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 5'  3'   		2  
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

tTTCACCAACCTCTATGGTCTGCATGACCCTTTTCTGAAAGGCGCGGTGAAGAGAGGTGACTGGTATAGGACCAAGGATTTGGTGATTAAGGGGGCAGACT

Basic information

species Zea mays
transcript GRMZM2G040209_T01
intron # 2
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|211125424|gb|FL376741.1|FL376741
EST:     CCCCTCCAGAGAAGACTCACTTTGGTGGTCTCAAAGATGAGGATCGCATT                         TTCACCAACCTCTATGGTCTGCATGACCCTTTTCTGAAAGGCGCGGTGAAG
genomic: CCCCTCCAGAGAAGACTCACTTTGGTGGTCTCAAAGATGAGGATCGCATTt ... tTTCACCAACCTCTATGGTCTGCATGACCCTTTTCTGAAAGGCGCGGTGAAGAGAGGTGACTGGTATAGG
EST: gi|32928785|gb|CF033597.1|CF033597
EST:     CCCCTCCAGAGAAGACTCACTTTGGTGGTCTCAAAGATGAGGATCGCATT                         TTCACCAACCTCTATGGTCTGCATGACCCTTTTCTGAAAGGCGCGGTGAAG
genomic: CCCCTCCAGAGAAGACTCACTTTGGTGGTCTCAAAGATGAGGATCGCATTt ... tTTCACCAACCTCTATGGTCTGCATGACCCTTTTCTGAAAGGCGCGGTGAAGAGAGGTGACTGGTATAGG
EST: gi|211413498|gb|FL407164.1|FL407164
EST:     CCCCTCCAGAGAAGACTCACTTTGGTGGTCTCAAAGATGAGGATCGCATT                         TTCACCAACCTCTATGGTCTGCATGACCCTTTTCTGAAAGGCGCGGTGAAG
genomic: CCCCTCCAGAGAAGACTCACTTTGGTGGTCTCAAAGATGAGGATCGCATTt ... tTTCACCAACCTCTATGGTCTGCATGACCCTTTTCTGAAAGGCGCGGTGAAGAGAGGTGACTGGTATAGG
EST: gi|78086164|gb|DV514557.1|DV514557
EST:     CCCCTCCAGAGAAGACTCACTTTGGTGGTCTCAAAGATGAGGATCGCATT                         TTCACCAACCTCTATGGTCTGCATGACCCTTTTCTGAAAGGCGCGGTGAAG
genomic: CCCCTCCAGAGAAGACTCACTTTGGTGGTCTCAAAGATGAGGATCGCATTt ... tTTCACCAACCTCTATGGTCTGCATGACCCTTTTCTGAAAGGCGCGGTGAAGAGAGGTGACTGGTATAGG
EST: gi|28910304|gb|CB331372.1|CB331372
EST:     CCCCTCCAGAGAAGACTCACTTTGGTGGTCTCAAAGATGAGGATCGCATT                         TTCACCAACCTCTATGGTCTGCATGACCCTTTTCTGAAAGGCGCGGTGAAG
genomic: CCCCTCCAGAGAAGACTCACTTTGGTGGTCTCAAAGATGAGGATCGCATTt ... tTTCACCAACCTCTATGGTCTGCATGACCCTTTTCTGAAAGGCGCGGTGAAGAGAGGTGACTGGTATAGG
EST: gi|71318463|gb|DR795997.1|DR795997
EST:     CCCCTCCAGAGAAGACTCACTTTGGTGGTCTCAAAGATGAGGATCGCATT                         TTCACCAACCTCTATGGTCTGCATGACCCTTTTCTGAAAGGCGCGGTGAAG
genomic: CCCCTCCAGAGAAGACTCACTTTGGTGGTCTCAAAGATGAGGATCGCATTt ... tTTCACCAACCTCTATGGTCTGCATGACCCTTTTCTGAAAGGCGCGGTGAAGAGAGGTGACTGGTATAGG
EST: gi|211240619|gb|FL389150.1|FL389150
EST:     CCCCTCCAGAGAAGACTCACTTTGGTGGCCTCAAAGATGAGGATCGCATT                         TTCACCAACCTCTATGGTCTGCATGACCCTTTTCTGAAAGGCGCGGTGAAG
genomic: CCCCTCCAGAGAAGACTCACTTTGGTGGTCTCAAAGATGAGGATCGCATTt ... tTTCACCAACCTCTATGGTCTGCATGACCCTTTTCTGAAAGGCGCGGTGAAGAGAGGTGACTGGTATAGG
EST: gi|211279377|gb|FL428423.1|FL428423
EST:     CCCCTCCAGAGAAGACTCACTTTGGTGGTCTCAAAGATGAGGATCGCATT                         TTCACCAACCTCTATGGTCTGCATGACCCTTTTCTGAAAGGCGCGGTGAAG
genomic: CCCCTCCAGAGAAGACTCACTTTGGTGGTCTCAAAGATGAGGATCGCATTt ... tTTCACCAACCTCTATGGTCTGCATGACCCTTTTCTGAAAGGCGCGGTGAAGAGAGGTGACTGGTATAGG
EST: gi|211504997|gb|FL428972.1|FL428972
EST:     CCCCTCCAGAGAAGACTCACTTTGGTGGCCTCAAAGATGAGGATCGCATT                         TTCACCAACCTCTATGGTCTGCATGACCCTTTTCTGAAAGGCGCGGTGAAG
genomic: CCCCTCCAGAGAAGACTCACTTTGGTGGTCTCAAAGATGAGGATCGCATTt ... tTTCACCAACCTCTATGGTCTGCATGACCCTTTTCTGAAAGGCGCGGTGAAGAGAGGTGA
EST: gi|9952646|gb|BE639334.1|BE639334
EST:     CCCCTCCAGAGAAGACTCACTTTGGTGGCCTCAAAGATGAGGATCGCATT                         TTCACCAACCTCTATGGTCTTCATGACCCTTTTCTGAAAGGCGCGATGAAG
genomic: CCCCTCCAGAGAAGACTCACTTTGGTGGTCTCAAAGATGAGGATCGCATTt ... tTTCACCAACCTCTATGGTCTGCATGACCCTTTTCTGAAAGGCGCGGTGAAGAGAGGTGACTGGTATAGG
EST: gi|149080018|gb|EE169038.2|EE169038
EST:     CCCCTCCAGAGAAGACTCACTTTGGTGGTCTCAAAGATGAGGATCGCATT                         TTCACCAACCTCTATGGTCTGCATGACCCTTTTCTGAAAGGCGCGGTGAAG
genomic: CCCCTCCAGAGAAGACTCACTTTGGTGGTCTCAAAGATGAGGATCGCATTt ... tTTCACCAACCTCTATGGTCTGCATGACCCTTTTCTGAAAGGCGCGGTGAAGAGAGGTGACTGGTATAGG
EST: gi|211498787|gb|FL369824.1|FL369824
EST:     CCCCTCCAGAGAAGA-TCACTTTGGTGGTCTCAAAGATGAGGATCGCATT                         TTCACCAACCTCTATGGTCTGCATGACCCTTTTCTGAAAGGCGCGGTGAAG
genomic: CCCCTCCAGAGAAGACTCACTTTGGTGGTCTCAAAGATGAGGATCGCATTt ... tTTCACCAACCTCTATGGTCTGCATGACCCTTTTCTGAAAGGCGCGGTGAAGAGAGGTGACTGGTATAGG
EST: gi|211225728|gb|FL398690.1|FL398690
EST:     CCCCTCCAGAGAAGAYTCACTTTGGTGGCCTCAAAGATGAGGATCGCATT                         TTCACCAACCTCTATGGTCTGCATGACCCTTTTCTGAAAGGCGCGGTGAAG
genomic: CCCCTCCAGAGAAGACTCACTTTGGTGGTCTCAAAGATGAGGATCGCATTt ... tTTCACCAACCTCTATGGTCTGCATGACCCTTTTCTGAAAGGCGCGGTGAAGAGAGGTGACTGGTATAGG
EST: gi|211360524|gb|FL385277.1|FL385277
EST:     CCCCTCCAGAGAAGACTCACTTTGGTGGTCTCAAAGATGAGGATCGCATT                         TTCACCAACCTCTATGGTCTGCATGACCCTTTTCTGAAAGGCGCGGTGAAG
genomic: CCCCTCCAGAGAAGACTCACTTTGGTGGTCTCAAAGATGAGGATCGCATTt ... tTTCACCAACCTCTATGGTCTGCATGACCCTTTTCTGAAAGGCGCGGTGAAGAGAGGTGACTGGTATAGG
EST: gi|211464176|gb|FL410755.1|FL410755
EST:     CCCCTCCAGAGAAGACTCACTTTGGTGGCCTCAAAGATGAGGATCGCATT                         TTCACCAACCTCTATGGTCTTCATGACCCTTTTCTGAAAGGCGCGATGAAG
genomic: CCCCTCCAGAGAAGACTCACTTTGGTGGTCTCAAAGATGAGGATCGCATTt ... tTTCACCAACCTCTATGGTCTGCATGACCCTTTTCTGAAAGGCGCGGTGAAGAGAGGTGACTGGTATAGG
EST: gi|211169299|gb|FL375027.1|FL375027
EST:     CCCCTCCAGAGAAGACTCACTTTGGTGGTCTCAAAGATGAGGATCGCATT                         TTCACCAACCTCTATGGTCTGCATGACCCTTTTCTGAAAGGCGCGGTGAAG
genomic: CCCCTCCAGAGAAGACTCACTTTGGTGGTCTCAAAGATGAGGATCGCATTt ... tTTCACCAACCTCTATGGTCTGCATGACCCTTTTCTGAAAGGCGCGGTGAAGAGAGGTGACTGGTATAGG
EST: gi|211201667|gb|FL383393.1|FL383393
EST:     CCCCTCCAGAGAAGACTCACTTTGGTGGTCTCAAAGATGAGGATCGCATT                         TTCACCAACCTCTATGGTCTGCATGACCCTTTTCTGAAAGGCGCGGTGAAG
genomic: CCCCTCCAGAGAAGACTCACTTTGGTGGTCTCAAAGATGAGGATCGCATTt ... tTTCACCAACCTCTATGGTCTGCATGACCCTTTTCTGAAAGGCGCGGTGAAGAGAGGTGACTGGTATAGG
EST: gi|211065293|gb|FL377931.1|FL377931
EST:     CCCCTCCAGAGAAGACTCACTTTGGTGGTCTCAAAGATGAGGATCGCATT                         TTCACCAACCTCTATGGTCTGCATGACCCTTTTCTGAAAGGCGCGGTGAAG
genomic: CCCCTCCAGAGAAGACTCACTTTGGTGGTCTCAAAGATGAGGATCGCATTt ... tTTCACCAACCTCTATGGTCTGCATGACCCTTTTCTGAAAGGCGCGGTGAAGAGAGGTGACTGGTATAGG
EST: gi|211438872|gb|FL372183.1|FL372183
EST:     CCCCTCCAGAGAAGACTCACTTTGGTGGCCTCAAAGATGAGGATCGCATT                         TTCACCAACCTCTATGGTCTGCATGACCCTTTTCTGAAAGGCGCGGTGAAG
genomic: CCCCTCCAGAGAAGACTCACTTTGGTGGTCTCAAAGATGAGGATCGCATTt ... tTTCACCAACCTCTATGGTCTGCATGACCCTTTTCTGAAAGGCGCGGTGAAGAGAGGTGACTGGTATAGG
EST: gi|31250314|gb|CD219338.1|CD219338
EST:     CCCCTCCAGAGAAGACTCACTTTGGTGGCCTCAAAGATGAGGATCGCATT                         TTCACCAACCTCTATGGTCTTCATGACCCTTTTCTGAAAGGCGCGATGAAG
genomic: CCCCTCCAGAGAAGACTCACTTTGGTGGTCTCAAAGATGAGGATCGCATTt ... tTTCACCAACCTCTATGGTCTGCATGACCCTTTTCTGAAAGGCGCGGTGAAGAGAGGTGACTGGTATAGG
EST: gi|211060366|gb|FL403446.1|FL403446
EST:     CCCCTCCAGAGAAGACTCACTTTGGTGGTCTCAAAGATGAGGATCGCATT                         TTCACCAACCT
genomic: CCCCTCCAGAGAAGACTCACTTTGGTGGTCTCAAAGATGAGGATCGCATTt ... tTTCACCAACCT
EST: gi|211506477|gb|FL386350.1|FL386350
EST:     CCCCTCCAGAGAAGACTCACTTTGGTGGCCTCAAAGATGAGGATCGCATT                         TTCACCAACCTCTATGGTCTGCATGACCCTTTTCTGAAAGGCGCGGTGAAG
genomic: CCCCTCCAGAGAAGACTCACTTTGGTGGTCTCAAAGATGAGGATCGCATTt ... tTTCACCAACCTCTATGGTCTGCATGACCCTTTTCTGAAAGGCGCGGTGAAGAGAGGTGACTGGTATAGG
EST: gi|33467475|gb|CF244524.1|CF244524
EST:     CCCCTCCAGAGAAGACTCACTTTGGTGGTCTCAAAGATGAGGATCGCATT                         TTCACCAACCTCTATGGTCTGCATGACCCTTTTCTGAAAGGCGCG
genomic: CCCCTCCAGAGAAGACTCACTTTGGTGGTCTCAAAGATGAGGATCGCATTt ... tTTCACCAACCTCTATGGTCTGCATGACCCTTTTCTGAAAGGCGCG
EST: gi|211496244|gb|FL383704.1|FL383704
EST:     CCCCTCCAGAGAAGACTCACTTTGGTGGTCTCAAAGATGAGGATCGCATT                         TTCACCAACCTCTATGGTCTGCATGACCCTTTTCTGAAAGGCGCGGTGAAG
genomic: CCCCTCCAGAGAAGACTCACTTTGGTGGTCTCAAAGATGAGGATCGCATTt ... tTTCACCAACCTCTATGGTCTGCATGACCCTTTTCTGAAAGGCGCGGTGAAGAGAGGTGACTGGTATAGG
EST: gi|60345785|gb|DN212758.1|DN212758
EST:     CCCCTCCAGAGAAGACTCACTTTGGTGGTCTCAAAGATGAGGATCGCATT                         TTCACCAACCTCTATGGTCTGCATGACCCTTTTCTGAAAGGCGCGGTGAAG
genomic: CCCCTCCAGAGAAGACTCACTTTGGTGGTCTCAAAGATGAGGATCGCATTt ... tTTCACCAACCTCTATGGTCTGCATGACCCTTTTCTGAAAGGCGCGGTGAAGAGAGGTGACTGGTATAGG

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), 48 (downstream exon)
Score: 426

CACCCAGGCTGCCACTACGTCAAGCACACCACAGCCTCCACCTCCACCACCCCCTCCAGAGAAGACTCACTTTGGTGGTCTCAAAGATGAGGATCGCATTt ... tTTCACCAACCTCTATGGTCTGCATGACCCTTTTCTGAAAGGCGCGGTGAAGAGAGGTGACTGGTATAGGACCAAGGATTTGGTGATTAAGGGGGCAGACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 442

CACCCAGGCTGCCACTACGTCAAGCACACCACAGCCTCCACCTCCACCACCCCCTCCAGAGAAGACTCACTTTGGTGGTCTCAAAGATGAGGATCGCATTt ... tTTCACCAACCTCTATGGTCTGCATGACCCTTTTCTGAAAGGCGCGGTGAAGAGAGGTGACTGGTATAGGACCAAGGATTTGGTGATTAAGGGGGCAGACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 345

CACCCAGGCTGCCACTACGTCAAGCACACCACAGCCTCCACCTCCACCACCCCCTCCAGAGAAGACTCACTTTGGTGGTCTCAAAGATGAGGATCGCATTt ... tTTCACCAACCTCTATGGTCTGCATGACCCTTTTCTGAAAGGCGCGGTGAAGAGAGGTGACTGGTATAGGACCAAGGATTTGGTGATTAAGGGGGCAGACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 501

CACCCAGGCTGCCACTACGTCAAGCACACCACAGCCTCCACCTCCACCACCCCCTCCAGAGAAGACTCACTTTGGTGGTCTCAAAGATGAGGATCGCATTt ... tTTCACCAACCTCTATGGTCTGCATGACCCTTTTCTGAAAGGCGCGGTGAAGAGAGGTGACTGGTATAGGACCAAGGATTTGGTGATTAAGGGGGCAGACT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tTTCACCAACCTCTATGGTCTGCATGACCCTTTTCTGAAAGGCGCGGTGAAGAGAGGTGACTGGTATAGGACCAAGGATTTGGTGATTAAGGGGGCAGACT

- - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG