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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggatgcccttttttttgtctacatgcacatattattggacatatatggagtttatatttcagacaaaccttatttgttccagcattggtatttgttgtagATCCCCCCAACCAGAGCTAAATCACCAAAGCTTGGTCGGTCTAAAAACAAGTCCATATCAGAGACTGAAGAAAATACTACTACGGACCAACCTGCCCGTC

Basic information

species Zea mays
transcript GRMZM2G452633_T02
intron # 6
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|6102057|gb|AW126527.1|AW126527
EST:     CCAAGGTTGAATTGAAAAAG                         ATCCCCCCAACCAGAGCTAAATCNCCAAAGCTTGGTCGGTCTAAAANCAAG
genomic: CCAAGGTTGAATTGAAAAAGgtaacttagt ... tttgttgtagATCCCCCCAACCAGAGCTAAATCACCAAAGCTTGGTCGGTCTAAAAACAAG
EST: gi|5895672|gb|AW036918.1|AW036918
EST:     TGCCAAGCTTTTATAAGGAACCAACCCCTGCCAAGGTTGAATTGAAAAAG                         ATCCCCCCAACCAGAGCTAAATCACCAAAGCTTGGTCGGTCTAAAAACAAG
genomic: TGCCAAGCTTTTATAAGGAACCAACCCCTGCCAAGGTTGAATTGAAAAAGgtaacttagt ... tttgttgtagATCCCCCCAACCAGAGCTAAATCACCAAAGCTTGGTCGGTCTAAAAACAAG
EST: gi|211489831|gb|FL359783.1|FL359783
EST:     TGCCAAGCTTTTATAAGGAACCAACCCCTGCCAAGGTTGAATTGAAAAAG                         ATCCCCCCAACCAGAGCTAAATCACCAAAGCTTGGTCGGTCTAAAAACAAG
genomic: TGCCAAGCTTTTATAAGGAACCAACCCCTGCCAAGGTTGAATTGAAAAAGgtaacttagt ... tttgttgtagATCCCCCCAACCAGAGCTAAATCACCAAAGCTTGGTCGGTCTAAAAACAAG
EST: gi|30088240|gb|CB886445.1|CB886445
EST:     GTTGAATTGAAAAAG                         ATCCCCCCAACCAGAGCTAAATCACCAAAGCTTGGTCGGTCTAAAAACAAG
genomic: GTTGAATTGAAAAAGgtaacttagt ... tttgttgtagATCCCCCCAACCAGAGCTAAATCACCAAAGCTTGGTCGGTCTAAAAACAAG
EST: gi|211020738|gb|FL318488.1|FL318488
EST:     TGCCAAGCTTTTATAAGGAACCAACCCCTGCCAA-GTTGAATTGAAAAAG                         ATCCCCCCAACCAGAGCTAAATCACCAAAGCTTGGTCGGTCTAAAAACAAG
genomic: TGCCAAGCTTTTATAAGGAACCAACCCCTGCCAAGGTTGAATTGAAAAAGgtaacttagt ... tttgttgtagATCCCCCCAACCAGAGCTAAATCACCAAAGCTTGGTCGGTCTAAAAACAAG
EST: gi|211389178|gb|FL466818.1|FL466818
EST:     TGCCAAGCTTTTATAAGGAACCAACCCCTGCCAAGGTTGAATTGAAAAAG                         ATCCCCCCAACCAGAGCTAAATCACCAAAGCTTGGTCGGTCTAAAAACAAG
genomic: TGCCAAGCTTTTATAAGGAACCAACCCCTGCCAAGGTTGAATTGAAAAAGgtaacttagt ... tttgttgtagATCCCCCCAACCAGAGCTAAATCACCAAAGCTTGGTCGGTCTAAAAACAAG
EST: gi|33092930|gb|CF052924.1|CF052924
EST:     TGCCAAGCTTTTATAAGGAACCAACCCCTGCCAAGGTTGAATTGAAAAAG                         ATCCCCCCAACCAGAGCTAAATCACCAAAGCTTGGTCGGTCTAAAA-CAAG
genomic: TGCCAAGCTTTTATAAGGAACCAACCCCTGCCAAGGTTGAATTGAAAAAGgtaacttagt ... tttgttgtagATCCCCCCAACCAGAGCTAAATCACCAAAGCTTGGTCGGTCTAAAAACAAG
EST: gi|211190617|gb|FL326446.1|FL326446
EST:     TGCCAAGCTTTTATAAGGAACCAACCCCTGCCAA-GTTGAATTGAAAAAG                         ATCCCCCCAACCAGAGCTAAATCACCAAAGCTTGGTCGGTCTAAAAACAAG
genomic: TGCCAAGCTTTTATAAGGAACCAACCCCTGCCAAGGTTGAATTGAAAAAGgtaacttagt ... tttgttgtagATCCCCCCAACCAGAGCTAAATCACCAAAGCTTGGTCGGTCTAAAAACAAG
EST: gi|211322617|gb|FL345965.1|FL345965
EST:     TGCCAAGCTTTTATAAGGAACCAACCCCTGCCAAGGTTGAATTGAAAAAG                         ATCCCCCCAACCAGAGCTAAATCACCAAAGCTTGGTCGGTCTAAAAACAAG
genomic: TGCCAAGCTTTTATAAGGAACCAACCCCTGCCAAGGTTGAATTGAAAAAGgtaacttagt ... tttgttgtagATCCCCCCAACCAGAGCTAAATCACCAAAGCTTGGTCGGTCTAAAAACAAG
EST: gi|32934224|gb|CF039036.1|CF039036
EST:     TGCCAAGCTTTTATAAGGAACCAACCCCTGCCAAGGTTGAATTGAAAAAG                         ATCCCCCCAACCAGAGCTAAATCACCAAAGCTTGGTCGGTCTAAAAACAAG
genomic: TGCCAAGCTTTTATAAGGAACCAACCCCTGCCAAGGTTGAATTGAAAAAGgtaacttagt ... tttgttgtagATCCCCCCAACCAGAGCTAAATCACCAAAGCTTGGTCGGTCTAAAAACAAG
EST: gi|211526230|gb|FL353915.1|FL353915
EST:     TGCCAAGCTTTTATAAGGAACCAACCCCTGCCAAGGTTGAATTGAAAAAG                         ATCCCCCCAACCAGAGCTAAATCACCAAAGCTTGGTCGGTCTAAAAACAAG
genomic: TGCCAAGCTTTTATAAGGAACCAACCCCTGCCAAGGTTGAATTGAAAAAGgtaacttagt ... tttgttgtagATCCCCCCAACCAGAGCTAAATCACCAAAGCTTGGTCGGTCTAAAAACAAG
EST: gi|60358926|gb|DN225899.1|DN225899
EST:     TGCCAAGCTTTTATAAGGAACCAACCCCTGCCAAGGTTGAATTGAAAAAG                         ATCCCCCCAACCAGAGCTAAATCACCAAAGCTTGGTCGGTCTAAAAACAAG
genomic: TGCCAAGCTTTTATAAGGAACCAACCCCTGCCAAGGTTGAATTGAAAAAGgtaacttagt ... tttgttgtagATCCCCCCAACCAGAGCTAAATCACCAAAGCTTGGTCGGTCTAAAAACAAG

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: 47 (upstream exon), 49 (downstream exon)
Score: 195

AGCAGAACTCAAAATGCTGAGAAAGAGTTTGAATTTCAAGGCAACACCAATGCCAAGCTTTTATAAGGAACCAACCCCTGCCAAGGTTGAATTGAAAAAGgtaacttagt ... tttgttgtagATCCCCCCAACCAGAGCTAAATCACCAAAGCTTGGTCGGTCTAAAAACAAGTCCATATCAGAGACTGAAGAAAATACTACTACGGACCAACCTGCCCGTC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 33

AGCAGAACTCAAAATGCTGAGAAAGAGTTTGAATTTCAAGGCAACACCAATGCCAAGCTTTTATAAGGAACCAACCCCTGCCAAGGTTGAATTGAAAAAGgtaacttagt ... tttgttgtagATCCCCCCAACCAGAGCTAAATCACCAAAGCTTGGTCGGTCTAAAAACAAGTCCATATCAGAGACTGAAGAAAATACTACTACGGACCAACCTGCCCGTC


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 30

AGCAGAACTCAAAATGCTGAGAAAGAGTTTGAATTTCAAGGCAACACCAATGCCAAGCTTTTATAAGGAACCAACCCCTGCCAAGGTTGAATTGAAAAAGgtaacttagt ... tttgttgtagATCCCCCCAACCAGAGCTAAATCACCAAAGCTTGGTCGGTCTAAAAACAAGTCCATATCAGAGACTGAAGAAAATACTACTACGGACCAACCTGCCCGTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 91

AGCAGAACTCAAAATGCTGAGAAAGAGTTTGAATTTCAAGGCAACACCAATGCCAAGCTTTTATAAGGAACCAACCCCTGCCAAGGTTGAATTGAAAAAGgtaacttagt ... tttgttgtagATCCCCCCAACCAGAGCTAAATCACCAAAGCTTGGTCGGTCTAAAAACAAGTCCATATCAGAGACTGAAGAAAATACTACTACGGACCAACCTGCCCGTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggagtttatatttcagacaaaccttatttgttccagcattggtatttgttgtagATCCCCCCAACCAGAGCTAAATCACCAAAGCTTGGTCGGTCTAAAAACAAGTCCATATCAGAGACTGAAGAAAATACTACTACGGACCAACCTGCCCGTC
     tttatatttca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggatgcccttttttttgtctacatgcacatattattggacatatatggagtttatatttcagacaaaccttatttgttccagcattggtatttgttgtagATCCCCCCAACCAGAGCTAAATCACCAAAGCTTGGTCGGTCTAAAAACAAGTCCATATCAGAGACTGAAGAAAATACTACTACGGACCAACCTGCCCGTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
ggatgcc
- - - - - - - - - -tacatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tccagca