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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acaaaaccataatgcataggctccttcatatccaaaaacctttttgttgccaaacaaatgagcctgcattaataccgtcattcctgtaatatgcatttagGTCCATCCCCAGCAAAATGATACAACGAACACTCCGGGTATGTTACCTGTGGAACCTGCAGAAGAACCAATATATGTTAATGCAAAACAATACCATGCAA

Basic information

species Zea mays
transcript GRMZM2G040349_T01
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|149028984|gb|EE286170.2|EE286170
EST:     CTTATTATAGTGCGGTTGGGGTCTTGACAGGATATCCTCCACATGCCATT                         GTCCATCCCCAGCAAAATGATACAACGAACACTCCGGGTATGTTACCTGTG
genomic: CTTATTATAGTGCGGTTGGGGTCTTGACAGGATATCCTCCACATGCCATTgtatgttcac ... atgcatttagGTCCATCCCCAGCAAAATGATACAACGAACACTCCGGGTATGTTACCTGTG
EST: gi|89762792|gb|DY690244.1|DY690244
EST:     CTTATTATAGTGCGGTTGGGGTCTTGACAGGATATCCTCCACATGCCATT                         GTCCATCCCCAGCAAAATGATACAACGAACACTCCGGGTATGTTACCTGTG
genomic: CTTATTATAGTGCGGTTGGGGTCTTGACAGGATATCCTCCACATGCCATTgtatgttcac ... atgcatttagGTCCATCCCCAGCAAAATGATACAACGAACACTCCGGGTATGTTACCTGTG
EST: gi|211340500|gb|FL126029.1|FL126029
EST:     TTATTATAGTGGGGGTTGGGGTCTTGACAGGATATGCTCCACATGCCATT                         GTCCATCCCCAGCA
genomic: TTATTATAGTGCGG-TTGGGGTCTTGACAGGATATCCTCCACATGCCATTgtatgttcac ... atgcatttagGTCCATCCCCAGCA
EST: gi|211338112|gb|FL126025.1|FL126025
EST:     TATTATAGTGGCGGTTGGGGTCTTGACAAGATATCCTCCACATGCCCATT                         GTCCATCCCCAGCAAAATGATACAACGAAACCCTCCGGGGTATGTTACCC
genomic: TATTATAGTG-CGGTTGGGGTCTTGACAGGATATCCTCCACATGCC-ATTgtatgttcac ... atgcatttagGTCCATCCCCAGCAAAATGATACAACGAA-CACTCCGGG-TATGTTACC-
EST: gi|76012499|gb|DT939669.1|DT939669
EST:     CTTATTATAGTGCGGTTGGGGTCTTGACAGGATATCCTCCACATGCCATT                         GTCCATCCCCAGCAAAATGATACAACGAACACTCCGGGTATGTTACCTGTG
genomic: CTTATTATAGTGCGGTTGGGGTCTTGACAGGATATCCTCCACATGCCATTgtatgttcac ... atgcatttagGTCCATCCCCAGCAAAATGATACAACGAACACTCCGGGTATGTTACCTGTG
EST: gi|50333900|gb|CO529026.1|CO529026
EST:     CTTATTATAGTGCGGTTGGGGTCTTGACAGGATATCCTCCACATGCCATT                         GTCCATCCCCAGCAAAATGATACAACGAACACTCCGGGTATGTTACCTGTG
genomic: CTTATTATAGTGCGGTTGGGGTCTTGACAGGATATCCTCCACATGCCATTgtatgttcac ... atgcatttagGTCCATCCCCAGCAAAATGATACAACGAACACTCCGGGTATGTTACCTGTG
EST: gi|30088407|gb|CB886612.1|CB886612
EST:     CTTATTATAGTGCGGTTGGGGTCTTGACAGGATATCCTCCACATGCCATT                         GTCCATCCCCAGCAAAATGATACAACGAACACTCCGGGTATGT
genomic: CTTATTATAGTGCGGTTGGGGTCTTGACAGGATATCCTCCACATGCCATTgtatgttcac ... atgcatttagGTCCATCCCCAGCAAAATGATACAACGAACACTCCGGGTATGT
EST: gi|76015258|gb|DT942428.1|DT942428
EST:     CTTATTATAGTGCGGTTGGGGTCTTGACAGGATATCCTCCACATGCCATT                         GTCCATCCCCAGCAAAATGATACAACGAACACTCCGGGTATGTTACCTGTG
genomic: CTTATTATAGTGCGGTTGGGGTCTTGACAGGATATCCTCCACATGCCATTgtatgttcac ... atgcatttagGTCCATCCCCAGCAAAATGATACAACGAACACTCCGGGTATGTTACCTGTG
EST: gi|78108019|gb|DV526437.1|DV526437
EST:     CTTATTATAGTGCGGTTGGGGTCTTGACAGGATATCCTCCACATGCCATT                         GTCCATCCCCAGCAAAATGATACAACGAACACTCCGGGTATGTTACCTGTG
genomic: CTTATTATAGTGCGGTTGGGGTCTTGACAGGATATCCTCCACATGCCATTgtatgttcac ... atgcatttagGTCCATCCCCAGCAAAATGATACAACGAACACTCCGGGTATGTTACCTGTG
EST: gi|31359967|gb|CD444324.1|CD444324
EST:     CTTATTATAGTGGGGTTGGGGTCTTGACAGGATG-C-TCCACATGCCATT                         GTCCATCCCCAGCAAAATGATACAACGAACACTCCGGGTATGTTACCTGTG
genomic: CTTATTATAGTGCGGTTGGGGTCTTGACAGGATATCCTCCACATGCCATTgtatgttcac ... atgcatttagGTCCATCCCCAGCAAAATGATACAACGAACACTCCGGGTATGTTACCTGTG
EST: gi|91057234|gb|EB167652.1|EB167652
EST:     CTTATTATAGTGCGGTTGGGGTCTTGACAGGATATCCTCCACATGCCATT                         GTCCATCCCCAGCAAAATGATACAACGAACACTCCGGGTATGTTACCTGTG
genomic: CTTATTATAGTGCGGTTGGGGTCTTGACAGGATATCCTCCACATGCCATTgtatgttcac ... atgcatttagGTCCATCCCCAGCAAAATGATACAACGAACACTCCGGGTATGTTACCTGTG
EST: gi|74233446|gb|DT641360.1|DT641360
EST:     CTTATTATAGTGCGGTTGGGGTCTTGACAGGATATCCTCCACATGCCATT                         GTCCATCCCCAGCAAAATGATACAACGAACACTCCGGGTATGTTACCTGTG
genomic: CTTATTATAGTGCGGTTGGGGTCTTGACAGGATATCCTCCACATGCCATTgtatgttcac ... atgcatttagGTCCATCCCCAGCAAAATGATACAACGAACACTCCGGGTATGTTACCTGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgccaaacaaatgagcctgcattaataccgtcattcctgtaatatgcatttagGTCCATCCCCAGCAAAATGATACAACGAACACTCCGGGTATGTTACCTGTGGAACCTGCAGAAGAACCAATATATGTTAATGCAAAACAATACCATGCAA
                     cattaat  putative branch site (score: 3)
                      attaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acaaaaccataatgcataggctccttcatatccaaaaacctttttgttgccaaacaaatgagcctgcattaataccgtcattcctgtaatatgcatttagGTCCATCCCCAGCAAAATGATACAACGAACACTCCGGGTATGTTACCTGTGGAACCTGCAGAAGAACCAATATATGTTAATGCAAAACAATACCATGCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC