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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgatcacggcaccttttcactgtgtatttacatcaatggctgtttcttttcaagtctagcagctgtgctcacgcaacttcgtgttatttgttcatagcagGTTGAGGGAAGTTGAAGCAAAAGTCTAAGCAAAAATG

Basic information

species Zea mays
transcript GRMZM2G114220_T02
intron # 1
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|76909136|gb|DV163240.1|DV163240
EST:     GATCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGTCA                         GTTGAGGGAAGTTGAAGCAAAAGTCTAAGCAAAAATG
genomic: GATCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGTCAgtaaggaacc ... ttcatagcagGTTGAGGGAAGTTGAAGCAAAAGTCTAAGCAAAAATG
EST: gi|211392498|gb|FL156787.1|FL156787
EST:     GATCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGTCA                         C
genomic: GATCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGTCAgtaaggaacc ... ttcatagcag-
EST: gi|211392498|gb|FL156787.1|FL156787
EST:     GATCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGTCA                         C
genomic: GATCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGTCAgtaaggaacc ... ttcatagcag-
EST: gi|211392498|gb|FL156787.1|FL156787
EST:     GATCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGTCA                         C
genomic: GATCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGTCAgtaaggaacc ... ttcatagcag-
EST: gi|211392504|gb|FL156793.1|FL156793
EST:     GATCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGTCACA                        
genomic: GATCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGT--CAgtaaggaacc ... ttcatagca
EST: gi|211392504|gb|FL156793.1|FL156793
EST:     GATCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGTCACA                        
genomic: GATCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGT--CAgtaaggaacc ... ttcatagca
EST: gi|211395124|gb|FL156801.1|FL156801
EST:     GATCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGTCACA                        
genomic: GATCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGT--CAgtaaggaacc ... ttcatagca
EST: gi|211395124|gb|FL156801.1|FL156801
EST:     GATCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGTCACA                        
genomic: GATCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGT--CAgtaaggaacc ... ttcatagca
EST: gi|211389877|gb|FL156782.1|FL156782
EST:     GATCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGTCA                         C
genomic: GATCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGTCAgtaaggaacc ... ttcatagcag-
EST: gi|211389877|gb|FL156782.1|FL156782
EST:     GATCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGTCA                         C
genomic: GATCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGTCAgtaaggaacc ... ttcatagcag-
EST: gi|211389877|gb|FL156782.1|FL156782
EST:     GATCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGTCA                         C
genomic: GATCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGTCAgtaaggaacc ... ttcatagcag-
EST: gi|211392507|gb|FL156796.1|FL156796
EST:     GATCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGTCACA                        
genomic: GATCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGT--CAgtaaggaacc ... ttcatagca
EST: gi|211392507|gb|FL156796.1|FL156796
EST:     GATCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGTCACA                        
genomic: GATCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGT--CAgtaaggaacc ... ttcatagca
EST: gi|91873355|gb|EB403312.1|EB403312
EST:     GATCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGTCACA                        
genomic: GATCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGT--CAgtaaggaacc ... ttcatagca
EST: gi|91873355|gb|EB403312.1|EB403312
EST:     GATCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGTCACA                        
genomic: GATCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGT--CAgtaaggaacc ... ttcatagca
EST: gi|14242735|gb|BG840580.2|BG840580
EST:     CAAGATTCCAAGCTCTTCTGTCACA                        
genomic: CAAGATTCCAAGCTCTTCTGT--CAgtaaggaacc ... ttcatagca
EST: gi|14242735|gb|BG840580.2|BG840580
EST:     CAAGATTCCAAGCTCTTCTGTCACA                        
genomic: CAAGATTCCAAGCTCTTCTGT--CAgtaaggaacc ... ttcatagca
EST: gi|211392505|gb|FL156794.1|FL156794
EST:     GATCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGTCACA                        
genomic: GATCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGT--CAgtaaggaacc ... ttcatagca
EST: gi|211392505|gb|FL156794.1|FL156794
EST:     GATCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGTCACA                        
genomic: GATCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGT--CAgtaaggaacc ... ttcatagca
EST: gi|71417924|gb|DR804257.1|DR804257
EST:     GATCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGTCA                         GTTGAGGGAAGTTGAAGCAAAAGTCTAAGCAAAAATG
genomic: GATCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGTCAgtaaggaacc ... ttcatagcagGTTGAGGGAAGTTGAAGCAAAAGTCTAAGCAAAAATG
EST: gi|50338446|gb|CO533572.1|CO533572
EST:     GATCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGTCA                         GTTGAGGGAAGTTGAAGCAAAAGTCTAAGCAAAAATG
genomic: GATCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGTCAgtaaggaacc ... ttcatagcagGTTGAGGGAAGTTGAAGCAAAAGTCTAAGCAAAAATG
EST: gi|211392501|gb|FL156790.1|FL156790
EST:     GATCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGTCA                         GTTGAGGGAAGTTGAAGCAAAAGTCTAAGCAAAAATG
genomic: GATCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGTCAgtaaggaacc ... ttcatagcagGTTGAGGGAAGTTGAAGCAAAAGTCTAAGCAAAAATG
EST: gi|211389876|gb|FL156781.1|FL156781
EST:     GATCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGTCA                         GTTGAGGGAAGTTGAAGCAAAAGTCTAAGCAAAAATG
genomic: GATCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGTCAgtaaggaacc ... ttcatagcagGTTGAGGGAAGTTGAAGCAAAAGTCTAAGCAAAAATG
