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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaccgacttgcctcctcattctccattttaattaccaacaactattcatagagactgaagtttattttctggatttgaccaatgtgcatgcagGTTCACAGAGAGCTGAATTTGGATGCTGCTAAGAAGTTCCTGAGCGCATATGAGAGCTGATGATGAACAATAG

Basic information

species Zea mays
transcript GRMZM2G039954_T03
intron # 5
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|211071792|gb|FK959263.1|FK959263
EST:     CAAAGGCAGAGTTCTTCTGCAAGACATTCGAAGAAGTTCATGAGAAACTT                         GTTCACAGAGAGCTGAATTTGGATGCTGCTAAGAAGTTCCTGAGCGCATAT
genomic: CAAAGGCAGAGTTCTTCTGCAAGACATTCGAAGAAGTTCATGAGAAACTTgtaccgactt ... gtgcatgcagGTTCACAGAGAGCTGAATTTGGATGCTGCTAAGAAGTTCCTGAGCGCATAT
EST: gi|211071798|gb|FK959269.1|FK959269
EST:     CAAAGGCAGAGTTCTTCTGCAAGACATTCGAAGAAGTTCATGAGAAACTT                         GTTCACAGAGAGCTGAATTTGGATGCTGCTAAGAAGTTYCTGAGCGCATAT
genomic: CAAAGGCAGAGTTCTTCTGCAAGACATTCGAAGAAGTTCATGAGAAACTTgtaccgactt ... gtgcatgcagGTTCACAGAGAGCTGAATTTGGATGCTGCTAAGAAGTTCCTGAGCGCATAT
EST: gi|211452548|gb|FK959198.1|FK959198
EST:     CAAAGGCAGAGTTCTTCTGCAAGACATTCGAAGAAGTTCATGAGAAACTT                         GTTCACAGAGAGCTGAATTTGGATGTTGCTAAGAAGTTCCTGAGCGCATAT
genomic: CAAAGGCAGAGTTCTTCTGCAAGACATTCGAAGAAGTTCATGAGAAACTTgtaccgactt ... gtgcatgcagGTTCACAGAGAGCTGAATTTGGATGCTGCTAAGAAGTTCCTGAGCGCATAT
EST: gi|211456807|gb|FK959226.1|FK959226
EST:     CAAAGGCAGAGTTCTTCTGCAAGACATTCGAAGAAGTTCATGAGAAACTT                         GTTCACAGAGAGCTGAATTTGGATGCTGCTAAGAAGTTCCTGAGCGCATAT
genomic: CAAAGGCAGAGTTCTTCTGCAAGACATTCGAAGAAGTTCATGAGAAACTTgtaccgactt ... gtgcatgcagGTTCACAGAGAGCTGAATTTGGATGCTGCTAAGAAGTTCCTGAGCGCATAT
EST: gi|211452545|gb|FK959195.1|FK959195
EST:     CAAAGGCAGAGTTCTTCTGCAAGACATTCGAAGAAGTTCATGAGAAACTT                         GTTCACAGAGAGCTGAATTTGGATGCTGCTAAGAAGTTCCTGAGCGCATAT
genomic: CAAAGGCAGAGTTCTTCTGCAAGACATTCGAAGAAGTTCATGAGAAACTTgtaccgactt ... gtgcatgcagGTTCACAGAGAGCTGAATTTGGATGCTGCTAAGAAGTTCCTGAGCGCATAT
EST: gi|211450408|gb|FK959184.1|FK959184
EST:     CAAAGGCAGAGTTCTTCTGCAAGACATTCGAAGAAGTTCATGAGAAACTT                         GTTCACAGAGAGCTGAAATTTGGATGCTGCTAAGAAGTTCCTGAGCGCATA
genomic: CAAAGGCAGAGTTCTTCTGCAAGACATTCGAAGAAGTTCATGAGAAACTTgtaccgactt ... gtgcatgcagGTTCACAGAGAGCTGAA-TTTGGATGCTGCTAAGAAGTTCCTGAGCGCATA
EST: gi|211454673|gb|FK959208.1|FK959208
EST:     CAAAGGCAGAGTTCTTCTGCAAGACATTCGAAGAAGTTCATGAGAAACTT                         GTTCACAGAGAGCTGAATTTGGATGCTGCTAAGAAGTTCCTGAGCGCATAC
genomic: CAAAGGCAGAGTTCTTCTGCAAGACATTCGAAGAAGTTCATGAGAAACTTgtaccgactt ... gtgcatgcagGTTCACAGAGAGCTGAATTTGGATGCTGCTAAGAAGTTCCTGAGCGCATAT
EST: gi|211454670|gb|FK959205.1|FK959205
EST:     CAAAGGCAGAGTTCTTCTGCAAGACATTCGAAGAAGTTCATGAGAAACTT                         GTTCACAGAGAGCTGAATTTGGATGCTGCTAAGAAGTTCCTGAGCGCATAT
genomic: CAAAGGCAGAGTTCTTCTGCAAGACATTCGAAGAAGTTCATGAGAAACTTgtaccgactt ... gtgcatgcagGTTCACAGAGAGCTGAATTTGGATGCTGCTAAGAAGTTCCTGAGCGCATAT
EST: gi|211071794|gb|FK959265.1|FK959265
EST:     CAAAGGCAGAGTTCTTCTGCAAGACATTCGAAGAAGTTCATGAGAAACTT                         GTTCACAGAGAGCTGAATTTGGATGCTGCTAAGAAGTTCCTGAGCGCATAT
genomic: CAAAGGCAGAGTTCTTCTGCAAGACATTCGAAGAAGTTCATGAGAAACTTgtaccgactt ... gtgcatgcagGTTCACAGAGAGCTGAATTTGGATGCTGCTAAGAAGTTCCTGAGCGCATAT
EST: gi|211066314|gb|FK959237.1|FK959237
EST:     CAAAGGCAGAGTTCTTCTGCAAGACATTCGAAGAAGTTCATGAGAAACTT                         GTTCACAGAGAGCTGAATTTGGATGCTGCTMAGAAGTTCCTGAGCGCATAT
genomic: CAAAGGCAGAGTTCTTCTGCAAGACATTCGAAGAAGTTCATGAGAAACTTgtaccgactt ... gtgcatgcagGTTCACAGAGAGCTGAATTTGGATGCTGCTAAGAAGTTCCTGAGCGCATAT
EST: gi|211302619|gb|FL366312.1|FL366312
EST:     CAAAGGCAGAGTTCTTCTGCAAGACATTCGAAGAAGTTCATGAGAAACTT                         GTTCACAGAGAGCTGAATTTGGATGCTGCTAAGAAGYTCCTGAGCGCATAT
genomic: CAAAGGCAGAGTTCTTCTGCAAGACATTCGAAGAAGTTCATGAGAAACTTgtaccgactt ... gtgcatgcagGTTCACAGAGAGCTGAATTTGGATGCTGCTAAGAAGTTCCTGAGCGCATAT
EST: gi|211074537|gb|FK959287.1|FK959287
EST:     CAAAGGCAGAGTTCTTCTGCAAGACATTCGAAGAAGTTCATGAGAAACTT                         GTTCACAGAGAGCTGAATTTGGATGCTGCTAAGAAGTTCCTGAGCGCATAT
genomic: CAAAGGCAGAGTTCTTCTGCAAGACATTCGAAGAAGTTCATGAGAAACTTgtaccgactt ... gtgcatgcagGTTCACAGAGAGCTGAATTTGGATGCTGCTAAGAAGTTCCTGAGCGCATAT
EST: gi|116824448|gb|EC868068.1|EC868068
EST:     CAAAGGCAGAGTTCTTCTGCAAGACATTCGAAGAAGTTCATGAGAAACTT                         GTTCACAGAGAGCTGAATTTGGATGCTGCTAAGAAGTTCCTGAGCGCATAT
genomic: CAAAGGCAGAGTTCTTCTGCAAGACATTCGAAGAAGTTCATGAGAAACTTgtaccgactt ... gtgcatgcagGTTCACAGAGAGCTGAATTTGGATGCTGCTAAGAAGTTCCTGAGCGCATAT
EST: gi|211066323|gb|FK959246.1|FK959246
EST:     AAAGGCAGAAGTTCTTCTGCAAGACATTCGAAGAAGTTCATGAGAAACTT                         GTTCACAGAGAGCTGAATTTGGATGCTGCTAAGAAGTTCCTGAGCGCATAT
genomic: AAAGGCAGA-GTTCTTCTGCAAGACATTCGAAGAAGTTCATGAGAAACTTgtaccgactt ... gtgcatgcagGTTCACAGAGAGCTGAATTTGGATGCTGCTAAGAAGTTCCTGAGCGCATAT
EST: gi|211069063|gb|FK959256.1|FK959256
EST:     CAAAGGCAGAGTTCTTCTGCAAGACATTCGAAGAAGTTCATGAGAAACTT                         GTTCACAGAGAGCTGAATTTGGATGCTGCTAAGAAGTTCCTGAGCGCATAT
genomic: CAAAGGCAGAGTTCTTCTGCAAGACATTCGAAGAAGTTCATGAGAAACTTgtaccgactt ... gtgcatgcagGTTCACAGAGAGCTGAATTTGGATGCTGCTAAGAAGTTCCTGAGCGCATAT
EST: gi|211074529|gb|FK959279.1|FK959279
EST:     CAAAGGCAGAGTTCTTCTGCAAGACATTCGAAGAAGTTCATGAGAAACTT                         GTTCACAGAGAGCTGAATTTGGATGCTGCTAAGAAGTTCCTGAGCGCATAT
genomic: CAAAGGCAGAGTTCTTCTGCAAGACATTCGAAGAAGTTCATGAGAAACTTgtaccgactt ... gtgcatgcagGTTCACAGAGAGCTGAATTTGGATGCTGCTAAGAAGTTCCTGAGCGCATAT
EST: gi|211450409|gb|FK959185.1|FK959185
EST:     CAAAGGCAGAGTTCTTCTGCAAGACATTCGAAGAAGTTCATGAGAAACTT                         GTTCACAGAGAGCTGAATTTGGATGCTGCTAAGAAGTTCCTGAGCGCATAT
genomic: CAAAGGCAGAGTTCTTCTGCAAGACATTCGAAGAAGTTCATGAGAAACTTgtaccgactt ... gtgcatgcagGTTCACAGAGAGCTGAATTTGGATGCTGCTAAGAAGTTCCTGAGCGCATAT
EST: gi|211071802|gb|FK959273.1|FK959273
EST:     CAAAGGCAGAGTTCTTCTGCAAGACATTCGAAGAAGTTCATGAGAAACTT                         GTTCACAGAGAGCTGAATTTGGATGCTGCTAAGAAGTTCCTGAGCGCATAT
genomic: CAAAGGCAGAGTTCTTCTGCAAGACATTCGAAGAAGTTCATGAGAAACTTgtaccgactt ... gtgcatgcagGTTCACAGAGAGCTGAATTTGGATGCTGCTAAGAAGTTCCTGAGCGCATAT
EST: gi|211066317|gb|FK959240.1|FK959240
EST:     AAAGGCAGAGTTCTTCTGCAAGACATTCGGAAGAAGTTCATGAGAAACTT                         GTTCACAGGAGAGCTGAATTTGGATGCTGCT
genomic: AAAGGCAGAGTTCTTCTGCAAGACATTCG-AAGAAGTTCATGAGAAACTTgtaccgactt ... gtgcatgcagGTTCACAG-AGAGCTGAATTTGGATGCTGCT
EST: gi|211450407|gb|FK959183.1|FK959183
EST:     AAAGGCAGAGTTCTTCTGCAAGACATTCNGAAGAAGTTCATGAGAAACTT                         GTTCACAGAGAGCTGAATTTTGATGCTGCTAAGAAGTTCCTGAGCGCATAT
genomic: AAAGGCAGAGTTCTTCTGCAAGACATTC-GAAGAAGTTCATGAGAAACTTgtaccgactt ... gtgcatgcagGTTCACAGAGAGCTGAATTTGGATGCTGCTAAGAAGTTCCTGAGCGCATAT
EST: gi|211071805|gb|FK959276.1|FK959276
EST:     AAAGGCAGAGTTCTTCTGCAAGACATTCCGAAGAAGTTCATGAGAAACTT                         GTTCACAGAGAGCTGAATTTGGATGCTGCTAAGAAGTTCCTGAGCGCATAT
genomic: AAAGGCAGAGTTCTTCTGCAAGACATTC-GAAGAAGTTCATGAGAAACTTgtaccgactt ... gtgcatgcagGTTCACAGAGAGCTGAATTTGGATGCTGCTAAGAAGTTCCTGAGCGCATAT
EST: gi|211452538|gb|FK959188.1|FK959188
EST:     CAAAGGCAGAGTTCTTCTGCAAGACATTCGAAGAAGTTCATGAGAAACTT                         GTTCACAGAGAGCTGAATTTGGATGCTGCTAAGAAGTTCCTGARGCGCATA
genomic: CAAAGGCAGAGTTCTTCTGCAAGACATTCGAAGAAGTTCATGAGAAACTTgtaccgactt ... gtgcatgcagGTTCACAGAGAGCTGAATTTGGATGCTGCTAAGAAGTTCCTGA-GCGCATA
EST: gi|211069062|gb|FK959255.1|FK959255
EST:     CAAAGGCAGAGTTCTTCTGCAAGACATTCGAAGAAGTTCATGAGAAACTT                         GTTCACAGAGAGCTGAATTTGGATGCTGCTAA
genomic: CAAAGGCAGAGTTCTTCTGCAAGACATTCGAAGAAGTTCATGAGAAACTTgtaccgactt ... gtgcatgcagGTTCACAGAGAGCTGAATTTGGATGCTGCTAA
EST: gi|211452540|gb|FK959190.1|FK959190
EST:     CAAAGGCAGAGTTCTTCTGCAAGACATTCGAAGAAGTTCATGAGAAACTT                         GTTCACAGAGAGCTGAATTTGGATGCTGCTAAGAAGTTCCTGAGCGCATAT
genomic: CAAAGGCAGAGTTCTTCTGCAAGACATTCGAAGAAGTTCATGAGAAACTTgtaccgactt ... gtgcatgcagGTTCACAGAGAGCTGAATTTGGATGCTGCTAAGAAGTTCCTGAGCGCATAT
EST: gi|211069056|gb|FK959249.1|FK959249
EST:     CAAAGGCAGAGTTCTTCTGCAAGACATTCGAAGAAGTTCATGAGAAACTT                         GTTCACAGAGAGCTGAATTTGGATGCTGCTAAGAAGTTCCTGAGCGCATAC
genomic: CAAAGGCAGAGTTCTTCTGCAAGACATTCGAAGAAGTTCATGAGAAACTTgtaccgactt ... gtgcatgcagGTTCACAGAGAGCTGAATTTGGATGCTGCTAAGAAGTTCCTGAGCGCATAT
EST: gi|211452543|gb|FK959193.1|FK959193
EST:     CAAAGGCAGAGTTCTTCTGCAAGACATTCGAAGAAGTTCATGAGAAACTT                         GTTTCACAGAGAGCTGAATTTGGATGCTGCTAAGAAGTTCCTGAGCGCATA
genomic: CAAAGGCAGAGTTCTTCTGCAAGACATTCGAAGAAGTTCATGAGAAACTTgtaccgactt ... gtgcatgcagGTT-CACAGAGAGCTGAATTTGGATGCTGCTAAGAAGTTCCTGAGCGCATA
EST: gi|211066319|gb|FK959242.1|FK959242
EST:     CAAAGGCAGAGTTCTTCTGCAAGACATTCGAAGAAGTTCATGAGAAACTT                         GTTCACAGAGAGCTGAATTTGGATGCTGCTAAGAAGTTCCTGAGCGCATAT
genomic: CAAAGGCAGAGTTCTTCTGCAAGACATTCGAAGAAGTTCATGAGAAACTTgtaccgactt ... gtgcatgcagGTTCACAGAGAGCTGAATTTGGATGCTGCTAAGAAGTTCCTGAGCGCATAT
EST: gi|211452550|gb|FK959200.1|FK959200
EST:     CAAAGGCAGAGTTCTTCTGCAAGACATTCGAAGAAGTTCATGAGAAACTT                         GTTCACAGAGAGCTGAATTTGGATGCTGCTAAGAAGTTCCTGAGCGC
genomic: CAAAGGCAGAGTTCTTCTGCAAGACATTCGAAGAAGTTCATGAGAAACTTgtaccgactt ... gtgcatgcagGTTCACAGAGAGCTGAATTTGGATGCTGCTAAGAAGTTCCTGAGCGC
EST: gi|211066311|gb|FK959234.1|FK959234
EST:     AAAGGCAGARTTCTTCTGCAAGACATTCCGAAGAAGTTCATGAGAAACYT                         GTTCACAGAGAGCTGAATTTGGATGC
genomic: AAAGGCAGAGTTCTTCTGCAAGACATTC-GAAGAAGTTCATGAGAAACTTgtaccgactt ... gtgcatgcagGTTCACAGAGAGCTGAATTTGGATGC
EST: gi|211454677|gb|FK959212.1|FK959212
EST:     CAAAGACAGAGTTCTTCTGCAAGACATTCGAAGAAGTTCATGAGAAACTT                         GTTCACAGAGAGCTGAATTTGGATGCTGCTAAGAAGT-CCTGAGCGCATAT
genomic: CAAAGGCAGAGTTCTTCTGCAAGACATTCGAAGAAGTTCATGAGAAACTTgtaccgactt ... gtgcatgcagGTTCACAGAGAGCTGAATTTGGATGCTGCTAAGAAGTTCCTGAGCGCATAT
EST: gi|211452546|gb|FK959196.1|FK959196
EST:     CAAAGGCAGAGTTCTTCTGCAAGACATTCGAAGAAGTTCATGAGAAACTT                         GTTCACAGAGAGCTGAATTTGGATGCTGCTAAGAAGTTCCTGAGCGCATAT
genomic: CAAAGGCAGAGTTCTTCTGCAAGACATTCGAAGAAGTTCATGAGAAACTTgtaccgactt ... gtgcatgcagGTTCACAGAGAGCTGAATTTGGATGCTGCTAAGAAGTTCCTGAGCGCATAT
EST: gi|116813303|gb|EC855734.1|EC855734
EST:     CAAAGGCAGAGTTCTTCTGCAAGACATTCGAAGAAGTTCATGAGAAACTT                         GTTCACAGAGAGCTGAATTTGGATGCTGCTAGGAAGTTCCTGAGCGCATAT
genomic: CAAAGGCAGAGTTCTTCTGCAAGACATTCGAAGAAGTTCATGAGAAACTTgtaccgactt ... gtgcatgcagGTTCACAGAGAGCTGAATTTGGATGCTGCTAAGAAGTTCCTGAGCGCATAT
EST: gi|211009739|gb|FL437062.1|FL437062
EST:     CAAAGGCAGAGTTCTTCTGCAAGACATTCGAAGAAGTTCATGAGAAACTT                         GTTCACAGAGAGCTGAATTTGGATGCTGCTAAGAAGTTCCTGAGCGCATAT
genomic: CAAAGGCAGAGTTCTTCTGCAAGACATTCGAAGAAGTTCATGAGAAACTTgtaccgactt ... gtgcatgcagGTTCACAGAGAGCTGAATTTGGATGCTGCTAAGAAGTTCCTGAGCGCATAT
EST: gi|211450404|gb|FK959180.1|FK959180
EST:     AAAGGCAGAGTTCTTCTGCAAGACATTCNGAAGAAGTTCATGAGAAACTT                         GTTCACAGAGAGCTGAATTTGGATGCTGCTAAGAAGTTCCTGAGCGCATAT
genomic: AAAGGCAGAGTTCTTCTGCAAGACATTC-GAAGAAGTTCATGAGAAACTTgtaccgactt ... gtgcatgcagGTTCACAGAGAGCTGAATTTGGATGCTGCTAAGAAGTTCCTGAGCGCATAT
EST: gi|211074535|gb|FK959285.1|FK959285
EST:     CAAAGGGMGAGTTCTTCTGCMAGACATTCGAAGAAGTTCATGAGAAACTT                         GTTCACAGAGAGCCTGAATTTGGATGCTGC
genomic: CAAAGGCAGAGTTCTTCTGCAAGACATTCGAAGAAGTTCATGAGAAACTTgtaccgactt ... gtgcatgcagGTTCACAGAGAGC-TGAATTTGGATGCTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caactattcatagagactgaagtttattttctggatttgaccaatgtgcatgcagGTTCACAGAGAGCTGAATTTGGATGCTGCTAAGAAGTTCCTGAGCGCATATGAGAGCTGATGATGAACAATAG
                                  atttgac  putative branch site (score: 4)
                   aagtttatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaccgacttgcctcctcattctccattttaattaccaacaactattcatagagactgaagtttattttctggatttgaccaatgtgcatgcagGTTCACAGAGAGCTGAATTTGGATGCTGCTAAGAAGTTCCTGAGCGCATATGAGAGCTGATGATGAACAATAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT