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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttgattgtccatgtaagctatatacttgtaagttagaattacaattcttattcatacttcatacactaataatttgttcgttgactttattatatttagGTTGAGCCGTCAAAAAAGAAAGTTAAGAAAATTACTGTTCCGGTCCATGAGTTGGTCTATGGGGCCTTGGCTGCGGCTGACCTGCAGAAGGCTGTAGAGA

Basic information

species Zea mays
transcript GRMZM2G023232_T01
intron # 5
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|32931686|gb|CF036498.1|CF036498
EST:     GACCACAAGATACTGAGGAAAAATCTGTTCCGATGGAAACTGATGCAAAG                         GTTGAGCCGTCAAAAAAGAAAGTTAAGAAAATTACTGTTCCGGTCCATGAG
genomic: GACCACAAGATACTGAGGAAAAATCTGTTCCGATGGAAACTGATGCAAAGgtatgatatg ... ttatatttagGTTGAGCCGTCAAAAAAGAAAGTTAAGAAAATTACTGTTCCGGTCCATGAG
EST: gi|9952046|gb|BE638629.1|BE638629
EST:     GACCACAAGATACTGAGGAAAAATCTGTTCCGATGGAAACTGATGCAAAG                         GTTGAGCCGTCAAAAAAGAAAGTTAAGAAAATTACTGTTCCGGTCCATGAG
genomic: GACCACAAGATACTGAGGAAAAATCTGTTCCGATGGAAACTGATGCAAAGgtatgatatg ... ttatatttagGTTGAGCCGTCAAAAAAGAAAGTTAAGAAAATTACTGTTCCGGTCCATGAG
EST: gi|89251181|gb|DY622967.1|DY622967
EST:     GACCACAAGATACTGAGGAAAAATCTGTTCCGATGGAAACTGATGCAAAG                         GTTGAGCCGTCAAAAAAGAAAGTTAAGAAAATTACTGTTCCGGTCCATGAG
genomic: GACCACAAGATACTGAGGAAAAATCTGTTCCGATGGAAACTGATGCAAAGgtatgatatg ... ttatatttagGTTGAGCCGTCAAAAAAGAAAGTTAAGAAAATTACTGTTCCGGTCCATGAG
EST: gi|32945492|gb|CF050311.1|CF050311
EST:     GACCACAAGATACTGAGGAAAAATCTGTTCCGATGGAAACTGATGCAAAG                         GTTGAGCCGTC
genomic: GACCACAAGATACTGAGGAAAAATCTGTTCCGATGGAAACTGATGCAAAGgtatgatatg ... ttatatttagGTTGAGCCGTC
EST: gi|20803202|gb|BQ294252.1|BQ294252
EST:     CACAAGATACTGAGGAAAAATCTGTTCCGATGGAAACTGATGCAAAG                         GTTGAGCCGTCAAAAAAGAAAGTTAAGAAAATTACTGTTCCGGTCCATGAG
genomic: CACAAGATACTGAGGAAAAATCTGTTCCGATGGAAACTGATGCAAAGgtatgatatg ... ttatatttagGTTGAGCCGTCAAAAAAGAAAGTTAAGAAAATTACTGTTCCGGTCCATGAG
EST: gi|67021901|gb|CO450650.1|CO450650
EST:     GACCACAAGATACTGAGGAAAAATCTGTTCCGATGGAAACTGATGCAAAG                         GTTGAGCCGTCAAAAAAGAAAGTTAAGAAAATTACTGTTCCGGTCCATGAG
genomic: GACCACAAGATACTGAGGAAAAATCTGTTCCGATGGAAACTGATGCAAAGgtatgatatg ... ttatatttagGTTGAGCCGTCAAAAAAGAAAGTTAAGAAAATTACTGTTCCGGTCCATGAG
EST: gi|67016035|gb|CO444784.1|CO444784
EST:     GACCACAAGATACTGAGGAAAAATCTGTTCCGATGGAAACTGATGCAAAG                         GTTGAGCCGTCAAAAAAGAAAGTTAAGAAAATTACTGTTCCGGTCCATGAG
genomic: GACCACAAGATACTGAGGAAAAATCTGTTCCGATGGAAACTGATGCAAAGgtatgatatg ... ttatatttagGTTGAGCCGTCAAAAAAGAAAGTTAAGAAAATTACTGTTCCGGTCCATGAG
EST: gi|67025370|gb|CO454119.1|CO454119
EST:     GACCACAAGATACTGAGGAAAAATCTGTTCCGATGGAAACTGATGCAAAG                         GTTGAGCCGTCAAAAAAGAAAGTTAAGAAAATTACTGTTCCGGTCCATGAG
genomic: GACCACAAGATACTGAGGAAAAATCTGTTCCGATGGAAACTGATGCAAAGgtatgatatg ... ttatatttagGTTGAGCCGTCAAAAAAGAAAGTTAAGAAAATTACTGTTCCGGTCCATGAG
EST: gi|18175444|gb|BM350773.1|BM350773
EST:     GACCACAAGATACTGAGGAAAAATCTGTTCCGATGGAAACTGATGCAAAG                         GTTGAGCCGTCAAAAAAGAAAGTTAAGAAAATTACTGTTC
genomic: GACCACAAGATACTGAGGAAAAATCTGTTCCGATGGAAACTGATGCAAAGgtatgatatg ... ttatatttagGTTGAGCCGTCAAAAAAGAAAGTTAAGAAAATTACTGTTC
EST: gi|33094410|gb|CF054404.1|CF054404
EST:     GACCACAAGATACTGAGGAAAAATCTGTTCCGATGGAAACTGATGCAAAG                         GTTGAGCCGTCAAAAAAGAAAGTTAAGAAAATTACTGTTCCGGTCCATGAG
genomic: GACCACAAGATACTGAGGAAAAATCTGTTCCGATGGAAACTGATGCAAAGgtatgatatg ... ttatatttagGTTGAGCCGTCAAAAAAGAAAGTTAAGAAAATTACTGTTCCGGTCCATGAG
EST: gi|211343665|gb|FL392042.1|FL392042
EST:     TACTGAGGAAAAATCTGTTCCGATGGAAACTGATGCAAAG                         GTTGAGCCGTCAAAAAAGAAAGTTAAGAAAATTACTGTTCCGGTCCATGAG
genomic: TACTGAGGAAAAATCTGTTCCGATGGAAACTGATGCAAAGgtatgatatg ... ttatatttagGTTGAGCCGTCAAAAAAGAAAGTTAAGAAAATTACTGTTCCGGTCCATGAG
EST: gi|78106114|gb|DV524532.1|DV524532
EST:     GACCACAAGATACTGAGGAAAAATCTGTTCCGATGGAAACTGATGCAAAG                         GTTGAGCCGTCAAAAAAGAAAGTTAAGAAAATTACTGTTCCGGTCCATGAG
genomic: GACCACAAGATACTGAGGAAAAATCTGTTCCGATGGAAACTGATGCAAAGgtatgatatg ... ttatatttagGTTGAGCCGTCAAAAAAGAAAGTTAAGAAAATTACTGTTCCGGTCCATGAG
EST: gi|213174387|gb|FM187872.1|FM187872
EST:     GACCACAAGATACTGAGGAAAAATCTGTTCCGATGGAAACTGATGCAAAG                         GTTGAGCCGTCAAAAAAGAAAGTTAAGAAAATTACTGTTCCGGTCCATGAG
genomic: GACCACAAGATACTGAGGAAAAATCTGTTCCGATGGAAACTGATGCAAAGgtatgatatg ... ttatatttagGTTGAGCCGTCAAAAAAGAAAGTTAAGAAAATTACTGTTCCGGTCCATGAG

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: 48 (upstream exon), 49 (downstream exon)
Score: 650

GGAGCCTAAAAGCGCTGATACCGCTGAGGCTGCTCATGCAGCTGAAAATGGACCACAAGATACTGAGGAAAAATCTGTTCCGATGGAAACTGATGCAAAGgtatgatatg ... ttatatttagGTTGAGCCGTCAAAAAAGAAAGTTAAGAAAATTACTGTTCCGGTCCATGAGTTGGTCTATGGGGCCTTGGCTGCGGCTGACCTGCAGAAGGCTGTAGAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 420

GGAGCCTAAAAGCGCTGATACCGCTGAGGCTGCTCATGCAGCTGAAAATGGACCACAAGATACTGAGGAAAAATCTGTTCCGATGGAAACTGATGCAAAGgtatgatatg ... ttatatttagGTTGAGCCGTCAAAAAAGAAAGTTAAGAAAATTACTGTTCCGGTCCATGAGTTGGTCTATGGGGCCTTGGCTGCGGCTGACCTGCAGAAGGCTGTAGAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 398

GGAGCCTAAAAGCGCTGATACCGCTGAGGCTGCTCATGCAGCTGAAAATGGACCACAAGATACTGAGGAAAAATCTGTTCCGATGGAAACTGATGCAAAGgtatgatatg ... ttatatttagGTTGAGCCGTCAAAAAAGAAAGTTAAGAAAATTACTGTTCCGGTCCATGAGTTGGTCTATGGGGCCTTGGCTGCGGCTGACCTGCAGAAGGCTGTAGAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 510

GGAGCCTAAAAGCGCTGATACCGCTGAGGCTGCTCATGCAGCTGAAAATGGACCACAAGATACTGAGGAAAAATCTGTTCCGATGGAAACTGATGCAAAGgtatgatatg ... ttatatttagGTTGAGCCGTCAAAAAAGAAAGTTAAGAAAATTACTGTTCCGGTCCATGAGTTGGTCTATGGGGCCTTGGCTGCGGCTGACCTGCAGAAGGCTGTAGAGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcttattcatacttcatacactaataatttgttcgttgactttattatatttagGTTGAGCCGTCAAAAAAGAAAGTTAAGAAAATTACTGTTCCGGTCCATGAGTTGGTCTATGGGGCCTTGGCTGCGGCTGACCTGCAGAAGGCTGTAGAGA
                                        ctttatt  CT-rich tract
                                    ttgactttattatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttgattgtccatgtaagctatatacttgtaagttagaattacaattcttattcatacttcatacactaataatttgttcgttgactttattatatttagGTTGAGCCGTCAAAAAAGAAAGTTAAGAAAATTACTGTTCCGGTCCATGAGTTGGTCTATGGGGCCTTGGCTGCGGCTGACCTGCAGAAGGCTGTAGAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - -gtccatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catacac