EST: gi|211392496|gb|FL156785.1|FL156785
EST:     GATCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGTCACA                        
genomic: GATCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGT--CAgtaaggaacc ... ttcatagca
EST: gi|211392496|gb|FL156785.1|FL156785
EST:     GATCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGTCACA                        
genomic: GATCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGT--CAgtaaggaacc ... ttcatagca
EST: gi|93015584|gb|EB641104.1|EB641104
EST:     GATCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGTCA                         GTTGAGGGAAGTTGAAGCAAAAGTCTAAGCAAAAATG
genomic: GATCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGTCAgtaaggaacc ... ttcatagcagGTTGAGGGAAGTTGAAGCAAAAGTCTAAGCAAAAATG
EST: gi|211389879|gb|FL156784.1|FL156784
EST:     GATCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGTCA                         C
genomic: GATCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGTCAgtaaggaacc ... ttcatagcag-
EST: gi|211389879|gb|FL156784.1|FL156784
EST:     GATCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGTCA                         C
genomic: GATCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGTCAgtaaggaacc ... ttcatagcag-
EST: gi|211389879|gb|FL156784.1|FL156784
EST:     GATCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGTCA                         C
genomic: GATCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGTCAgtaaggaacc ... ttcatagcag-
EST: gi|32862738|gb|CF002420.1|CF002420
EST:     GATCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGTCA                         GTTGAGGGAAGTTGAAGCAAAAGTCTAAGCAAAAATG
genomic: GATCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGTCAgtaaggaacc ... ttcatagcagGTTGAGGGAAGTTGAAGCAAAAGTCTAAGCAAAAATG
EST: gi|211392502|gb|FL156791.1|FL156791
EST:     GATCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGTCACA                        
genomic: GATCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGT--CAgtaaggaacc ... ttcatagca
EST: gi|211392502|gb|FL156791.1|FL156791
EST:     GATCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGTCACA                        
genomic: GATCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGT--CAgtaaggaacc ... ttcatagca
EST: gi|91049005|gb|EB159423.1|EB159423
EST:     GATCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGTCACA                        
genomic: GATCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGT--CAgtaaggaacc ... ttcatagca
EST: gi|91049005|gb|EB159423.1|EB159423
EST:     GATCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGTCACA                        
genomic: GATCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGT--CAgtaaggaacc ... ttcatagca
EST: gi|6637070|gb|AW261342.1|AW261342
EST:     GATCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGTCA                         GTTGAGGGAAGTTGAAGCAAAAGTCTAACCAAAAATG
genomic: GATCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGTCAgtaaggaacc ... ttcatagcagGTTGAGGGAAGTTGAAGCAAAAGTCTAAGCAAAAATG
EST: gi|211395123|gb|FL156800.1|FL156800
EST:     GDNCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGTCACA                        
genomic: GATCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGT--CAgtaaggaacc ... ttcatagca
EST: gi|211395123|gb|FL156800.1|FL156800
EST:     GDNCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGTCACA                        
genomic: GATCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGT--CAgtaaggaacc ... ttcatagca
EST: gi|211392503|gb|FL156792.1|FL156792
EST:     GATCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGTCACA                        
genomic: GATCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGT--CAgtaaggaacc ... ttcatagca
EST: gi|211392503|gb|FL156792.1|FL156792
EST:     GATCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGTCACA                        
genomic: GATCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGT--CAgtaaggaacc ... ttcatagca
EST: gi|211392499|gb|FL156788.1|FL156788
EST:     GATCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGTCACA                        
genomic: GATCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGT--CAgtaaggaacc ... ttcatagca
EST: gi|211392499|gb|FL156788.1|FL156788
EST:     GATCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGTCACA                        
genomic: GATCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGT--CAgtaaggaacc ... ttcatagca
EST: gi|211392510|gb|FL156799.1|FL156799
EST:     GATCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGTCACA                        
genomic: GATCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGT--CAgtaaggaacc ... ttcatagca
EST: gi|211392510|gb|FL156799.1|FL156799
EST:     GATCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGTCACA                        
genomic: GATCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGT--CAgtaaggaacc ... ttcatagca
EST: gi|213183590|gb|FM196389.1|FM196389
EST:     GATCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGTCA                         GTTGAGGGAAGTTGAAGCAAAAGTCTAAGCAAAAATG
genomic: GATCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGTCAgtaaggaacc ... ttcatagcagGTTGAGGGAAGTTGAAGCAAAAGTCTAAGCAAAAATG
EST: gi|32859779|gb|CD999460.1|CD999460
EST:     GATCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGTCACA                        
genomic: GATCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGT--CAgtaaggaacc ... ttcatagca
EST: gi|32859779|gb|CD999460.1|CD999460
EST:     GATCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGTCACA                        
genomic: GATCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGT--CAgtaaggaacc ... ttcatagca
EST: gi|211392508|gb|FL156797.1|FL156797
EST:     GATCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGTCA                         GTTGAGGGAAGTTGAAGCAAAAGTCTAA-CAAAAAATG
genomic: GATCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGTCAgtaaggaacc ... ttcatagcagGTTGAGGGAAGTTGAAGCAAAAGTCTAAGCAAAAA-TG

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), 46 (downstream exon)
Score: 72

ACCTGCGCCCGAACACTTCGAGCTCACCCGCAACCTCCTCCGGGAAGCGCGATCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGTCAgtaaggaacc ... ttcatagcagGTTGAGGGAAGTTGAAGCAAAAGTCTAAGCAAAAATG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 102

ACCTGCGCCCGAACACTTCGAGCTCACCCGCAACCTCCTCCGGGAAGCGCGATCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGTCAgtaaggaacc ... ttcatagcagGTTGAGGGAAGTTGAAGCAAAAGTCTAAGCAAAAATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 121

ACCTGCGCCCGAACACTTCGAGCTCACCCGCAACCTCCTCCGGGAAGCGCGATCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGTCAgtaaggaacc ... ttcatagcagGTTGAGGGAAGTTGAAGCAAAAGTCTAAGCAAAAATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 111

ACCTGCGCCCGAACACTTCGAGCTCACCCGCAACCTCCTCCGGGAAGCGCGATCGCCGTCTCGAAGGAGCTGAAATCCAAGATTCCAAGCTCTTCTGTCAgtaaggaacc ... ttcatagcagGTTGAGGGAAGTTGAAGCAAAAGTCTAAGCAAAAATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttttcaagtctagcagctgtgctcacgcaacttcgtgttatttgttcatagcagGTTGAGGGAAGTTGAAGCAAAAGTCTAAGCAAAAATG
                    tgctcac  putative branch site (score: 111)
                                         tttgttc  putative PPT
                                      ttatttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgatcacggcaccttttcactgtgtatttacatcaatggctgtttcttttcaagtctagcagctgtgctcacgcaacttcgtgttatttgttcatagcagGTTGAGGGAAGTTGAAGCAAAAGTCTAAGCAAAAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - cggcacc
- - - - - - - -ttcactg
- - - - - - - - - - - tgtattt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcagctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cacgcaa