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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTTTGCGTCATCCTTGGGATGGACATGATGACCACTCTCATGGTCATGGACACGGGCATGAGgtagtaccatttgatcccttctatttacttggcattacataatgcgttcttttaacttgttttgttaatgaattgctgtttgactgtcgttaatttgcaa...

Basic information

species Zea mays
transcript GRMZM2G106607_T01
intron # 3
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|211525323|gb|FL320981.1|FL320981
EST:     GGGATGGACATGATGACCACTCTCATGGTCATGGACACGGGCATGAG                         GCATCATCATCGTCATCTTCACATTAAGTTCCTTACTGGCTGCGGACGATG
genomic: GGGATGGACATGATGACCACTCTCATGGTCATGGACACGGGCATGAGgtagtaccat ... tttcgtgtagGCATCATCATCGTCATCTTCACATTAAGTTCCTTACTGGCTGCGGACGATG
EST: gi|14244444|gb|BG842499.2|BG842499
EST:     CTTGGGATGGACATGATGACCACTCTCATGGTCATGGACACGGGCATGAG                         GCATCATCATCGTCATCTTCACATTAAGTTCCTTACTGGCTGCGGACGATG
genomic: CTTGGGATGGACATGATGACCACTCTCATGGTCATGGACACGGGCATGAGgtagtaccat ... tttcgtgtagGCATCATCATCGTCATCTTCACATTAAGTTCCTTACTGGCTGCGGACGATG
EST: gi|9794379|gb|BE552687.1|BE552687
EST:     CTTGGGATGGACATGATGACCACTCTCATGGTCATGGACACGGGCATGAG                         GCATCATCATCGTCATCTTCACATTAAGTTCCTTACTGGCTGCGGACGATG
genomic: CTTGGGATGGACATGATGACCACTCTCATGGTCATGGACACGGGCATGAGgtagtaccat ... tttcgtgtagGCATCATCATCGTCATCTTCACATTAAGTTCCTTACTGGCTGCGGACGATG
EST: gi|44900467|gb|CK827012.1|CK827012
EST:     TGGGATGGACATGATGACCACTCTCATGGTCATGGACACGGGCATGAG                         GCATCATCATCGTCATCTTCACATTAAGTTCCTTACTGGCTGCGGACGATG
genomic: TGGGATGGACATGATGACCACTCTCATGGTCATGGACACGGGCATGAGgtagtaccat ... tttcgtgtagGCATCATCATCGTCATCTTCACATTAAGTTCCTTACTGGCTGCGGACGATG
EST: gi|211347602|gb|FL351939.1|FL351939
EST:     CTTGGGATGGACATGATGACCACTCTCATGGTCATGGACACGGGCATGAG                         GCATCATCATCGTCATCTTCACATTAAGTTCCTTACTGGCTGCGGACGATG
genomic: CTTGGGATGGACATGATGACCACTCTCATGGTCATGGACACGGGCATGAGgtagtaccat ... tttcgtgtagGCATCATCATCGTCATCTTCACATTAAGTTCCTTACTGGCTGCGGACGATG
EST: gi|60339461|gb|DN206434.1|DN206434
EST:     CTCATGGTCATGGGCACGGGCCTGAG                         GCATCATCATCGTCATCTTCACATTAAGTTCCTTACTGGCTGCGGACGATG
genomic: CTCATGGTCATGGACACGGGCATGAGgtagtaccat ... tttcgtgtagGCATCATCATCGTCATCTTCACATTAAGTTCCTTACTGGCTGCGGACGATG
EST: gi|211250380|gb|FL431482.1|FL431482
EST:     CTTGGGATGGACATGATGACCACTCTCATGGTCATGGACACGGGCATGAG                         GCATCATCATCGTCATCTTCACATTAAGTTCCTTACTGGCTGCGGACGATG
genomic: CTTGGGATGGACATGATGACCACTCTCATGGTCATGGACACGGGCATGAGgtagtaccat ... tttcgtgtagGCATCATCATCGTCATCTTCACATTAAGTTCCTTACTGGCTGCGGACGATG
EST: gi|19822006|gb|BQ048030.1|BQ048030
EST:     CTTGGGAGGGACATGATGACCACTCTCATGGTCATGGACACGGGCATGAG                         GCATCATCATCGTCATCTTCACATTAAGTTCCTTACTGGCTGCGGACGATG
genomic: CTTGGGATGGACATGATGACCACTCTCATGGTCATGGACACGGGCATGAGgtagtaccat ... tttcgtgtagGCATCATCATCGTCATCTTCACATTAAGTTCCTTACTGGCTGCGGACGATG
EST: gi|28983268|gb|BQ539469.2|BQ539469
EST:     CTTGGGATGGACATGATGACCACTCTCATGGTCATGGACACGGGCATGAG                         GCATCATCATCGTCATCTTCACAATAAGTTCCTTACTGGCTGCGGACGATG
genomic: CTTGGGATGGACATGATGACCACTCTCATGGTCATGGACACGGGCATGAGgtagtaccat ... tttcgtgtagGCATCATCATCGTCATCTTCACATTAAGTTCCTTACTGGCTGCGGACGATG
EST: gi|32917542|gb|CF022354.1|CF022354
EST:     CTTGGGATGGACATGATGACCACTCTCATGGTCATGGACACGGGCATGAG                         GCATCATCATCGTCATCTTCACATTAAGTTCCTTACTGGCTGCGGACGATG
genomic: CTTGGGATGGACATGATGACCACTCTCATGGTCATGGACACGGGCATGAGgtagtaccat ... tttcgtgtagGCATCATCATCGTCATCTTCACATTAAGTTCCTTACTGGCTGCGGACGATG
EST: gi|88756199|gb|DY540340.1|DY540340
EST:     CTTGGGATGGACATGATGACCACTCTCATGGTCATGGACACGGGCATGAG                         GCATCATCATCGTCATCTTCACATTAAGTTCCTTACTGGCTGCGGACGATG
genomic: CTTGGGATGGACATGATGACCACTCTCATGGTCATGGACACGGGCATGAGgtagtaccat ... tttcgtgtagGCATCATCATCGTCATCTTCACATTAAGTTCCTTACTGGCTGCGGACGATG
EST: gi|18181469|gb|BM382679.1|BM382679
EST:     CTTGGGATGGACATGATGACCACTCTCATGGTCATGGACACGGGCATGAG                         GCATCATCATCGTCATCTTCACATTAAGTTCCTTACTGGCTGCGGACGATG
genomic: CTTGGGATGGACATGATGACCACTCTCATGGTCATGGACACGGGCATGAGgtagtaccat ... tttcgtgtagGCATCATCATCGTCATCTTCACATTAAGTTCCTTACTGGCTGCGGACGATG
EST: gi|37384237|gb|CF629177.1|CF629177
EST:     CTTGGGATGGACATGATGACCACTCTCATGGTCATGGACACGGGCATGAG                         GCATCATCATCGTCATCTTCACATTAAGTTCCTTACTGGCTGCGGACGATG
genomic: CTTGGGATGGACATGATGACCACTCTCATGGTCATGGACACGGGCATGAGgtagtaccat ... tttcgtgtagGCATCATCATCGTCATCTTCACATTAAGTTCCTTACTGGCTGCGGACGATG
EST: gi|18177825|gb|BM379035.1|BM379035
EST:     TGGACACGGGCATGAG                         GCATCATCATCGTCATCTTCACATTAAGTTCCTTACTGGCTGCGGACGATG
genomic: TGGACACGGGCATGAGgtagtaccat ... tttcgtgtagGCATCATCATCGTCATCTTCACATTAAGTTCCTTACTGGCTGCGGACGATG
EST: gi|211352177|gb|FL343460.1|FL343460
EST:     CTTGGGAGGGACATGATGACCACTCTCATGGTCATGGACACGGGCATGAG                         GCATCATCATCGTCATCTTCACATTAAGTTCCTTACTGGCTGCGGACGATG
genomic: CTTGGGATGGACATGATGACCACTCTCATGGTCATGGACACGGGCATGAGgtagtaccat ... tttcgtgtagGCATCATCATCGTCATCTTCACATTAAGTTCCTTACTGGCTGCGGACGATG
EST: gi|67024511|gb|CO453260.1|CO453260
EST:     CTTGGGATGGACATGATGACCACTCTCATGGTCATGGACACGGGCATGAG                         GCATCATCATCGTCATCTTCACATTAAGTTCCTTACTGGCTGCGGACGATG
genomic: CTTGGGATGGACATGATGACCACTCTCATGGTCATGGACACGGGCATGAGgtagtaccat ... tttcgtgtagGCATCATCATCGTCATCTTCACATTAAGTTCCTTACTGGCTGCGGACGATG
EST: gi|166541040|gb|EG167162.1|EG167162
EST:     CTTGGGATGGACATGATGACCACTCTCATGGTCATGGACACGGGCATGAG                         GCATCATCATCGTCATCTTCACA
genomic: CTTGGGATGGACATGATGACCACTCTCATGGTCATGGACACGGGCATGAGgtagtaccat ... tttcgtgtagGCATCATCATCGTCATCTTCACA
EST: gi|18177443|gb|BM378653.1|BM378653
EST:     TGGACACGGGCATAAG                         GCATCATCATCGTCATCTTCACATTAAGTTCCTTACTGGCTGCGGACGATG
genomic: TGGACACGGGCATGAGgtagtaccat ... tttcgtgtagGCATCATCATCGTCATCTTCACATTAAGTTCCTTACTGGCTGCGGACGATG
EST: gi|9254565|gb|BE345033.1|BE345033
EST:     CTTGGGATGGACATGATGACCACTCTCATGGTCATGGACACGGGCATGAG                         GCATCATCATCGTCATCTTCACATTAAGTTCCTTACTGGCTGCGGACGATG
genomic: CTTGGGATGGACATGATGACCACTCTCATGGTCATGGACACGGGCATGAGgtagtaccat ... tttcgtgtagGCATCATCATCGTCATCTTCACATTAAGTTCCTTACTGGCTGCGGACGATG
EST: gi|33096743|gb|CF056721.1|CF056721
EST:     CTTGGGATGGACATGATGACCACTCTCATGGTCATGGACACGGGCATGAG                         GCATCATCATCGTCATCTTCACATTAAGTTCCTTACTGGCTGCGGACGATG
genomic: CTTGGGATGGACATGATGACCACTCTCATGGTCATGGACACGGGCATGAGgtagtaccat ... tttcgtgtagGCATCATCATCGTCATCTTCACATTAAGTTCCTTACTGGCTGCGGACGATG
EST: gi|19822025|gb|BQ048049.1|BQ048049
EST:     CTTGGGAGGGACATGATGACCACTCTCATGGTCATGGACACGGGCATGAG                         GCATCATCATCGTCATCTTCACATTAAGTTCCTTACTGGCTGCGGACGATG
genomic: CTTGGGATGGACATGATGACCACTCTCATGGTCATGGACACGGGCATGAGgtagtaccat ... tttcgtgtagGCATCATCATCGTCATCTTCACATTAAGTTCCTTACTGGCTGCGGACGATG
EST: gi|211432000|gb|FL306578.1|FL306578
EST:     CTTGGGATGGACATGATGACCACTCTCATGGTCATGGACACGGGCATGAG                         GCATCATCATCGTCATCTTCACATTAAGTTCCTTACTGGCTGCGGACGATG
genomic: CTTGGGATGGACATGATGACCACTCTCATGGTCATGGACACGGGCATGAGgtagtaccat ... tttcgtgtagGCATCATCATCGTCATCTTCACATTAAGTTCCTTACTGGCTGCGGACGATG
EST: gi|38502640|gb|CF972500.1|CF972500
EST:     CTTGGGATGGACATGATGACCACTCTCATGGTCATGGACACGGGCATGAG                         GCATCATCATCGTCATCTTCACATTAAGTTCCTTACTGGCTGCGGACGATG
genomic: CTTGGGATGGACATGATGACCACTCTCATGGTCATGGACACGGGCATGAGgtagtaccat ... tttcgtgtagGCATCATCATCGTCATCTTCACATTAAGTTCCTTACTGGCTGCGGACGATG
EST: gi|113700980|gb|EE678484.1|EE678484
EST:     CTTGGGATGGACATGATGACCACTCTCATGGTCATGGACACGGGCATGAG                         GCATCATCATCGTCATCTTCACATTAAGTTCCTTACTGGCTGCGGACGATG
genomic: CTTGGGATGGACATGATGACCACTCTCATGGTCATGGACACGGGCATGAGgtagtaccat ... tttcgtgtagGCATCATCATCGTCATCTTCACATTAAGTTCCTTACTGGCTGCGGACGATG

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: 46 (upstream exon), 49 (downstream exon)
Score: 386

GGTTTGCGTCATCCTTGGGATGGACATGATGACCACTCTCATGGTCATGGACACGGGCATGAGgtagtaccat ... tttcgtgtagGCATCATCATCGTCATCTTCACATTAAGTTCCTTACTGGCTGCGGACGATGCTTGGCATGTTCCAACAGCTAAAGTTTGAGTTAATAAATTCTATCACCC


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 360

GGTTTGCGTCATCCTTGGGATGGACATGATGACCACTCTCATGGTCATGGACACGGGCATGAGgtagtaccat ... tttcgtgtagGCATCATCATCGTCATCTTCACATTAAGTTCCTTACTGGCTGCGGACGATGCTTGGCATGTTCCAACAGCTAAAGTTTGAGTTAATAAATTCTATCACCC


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 322

GGTTTGCGTCATCCTTGGGATGGACATGATGACCACTCTCATGGTCATGGACACGGGCATGAGgtagtaccat ... tttcgtgtagGCATCATCATCGTCATCTTCACATTAAGTTCCTTACTGGCTGCGGACGATGCTTGGCATGTTCCAACAGCTAAAGTTTGAGTTAATAAATTCTATCACCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 388

GGTTTGCGTCATCCTTGGGATGGACATGATGACCACTCTCATGGTCATGGACACGGGCATGAGgtagtaccat ... tttcgtgtagGCATCATCATCGTCATCTTCACATTAAGTTCCTTACTGGCTGCGGACGATGCTTGGCATGTTCCAACAGCTAAAGTTTGAGTTAATAAATTCTATCACCC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTTTGCGTCATCCTTGGGATGGACATGATGACCACTCTCATGGTCATGGACACGGGCATGAGgtagtaccatttgatcccttctatttacttggcattacataatgcgttcttttaacttgttttgttaatgaattgctgtttgactgtcgttaatttgcaa

- - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - -  CATGGA