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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcacccacgccgccaactccctcggctccacgatgcaggcaattgattcaaccgccgtgctaatctgcgtgtctctcctgatcagGGGATGTGCCTGCTGTGGCTGACGGCGATCCTTCCGGTGTACAAGAACACCCCGGAGTGCGCGCCGGGGCGGCCGGTAGGGTGCGCGGTGCTGCCGTGGC

Basic information

species Zea mays
transcript GRMZM2G035790_T02
intron # 2
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|149071140|gb|EE159538.2|EE159538
EST:     GCCTCGGCCGGTTCCGGGTCATCACCCTCGGCTCCTGCGTTAGCCTCTTC                         GGGATGTGCCTGCTGTGGCTGACGGCGATCCTTCCGGTGTACAAGAACACC
genomic: GCCTCGGCCGGTTCCGGGTCATCACCCTCGGCTCCTGCGTTAGCCTCTTCgtgagcaccc ... tcctgatcagGGGATGTGCCTGCTGTGGCTGACGGCGATCCTTCCGGTGTACAAGAACACC
EST: gi|211539680|gb|FL070739.1|FL070739
EST:     GCCTCGGCCGGTTCCGGGTCATCACCCTCGGCTCCTGCGTTAGCCTCTTC                         GGGATGTGCCTGCTGTGGCTGACGGCGATCCTTCCGGTGTACAAGAACACC
genomic: GCCTCGGCCGGTTCCGGGTCATCACCCTCGGCTCCTGCGTTAGCCTCTTCgtgagcaccc ... tcctgatcagGGGATGTGCCTGCTGTGGCTGACGGCGATCCTTCCGGTGTACAAGAACACC
EST: gi|211533673|gb|FL070722.1|FL070722
EST:     GCCTCGGCCGGTTCCGGGTCATCACCCTCGGCTCCTGCGTTAGCCTCTTC                         GGGATGTGCCTGCTGTGGCTGACGGCGATCCTTCCGGTGGACAAGAACACC
genomic: GCCTCGGCCGGTTCCGGGTCATCACCCTCGGCTCCTGCGTTAGCCTCTTCgtgagcaccc ... tcctgatcagGGGATGTGCCTGCTGTGGCTGACGGCGATCCTTCCGGTGTACAAGAACACC
EST: gi|211536680|gb|FL070733.1|FL070733
EST:     GCCTCGGCCGGTTCCGGGTCATCACCCTCGGCTCCTGCGTTAGCCTCTTC                         GGGATGTGCCTGCTGTGGCTGACGGCGATCCTTCCGGTGTACAAGAACACC
genomic: GCCTCGGCCGGTTCCGGGTCATCACCCTCGGCTCCTGCGTTAGCCTCTTCgtgagcaccc ... tcctgatcagGGGATGTGCCTGCTGTGGCTGACGGCGATCCTTCCGGTGTACAAGAACACC
EST: gi|211536681|gb|FL070734.1|FL070734
EST:     GCCTCGGCCGGTTCCGGGTCATCACCCTCGGCTCCTGCGTTAGCCTCTTC                         GGGATGTGCCTGCTGTGGCTGACGNCGATCTTTCCGGTGTANCA-GAACAC
genomic: GCCTCGGCCGGTTCCGGGTCATCACCCTCGGCTCCTGCGTTAGCCTCTTCgtgagcaccc ... tcctgatcagGGGATGTGCCTGCTGTGGCTGACGGCGATCCTTCCGGTGTA-CAAGAACAC
EST: gi|211533666|gb|FL070715.1|FL070715
EST:     GCCTCGGCCGGTTCCGGGTCATCACCCTCGGCTCCTGCGTTAGCCTCTTC                         GGGATGTGCCTGCTGTGGCTGACGGCGATCCTTCCGGTGTACAAGAACACC
genomic: GCCTCGGCCGGTTCCGGGTCATCACCCTCGGCTCCTGCGTTAGCCTCTTCgtgagcaccc ... tcctgatcagGGGATGTGCCTGCTGTGGCTGACGGCGATCCTTCCGGTGTACAAGAACACC
EST: gi|211533667|gb|FL070716.1|FL070716
EST:     GCCTCGGCCGGTTCCGGGTCATCACCCTCGGCTCCTGCGTTAGCCTCTTC                         GGGATGTGCCTGCTGTGGCTGACGGCGATCCTTCCGGTGTACAAGAACACC
genomic: GCCTCGGCCGGTTCCGGGTCATCACCCTCGGCTCCTGCGTTAGCCTCTTCgtgagcaccc ... tcctgatcagGGGATGTGCCTGCTGTGGCTGACGGCGATCCTTCCGGTGTACAAGAACACC
EST: gi|149011546|gb|EE042369.2|EE042369
EST:     GCCTCGGCCGGTTCCGGGTCATCACCCTCGGCTCCTGCGTTAGCCTCTTC                         GGGATGTGCCTGCTGTGGCTGACGGCGATCCTTCCGGTGTACAAGAACACC
genomic: GCCTCGGCCGGTTCCGGGTCATCACCCTCGGCTCCTGCGTTAGCCTCTTCgtgagcaccc ... tcctgatcagGGGATGTGCCTGCTGTGGCTGACGGCGATCCTTCCGGTGTACAAGAACACC
EST: gi|211536679|gb|FL070732.1|FL070732
EST:     GCCTCGGCCGGTTCCGGGTCATCACCCTCGGCTCCTGCGTTAGCCTCTTC                         GGGATGTGCCTGCTGTGGCTGACGGCGATCCTTCCGGTGTA-AAGAACACC
genomic: GCCTCGGCCGGTTCCGGGTCATCACCCTCGGCTCCTGCGTTAGCCTCTTCgtgagcaccc ... tcctgatcagGGGATGTGCCTGCTGTGGCTGACGGCGATCCTTCCGGTGTACAAGAACACC
EST: gi|211536673|gb|FL070726.1|FL070726
EST:     GCCTCGGCCGGTTCCGGGTCATCACCCTCGGCTCCTGCGTTAGCCTCTTC                         GGGATGTGCCTGCTGTGGCTGACGGCGATCCTTCCGGTGTACAAGAACACC
genomic: GCCTCGGCCGGTTCCGGGTCATCACCCTCGGCTCCTGCGTTAGCCTCTTCgtgagcaccc ... tcctgatcagGGGATGTGCCTGCTGTGGCTGACGGCGATCCTTCCGGTGTACAAGAACACC
EST: gi|211536675|gb|FL070728.1|FL070728
EST:     GCCTCGGCCGGTTCCGGGTCATCACCCTCGGCTCCTGCGTTAGCCTCTTC                         GGGATGTGCCTGCTGTGGCTGACGGCGATCCTTCCGGTGTACAAGAACACC
genomic: GCCTCGGCCGGTTCCGGGTCATCACCCTCGGCTCCTGCGTTAGCCTCTTCgtgagcaccc ... tcctgatcagGGGATGTGCCTGCTGTGGCTGACGGCGATCCTTCCGGTGTACAAGAACACC
EST: gi|211530666|gb|FL070708.1|FL070708
EST:     GCCTCGGCCGGTTCCGGGTCATCACCCTCGGCTCCTGCGTTAGCCTCTTC                         GGGATGTGCCTGCTGTGGCTGACGGCGATCCTTCCGGTGTACAAGAACACC
genomic: GCCTCGGCCGGTTCCGGGTCATCACCCTCGGCTCCTGCGTTAGCCTCTTCgtgagcaccc ... tcctgatcagGGGATGTGCCTGCTGTGGCTGACGGCGATCCTTCCGGTGTACAAGAACACC
EST: gi|211530661|gb|FL070703.1|FL070703
EST:     GCCTCGGCCGNNTCCGGGNCATCACCCTCGGCTCCTGCGTTAGCCTCTTC                         GGGATGTGCCTGCTGTGGCTGACGGCGATCCTTCCGGATG-ACAAAAACAC
genomic: GCCTCGGCCGGTTCCGGGTCATCACCCTCGGCTCCTGCGTTAGCCTCTTCgtgagcaccc ... tcctgatcagGGGATGTGCCTGCTGTGGCTGACGGCGATCCTTCCGG-TGTACAAGAACAC
EST: gi|148968167|gb|EE019456.2|EE019456
EST:     GCCTCGGCCGGTTCCGGGTCATCACCCTCGGCTCCTGCGTTAGCCTCTTC                         GGGATGTGCCTGCTGTGGCTGACGGCGATCCTTCCGGTGTACAAGAACACC
genomic: GCCTCGGCCGGTTCCGGGTCATCACCCTCGGCTCCTGCGTTAGCCTCTTCgtgagcaccc ... tcctgatcagGGGATGTGCCTGCTGTGGCTGACGGCGATCCTTCCGGTGTACAAGAACACC
EST: gi|211527668|gb|FL070695.1|FL070695
EST:     GCCTCGGCCGGTTCCGGGTCATCACCCTCGGCTCCTGCGTTAGCCTCTTC                         GGGATGTGCCTGCTGTGGCTGACGGCGATCCTTCCGGTGTACAAGAACACC
genomic: GCCTCGGCCGGTTCCGGGTCATCACCCTCGGCTCCTGCGTTAGCCTCTTCgtgagcaccc ... tcctgatcagGGGATGTGCCTGCTGTGGCTGACGGCGATCCTTCCGGTGTACAAGAACACC
EST: gi|211530656|gb|FL070698.1|FL070698
EST:     GCCTCGGCCGGTTCCGGGTCATCACCCTCGGCTCCTGCGTTAGCCTCTTC                         GGGATGTGCCTGCTGTGGCTGACGGCGATCCTTCCGGTGTACAAGAACACC
genomic: GCCTCGGCCGGTTCCGGGTCATCACCCTCGGCTCCTGCGTTAGCCTCTTCgtgagcaccc ... tcctgatcagGGGATGTGCCTGCTGTGGCTGACGGCGATCCTTCCGGTGTACAAGAACACC
EST: gi|149078326|gb|EE167093.2|EE167093
EST:     GCCTCGGCCGGTTCCGGGTCATCACCCTCGGCTCCTGCGTTAGCCTCTTC                         GGGATGTGCCTGCTGTGGCTGACGGCGATCCTTCCGGTGTACAAGAACACC
genomic: GCCTCGGCCGGTTCCGGGTCATCACCCTCGGCTCCTGCGTTAGCCTCTTCgtgagcaccc ... tcctgatcagGGGATGTGCCTGCTGTGGCTGACGGCGATCCTTCCGGTGTACAAGAACACC
EST: gi|211536682|gb|FL070735.1|FL070735
EST:     GCCTCGGCCGGTTCCGGGTCATCACCCTCGGCTCCTGCGTTAGCCTCTTC                         GGGATGTGCCTGCTGTGGCTGACGGCGATCCTTCCGGTGTACAAGAACACC
genomic: GCCTCGGCCGGTTCCGGGTCATCACCCTCGGCTCCTGCGTTAGCCTCTTCgtgagcaccc ... tcctgatcagGGGATGTGCCTGCTGTGGCTGACGGCGATCCTTCCGGTGTACAAGAACACC
EST: gi|211530657|gb|FL070699.1|FL070699
EST:     GCCTCGGCCGGTTCCGGGTCATCACCCTCGGCTCCTGCGTTAGCCTCTTC                         GGGATGTGCCTGCTGTGGCTGACGGCNGATCCTTCCGGTGTACAAGAACAC
genomic: GCCTCGGCCGGTTCCGGGTCATCACCCTCGGCTCCTGCGTTAGCCTCTTCgtgagcaccc ... tcctgatcagGGGATGTGCCTGCTGTGGCTGACGGC-GATCCTTCCGGTGTACAAGAACAC
EST: gi|211530664|gb|FL070706.1|FL070706
EST:     GCCTCGGCCGGTTCCGGGTCATCACCCTCGGCTCCTGCGTTAGCCTCTTC                         GGGATGTGCCTGCTGTGGCTGACGGCGATCCTTCCGGTGTACAAGAACACC
genomic: GCCTCGGCCGGTTCCGGGTCATCACCCTCGGCTCCTGCGTTAGCCTCTTCgtgagcaccc ... tcctgatcagGGGATGTGCCTGCTGTGGCTGACGGCGATCCTTCCGGTGTACAAGAACACC
EST: gi|148931856|gb|EC877314.2|EC877314
EST:     GCCTCGGCCGGTTCCGGGTCATCACCCTCGGCTCCTGCGTTAGCCTCTTC                         GGGATGTGCCTGCTGTGGCTGACGGCGATCCTTCCGGTGTACAAGAACACC
genomic: GCCTCGGCCGGTTCCGGGTCATCACCCTCGGCTCCTGCGTTAGCCTCTTCgtgagcaccc ... tcctgatcagGGGATGTGCCTGCTGTGGCTGACGGCGATCCTTCCGGTGTACAAGAACACC
EST: gi|211536684|gb|FL070737.1|FL070737
EST:     GCCTCGGCCGGTTCCGGGTCATCACCCTCGGCTCCTGCGTTAGCCTCTTC                         GGGATGTGCCTGCTGTGGCTGACGGCGATCCTTCCGGTGTACAAGAACACC
genomic: GCCTCGGCCGGTTCCGGGTCATCACCCTCGGCTCCTGCGTTAGCCTCTTCgtgagcaccc ... tcctgatcagGGGATGTGCCTGCTGTGGCTGACGGCGATCCTTCCGGTGTACAAGAACACC
EST: gi|211536683|gb|FL070736.1|FL070736
EST:     GCCTCGGCCGGTTCCGGGTCATCACCCTCGGCTCCTGCGTTAGCCTCTTC                         GGGATGTGCCTGCTGTGGCTGACGGCGATCCTTCCGGTGTACAAGAACACC
genomic: GCCTCGGCCGGTTCCGGGTCATCACCCTCGGCTCCTGCGTTAGCCTCTTCgtgagcaccc ... tcctgatcagGGGATGTGCCTGCTGTGGCTGACGGCGATCCTTCCGGTGTACAAGAACACC
EST: gi|211530659|gb|FL070701.1|FL070701
EST:     GCCTCGGCCGGTTCCGGGTCATCACCCTCGGCTCCTGCGTTAGCCTCTTC                         GGGATGTGCCTGCTGTGGCTGACGGCGATCCTTCCGGTGTACAAGAACACC
genomic: GCCTCGGCCGGTTCCGGGTCATCACCCTCGGCTCCTGCGTTAGCCTCTTCgtgagcaccc ... tcctgatcagGGGATGTGCCTGCTGTGGCTGACGGCGATCCTTCCGGTGTACAAGAACACC
EST: gi|149008814|gb|EE041018.2|EE041018
EST:     GCCTCGGCCGGTTCCGGGTCATCACCCTCGGCTCCTGCGTTAGCCTCTTC                         GGGATGTGCCTGCTGTGGCTGACGGCGATCCTTCCGGTGTACAAGAACACC
genomic: GCCTCGGCCGGTTCCGGGTCATCACCCTCGGCTCCTGCGTTAGCCTCTTCgtgagcaccc ... tcctgatcagGGGATGTGCCTGCTGTGGCTGACGGCGATCCTTCCGGTGTACAAGAACACC
EST: gi|211536676|gb|FL070729.1|FL070729
EST:     GCCTCGGCCGGTTCCGGGTCATCACCCTCGGCTCCTGCGTTAGCCTCTTC                         GGGATGTGCCTGCTGTGGCTGACGGCGATCCTTCCGGTGTACAAGAACACC
genomic: GCCTCGGCCGGTTCCGGGTCATCACCCTCGGCTCCTGCGTTAGCCTCTTCgtgagcaccc ... tcctgatcagGGGATGTGCCTGCTGTGGCTGACGGCGATCCTTCCGGTGTACAAGAACACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgatgcaggcaattgattcaaccgccgtgctaatctgcgtgtctctcctgatcagGGGATGTGCCTGCTGTGGCTGACGGCGATCCTTCCGGTGTACAAGAACACCCCGGAGTGCGCGCCGGGGCGGCCGGTAGGGTGCGCGGTGCTGCCGTGGC
                           tgctaat  putative branch site (score: 2)
                                       tgtctctcct  putative PPT
          aattgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagcacccacgccgccaactccctcggctccacgatgcaggcaattgattcaaccgccgtgctaatctgcgtgtctctcctgatcagGGGATGTGCCTGCTGTGGCTGACGGCGATCCTTCCGGTGTACAAGAACACCCCGGAGTGCGCGCCGGGGCGGCCGGTAGGGTGCGCGGTGCTGCCGTGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC