL134691.1|FL134691
EST:     TCCTCCCAGGCGGCGTCAGCCCTTTCCTCGCCCTCCTCCGTTTCTCTCCG                         GCGTATATATGGGTTCGAAATCGGTAGATGAGGTGCTCGATGCCGCCGCCG
genomic: TCCTCCCAGGCGGCGTCGGCCCTTTCCTCGCCCTCCTCCGTTTCTCTCCGgtaaaaaaag ... cccctgctagGCGTATATATGGGTTCGAAATCGGTAGATGAGGTGCTCGATGCCGCCGCCG
EST: gi|71439660|gb|DR820710.1|DR820710
EST:     TCCTCCCAGGCGGCGTCGGCCCTTTCCTCGCCCTCCTCCGTTTCTCTCCG                         GCGTATATATGGGTTCGAAATCGGTAGATGAGGTGCTCGATGCCGCCGCCG
genomic: TCCTCCCAGGCGGCGTCGGCCCTTTCCTCGCCCTCCTCCGTTTCTCTCCGgtaaaaaaag ... cccctgctagGCGTATATATGGGTTCGAAATCGGTAGATGAGGTGCTCGATGCCGCCGCCG
EST: gi|148995152|gb|EE034432.2|EE034432
EST:     TCCTCCCAGGCGGCGTCGGCCCTTTCCTCGCCCTCCTCCGTTTCTCTCCG                         GCGTATATATGGGTTCGAAATCGGTAGATGAGGTGCTCGATGCCGCCGCCG
genomic: TCCTCCCAGGCGGCGTCGGCCCTTTCCTCGCCCTCCTCCGTTTCTCTCCGgtaaaaaaag ... cccctgctagGCGTATATATGGGTTCGAAATCGGTAGATGAGGTGCTCGATGCCGCCGCCG
EST: gi|211489870|gb|FL134684.1|FL134684
EST:     TCCTCCCAGGCGGCGTCGGCCCTTTCCTCGCCCTCCTCCGTTTCTCTCCG                         GCGTATATATGGGTTCGAAATCGGTAGATGAGGTGCTCGATGCCGCCGCCG
genomic: TCCTCCCAGGCGGCGTCGGCCCTTTCCTCGCCCTCCTCCGTTTCTCTCCGgtaaaaaaag ... cccctgctagGCGTATATATGGGTTCGAAATCGGTAGATGAGGTGCTCGATGCCGCCGCCG
EST: gi|211489869|gb|FL134683.1|FL134683
EST:     TCCTCCCAGGCGGCGTCGGCCCTTTCCTCGCCCTCCTCCGTTTCTCTCCG                         GCGTATATATGGGTTCGAAATCGGTAGATGAGGTGCTCGATGCCGCCGCCG
genomic: TCCTCCCAGGCGGCGTCGGCCCTTTCCTCGCCCTCCTCCGTTTCTCTCCGgtaaaaaaag ... cccctgctagGCGTATATATGGGTTCGAAATCGGTAGATGAGGTGCTCGATGCCGCCGCCG
EST: gi|211492744|gb|FL134687.1|FL134687
EST:     TCCTCCCAGGCGGCGTCGGCCCTTTCCTCGCCCTCCTCCGTTTCTCTCCG                         GCGTATATATGGGTTCGAAATCGGTAGATGAGGTGCTCGATGCCGCCGCCG
genomic: TCCTCCCAGGCGGCGTCGGCCCTTTCCTCGCCCTCCTCCGTTTCTCTCCGgtaaaaaaag ... cccctgctagGCGTATATATGGGTTCGAAATCGGTAGATGAGGTGCTCGATGCCGCCGCCG
EST: gi|211489866|gb|FL134680.1|FL134680
EST:     TCCTCCCAGGCGGCGTCGGCCCTTTCCTCGCCCTCCTCCGTTTCTCTCCG                         GCGTATATATGGGTTCGAAATCGGTAGATGAGGTGCTCGATGCCGCCGCCG
genomic: TCCTCCCAGGCGGCGTCGGCCCTTTCCTCGCCCTCCTCCGTTTCTCTCCGgtaaaaaaag ... cccctgctagGCGTATATATGGGTTCGAAATCGGTAGATGAGGTGCTCGATGCCGCCGCCG
EST: gi|31359325|gb|CD443682.1|CD443682
EST:     GTCGGGCCTTTCCTCGCCCTCCTCCGTTTCTCTCCG                         GCGTATATATGGGTTCGAAATCGGTAGATGAGGTGCTCGATGCCGCCGCCG
genomic: GTCGGCCCTTTCCTCGCCCTCCTCCGTTTCTCTCCGgtaaaaaaag ... cccctgctagGCGTATATATGGGTTCGAAATCGGTAGATGAGGTGCTCGATGCCGCCGCCG
EST: gi|149020749|gb|EE045750.2|EE045750
EST:     TCCTCCCAGGCGGCGTCGGCCCTTTCCTCGCCCTCCTCCGTTTCTCTCCG                         GCGTATATATGGGTTCGAAATCGGTAGATGAGGTGCTCGATGCCGCCGCCG
genomic: TCCTCCCAGGCGGCGTCGGCCCTTTCCTCGCCCTCCTCCGTTTCTCTCCGgtaaaaaaag ... cccctgctagGCGTATATATGGGTTCGAAATCGGTAGATGAGGTGCTCGATGCCGCCGCCG
EST: gi|211492749|gb|FL134692.1|FL134692
EST:     TCCTCCCAGGCGGCGTCGGCCCTTTCCTCGCCCTCCTCCGTTTCTCTCCG                         GCGTATATATGGGTTCGAAATCGGTAGATGAGGTGCTCGATGCCGCCGCCG
genomic: TCCTCCCAGGCGGCGTCGGCCCTTTCCTCGCCCTCCTCCGTTTCTCTCCGgtaaaaaaag ... cccctgctagGCGTATATATGGGTTCGAAATCGGTAGATGAGGTGCTCGATGCCGCCGCCG
EST: gi|148943394|gb|EC888453.2|EC888453
EST:     TCCTCCCAGGCGGCGTCGGCCCTTTCCTCGCCCTCCTCCGTTTCTCTCCG                         GCGTATATATGGGTTCGAAATCGGTAGATGAGGTGCTCGATGCCGCCGCCG
genomic: TCCTCCCAGGCGGCGTCGGCCCTTTCCTCGCCCTCCTCCGTTTCTCTCCGgtaaaaaaag ... cccctgctagGCGTATATATGGGTTCGAAATCGGTAGATGAGGTGCTCGATGCCGCCGCCG
EST: gi|149088610|gb|EE177727.2|EE177727
EST:     TCCTCCCAGGCGGCGTCGGCCCTTTCCTCGCCCTCCTCCGTTTCTCTCCG                         GCGTATATATGGGTTCGAAATCGGTAGATGAGGTGCTCGATGCCGCCGCCG
genomic: TCCTCCCAGGCGGCGTCGGCCCTTTCCTCGCCCTCCTCCGTTTCTCTCCGgtaaaaaaag ... cccctgctagGCGTATATATGGGTTCGAAATCGGTAGATGAGGTGCTCGATGCCGCCGCCG
EST: gi|211489865|gb|FL134679.1|FL134679
EST:     TCCTCCCAGGCGGCGTCGGCCCTTTCCTCGCCCTCCTCCGTTTCTCTCCG                         GCGTATATATGGGTTCGAAATCGGTAGATGAGGTGCTCGATGCCGCCGCCG
genomic: TCCTCCCAGGCGGCGTCGGCCCTTTCCTCGCCCTCCTCCGTTTCTCTCCGgtaaaaaaag ... cccctgctagGCGTATATATGGGTTCGAAATCGGTAGATGAGGTGCTCGATGCCGCCGCCG
EST: gi|211492751|gb|FL134694.1|FL134694
EST:     TCCTCCCAGGCGGCGTCGGCCCTTTCCTCGCCCTCCTCCGTTTCTCTCCG                         GCGTATATATGGGTTCGAAATCGGTAGATGAGGTGCTCGATGCCGCCGCCG
genomic: TCCTCCCAGGCGGCGTCGGCCCTTTCCTCGCCCTCCTCCGTTTCTCTCCGgtaaaaaaag ... cccctgctagGCGTATATATGGGTTCGAAATCGGTAGATGAGGTGCTCGATGCCGCCGCCG

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), 49 (downstream exon)
Score: 91

TTCCCCTTTTCCTCTCCCCCAGATCCACCCGCCGCGCCACCCCTCTCGGCTCCTCCCAGGCGGCGTCGGCCCTTTCCTCGCCCTCCTCCGTTTCTCTCCGgtaaaaaaag ... cccctgctagGCGTATATATGGGTTCGAAATCGGTAGATGAGGTGCTCGATGCCGCCGCCGGAGTCCATTGCTCTGCTCTCCGTCTGGACGGTCCCAACGTCCAGTTTTC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 33

TTCCCCTTTTCCTCTCCCCCAGATCCACCCGCCGCGCCACCCCTCTCGGCTCCTCCCAGGCGGCGTCGGCCCTTTCCTCGCCCTCCTCCGTTTCTCTCCGgtaaaaaaag ... cccctgctagGCGTATATATGGGTTCGAAATCGGTAGATGAGGTGCTCGATGCCGCCGCCGGAGTCCATTGCTCTGCTCTCCGTCTGGACGGTCCCAACGTCCAGTTTTC


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 32

TTCCCCTTTTCCTCTCCCCCAGATCCACCCGCCGCGCCACCCCTCTCGGCTCCTCCCAGGCGGCGTCGGCCCTTTCCTCGCCCTCCTCCGTTTCTCTCCGgtaaaaaaag ... cccctgctagGCGTATATATGGGTTCGAAATCGGTAGATGAGGTGCTCGATGCCGCCGCCGGAGTCCATTGCTCTGCTCTCCGTCTGGACGGTCCCAACGTCCAGTTTTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 35

TTCCCCTTTTCCTCTCCCCCAGATCCACCCGCCGCGCCACCCCTCTCGGCTCCTCCCAGGCGGCGTCGGCCCTTTCCTCGCCCTCCTCCGTTTCTCTCCGgtaaaaaaag ... cccctgctagGCGTATATATGGGTTCGAAATCGGTAGATGAGGTGCTCGATGCCGCCGCCGGAGTCCATTGCTCTGCTCTCCGTCTGGACGGTCCCAACGTCCAGTTTTC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCCCCTTTTCCTCTCCCCCAGATCCACCCGCCGCGCCACCCCTCTCGGCTCCTCCCAGGCGGCGTCGGCCCTTTCCTCGCCCTCCTCCGTTTCTCTCCGgtaaaaaaagaaacatccttgcttgcctgatttgcgatacctctaaagccaaatctttgttggcatacaatttatttcggatttgtttgacgctcacactcccctgctag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC