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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgaacaagttctaaattctgtattaccagtggtatggatttgtaagtcctacatttatttagtagtgaatgtgtaatcttttggcaaacccacaaagtctactacacttcagttttatttgtttctcctttcatgtcatgtataaccatgctttatcgtttgcttgggattgcagAAGTTTTCGCCAGATGGACGGTTCATTGCTACTGCTGATAGGGACTTCAAAATACGAGT

Basic information

species Zea mays
transcript GRMZM2G131998_T04
intron # 3
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|78091377|gb|DV519751.1|DV519751
EST:     ACAAACCTGTGTCAATTCTTGGTCACTATTGCAGTATCATCACTAGCATG                         AAGTTTTCGCCAGATGGACGGTTCATTGCTACTGCTGATAGGGACTTCAAA
genomic: ACAAACCTGTGTCAATTCTTGGTCACTATTGCAGTATCATCACTAGCATGgtatgaacaa ... gggattgcagAAGTTTTCGCCAGATGGACGGTTCATTGCTACTGCTGATAGGGACTTCAAA
EST: gi|87156923|gb|DY401712.1|DY401712
EST:     ACAAACCTGTGTCAATTCTTGGTCACTATTGCAGTATCATCACTAGCATG                         AAGTTTTCGCCAGATGGACGGTTCATTGCTACTGCTGATAGGGACTTCAAA
genomic: ACAAACCTGTGTCAATTCTTGGTCACTATTGCAGTATCATCACTAGCATGgtatgaacaa ... gggattgcagAAGTTTTCGCCAGATGGACGGTTCATTGCTACTGCTGATAGGGACTTCAAA
EST: gi|89761079|gb|DY689237.1|DY689237
EST:     ACAAACCTGTGTCAATTCTTGGTCACTATTGCAGTATCATCACTAGCATG                         AAGTTTTCGCCAGATGGACGGTTCATTGCTACTGCTGATAGGGACTTCAAA
genomic: ACAAACCTGTGTCAATTCTTGGTCACTATTGCAGTATCATCACTAGCATGgtatgaacaa ... gggattgcagAAGTTTTCGCCAGATGGACGGTTCATTGCTACTGCTGATAGGGACTTCAAA
EST: gi|89249366|gb|DY621152.1|DY621152
EST:     ACAAACCTGTGTCAATTCTTGGTCACTATTGCAGTATCATCACTAGCATG                         AAGTTTTTCGCCAGATGGACGGTTCATTGCTACTGCTGATAGGGACTTCAA
genomic: ACAAACCTGTGTCAATTCTTGGTCACTATTGCAGTATCATCACTAGCATGgtatgaacaa ... gggattgcagAAGTTTT-CGCCAGATGGACGGTTCATTGCTACTGCTGATAGGGACTTCAA
EST: gi|211051635|gb|FL294354.1|FL294354
EST:     ACAAACCTGTGTCAATTCTTGGTCACTATTGCAGTATCATCACTAGCATG                         AAGTTTTCGCCAGATGGACGGTTCATTGCTACTGCTG
genomic: ACAAACCTGTGTCAATTCTTGGTCACTATTGCAGTATCATCACTAGCATGgtatgaacaa ... gggattgcagAAGTTTTCGCCAGATGGACGGTTCATTGCTACTGCTG
EST: gi|148936297|gb|EC880380.2|EC880380
EST:     ACAAACCTGTGTCAATTCTTGGTCACTATTGCAGTATCATCACTAGCATG                         AAGTTTTCGCCAGATGGACGGTTCATTGCTACTGCTGATAGGGACTTCAAA
genomic: ACAAACCTGTGTCAATTCTTGGTCACTATTGCAGTATCATCACTAGCATGgtatgaacaa ... gggattgcagAAGTTTTCGCCAGATGGACGGTTCATTGCTACTGCTGATAGGGACTTCAAA
EST: gi|211051632|gb|FL294351.1|FL294351
EST:     ACAAACCTGTGTCAATTCTTGGTCACTATTGCAGTATCATCACTAGCATG                         AAGTTTTCGCCAGATGGACGGTTCATTGCTACTGCTGATAGGGACTTCAAA
genomic: ACAAACCTGTGTCAATTCTTGGTCACTATTGCAGTATCATCACTAGCATGgtatgaacaa ... gggattgcagAAGTTTTCGCCAGATGGACGGTTCATTGCTACTGCTGATAGGGACTTCAAA
EST: gi|71437750|gb|DR818800.1|DR818800
EST:     ACAAACCTGTGTCAATTCTTGGTCACTATTGCAGTATCATCACTAGCATG                         AAGTTTTCGCCAGATGGACGGTTCATTGCTACTGCTGATAGGGACTTCAAA
genomic: ACAAACCTGTGTCAATTCTTGGTCACTATTGCAGTATCATCACTAGCATGgtatgaacaa ... gggattgcagAAGTTTTCGCCAGATGGACGGTTCATTGCTACTGCTGATAGGGACTTCAAA
EST: gi|148959295|gb|EE010708.2|EE010708
EST:     ACAAACCTGTGTCAATTCTTGGTCACTATTGCAGTATCATCACTAGCATG                         AAGTTTTCGCCAGATGGACGGTTCATTGCTACTGCTGATAGGGACTTTCAA
genomic: ACAAACCTGTGTCAATTCTTGGTCACTATTGCAGTATCATCACTAGCATGgtatgaacaa ... gggattgcagAAGTTTTCGCCAGATGGACGGTTCATTGCTACTGCTGATAGGGACTT-CAA
EST: gi|22546288|gb|BU098599.1|BU098599
EST:     ACAAACCTGTGTCAATTCTTGGTCACTATTGCAGTATCATCACTAGCATG                         AAGTTTTCGCCAGATGGACGGGTCATTGCTACTGCTGATAGGGACT
genomic: ACAAACCTGTGTCAATTCTTGGTCACTATTGCAGTATCATCACTAGCATGgtatgaacaa ... gggattgcagAAGTTTTCGCCAGATGGACGGTTCATTGCTACTGCTGATAGGGACT
EST: gi|4753448|gb|AI657358.1|AI657358
EST:     ACAAACCTGTGTCAATTCTTGGTCACTATTGCAGTATCATCACTAGCATG                         AAGTTTTCGCCAGATGGACGGTTCATTGCTACTGCTGATAGGGACTTC
genomic: ACAAACCTGTGTCAATTCTTGGTCACTATTGCAGTATCATCACTAGCATGgtatgaacaa ... gggattgcagAAGTTTTCGCCAGATGGACGGTTCATTGCTACTGCTGATAGGGACTTC
EST: gi|148945698|gb|EC890971.2|EC890971
EST:     ACAAACCTGTGTCAATTCTTGGTCACTATTGCAGTATCATCACTAGCATG                         AAGTTTTCGCCAGATGGACGGTTCATTGCTACTGCTGATAGGGACTTCAAA
genomic: ACAAACCTGTGTCAATTCTTGGTCACTATTGCAGTATCATCACTAGCATGgtatgaacaa ... gggattgcagAAGTTTTCGCCAGATGGACGGTTCATTGCTACTGCTGATAGGGACTTCAAA
EST: gi|148973467|gb|EE024565.2|EE024565
EST:     ACAAACCTGTGTCAATTCTTGGTCACTATTGCAGTATCATCACTAGCATG                         AAGTTTTCGCCAGATGGACGGTTCATTGCTACTGCTGATAGGGACTTCAAA
genomic: ACAAACCTGTGTCAATTCTTGGTCACTATTGCAGTATCATCACTAGCATGgtatgaacaa ... gggattgcagAAGTTTTCGCCAGATGGACGGTTCATTGCTACTGCTGATAGGGACTTCAAA
EST: gi|149081963|gb|EE171128.2|EE171128
EST:     CAAACCTGTGTCAATTCTTGGTCACTATTGCAGTATCATCACCTAGCATG                         AAGTTTTCGCCGGATGGACGGTTCATTGCTACTGCTGATAGGGACTTCAA
genomic: CAAACCTGTGTCAATTCTTGGTCACTATTGCAGTATCATCAC-TAGCATGgtatgaacaa ... gggattgcagAAGTTTTCGCCAGATGGACGGTTCATTGCTACTGCTGATAGGGACTTCAA
EST: gi|78106892|gb|DV525310.1|DV525310
EST:     ACAAACCTGTGTCAATTCTTGGTCACTATTGCAGTATCATCACTAGCATG                         AAGTTTTCGCCAGATGGACGGTTCATTGCTACTGCTGATAGGGACTTCAAA
genomic: ACAAACCTGTGTCAATTCTTGGTCACTATTGCAGTATCATCACTAGCATGgtatgaacaa ... gggattgcagAAGTTTTCGCCAGATGGACGGTTCATTGCTACTGCTGATAGGGACTTCAAA
EST: gi|78081795|gb|DV510207.1|DV510207
EST:     ACAAACCTGTGTCAATTCTTGGTCACTATTGCAGTATCATCACTAGCATG                         AAGTTTTCGCCAGATGGACGGTTCATTGCTACTGCTGATAGGGACTTCAAA
genomic: ACAAACCTGTGTCAATTCTTGGTCACTATTGCAGTATCATCACTAGCATGgtatgaacaa ... gggattgcagAAGTTTTCGCCAGATGGACGGTTCATTGCTACTGCTGATAGGGACTTCAAA
EST: gi|20811129|gb|BQ295607.1|BQ295607
EST:     ACAAACCTGTGTCAATTCTTGGTCACTATTGCAGTATCATCACTAGCATG                         AAGTTTTCGCCAGATGGACGGNTCATTGCTACTGCTGATAGGGACTTCAAA
genomic: ACAAACCTGTGTCAATTCTTGGTCACTATTGCAGTATCATCACTAGCATGgtatgaacaa ... gggattgcagAAGTTTTCGCCAGATGGACGGTTCATTGCTACTGCTGATAGGGACTTCAAA
EST: gi|149111910|gb|EE191066.2|EE191066
EST:     ACAAACCTGTGTCAATTCTTGGTCACTATTGCAGTATCATCACTAGCATG                         AAGTTTTCGCCAGATGGACGGTTCATTGCTACTGCTGATAGGGACTTCAAA
genomic: ACAAACCTGTGTCAATTCTTGGTCACTATTGCAGTATCATCACTAGCATGgtatgaacaa ... gggattgcagAAGTTTTCGCCAGATGGACGGTTCATTGCTACTGCTGATAGGGACTTCAAA
EST: gi|89759711|gb|DY688443.1|DY688443
EST:     ACAAACCTGTGTCAATTCTTGGTCACTATTGCAGTATCATCACTAGCATG                         AAGTTTTCGCCAGATGGACGGTTCATTGCTACTGCTGATAGGGACTTCAAA
genomic: ACAAACCTGTGTCAATTCTTGGTCACTATTGCAGTATCATCACTAGCATGgtatgaacaa ... gggattgcagAAGTTTTCGCCAGATGGACGGTTCATTGCTACTGCTGATAGGGACTTCAAA
EST: gi|148964964|gb|EE015811.2|EE015811
EST:     ACAAACCTGTGTCAATTCTTGGTCACTATTGCAGTATCATCACTAGCATG                         AAGTTTTCGCCAGATGGACGGTTCATTGCTACTGCTGATAGGGACTTCAAA
genomic: ACAAACCTGTGTCAATTCTTGGTCACTATTGCAGTATCATCACTAGCATGgtatgaacaa ... gggattgcagAAGTTTTCGCCAGATGGACGGTTCATTGCTACTGCTGATAGGGACTTCAAA
EST: gi|76017216|gb|DT944386.1|DT944386
EST:     ACAAACCTGTGTCAATTCTTGGTCACTATTGCAGTATCATCACTAGCATG                         AAGTTTTCGCCAGATGGACGGTTCATTGCTACTGCTGATAGGGACTTCAAA
genomic: ACAAACCTGTGTCAATTCTTGGTCACTATTGCAGTATCATCACTAGCATGgtatgaacaa ... gggattgcagAAGTTTTCGCCAGATGGACGGTTCATTGCTACTGCTGATAGGGACTTCAAA
EST: gi|50331437|gb|CO526563.1|CO526563
EST:     ACAAACCTGTGTCAATTCTTGGTCACTATTGCAGTATCATCACTAGCATG                         AAGTTTTCGCCAGATGGACGGTTCATTGCTACTGCTGATAGGGACTTCAAA
genomic: ACAAACCTGTGTCAATTCTTGGTCACTATTGCAGTATCATCACTAGCATGgtatgaacaa ... gggattgcagAAGTTTTCGCCAGATGGACGGTTCATTGCTACTGCTGATAGGGACTTCAAA
EST: gi|71771570|gb|DR969507.1|DR969507
EST:     ACAAACCTGTGTCAATTCTTGGTCACTATTGCAGTATCATCACTAGCATG                         AAGTTTTCGCCAGATGGACGGTTCATTGCTACTGCTGATAGGGACTTCAAA
genomic: ACAAACCTGTGTCAATTCTTGGTCACTATTGCAGTATCATCACTAGCATGgtatgaacaa ... gggattgcagAAGTTTTCGCCAGATGGACGGTTCATTGCTACTGCTGATAGGGACTTCAAA

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), 48 (downstream exon)
Score: 71

TTGGTTAGTCACTTTGCGGGAAGATAGTGCAGAGCAGGTTTCAGTTGATAACAAACCTGTGTCAATTCTTGGTCACTATTGCAGTATCATCACTAGCATGgtatgaacaa ... gggattgcagAAGTTTTCGCCAGATGGACGGTTCATTGCTACTGCTGATAGGGACTTCAAAATACGAGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 61

TTGGTTAGTCACTTTGCGGGAAGATAGTGCAGAGCAGGTTTCAGTTGATAACAAACCTGTGTCAATTCTTGGTCACTATTGCAGTATCATCACTAGCATGgtatgaacaa ... gggattgcagAAGTTTTCGCCAGATGGACGGTTCATTGCTACTGCTGATAGGGACTTCAAAATACGAGT


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 68

TTGGTTAGTCACTTTGCGGGAAGATAGTGCAGAGCAGGTTTCAGTTGATAACAAACCTGTGTCAATTCTTGGTCACTATTGCAGTATCATCACTAGCATGgtatgaacaa ... gggattgcagAAGTTTTCGCCAGATGGACGGTTCATTGCTACTGCTGATAGGGACTTCAAAATACGAGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 65

TTGGTTAGTCACTTTGCGGGAAGATAGTGCAGAGCAGGTTTCAGTTGATAACAAACCTGTGTCAATTCTTGGTCACTATTGCAGTATCATCACTAGCATGgtatgaacaa ... gggattgcagAAGTTTTCGCCAGATGGACGGTTCATTGCTACTGCTGATAGGGACTTCAAAATACGAGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttctcctttcatgtcatgtataaccatgctttatcgtttgcttgggattgcagAAGTTTTCGCCAGATGGACGGTTCATTGCTACTGCTGATAGGGACTTCAAAATACGAGT
                   gtataac  putative branch site (score: 65)
                 atgtataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgaacaagttctaaattctgtattaccagtggtatggatttgtaagtcctacatttatttagtagtgaatgtgtaatcttttggcaaacccacaaagtctactacacttcagttttatttgtttctcctttcatgtcatgtataaccatgctttatcgtttgcttgggattgcagAAGTTTTCGCCAGATGGACGGTTCATTGCTACTGCTGATAGGGACTTCAAAATACGAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT