Skip to another splice site:
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actttctccacgattttgtctttccagttcagcatcatccgttttcgtttgatatttgaattttatacatttacaatttattaagtatctcttttggcagCTCCAGTTGAGACCTCGCAAGAGAAGAGCCAAGCTCTGGCGCTTTGGCATACGAGACCTGTTGATCCAACAGATACTGGTATCGGAAAATAGGCAACAGT

Basic information

species Zea mays
transcript GRMZM2G123709_T01
intron # 4
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|211121130|gb|FL435130.1|FL435130
EST:     TTTGGACTCCCTCTGCGATTGAGCGGGCACCTATGATACATGTTGATGAG                         CTCCAGTTGAGACCTCGCAAGAGAAGAGCCAAGCTCTGGCGCTTTGGCATA
genomic: TTTGGACTCCCTCTGCGATTGAGCGGGCACCTATGATACATGTTGATGAGgtaatatctt ... cttttggcagCTCCAGTTGAGACCTCGCAAGAGAAGAGCCAAGCTCTGGCGCTTTGGCATA
EST: gi|211507760|gb|FL332863.1|FL332863
EST:     TTGGACTCCCTCTGCGATTGAGCGGGCACCTATGATATCATGTTGATGAG                         -T----T-GAGACCTCGCAAGAGAAGAGCCAAGCTCTGGCGCTTTGGCATA
genomic: TTGGACTCCCTCTGCGATTGAGCGGGCACCTATGATA-CATGTTGATGAGgtaatatctt ... cttttggcagCTCCAGTTGAGACCTCGCAAGAGAAGAGCCAAGCTCTGGCGCTTTGGCATA
EST: gi|211281689|gb|FL458599.1|FL458599
EST:     TTTGGACTCCCTCTGCGATTGAGCGGGCACCTATGATACATGTTGAT--G                         ----AGTTGAGACCTCGCAAGAGAAGAGCCAAGCTCTGGCGCTTTGGCATA
genomic: TTTGGACTCCCTCTGCGATTGAGCGGGCACCTATGATACATGTTGATGAGgtaatatctt ... cttttggcagCTCCAGTTGAGACCTCGCAAGAGAAGAGCCAAGCTCTGGCGCTTTGGCATA
EST: gi|71533923|gb|DR784682.1|DR784682
EST:     TTTGGACTCCCTCTGCGATTGAGCGGGCACCTATGATACATGTTGATGAG                         CTCCAGTTGAGACCTCGCAAGAGAAGAGCCAAGCTCTGGCGCTTTGGCATA
genomic: TTTGGACTCCCTCTGCGATTGAGCGGGCACCTATGATACATGTTGATGAGgtaatatctt ... cttttggcagCTCCAGTTGAGACCTCGCAAGAGAAGAGCCAAGCTCTGGCGCTTTGGCATA
EST: gi|211224895|gb|FL345055.1|FL345055
EST:     TTTGGACTCCCTCTGCGATTGAGCGGGCACCTATGATACATGTTGATGAG                         CTCCAGTTGAGACCTCGCAAGAGAAGAGCCAAGCTCTGGCGCTTTGGCATA
genomic: TTTGGACTCCCTCTGCGATTGAGCGGGCACCTATGATACATGTTGATGAGgtaatatctt ... cttttggcagCTCCAGTTGAGACCTCGCAAGAGAAGAGCCAAGCTCTGGCGCTTTGGCATA
EST: gi|60354150|gb|DN221123.1|DN221123
EST:     TTTGGACTCCCTCTGCGATTGAGCGGGCACCTATGATACATGTTGATGAG                         CTCCAGTTGAGACCTCGCAAGAGAAGAGCCAAGCTCTGGCGCTTTGGCATA
genomic: TTTGGACTCCCTCTGCGATTGAGCGGGCACCTATGATACATGTTGATGAGgtaatatctt ... cttttggcagCTCCAGTTGAGACCTCGCAAGAGAAGAGCCAAGCTCTGGCGCTTTGGCATA
EST: gi|211257337|gb|FL311699.1|FL311699
EST:     TTTGGACTCCCTCTGCGATTGAGCGGGCACCTATGATACATGTTGATGAG                         CTCCAGTTGAGACCTCGCAAGAGAAGAGCCAAGCTCTGGCGCTTTGGCATA
genomic: TTTGGACTCCCTCTGCGATTGAGCGGGCACCTATGATACATGTTGATGAGgtaatatctt ... cttttggcagCTCCAGTTGAGACCTCGCAAGAGAAGAGCCAAGCTCTGGCGCTTTGGCATA
EST: gi|74236416|gb|DT644330.1|DT644330
EST:     TTTGGACTCCCTCTGCGATTGAGCGGGCACCTATGATACATGTTGATGAG                         CTCCAGTTGAGACCTCGCAAGAGAAGAGCCAAGCTCTGGCGCTTTGGCATA
genomic: TTTGGACTCCCTCTGCGATTGAGCGGGCACCTATGATACATGTTGATGAGgtaatatctt ... cttttggcagCTCCAGTTGAGACCTCGCAAGAGAAGAGCCAAGCTCTGGCGCTTTGGCATA
EST: gi|6742558|gb|AW313373.1|AW313373
EST:     TTTGGACTCCCTCTGCGATTGAGCGGGCACCTATGATACATGTTGAT--G                         ----AGTTGAGACCTCGCAAGAGAAGAGCCAAGCTCTGGCGCTTTGGCATA
genomic: TTTGGACTCCCTCTGCGATTGAGCGGGCACCTATGATACATGTTGATGAGgtaatatctt ... cttttggcagCTCCAGTTGAGACCTCGCAAGAGAAGAGCCAAGCTCTGGCGCTTTGGCATA
EST: gi|76924929|gb|DV170200.1|DV170200
EST:     TTTGGACTCCCTCTGCGATTGAGCGGGCACCTATGATACATGTTGATGAG                         CTCCAGTTGAGACCTCGCAAGAGAAGAGCCAAGCTCTGGCGCTTTGGCATA
genomic: TTTGGACTCCCTCTGCGATTGAGCGGGCACCTATGATACATGTTGATGAGgtaatatctt ... cttttggcagCTCCAGTTGAGACCTCGCAAGAGAAGAGCCAAGCTCTGGCGCTTTGGCATA
EST: gi|32915762|gb|CF020574.1|CF020574
EST:     TTTGGACTCCCTCTGCGATTGAGCGGGCACCTATGATACATGTTGATGAG                         CTCCAGTTGAGACCTCGCAAGAGAAGAGCCAAGCTCTGGCGCTTTGGCATA
genomic: TTTGGACTCCCTCTGCGATTGAGCGGGCACCTATGATACATGTTGATGAGgtaatatctt ... cttttggcagCTCCAGTTGAGACCTCGCAAGAGAAGAGCCAAGCTCTGGCGCTTTGGCATA
EST: gi|71763783|gb|DR961720.1|DR961720
EST:     TTTGGACTCCCTCTGCGATTGAGCGGGCACCTATGATACATGTTGATGAG                         CTCCAGTTGAGACCTCGCAAGAGAAGAGCCAAGCTCTGGCGCTTTGGCATA
genomic: TTTGGACTCCCTCTGCGATTGAGCGGGCACCTATGATACATGTTGATGAGgtaatatctt ... cttttggcagCTCCAGTTGAGACCTCGCAAGAGAAGAGCCAAGCTCTGGCGCTTTGGCATA
EST: gi|148940254|gb|EC885027.2|EC885027
EST:     TTTGGACTCCCTCTGCGATTGAGCGGGCACCTATGATACATGTTGATGAG                         CTCCAGTTGAGACCTCGCAAGAGAAGAGCCAAGCTCTGGCGCTTTGGCATA
genomic: TTTGGACTCCCTCTGCGATTGAGCGGGCACCTATGATACATGTTGATGAGgtaatatctt ... cttttggcagCTCCAGTTGAGACCTCGCAAGAGAAGAGCCAAGCTCTGGCGCTTTGGCATA
EST: gi|213179387|gb|FM183062.1|FM183062
EST:     TTTGGACTCCCTCTGCGATTGAGCGGGCACCTATGATACATGTTGATGAG                         CTCCAGTTGAGACCTCGCAAGAGAAGAGCCAAGCTCTGGCGCTTTGGCATA
genomic: TTTGGACTCCCTCTGCGATTGAGCGGGCACCTATGATACATGTTGATGAGgtaatatctt ... cttttggcagCTCCAGTTGAGACCTCGCAAGAGAAGAGCCAAGCTCTGGCGCTTTGGCATA
EST: gi|37399221|gb|CF636936.1|CF636936
EST:     TTTGGACTCCCTCTGCGATTGAGCGGGCACCTATGATACATGTTGAT--G                         ----AGTTGAGACCTCGCAAGAGAAGAGCCAAGCTCTGGCGCTTTGGCATA
genomic: TTTGGACTCCCTCTGCGATTGAGCGGGCACCTATGATACATGTTGATGAGgtaatatctt ... cttttggcagCTCCAGTTGAGACCTCGCAAGAGAAGAGCCAAGCTCTGGCGCTTTGGCATA
EST: gi|89250501|gb|DY622287.1|DY622287
EST:     TTGGGCCTCCCTCTGCGATTGAGCGGGCACCTATGATACATGTTGATGAG                         CTCCAGTTGAGACCTCGCAAGAGAAGAGCCAAGCTCTGGCGCTTTGGCATA
genomic: TTTGGACTCCCTCTGCGATTGAGCGGGCACCTATGATACATGTTGATGAGgtaatatctt ... cttttggcagCTCCAGTTGAGACCTCGCAAGAGAAGAGCCAAGCTCTGGCGCTTTGGCATA
EST: gi|78026890|gb|DV495277.1|DV495277
EST:     TTTGGACTCCCTCTGCGATTGAGCGGGCACCTATGATACATGTTGAT--G                         ----AGTTGAGACCTCGCAAGAGAAGAGCCAAGCTCTGGCGCTTTGGCATA
genomic: TTTGGACTCCCTCTGCGATTGAGCGGGCACCTATGATACATGTTGATGAGgtaatatctt ... cttttggcagCTCCAGTTGAGACCTCGCAAGAGAAGAGCCAAGCTCTGGCGCTTTGGCATA
EST: gi|76017450|gb|DT944620.1|DT944620
EST:     TTTGGACTCCCTCTGCGATTGAGCGGGCACCTATGATACATGTTGATGAG                         CTCCAGTTGAGACCTCGCAAGAGAAGAGCCAAGCTCTGGCGCTTTGGCATA
genomic: TTTGGACTCCCTCTGCGATTGAGCGGGCACCTATGATACATGTTGATGAGgtaatatctt ... cttttggcagCTCCAGTTGAGACCTCGCAAGAGAAGAGCCAAGCTCTGGCGCTTTGGCATA
EST: gi|60400074|gb|DN232881.1|DN232881
EST:     TTTGGACTCCCTCTGCGATTGAGCGGGCACCTATGATACATGTTGATGAG                         CTCCAGTTGAGACCTCGCAAGAGAAGAGCCAAGCTCTGGCGCTTTGGCATA
genomic: TTTGGACTCCCTCTGCGATTGAGCGGGCACCTATGATACATGTTGATGAGgtaatatctt ... cttttggcagCTCCAGTTGAGACCTCGCAAGAGAAGAGCCAAGCTCTGGCGCTTTGGCATA
EST: gi|211104219|gb|FL471983.1|FL471983
EST:     TTTGGACTCCCTCTGCGATTGAGCGGGCACCTATGATACATGTTGATGAG                         CTCCAGTTGAGACCTCGCAAGAGAAGAGCCAAGCTCTGGCGCTTTGGCATA
genomic: TTTGGACTCCCTCTGCGATTGAGCGGGCACCTATGATACATGTTGATGAGgtaatatctt ... cttttggcagCTCCAGTTGAGACCTCGCAAGAGAAGAGCCAAGCTCTGGCGCTTTGGCATA
EST: gi|148949178|gb|EC894615.2|EC894615
EST:     TTTGGACTCCCTCTGCGATTGAGCGGGCACCTATGATACATGTTGATGAG                         CTCCAGTTGAGACCTCGCAAGAGAAGAGCCAAGCTCTGGCGCTTTGGCATA
genomic: TTTGGACTCCCTCTGCGATTGAGCGGGCACCTATGATACATGTTGATGAGgtaatatctt ... cttttggcagCTCCAGTTGAGACCTCGCAAGAGAAGAGCCAAGCTCTGGCGCTTTGGCATA
EST: gi|78111954|gb|DV530350.1|DV530350
EST:     TTTGGACTCCCTCTGCGATTGAGCGGGCACCTATGATACATGTTGATGAG                         CTCCAGTTGAGACCTCGCAAGAGAAGAGCCAAGCTCTGGCGCTTTGGCATA
genomic: TTTGGACTCCCTCTGCGATTGAGCGGGCACCTATGATACATGTTGATGAGgtaatatctt ... cttttggcagCTCCAGTTGAGACCTCGCAAGAGAAGAGCCAAGCTCTGGCGCTTTGGCATA
EST: gi|148996164|gb|EE035434.2|EE035434
EST:     TTTGGACTCCCTCTGCGATTGAGCGGGCACCTATGATACATGTTGATGAG                         CTCCAGTTGAGACCTCGCAAGAGAAGAGCCAAGCTCTGGCGCTTTGGCATA
genomic: TTTGGACTCCCTCTGCGATTGAGCGGGCACCTATGATACATGTTGATGAGgtaatatctt ... cttttggcagCTCCAGTTGAGACCTCGCAAGAGAAGAGCCAAGCTCTGGCGCTTTGGCATA

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: 269

TCCTCATGCTATGGCAATCGCGAGCTGTGGAATTGATAATGATGTAAAAGTTTGGACTCCCTCTGCGATTGAGCGGGCACCTATGATACATGTTGATGAGgtaatatctt ... cttttggcagCTCCAGTTGAGACCTCGCAAGAGAAGAGCCAAGCTCTGGCGCTTTGGCATACGAGACCTGTTGATCCAACAGATACTGGTATCGGAAAATAGGCAACAGT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 201

TCCTCATGCTATGGCAATCGCGAGCTGTGGAATTGATAATGATGTAAAAGTTTGGACTCCCTCTGCGATTGAGCGGGCACCTATGATACATGTTGATGAGgtaatatctt ... cttttggcagCTCCAGTTGAGACCTCGCAAGAGAAGAGCCAAGCTCTGGCGCTTTGGCATACGAGACCTGTTGATCCAACAGATACTGGTATCGGAAAATAGGCAACAGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 244

TCCTCATGCTATGGCAATCGCGAGCTGTGGAATTGATAATGATGTAAAAGTTTGGACTCCCTCTGCGATTGAGCGGGCACCTATGATACATGTTGATGAGgtaatatctt ... cttttggcagCTCCAGTTGAGACCTCGCAAGAGAAGAGCCAAGCTCTGGCGCTTTGGCATACGAGACCTGTTGATCCAACAGATACTGGTATCGGAAAATAGGCAACAGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 359

TCCTCATGCTATGGCAATCGCGAGCTGTGGAATTGATAATGATGTAAAAGTTTGGACTCCCTCTGCGATTGAGCGGGCACCTATGATACATGTTGATGAGgtaatatctt ... cttttggcagCTCCAGTTGAGACCTCGCAAGAGAAGAGCCAAGCTCTGGCGCTTTGGCATACGAGACCTGTTGATCCAACAGATACTGGTATCGGAAAATAGGCAACAGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgtttgatatttgaattttatacatttacaatttattaagtatctcttttggcagCTCCAGTTGAGACCTCGCAAGAGAAGAGCCAAGCTCTGGCGCTTTGGCATACGAGACCTGTTGATCCAACAGATACTGGTATCGGAAAATAGGCAACAGT
 gtttgat  putative branch site (score: 359)
                                        tatctctttt  putative PPT
      atatttgaattttata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
actttctccacgattttgtctttccagttcagcatcatccgttttcgtttgatatttgaattttatacatttacaatttattaagtatctcttttggcagCTCCAGTTGAGACCTCGCAAGAGAAGAGCCAAGCTCTGGCGCTTTGGCATACGAGACCTGTTGATCCAACAGATACTGGTATCGGAAAATAGGCAACAGT

- - - - - - - - - - - - - - -cagcatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tacattt