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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgctctgtggttctccgtcgtcgattgccattttaacacctagtagttgttgttgacgatatgcttctctgtgcttccggttctgcatgatccaggcagCAGCCAGGAACAACAAGCTAGGCCCCCTCACGCAGACCGCACGACCGAGCGCGCGGCATTGACCGACCCATCGCCGCCGCCGCCGCCTCGATCGACCATG

Basic information

species Zea mays
transcript GRMZM2G060742_T01
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|148934122|gb|EC878137.2|EC878137
EST:     GCAGCTGCTAGCTCATCTGCTTGATCTCTAGCTGAGACTCCGAGCAAAAT                         T
genomic: GCAGCTGCTAGCTCATCTGCTTGATCTCTAGCTGAGACTCCGAGCAAAATgtaagttttc ... atccaggcag-
EST: gi|148934122|gb|EC878137.2|EC878137
EST:     GCAGCTGCTAGCTCATCTGCTTGATCTCTAGCTGAGACTCCGAGCAAAAT                         T
genomic: GCAGCTGCTAGCTCATCTGCTTGATCTCTAGCTGAGACTCCGAGCAAAATgtaagttttc ... atccaggcag-
EST: gi|148934122|gb|EC878137.2|EC878137
EST:     GCAGCTGCTAGCTCATCTGCTTGATCTCTAGCTGAGACTCCGAGCAAAAT                         T
genomic: GCAGCTGCTAGCTCATCTGCTTGATCTCTAGCTGAGACTCCGAGCAAAATgtaagttttc ... atccaggcag-
EST: gi|211317617|gb|FL072363.1|FL072363
EST:     GCAGCTGCTAGCTCATCTGCTTGATCTCTAGCTGAGACTCCGAGCAAAAT                         CAGCCAGGAACAACAAGCTAGGCCCCCTCACGCAGACCGCACGACCGAGCG
genomic: GCAGCTGCTAGCTCATCTGCTTGATCTCTAGCTGAGACTCCGAGCAAAATgtaagttttc ... atccaggcagCAGCCAGGAACAACAAGCTAGGCCCCCTCACGCAGACCGCACGACCGAGCG
EST: gi|211319641|gb|FL072373.1|FL072373
EST:     GCAGCTGCTAGCTCATCTGCTTGATCTCTAGCTGAGACTCCGAGCAAAAT                         G
genomic: GCAGCTGCTAGCTCATCTGCTTGATCTCTAGCTGAGACTCCGAGCAAAATgtaagttttc ... atccaggcag-
EST: gi|211319641|gb|FL072373.1|FL072373
EST:     GCAGCTGCTAGCTCATCTGCTTGATCTCTAGCTGAGACTCCGAGCAAAAT                         G
genomic: GCAGCTGCTAGCTCATCTGCTTGATCTCTAGCTGAGACTCCGAGCAAAATgtaagttttc ... atccaggcag-
EST: gi|211319641|gb|FL072373.1|FL072373
EST:     GCAGCTGCTAGCTCATCTGCTTGATCTCTAGCTGAGACTCCGAGCAAAAT                         G
genomic: GCAGCTGCTAGCTCATCTGCTTGATCTCTAGCTGAGACTCCGAGCAAAATgtaagttttc ... atccaggcag-
EST: gi|211319641|gb|FL072373.1|FL072373
EST:     GCAGCTGCTAGCTCATCTGCTTGATCTCTAGCTGAGACTCCGAGCAAAAT                         G
genomic: GCAGCTGCTAGCTCATCTGCTTGATCTCTAGCTGAGACTCCGAGCAAAATgtaagttttc ... atccaggcag-
EST: gi|211319641|gb|FL072373.1|FL072373
EST:     GCAGCTGCTAGCTCATCTGCTTGATCTCTAGCTGAGACTCCGAGCAAAAT                         G
genomic: GCAGCTGCTAGCTCATCTGCTTGATCTCTAGCTGAGACTCCGAGCAAAATgtaagttttc ... atccaggcag-
EST: gi|149111495|gb|EE294998.2|EE294998
EST:     GCAGCTGCTAGCTCATCTGCTTGATCTCTAGCTGAGACTCCGAGCAAAAT                         G
genomic: GCAGCTGCTAGCTCATCTGCTTGATCTCTAGCTGAGACTCCGAGCAAAATgtaagttttc ... atccaggcag-
EST: gi|149111495|gb|EE294998.2|EE294998
EST:     GCAGCTGCTAGCTCATCTGCTTGATCTCTAGCTGAGACTCCGAGCAAAAT                         G
genomic: GCAGCTGCTAGCTCATCTGCTTGATCTCTAGCTGAGACTCCGAGCAAAATgtaagttttc ... atccaggcag-
EST: gi|211317619|gb|FL072365.1|FL072365
EST:     GCAGCTGCTAGCTCATCTGCTTGATCTCTAGCTGAGACTCCGAGCAAAAT                         G
genomic: GCAGCTGCTAGCTCATCTGCTTGATCTCTAGCTGAGACTCCGAGCAAAATgtaagttttc ... atccaggcag-
EST: gi|211317619|gb|FL072365.1|FL072365
EST:     GCAGCTGCTAGCTCATCTGCTTGATCTCTAGCTGAGACTCCGAGCAAAAT                         G
genomic: GCAGCTGCTAGCTCATCTGCTTGATCTCTAGCTGAGACTCCGAGCAAAATgtaagttttc ... atccaggcag-
EST: gi|148965701|gb|EE016564.2|EE016564
EST:     GCAGCTGCTAGCTCATCTGCTTGATCTCTAGCTGAGACTCCGAGCAAAAT                         G
genomic: GCAGCTGCTAGCTCATCTGCTTGATCTCTAGCTGAGACTCCGAGCAAAATgtaagttttc ... atccaggcag-
EST: gi|148965701|gb|EE016564.2|EE016564
EST:     GCAGCTGCTAGCTCATCTGCTTGATCTCTAGCTGAGACTCCGAGCAAAAT                         G
genomic: GCAGCTGCTAGCTCATCTGCTTGATCTCTAGCTGAGACTCCGAGCAAAATgtaagttttc ... atccaggcag-
EST: gi|148990641|gb|EE032032.2|EE032032
EST:     GCAGCTGCTAGCTCATCTGCTTGATCTCTAGCTGAGACTCCGAGCAAAAT                         G
genomic: GCAGCTGCTAGCTCATCTGCTTGATCTCTAGCTGAGACTCCGAGCAAAATgtaagttttc ... atccaggcag-
EST: gi|148990641|gb|EE032032.2|EE032032
EST:     GCAGCTGCTAGCTCATCTGCTTGATCTCTAGCTGAGACTCCGAGCAAAAT                         G
genomic: GCAGCTGCTAGCTCATCTGCTTGATCTCTAGCTGAGACTCCGAGCAAAATgtaagttttc ... atccaggcag-
EST: gi|71773770|gb|DR971665.1|DR971665
EST:     GCAGCTGCTAGCTCATCTGCTTGATCTCTAGCTGAGACTCCGAGCAAAAT                         G
genomic: GCAGCTGCTAGCTCATCTGCTTGATCTCTAGCTGAGACTCCGAGCAAAATgtaagttttc ... atccaggcag-
EST: gi|71773770|gb|DR971665.1|DR971665
EST:     GCAGCTGCTAGCTCATCTGCTTGATCTCTAGCTGAGACTCCGAGCAAAAT                         G
genomic: GCAGCTGCTAGCTCATCTGCTTGATCTCTAGCTGAGACTCCGAGCAAAATgtaagttttc ... atccaggcag-
EST: gi|149065590|gb|EE286713.2|EE286713
EST:     GCAGCTGCTAGCTCATCTGCTTGATCTCTAGCTGAGACTCCGAGCAAAAT                         G
genomic: GCAGCTGCTAGCTCATCTGCTTGATCTCTAGCTGAGACTCCGAGCAAAATgtaagttttc ... atccaggcag-
EST: gi|149065590|gb|EE286713.2|EE286713
EST:     GCAGCTGCTAGCTCATCTGCTTGATCTCTAGCTGAGACTCCGAGCAAAAT                         G
genomic: GCAGCTGCTAGCTCATCTGCTTGATCTCTAGCTGAGACTCCGAGCAAAATgtaagttttc ... atccaggcag-
EST: gi|211319640|gb|FL072372.1|FL072372
EST:     GCAGCTGCTAGCTCATCTGCTTGATCTCTAGCTGAGACTCCGAGCAAAAT                         G
genomic: GCAGCTGCTAGCTCATCTGCTTGATCTCTAGCTGAGACTCCGAGCAAAATgtaagttttc ... atccaggcag-
EST: gi|211319640|gb|FL072372.1|FL072372
EST:     GCAGCTGCTAGCTCATCTGCTTGATCTCTAGCTGAGACTCCGAGCAAAAT                         G
genomic: GCAGCTGCTAGCTCATCTGCTTGATCTCTAGCTGAGACTCCGAGCAAAATgtaagttttc ... atccaggcag-
EST: gi|211319638|gb|FL072370.1|FL072370
EST:     GCAGCTGCTAGCTCATCTGCTTGATCTCTAGCTGAGACTCCGAGCAAAAT                         G
genomic: GCAGCTGCTAGCTCATCTGCTTGATCTCTAGCTGAGACTCCGAGCAAAATgtaagttttc ... atccaggcag-
EST: gi|211319638|gb|FL072370.1|FL072370
EST:     GCAGCTGCTAGCTCATCTGCTTGATCTCTAGCTGAGACTCCGAGCAAAAT                         G
genomic: GCAGCTGCTAGCTCATCTGCTTGATCTCTAGCTGAGACTCCGAGCAAAATgtaagttttc ... atccaggcag-
EST: gi|149108439|gb|EE292776.2|EE292776
EST:     GCAGCTGCTAGCTCATCTGCTTGATCTCTAGCTGAGACTCCGAGCAAAAT                         G
genomic: GCAGCTGCTAGCTCATCTGCTTGATCTCTAGCTGAGACTCCGAGCAAAATgtaagttttc ... atccaggcag-
EST: gi|149108439|gb|EE292776.2|EE292776
EST:     GCAGCTGCTAGCTCATCTGCTTGATCTCTAGCTGAGACTCCGAGCAAAAT                         G
genomic: GCAGCTGCTAGCTCATCTGCTTGATCTCTAGCTGAGACTCCGAGCAAAATgtaagttttc ... atccaggcag-
EST: gi|149108439|gb|EE292776.2|EE292776
EST:     GCAGCTGCTAGCTCATCTGCTTGATCTCTAGCTGAGACTCCGAGCAAAAT                         G
genomic: GCAGCTGCTAGCTCATCTGCTTGATCTCTAGCTGAGACTCCGAGCAAAATgtaagttttc ... atccaggcag-
EST: gi|149108439|gb|EE292776.2|EE292776
EST:     GCAGCTGCTAGCTCATCTGCTTGATCTCTAGCTGAGACTCCGAGCAAAAT                         G
genomic: GCAGCTGCTAGCTCATCTGCTTGATCTCTAGCTGAGACTCCGAGCAAAATgtaagttttc ... atccaggcag-
EST: gi|149108439|gb|EE292776.2|EE292776
EST:     GCAGCTGCTAGCTCATCTGCTTGATCTCTAGCTGAGACTCCGAGCAAAAT                         G
genomic: GCAGCTGCTAGCTCATCTGCTTGATCTCTAGCTGAGACTCCGAGCAAAATgtaagttttc ... atccaggcag-
EST: gi|148931780|gb|EC875059.2|EC875059
EST:     GCAGCTGCTAGCTCATCTGCTTGATCTCTAGCTGAGACTCCGAGCAAAAT                         G
genomic: GCAGCTGCTAGCTCATCTGCTTGATCTCTAGCTGAGACTCCGAGCAAAATgtaagttttc ... atccaggcag-
EST: gi|148931780|gb|EC875059.2|EC875059
EST:     GCAGCTGCTAGCTCATCTGCTTGATCTCTAGCTGAGACTCCGAGCAAAAT                         G
genomic: GCAGCTGCTAGCTCATCTGCTTGATCTCTAGCTGAGACTCCGAGCAAAATgtaagttttc ... atccaggcag-
EST: gi|149014994|gb|EE044736.2|EE044736
EST:     GCAGCTGCTAGCTCATCTGCTTGATCTCTAGCTGAGACTCCGAGCAAAAT                         G
genomic: GCAGCTGCTAGCTCATCTGCTTGATCTCTAGCTGAGACTCCGAGCAAAATgtaagttttc ... atccaggcag-
EST: gi|149014994|gb|EE044736.2|EE044736
EST:     GCAGCTGCTAGCTCATCTGCTTGATCTCTAGCTGAGACTCCGAGCAAAAT                         G
genomic: GCAGCTGCTAGCTCATCTGCTTGATCTCTAGCTGAGACTCCGAGCAAAATgtaagttttc ... atccaggcag-


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttgttgttgacgatatgcttctctgtgcttccggttctgcatgatccaggcagCAGCCAGGAACAACAAGCTAGGCCCCCTCACGCAGACCGCACGACCGAGCGCGCGGCATTGACCGACCCATCGCCGCCGCCGCCGCCTCGATCGACCATG
      tgttgac  putative branch site (score: 3)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgctctgtggttctccgtcgtcgattgccattttaacacctagtagttgttgttgacgatatgcttctctgtgcttccggttctgcatgatccaggcagCAGCCAGGAACAACAAGCTAGGCCCCCTCACGCAGACCGCACGACCGAGCGCGCGGCATTGACCGACCCATCGCCGCCGCCGCCGCCTCGATCGACCATG

-tgctctg
- - - - tggttct
- - - - - - - - - - - - - tgccatt
- - - - - - - - - - - - - - - - - - - - - - - - tgttgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gttctgc