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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagctttgatgattatatattttcttatatgagtcccttaatttcattcagtacttaacttttaagattaacagGATTCTGAAGATGAAGCAGAGGTTAAGGGGATCAAAAGAAAAAGGAAAAATAAG

Basic information

species Zea mays
transcript GRMZM2G020606_T02
intron # 3
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|71331155|gb|DR802412.1|DR802412
EST:     CTTCAGGAAGAGTAGTACGACATGTTTCCTCATTTGTGGATGGAACTGAG                         GATTCTGAAGATGAAGCAGAGGTTAAGGGGATC
genomic: CTTCAGGAAGAGTAGTACGACATGTTTCCTCATTTGTGGATGGAACTGAGgtagctttga ... agattaacagGATTCTGAAGATGAAGCAGAGGTTAAGGGGATC
EST: gi|37376807|gb|CF624961.1|CF624961
EST:     CTTCAGGAAGAGTAGTACGACATGTTTCCTCATTTGTGGATGGAACTGAG                         GATTCTGAAGATGAAGCAGAGGTTAAGGGGATC
genomic: CTTCAGGAAGAGTAGTACGACATGTTTCCTCATTTGTGGATGGAACTGAGgtagctttga ... agattaacagGATTCTGAAGATGAAGCAGAGGTTAAGGGGATC
EST: gi|211299732|gb|FL213380.1|FL213380
EST:     CTTCAGGAAGAGTAGTACGACATGTTTCCTCATTTGTGGATGGAACTCAG                         GATTCTGAAGATGAAGCAGAGGT
genomic: CTTCAGGAAGAGTAGTACGACATGTTTCCTCATTTGTGGATGGAACTGAGgtagctttga ... agattaacagGATTCTGAAGATGAAGCAGAGGT
EST: gi|113863937|gb|DW981593.1|DW981593
EST:     ATGTTTCCTCATTTGTGGATGGAACTGAG                         GATTCTGAAGATGAAGCAGAGGTTAAGGGGATCAAAAGAAAA-GGTAAAAT
genomic: ATGTTTCCTCATTTGTGGATGGAACTGAGgtagctttga ... agattaacagGATTCTGAAGATGAAGCAGAGGTTAAGGGGATCAAAAGAAAAAGGAAAAAT
EST: gi|28187621|gb|CB179231.1|CB179231
EST:     CTTCAGGAAGAGTAGTACGACATGTTTCCTCATTTGTGGATGGAACTGAG                         GATTCTGAAGATGAAGCAGAGGTTAAGGGGATCCAAAGAAAAGGGAAAA
genomic: CTTCAGGAAGAGTAGTACGACATGTTTCCTCATTTGTGGATGGAACTGAGgtagctttga ... agattaacagGATTCTGAAGATGAAGCAGAGGTTAAGGGGATCAAAAGAAAAAGGAAAA

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: 87

GTGAGCCTTCAACTTCAGGAAGAGTAGTACGACATGTTTCCTCATTTGTGGATGGAACTGAGgtagctttga ... agattaacagGATTCTGAAGATGAAGCAGAGGTTAAGGGGATCAAAAGAAAAAGGAAAAATAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 73

GTGAGCCTTCAACTTCAGGAAGAGTAGTACGACATGTTTCCTCATTTGTGGATGGAACTGAGgtagctttga ... agattaacagGATTCTGAAGATGAAGCAGAGGTTAAGGGGATCAAAAGAAAAAGGAAAAATAAG


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 52

GTGAGCCTTCAACTTCAGGAAGAGTAGTACGACATGTTTCCTCATTTGTGGATGGAACTGAGgtagctttga ... agattaacagGATTCTGAAGATGAAGCAGAGGTTAAGGGGATCAAAAGAAAAAGGAAAAATAAG


Block sizes: 37 (upstream exon), 49 (downstream exon)
Score: 41

GTGAGCCTTCAACTTCAGGAAGAGTAGTACGACATGTTTCCTCATTTGTGGATGGAACTGAGgtagctttga ... agattaacagGATTCTGAAGATGAAGCAGAGGTTAAGGGGATCAAAAGAAAAAGGAAAAATAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttcttatatgagtcccttaatttcattcagtacttaacttttaagattaacagGATTCTGAAGATGAAGCAGAGGTTAAGGGGATCAAAAGAAAAAGGAAAAATAAG
                                 acttaac  putative branch site (score: 41)
                                   ttaacttttaagatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagctttgatgattatatattttcttatatgagtcccttaatttcattcagtacttaacttttaagattaacagGATTCTGAAGATGAAGCAGAGGTTAAGGGGATCAAAAGAAAAAGGAAAAATAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA