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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattaacctgcttattcgcgatctatatctgtatgtccattgtgtttgaaaaaaaaggactcactgttcattatgcagGCCAGCCCATCAGACCCAGAGAATTTCCCATTTGTTGTGCTTGGTAACAAGATCGATGTTGATGGTGGTAACAGCCGGACT

Basic information

species Zea mays
transcript GRMZM2G058366_T01
intron # 12
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|148965008|gb|EE015841.2|EE015841
EST:     CCAAGTCATTTGAAAAGCTCAACAACTGGCGTGAGGAATTCCTAATTCAA                         GCCAGCCCATCAGACCCAGAGAATTTCCCATTTGTTGTGCTTGGTAACAAG
genomic: CCAAGTCATTTGAAAAGCTCAACAACTGGCGTGAGGAATTCCTAATTCAAgtaattaacc ... cattatgcagGCCAGCCCATCAGACCCAGAGAATTTCCCATTTGTTGTGCTTGGTAACAAG
EST: gi|18163479|gb|BM333318.1|BM333318
EST:     CCAAGTCATTT-AAAAGCTCAACAACTGGCGTGAGGAATTCGTAATTCAA                         GCCAGCCCATCAGACCCAGAGAATTTCCCATTTGTTGTGCTTGGTAACAAG
genomic: CCAAGTCATTTGAAAAGCTCAACAACTGGCGTGAGGAATTCCTAATTCAAgtaattaacc ... cattatgcagGCCAGCCCATCAGACCCAGAGAATTTCCCATTTGTTGTGCTTGGTAACAAG
EST: gi|5069977|gb|AI737942.1|AI737942
EST:     GAGG-ATTCCTAATTCAA                         GCCAGCCCATCAGACCCAGAGAATTTCCCATTTGTTGTGCTTGGTAACAAG
genomic: GAGGAATTCCTAATTCAAgtaattaacc ... cattatgcagGCCAGCCCATCAGACCCAGAGAATTTCCCATTTGTTGTGCTTGGTAACAAG
EST: gi|211158731|gb|FL327701.1|FL327701
EST:     CCAAGTCATTTGAAAAGCTCAACAACTGGCGTGAGGAATTCCTAATTCAA                         GCCAGCCCATCAGACCCAGAGAATTTCCCATTTGTTGTGCTTGGTAACAAG
genomic: CCAAGTCATTTGAAAAGCTCAACAACTGGCGTGAGGAATTCCTAATTCAAgtaattaacc ... cattatgcagGCCAGCCCATCAGACCCAGAGAATTTCCCATTTGTTGTGCTTGGTAACAAG
EST: gi|32865528|gb|CF005210.1|CF005210
EST:     AAGCTCAACAACTGGCGTGAGGAATTCCTAATTCAA                         GCCAGCCCATCAGACCCAGAGAATTTCCCATTTGTTGTGCTTGGTAACAAG
genomic: AAGCTCAACAACTGGCGTGAGGAATTCCTAATTCAAgtaattaacc ... cattatgcagGCCAGCCCATCAGACCCAGAGAATTTCCCATTTGTTGTGCTTGGTAACAAG
EST: gi|211198572|gb|FL471183.1|FL471183
EST:     GCTCAACAACTGGCGTGAGGAATTCCTAATTCAA                         GCCAGCCCATCAGACCCAGAGAATTTCCCATTTGTTGTGCTTGGTAACAAG
genomic: GCTCAACAACTGGCGTGAGGAATTCCTAATTCAAgtaattaacc ... cattatgcagGCCAGCCCATCAGACCCAGAGAATTTCCCATTTGTTGTGCTTGGTAACAAG
EST: gi|211340444|gb|FL354255.1|FL354255
EST:     CCAAGTCATTTGAAAAGCTCAACAACTGGCGTGAGGAATTCCTAATTCAA                         GCCAGCCCATCAGACCCAGAGAATTTCCCATTTGTTGTGCTTGGTAACAAG
genomic: CCAAGTCATTTGAAAAGCTCAACAACTGGCGTGAGGAATTCCTAATTCAAgtaattaacc ... cattatgcagGCCAGCCCATCAGACCCAGAGAATTTCCCATTTGTTGTGCTTGGTAACAAG
EST: gi|211435902|gb|FL357604.1|FL357604
EST:     CCAAGTCATTTGAAAAGCTCAACAACTGGCGTGAGGAATTCCTAATTCAA                         GCCAGCCCATCAGACCCAGAGAATTTCCCATTTGTTGTGCTTGGTAACAAG
genomic: CCAAGTCATTTGAAAAGCTCAACAACTGGCGTGAGGAATTCCTAATTCAAgtaattaacc ... cattatgcagGCCAGCCCATCAGACCCAGAGAATTTCCCATTTGTTGTGCTTGGTAACAAG
EST: gi|20803409|gb|BQ294459.1|BQ294459
EST:     CCAAGTCATTTGAAAAGCTCAACAACTGGCGTGAGGAATTCCTAATTCAA                         GCCAGCCCATCAGACCCAGAGAATTTCCCATTTGTTGTGCTTGGTAACAAG
genomic: CCAAGTCATTTGAAAAGCTCAACAACTGGCGTGAGGAATTCCTAATTCAAgtaattaacc ... cattatgcagGCCAGCCCATCAGACCCAGAGAATTTCCCATTTGTTGTGCTTGGTAACAAG
EST: gi|211522124|gb|FL314742.1|FL314742
EST:     CCAAGTCATTTGAAAAGCTCAACAACTGGCGTGAGGAATTCCTAATTCAA                         GCCAGCCCATCAGACCCAGAGAATTTCCCATTTGTTGTGCTTGGTAACAAG
genomic: CCAAGTCATTTGAAAAGCTCAACAACTGGCGTGAGGAATTCCTAATTCAAgtaattaacc ... cattatgcagGCCAGCCCATCAGACCCAGAGAATTTCCCATTTGTTGTGCTTGGTAACAAG
EST: gi|15100485|gb|BI396276.1|BI396276
EST:     CCAAGTCATTTGAAAAGCTCAACAACTGGCGTGAGGAATTCCTAATTCAA                         GCCAGCCCATCAGACCCAGAGAATTTCCCATTTGTTGTGCTTGGTAACAAG
genomic: CCAAGTCATTTGAAAAGCTCAACAACTGGCGTGAGGAATTCCTAATTCAAgtaattaacc ... cattatgcagGCCAGCCCATCAGACCCAGAGAATTTCCCATTTGTTGTGCTTGGTAACAAG
EST: gi|60353761|gb|DN220734.1|DN220734
EST:     CCAAGTCATTTGAAAAGCTCAACAACTGGCGTGAGGAATTCCTAATTCAA                         GCCAGCCCATCAGACCCAGAGAATTTCCCATTTGTTGTGCTTGGTAACAAG
genomic: CCAAGTCATTTGAAAAGCTCAACAACTGGCGTGAGGAATTCCTAATTCAAgtaattaacc ... cattatgcagGCCAGCCCATCAGACCCAGAGAATTTCCCATTTGTTGTGCTTGGTAACAAG
EST: gi|211093130|gb|FL308874.1|FL308874
EST:     CCAAGTCATTTGAAAAGCTCAACAACTGGCGTGAGGAATTCCTAATTCAA                         GCCAGCCCATCAGACCCAGAGAATTTCCCATTTGTTGTGCTTGGTAACAAG
genomic: CCAAGTCATTTGAAAAGCTCAACAACTGGCGTGAGGAATTCCTAATTCAAgtaattaacc ... cattatgcagGCCAGCCCATCAGACCCAGAGAATTTCCCATTTGTTGTGCTTGGTAACAAG
EST: gi|16921014|gb|BM074941.1|BM074941
EST:     TGGCGTGAGGAAATCNTAA-TCAA                         GCCAGCCCATCAGACCCAGAGAATTTCCCATTTGTTGTGCTTGGTAACAAG
genomic: TGGCGTGAGGAATTCCTAATTCAAgtaattaacc ... cattatgcagGCCAGCCCATCAGACCCAGAGAATTTCCCATTTGTTGTGCTTGGTAACAAG
EST: gi|211514505|gb|FL430894.1|FL430894
EST:     CCAAGTCATTTGAAAAGCTCAACAACTGGCGTGAGGAATTCCTAATTCAA                         GCCAGCCCATCAGACCCAGAGAATTTCCCATTTGTTGTGCTTGGTAACAAG
genomic: CCAAGTCATTTGAAAAGCTCAACAACTGGCGTGAGGAATTCCTAATTCAAgtaattaacc ... cattatgcagGCCAGCCCATCAGACCCAGAGAATTTCCCATTTGTTGTGCTTGGTAACAAG
EST: gi|16916424|gb|BM072835.1|BM072835
EST:     CCAAGTCA-TTGAAAAGCTCAACAACTGGCGTGAGGAATTCTTAATTCAA                         GCCAGCCCATCAGACCCAGAGAATTTCCCATTTGTTGTGCTTGGTAACAAG
genomic: CCAAGTCATTTGAAAAGCTCAACAACTGGCGTGAGGAATTCCTAATTCAAgtaattaacc ... cattatgcagGCCAGCCCATCAGACCCAGAGAATTTCCCATTTGTTGTGCTTGGTAACAAG
EST: gi|211267809|gb|FL345566.1|FL345566
EST:     CCAAGTCATTTGAAAAGCTCAACAACTGGCGTGAGGAATTCCTAATTCAA                         GCCAGCCCATCAGACCCAGAGAATTTCCCATTTGTTGTGCTTGGTAACAAG
genomic: CCAAGTCATTTGAAAAGCTCAACAACTGGCGTGAGGAATTCCTAATTCAAgtaattaacc ... cattatgcagGCCAGCCCATCAGACCCAGAGAATTTCCCATTTGTTGTGCTTGGTAACAAG
EST: gi|211403760|gb|FL312287.1|FL312287
EST:     CCAAGTCATTTGAAAAGCTCAACAACTGGCGTGAGGAATTCCTAATTCAA                         GCCAGCCCATCAGACCCAGAGAATTTCCCCATTTGTTGTGCTTGGTAACAA
genomic: CCAAGTCATTTGAAAAGCTCAACAACTGGCGTGAGGAATTCCTAATTCAAgtaattaacc ... cattatgcagGCCAGCCCATCAGACCCAGAGAATTTCCC-ATTTGTTGTGCTTGGTAACAA
EST: gi|149062811|gb|EE157528.2|EE157528
EST:     CCAAGTCATTTGAAAAGCTCAACAACTGGCGTGAGGAGTTCCTAATTCAA                         GCCAGCCCATCAGACCCAGAGAATTTCCCATTTGTTGTGCTTGGTAACAAG
genomic: CCAAGTCATTTGAAAAGCTCAACAACTGGCGTGAGGAATTCCTAATTCAAgtaattaacc ... cattatgcagGCCAGCCCATCAGACCCAGAGAATTTCCCATTTGTTGTGCTTGGTAACAAG
EST: gi|148965007|gb|EE015840.2|EE015840
EST:     CCAAGTCATTTGAAAAGCTCAACAACTGGCGTGAGGAATTCCTAATTCAA                         GCCAGCCCATCAGACCCAGAGAATTTCCCATTTGTTGTGCTTGGTAACAAG
genomic: CCAAGTCATTTGAAAAGCTCAACAACTGGCGTGAGGAATTCCTAATTCAAgtaattaacc ... cattatgcagGCCAGCCCATCAGACCCAGAGAATTTCCCATTTGTTGTGCTTGGTAACAAG
EST: gi|78021263|gb|DV489650.1|DV489650
EST:     CCAAGTCA-TTGAAAAGCTCAACAACTGGCGTGAGGAATTCCTAATTCAA                         GCCAGCCCATCAGACCCAGAGAATTTCCCATTTGTTGTGCTTGGTAACAAG
genomic: CCAAGTCATTTGAAAAGCTCAACAACTGGCGTGAGGAATTCCTAATTCAAgtaattaacc ... cattatgcagGCCAGCCCATCAGACCCAGAGAATTTCCCATTTGTTGTGCTTGGTAACAAG
EST: gi|86469050|gb|DY235420.1|DY235420
EST:     CCAAGTCATTTGAAAAGCTCAACAACTGGCGTGAGGAATTCCTAATTCAA                         GCCAGCCCATCAGACCCAGAGAATTTCCCATTTGTTGTGCTTGGTAACAAG
genomic: CCAAGTCATTTGAAAAGCTCAACAACTGGCGTGAGGAATTCCTAATTCAAgtaattaacc ... cattatgcagGCCAGCCCATCAGACCCAGAGAATTTCCCATTTGTTGTGCTTGGTAACAAG
EST: gi|211495186|gb|FL341359.1|FL341359
EST:     CCAAGTCATTTGAAAAGCTCAACAACTGGCGTGAGGAATTCCTAATTCAA                         GCCAGCCCATCAGACCCAGAGAATTTCCCATTTGTTGTGCTTGGTAACAAG
genomic: CCAAGTCATTTGAAAAGCTCAACAACTGGCGTGAGGAATTCCTAATTCAAgtaattaacc ... cattatgcagGCCAGCCCATCAGACCCAGAGAATTTCCCATTTGTTGTGCTTGGTAACAAG
EST: gi|211477104|gb|FL313896.1|FL313896
EST:     CCAAGTCATTTGAAAAGCTCAACAACTGGCGTGAGGAATTCCTAATTCAA                         GCCAGCCCATCAGACCCAGAGAATTTCCCATTTGTTGTGCTTGGTAACAAG
genomic: CCAAGTCATTTGAAAAGCTCAACAACTGGCGTGAGGAATTCCTAATTCAAgtaattaacc ... cattatgcagGCCAGCCCATCAGACCCAGAGAATTTCCCATTTGTTGTGCTTGGTAACAAG
EST: gi|211165712|gb|FL359024.1|FL359024
EST:     CCAAGTCATTTGAAAAGCTCAACAACTGGCGTGAGGAATTCCTAATTCAA                         GCCAGCCCATCAGACCCAGAGAATTTCCCATTTGTTGTGCTTGGTAACAAG
genomic: CCAAGTCATTTGAAAAGCTCAACAACTGGCGTGAGGAATTCCTAATTCAAgtaattaacc ... cattatgcagGCCAGCCCATCAGACCCAGAGAATTTCCCATTTGTTGTGCTTGGTAACAAG

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: 49 (upstream exon), 49 (downstream exon)
Score: 317

ATTTTATAGGGGAGCTGACTGCTGTGTTCTTGTATATGATGTCAACGTATCCAAGTCATTTGAAAAGCTCAACAACTGGCGTGAGGAATTCCTAATTCAAgtaattaacc ... cattatgcagGCCAGCCCATCAGACCCAGAGAATTTCCCATTTGTTGTGCTTGGTAACAAGATCGATGTTGATGGTGGTAACAGCCGGACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 234

ATTTTATAGGGGAGCTGACTGCTGTGTTCTTGTATATGATGTCAACGTATCCAAGTCATTTGAAAAGCTCAACAACTGGCGTGAGGAATTCCTAATTCAAgtaattaacc ... cattatgcagGCCAGCCCATCAGACCCAGAGAATTTCCCATTTGTTGTGCTTGGTAACAAGATCGATGTTGATGGTGGTAACAGCCGGACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 253

ATTTTATAGGGGAGCTGACTGCTGTGTTCTTGTATATGATGTCAACGTATCCAAGTCATTTGAAAAGCTCAACAACTGGCGTGAGGAATTCCTAATTCAAgtaattaacc ... cattatgcagGCCAGCCCATCAGACCCAGAGAATTTCCCATTTGTTGTGCTTGGTAACAAGATCGATGTTGATGGTGGTAACAGCCGGACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 198

ATTTTATAGGGGAGCTGACTGCTGTGTTCTTGTATATGATGTCAACGTATCCAAGTCATTTGAAAAGCTCAACAACTGGCGTGAGGAATTCCTAATTCAAgtaattaacc ... cattatgcagGCCAGCCCATCAGACCCAGAGAATTTCCCATTTGTTGTGCTTGGTAACAAGATCGATGTTGATGGTGGTAACAGCCGGACT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatatctgtatgtccattgtgtttgaaaaaaaaggactcactgttcattatgcagGCCAGCCCATCAGACCCAGAGAATTTCCCATTTGTTGTGCTTGGTAACAAGATCGATGTTGATGGTGGTAACAGCCGGACT
                                  gactcac  putative branch site (score: 198)
                   tgtttgaaaaaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattaacctgcttattcgcgatctatatctgtatgtccattgtgtttgaaaaaaaaggactcactgttcattatgcagGCCAGCCCATCAGACCCAGAGAATTTCCCATTTGTTGTGCTTGGTAACAAGATCGATGTTGATGGTGGTAACAGCCGGACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG