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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tccctaatctgatattgatgcttgctttgctgggtgagcttggctggttgcatcacactgcacttataatatttatgattagtcacctcgctccctgcagTTCAAGCTTTGGATTCCCGGATCCCACACCACCGGTCTCTCTCGGGGAGTGTAATCCAGCGAGCGTTGAGTTGAAAGCCGCGCAAGTGGAGATGAGTACT

Basic information

species Zea mays
transcript GRMZM2G147446_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|211053591|gb|FL371314.1|FL371314
EST:     GCATCACCGGAGCAACGCGGGCGCGGAGAGGCCAGCCAGCGCAGGCGCAG                         TTCAAGCTTTGGATTCCCGGATCCCACACCACCGGTCTCTCTCGGGGAGTG
genomic: GCATCACCGGAGCAACGCGGGCGCGGAGAGGCCAGCCAGCGCAGGCGCAGgtaactgcag ... ctccctgcagTTCAAGCTTTGGATTCCCGGATCCCACACCACCGGTCTCTCTCGGGGAGTG
EST: gi|211217766|gb|FL412349.1|FL412349
EST:     GCATCACCGGAGCAACGCGGGCGCGGAGAGGCCAGCCAGCGCAGGCGCAG                         TTCAAGCTTTGGATTCCCGGATCCCACACCACCGGTCTCTCTCGGGGAGTG
genomic: GCATCACCGGAGCAACGCGGGCGCGGAGAGGCCAGCCAGCGCAGGCGCAGgtaactgcag ... ctccctgcagTTCAAGCTTTGGATTCCCGGATCCCACACCACCGGTCTCTCTCGGGGAGTG
EST: gi|149110810|gb|EE190620.2|EE190620
EST:     GCATCACCGGAGCAACGCGGGCGCGGAGAGGCCAGCCAGCGCAGGCGCAG                         TTCAAGCTTTGGATTCCCGGATCCCACACCACCGGTCTCTCTCGGGGAGTG
genomic: GCATCACCGGAGCAACGCGGGCGCGGAGAGGCCAGCCAGCGCAGGCGCAGgtaactgcag ... ctccctgcagTTCAAGCTTTGGATTCCCGGATCCCACACCACCGGTCTCTCTCGGGGAGTG
EST: gi|78076134|gb|DV504568.1|DV504568
EST:     GCATCACCGGAGCAACGCGGGCGCGGAGAGGCCAGCCAGCGCAGGCGCAG                         TTCAAGCTTTGGATTCCCGGATCCCACACCACCGGTCTCTCTCGGGGAGTG
genomic: GCATCACCGGAGCAACGCGGGCGCGGAGAGGCCAGCCAGCGCAGGCGCAGgtaactgcag ... ctccctgcagTTCAAGCTTTGGATTCCCGGATCCCACACCACCGGTCTCTCTCGGGGAGTG
EST: gi|91051991|gb|EB162409.1|EB162409
EST:     GCATCACCGGAGCAACGCGGGCGCGGAGAGGCCAGCCAGCGCAGGCGCAG                         TTCAAGCTTTGGATTCCCGGATCCCACACCACCGGTCTCTCTCGGGGAGTG
genomic: GCATCACCGGAGCAACGCGGGCGCGGAGAGGCCAGCCAGCGCAGGCGCAGgtaactgcag ... ctccctgcagTTCAAGCTTTGGATTCCCGGATCCCACACCACCGGTCTCTCTCGGGGAGTG
EST: gi|71321408|gb|DR797414.1|DR797414
EST:     GCATCACCGGAGCAACGCGGGCGCGGAGAGGCCAGCCAGCGCAGGCGCAG                         TTCAAGCTTTGGATTCCCGGATCCCACACCACCGGTCTCTCTCGGGGAGTG
genomic: GCATCACCGGAGCAACGCGGGCGCGGAGAGGCCAGCCAGCGCAGGCGCAGgtaactgcag ... ctccctgcagTTCAAGCTTTGGATTCCCGGATCCCACACCACCGGTCTCTCTCGGGGAGTG
EST: gi|91868221|gb|EB399951.1|EB399951
EST:     GCATCACCGGAGCAACGCGGGCGCGGAGAGGCCAGCCAGCGCAGGCGCAG                         TTCAAGCTTTGGATTCCCGGATCCCACACCACCGGTCTCTCTCGGGGAGTG
genomic: GCATCACCGGAGCAACGCGGGCGCGGAGAGGCCAGCCAGCGCAGGCGCAGgtaactgcag ... ctccctgcagTTCAAGCTTTGGATTCCCGGATCCCACACCACCGGTCTCTCTCGGGGAGTG
EST: gi|148986808|gb|EE030604.2|EE030604
EST:     GCATCACCGGAGCAACGCGGGCGCGGAGAGGCCAGCCAGCGCAGGCGCAG                         TTCAAGCTTTGGATTCCCGGATCCCACACCACCGGTCTCTCTCGGGGAGTG
genomic: GCATCACCGGAGCAACGCGGGCGCGGAGAGGCCAGCCAGCGCAGGCGCAGgtaactgcag ... ctccctgcagTTCAAGCTTTGGATTCCCGGATCCCACACCACCGGTCTCTCTCGGGGAGTG
EST: gi|149082248|gb|EE171434.2|EE171434
EST:     GCATCACCGGAGCAACGCGGGCGCGGAGAGGCCAGCCAGCGCAGGCGCAG                         TTCAAGCTTTGGATTCCCGGATCCCACACCACCGGTCTCTCTCGGGGAGTG
genomic: GCATCACCGGAGCAACGCGGGCGCGGAGAGGCCAGCCAGCGCAGGCGCAGgtaactgcag ... ctccctgcagTTCAAGCTTTGGATTCCCGGATCCCACACCACCGGTCTCTCTCGGGGAGTG
EST: gi|71426314|gb|DR807364.1|DR807364
EST:     GCATCACCGGAGCAACGCGGGCGCGGAGAGGCCAGCCAGCGCAGGCGCAG                         TTCAAGCTTTGGATTCCCGGATCCCACACCACCGGTCTCTCTCGGGGAGTG
genomic: GCATCACCGGAGCAACGCGGGCGCGGAGAGGCCAGCCAGCGCAGGCGCAGgtaactgcag ... ctccctgcagTTCAAGCTTTGGATTCCCGGATCCCACACCACCGGTCTCTCTCGGGGAGTG
EST: gi|101384748|gb|EB814420.1|EB814420
EST:     GCATCACCGGAGCAACGCGGGCGCGGAGAGGCCAGCCAGCGCAGGCGCAG                         TTCAAGCTTTGGATTCCCGGATCCCACACCACCGGTCTCTCTCGGGGAGTG
genomic: GCATCACCGGAGCAACGCGGGCGCGGAGAGGCCAGCCAGCGCAGGCGCAGgtaactgcag ... ctccctgcagTTCAAGCTTTGGATTCCCGGATCCCACACCACCGGTCTCTCTCGGGGAGTG
EST: gi|93282197|gb|EB674461.1|EB674461
EST:     GCATCACCGGAGCAACGCGGGCGCGGAGAGGCCAGCCAGCGCAGGCGCAG                         TTCAAGCTTTGGATTCCCGGATCCCACACCACCGGTCTCTCTCGGGGAGTG
genomic: GCATCACCGGAGCAACGCGGGCGCGGAGAGGCCAGCCAGCGCAGGCGCAGgtaactgcag ... ctccctgcagTTCAAGCTTTGGATTCCCGGATCCCACACCACCGGTCTCTCTCGGGGAGTG
EST: gi|211214768|gb|FL397948.1|FL397948
EST:     GCATCACCGGAGCAACGCGTGCGCGGAGAGGCCAGCCAGCGCAGGCGCAG                         TTCAAGCTTTGGATTCCCGGATCCCACACCACCGGTCTCTCTCGGGGAGTG
genomic: GCATCACCGGAGCAACGCGGGCGCGGAGAGGCCAGCCAGCGCAGGCGCAGgtaactgcag ... ctccctgcagTTCAAGCTTTGGATTCCCGGATCCCACACCACCGGTCTCTCTCGGGGAGTG
EST: gi|78076922|gb|DV505356.1|DV505356
EST:     GCATCACCGGAGCAACGCGGGCGCGGAGAGGCCAGCCAGCGCAGGCGCAG                         TTCAAGCTTTGGATTCCCGGATCCCACACCACCGGTCTCTCTCGGGGAGTG
genomic: GCATCACCGGAGCAACGCGGGCGCGGAGAGGCCAGCCAGCGCAGGCGCAGgtaactgcag ... ctccctgcagTTCAAGCTTTGGATTCCCGGATCCCACACCACCGGTCTCTCTCGGGGAGTG
EST: gi|149000630|gb|EE037833.2|EE037833
EST:     GCATCACCGGAGCAACGCGGGCGCGGAGAGGCCAGCCAGCGCAGGCGCAG                         TTCAAGCTTTGGATTCCCGGATCCCACACCACCGGTCTCTCTCGGGGAGTG
genomic: GCATCACCGGAGCAACGCGGGCGCGGAGAGGCCAGCCAGCGCAGGCGCAGgtaactgcag ... ctccctgcagTTCAAGCTTTGGATTCCCGGATCCCACACCACCGGTCTCTCTCGGGGAGTG
EST: gi|148947730|gb|EC893211.2|EC893211
EST:     GCATCACCGGAGCAACGCGGGCGCGGAGAGGCCAGCCAGCGCAGGCGCAG                         TTCAAGCTTTGGATTCCCGGATCCCACACCACCGGTCTCTCTCGGGGAGTG
genomic: GCATCACCGGAGCAACGCGGGCGCGGAGAGGCCAGCCAGCGCAGGCGCAGgtaactgcag ... ctccctgcagTTCAAGCTTTGGATTCCCGGATCCCACACCACCGGTCTCTCTCGGGGAGTG
EST: gi|211301329|gb|FL412804.1|FL412804
EST:     GCATCACCGGAGCAACGCGGGCGCGGAGAGGCCAGCCAGCGCAGGCGCAG                         TTCAAGCTTTGGATTCCCGGATCCCACACCACCGGTCTCTCTCGGGGAGTG
genomic: GCATCACCGGAGCAACGCGGGCGCGGAGAGGCCAGCCAGCGCAGGCGCAGgtaactgcag ... ctccctgcagTTCAAGCTTTGGATTCCCGGATCCCACACCACCGGTCTCTCTCGGGGAGTG
EST: gi|89764132|gb|DY691050.1|DY691050
EST:     ACATCACCGGAGCAACGCGGGCGCGGAGAGGCCAGCCAGCGCAGGCGCAG                         TTCAAGCTTTGGATTCCCGGATCCCACACCACCGGTCTCTCTCGGGGAGTG
genomic: -CATCACCGGAGCAACGCGGGCGCGGAGAGGCCAGCCAGCGCAGGCGCAGgtaactgcag ... ctccctgcagTTCAAGCTTTGGATTCCCGGATCCCACACCACCGGTCTCTCTCGGGGAGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggttgcatcacactgcacttataatatttatgattagtcacctcgctccctgcagTTCAAGCTTTGGATTCCCGGATCCCACACCACCGGTCTCTCTCGGGGAGTGTAATCCAGCGAGCGTTGAGTTGAAAGCCGCGCAAGTGGAGATGAGTACT
                                     tcacctcgctccct  CT-rich tract
                acttataatatttatg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tccctaatctgatattgatgcttgctttgctgggtgagcttggctggttgcatcacactgcacttataatatttatgattagtcacctcgctccctgcagTTCAAGCTTTGGATTCCCGGATCCCACACCACCGGTCTCTCTCGGGGAGTGTAATCCAGCGAGCGTTGAGTTGAAAGCCGCGCAAGTGGAGATGAGTACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG