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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attcacatcccatctgatctatgcatgttccttctcttctttctttgcttcttcagtttaatgataacggaactttatatattctgtcccatttctcaagGTTCAAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTATCTC

Basic information

species Zea mays
transcript GRMZM2G484880_T04
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|211058544|gb|FK994409.1|FK994409
EST:     AGAACGAAAGGGTCCTCGCCTACCACGGCCCCCTCCTCTACGAGGCCAAG                         GTTCAAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTAT
genomic: AGAACGAAAGGGTCCTCGCCTACCACGGCCCCCTCCTCTACGAGGCCAAGgttcgctatt ... atttctcaagGTTCAAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTAT
EST: gi|211061512|gb|FK994428.1|FK994428
EST:     AGAACGAAAGGGTCCTCGCCTACCACGGCCCCCTCCTCTACGAGGCCAAG                         GTTCAAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTAT
genomic: AGAACGAAAGGGTCCTCGCCTACCACGGCCCCCTCCTCTACGAGGCCAAGgttcgctatt ... atttctcaagGTTCAAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTAT
EST: gi|76912438|gb|DV164732.1|DV164732
EST:     AGAACGAAAGGGTCCTCGCCTACCACGGCCCCCTCCTCTACGAGGCCAAG                         GTTCAAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTAT
genomic: AGAACGAAAGGGTCCTCGCCTACCACGGCCCCCTCCTCTACGAGGCCAAGgttcgctatt ... atttctcaagGTTCAAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTAT
EST: gi|71434326|gb|DR815376.1|DR815376
EST:     AGAACGAAAGGGTCCTCGCCTACCACGGCCCCCTCCTCTACGAGGCCAAG                         GTTCAAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTAT
genomic: AGAACGAAAGGGTCCTCGCCTACCACGGCCCCCTCCTCTACGAGGCCAAGgttcgctatt ... atttctcaagGTTCAAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTAT
EST: gi|211058550|gb|FK994415.1|FK994415
EST:     AGAACGAAAGGGTCCTCGCCTACCACGGCCCCCTCCTCTACGAGGCCAAG                         GTTCAAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTAT
genomic: AGAACGAAAGGGTCCTCGCCTACCACGGCCCCCTCCTCTACGAGGCCAAGgttcgctatt ... atttctcaagGTTCAAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTAT
EST: gi|6031476|gb|AW076378.1|AW076378
EST:     AGAACGAAAGGGTCCTCGCCTACCACGGCCCCCTCCTCTACGAGGCCATT                         GTTCAAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTAT
genomic: AGAACGAAAGGGTCCTCGCCTACCACGGCCCCCTCCTCTACGAGGCCAAGgttcgctatt ... atttctcaagGTTCAAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTAT
EST: gi|211061507|gb|FK994423.1|FK994423
EST:     AGAACGAAAGGGTCCTCGCCTACCACGGCCCCCTCCTCTACGAGGCCAAG                         GTTCAAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTAT
genomic: AGAACGAAAGGGTCCTCGCCTACCACGGCCCCCTCCTCTACGAGGCCAAGgttcgctatt ... atttctcaagGTTCAAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTAT
EST: gi|211061514|gb|FK994430.1|FK994430
EST:     AGAACGAWAGGGTCCTCGCCTACCACGGCCCCCTCCTCTACGAGGCCAAG                         GTTCAAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTAT
genomic: AGAACGAAAGGGTCCTCGCCTACCACGGCCCCCTCCTCTACGAGGCCAAGgttcgctatt ... atttctcaagGTTCAAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTAT
EST: gi|211058549|gb|FK994414.1|FK994414
EST:     AGAACGAAAGGGTCCTCGCCTACCACGGCCCCCTCCTCTACGAGGCCAAG                         GTTCAAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTAT
genomic: AGAACGAAAGGGTCCTCGCCTACCACGGCCCCCTCCTCTACGAGGCCAAGgttcgctatt ... atttctcaagGTTCAAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTAT
EST: gi|211058545|gb|FK994410.1|FK994410
EST:     AGAACGAAAGGGTCCTCGCCTACCACGGCCCCCTCCTCTACGAGGCCAAG                         GTTCAAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTAT
genomic: AGAACGAAAGGGTCCTCGCCTACCACGGCCCCCTCCTCTACGAGGCCAAGgttcgctatt ... atttctcaagGTTCAAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTAT
EST: gi|93284203|gb|EB676467.1|EB676467
EST:     AGAACGAAAGGGTCCTCGCCTACCACGGCCCCCTCCTCTACGAGGCCAAG                         GTTCAAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTAT
genomic: AGAACGAAAGGGTCCTCGCCTACCACGGCCCCCTCCTCTACGAGGCCAAGgttcgctatt ... atttctcaagGTTCAAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTAT
EST: gi|211058554|gb|FK994419.1|FK994419
EST:     AGAACGAAAGGGTCCTCGCCTACCACGGCCCCCTCCTCTACGAGGCCAAG                         GTTCAAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTAT
genomic: AGAACGAAAGGGTCCTCGCCTACCACGGCCCCCTCCTCTACGAGGCCAAGgttcgctatt ... atttctcaagGTTCAAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTAT
EST: gi|13178287|gb|BG349545.1|BG349545
EST:     AGAACGAAAGGGTCCTCGCCTACCACGGCCCCCTCCTCTACGAGGCCAAG                         GTTCAAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTAT
genomic: AGAACGAAAGGGTCCTCGCCTACCACGGCCCCCTCCTCTACGAGGCCAAGgttcgctatt ... atttctcaagGTTCAAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTAT
EST: gi|211058547|gb|FK994412.1|FK994412
EST:     AGAACGAAAGGGTCCTCGCCTACCACGGCCCCCTCCTCTACGAGGCCAAG                         GTTCAAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTAT
genomic: AGAACGAAAGGGTCCTCGCCTACCACGGCCCCCTCCTCTACGAGGCCAAGgttcgctatt ... atttctcaagGTTCAAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTAT
EST: gi|32913308|gb|CF018120.1|CF018120
EST:     AGAACGAAAGGGTCCTCGCCTACCACGGCCCCCTCCTCTACGAGGCCAAG                         GTTCAAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTAT
genomic: AGAACGAAAGGGTCCTCGCCTACCACGGCCCCCTCCTCTACGAGGCCAAGgttcgctatt ... atttctcaagGTTCAAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTAT
EST: gi|26456042|gb|CA827625.1|CA827625
EST:     AGAACGAAAGGGTCCTCGCCTACCACGGCCCCCTCCTCTACGAGGCCAAG                         GTTCAAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTAT
genomic: AGAACGAAAGGGTCCTCGCCTACCACGGCCCCCTCCTCTACGAGGCCAAGgttcgctatt ... atttctcaagGTTCAAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTAT
EST: gi|211061508|gb|FK994424.1|FK994424
EST:     AGAACGAAAGGGTCCTCGCCTACCACGGCCCCCTCCTCTACGAGGCCAAG                         GTTCAAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTAT
genomic: AGAACGAAAGGGTCCTCGCCTACCACGGCCCCCTCCTCTACGAGGCCAAGgttcgctatt ... atttctcaagGTTCAAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTAT
EST: gi|211061515|gb|FK994431.1|FK994431
EST:     AGAACGAAAGGGTCCTCGCCTACCACGGCCCCCTCCTCTACGAGGCCAAG                         GTTCAAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTAT
genomic: AGAACGAAAGGGTCCTCGCCTACCACGGCCCCCTCCTCTACGAGGCCAAGgttcgctatt ... atttctcaagGTTCAAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTAT
EST: gi|211058555|gb|FK994420.1|FK994420
EST:     AGAACGAAAGGGTCCTCGCCTACCACGGCCCCCTCCTCTACGAGGCCAAG                         GTTCAAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTAT
genomic: AGAACGAAAGGGTCCTCGCCTACCACGGCCCCCTCCTCTACGAGGCCAAGgttcgctatt ... atttctcaagGTTCAAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTAT
EST: gi|211061509|gb|FK994425.1|FK994425
EST:     AGAACGAAAGGGTCCTCGCCTACCACGGCCCCCTCCTCTACGAGGCCAAG                         GTTCAAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTAT
genomic: AGAACGAAAGGGTCCTCGCCTACCACGGCCCCCTCCTCTACGAGGCCAAGgttcgctatt ... atttctcaagGTTCAAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTAT
EST: gi|71331879|gb|DR802817.1|DR802817
EST:     AGAACGAAAGGGTCCTCGCCTACCACGGCCCCCTCCTCTACGAGGCCAAG                         GTTCAAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTAT
genomic: AGAACGAAAGGGTCCTCGCCTACCACGGCCCCCTCCTCTACGAGGCCAAGgttcgctatt ... atttctcaagGTTCAAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTAT
EST: gi|32865668|gb|CF005350.1|CF005350
EST:     AGAACGAAAGGGTCCTCGCCTACCACGGCCCCCTCCTCTACGAGGCCAAG                         GTTCAAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTAT
genomic: AGAACGAAAGGGTCCTCGCCTACCACGGCCCCCTCCTCTACGAGGCCAAGgttcgctatt ... atttctcaagGTTCAAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTAT
EST: gi|31997934|gb|CD661839.1|CD661839
EST:     AGAACGAAAGGGTCCTCGCCTACCACGGCCCCCTCCTCTACGAGGCCAAG                         GTTCAAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTAT
genomic: AGAACGAAAGGGTCCTCGCCTACCACGGCCCCCTCCTCTACGAGGCCAAGgttcgctatt ... atttctcaagGTTCAAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTAT
EST: gi|211058548|gb|FK994413.1|FK994413
EST:     AGAACGAAAGGGTCCTCGCCTACCACGGCCCCCTCCTCTACGAGGCCAAG                         GTTCAAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTAT
genomic: AGAACGAAAGGGTCCTCGCCTACCACGGCCCCCTCCTCTACGAGGCCAAGgttcgctatt ... atttctcaagGTTCAAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTAT

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), 46 (downstream exon)
Score: 585

GAAGGAGGACAAGATCAAAGGCAAGGACTCGTCGGGGCCATCCTTCAAGGAGAACGAAAGGGTCCTCGCCTACCACGGCCCCCTCCTCTACGAGGCCAAGgttcgctatt ... atttctcaagGTTCAAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTATCTC


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 274

GAAGGAGGACAAGATCAAAGGCAAGGACTCGTCGGGGCCATCCTTCAAGGAGAACGAAAGGGTCCTCGCCTACCACGGCCCCCTCCTCTACGAGGCCAAGgttcgctatt ... atttctcaagGTTCAAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTATCTC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 255

GAAGGAGGACAAGATCAAAGGCAAGGACTCGTCGGGGCCATCCTTCAAGGAGAACGAAAGGGTCCTCGCCTACCACGGCCCCCTCCTCTACGAGGCCAAGgttcgctatt ... atttctcaagGTTCAAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTATCTC


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 320

GAAGGAGGACAAGATCAAAGGCAAGGACTCGTCGGGGCCATCCTTCAAGGAGAACGAAAGGGTCCTCGCCTACCACGGCCCCCTCCTCTACGAGGCCAAGgttcgctatt ... atttctcaagGTTCAAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTATCTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcttcttcagtttaatgataacggaactttatatattctgtcccatttctcaagGTTCAAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTATCTC
                tgataac  putative branch site (score: 320)
                                    ttctgtcccatttctc  putative PPT
                         aactttatatattct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attcacatcccatctgatctatgcatgttccttctcttctttctttgcttcttcagtttaatgataacggaactttatatattctgtcccatttctcaagGTTCAAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTATCTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG