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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtagacactcttgttgtttgcgttgtgtcccctgtttcttttcgtttcaccgtcgtgtcgaggcatccattgatcgatatatgtcatcgccagAGCTTGCATCCGGCGGCGGAGTACCACGGCGCGGCGAGGGCCATCGGTGGCTGCCCGATATACGTCAGCGACAAGCCGGGGAACCACAACTTCGAGCTGC

Basic information

species Zea mays
transcript GRMZM2G340656_T04
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G340656_T05 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os07g10840.1 (Oryza sativa), 3'ss of exon 6
gtgagtagacactcttgttgtttgcgttgtgtcccctgtttcttttcgtttcaccgtcgtgtcgaggcatccattgatcgatatatgtcatcgccagAGCTTGCATCCGGCGGCGGAGTACCACGGCGCGGCGAGGGCCATCGGTGGCTGCCCGATATACGTCAGCGACAAGCCGGGGAACCACAACTTCGAGCTGC
|| || |   || | | | || | ||  |    | |  |||||| |  || |  | |       |||  |       ||||| | ||   |   ||||||||||| |||||||||||||||||||||||||||||||| ||||| || || ||||| ||||||||||||||||||||||||||||||||||| ||||
gtaagcatcaacccct-tcgtgtccgacgccggcgccatttcttcttcttgcttctt-------aggtgt-------tcgatgtgtggtttttgcagAGCTTGCACCCGGCGGCGGAGTACCACGGCGCGGCGAGGGCGATCGGCGGGTGTCCGATCTACGTCAGCGACAAGCCGGGGAACCACAACTTCGATCTGC
















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|154130378|gb|EC872174.2|EC872174
EST:     ACACCGTCTTCCTCGGCGAGTTCATGCAGCCCGATTGGGACATGTTCCAT                         AGCTTGCATCCGGCGGCGGAGTACCACGGCGCGGCGAGGGCCATCGGTGGC
genomic: ACACCGTCTTCCTCGGCGAGTTCATGCAGCCCGATTGGGACATGTTCCATgtgagtagac ... tcatcgccagAGCTTGCATCCGGCGGCGGAGTACCACGGCGCGGCGAGGGCCATCGGTGGC
EST: gi|148996151|gb|EE035420.2|EE035420
EST:     ACACCGTCTTCCTCGGCGAGTTCATGCAGCCCGATTGGGACATGTTCCAT                         AGCTTGCATCCGGCGGCGGAGTACCACGGCGCGGCGAGGGCCATCGGTGGC
genomic: ACACCGTCTTCCTCGGCGAGTTCATGCAGCCCGATTGGGACATGTTCCATgtgagtagac ... tcatcgccagAGCTTGCATCCGGCGGCGGAGTACCACGGCGCGGCGAGGGCCATCGGTGGC
EST: gi|149086838|gb|EE176387.2|EE176387
EST:     ACACCGTCTTCCTCGGCGAGTTCATGCAGCCCGATTGGGACATGTTCCAT                         AGCTTGCATCCGGCGGCGGAGTACCACGGCGCGGCGAGGGCCATCGGTGGC
genomic: ACACCGTCTTCCTCGGCGAGTTCATGCAGCCCGATTGGGACATGTTCCATgtgagtagac ... tcatcgccagAGCTTGCATCCGGCGGCGGAGTACCACGGCGCGGCGAGGGCCATCGGTGGC
EST: gi|149084331|gb|EE173770.2|EE173770
EST:     ACACCGTCTTCCTCGGCGAGTTCATGCAGCCCGATTGGGACATGTTCCAT                         AGCTTGCATCCGGCGGCGGAGTACCACGGCGCGGCGAGGGCCATCGGTGGC
genomic: ACACCGTCTTCCTCGGCGAGTTCATGCAGCCCGATTGGGACATGTTCCATgtgagtagac ... tcatcgccagAGCTTGCATCCGGCGGCGGAGTACCACGGCGCGGCGAGGGCCATCGGTGGC
EST: gi|211172040|gb|FL103285.1|FL103285
EST:     ANACCGTCTTCCTCGGNGAGTTCATGCAGCCCGATTGGGACATGTTCCAT                         AGCTTGCATCCGGCGGAGGAGTACCACGGCGCGGCGAGGGCCATCGGTGGC
genomic: ACACCGTCTTCCTCGGCGAGTTCATGCAGCCCGATTGGGACATGTTCCATgtgagtagac ... tcatcgccagAGCTTGCATCCGGCGGCGGAGTACCACGGCGCGGCGAGGGCCATCGGTGGC
EST: gi|12047418|gb|BF729557.1|BF729557
EST:     ACACCGTCTTCCTCGGCGAGTTCATGCAGCCCGA-TGGGACATGTTCCAT                         AGCTTGCATCCGGCGGCGGAGTACCACGGCGCGGCGAGGGCCATCGGTGGC
genomic: ACACCGTCTTCCTCGGCGAGTTCATGCAGCCCGATTGGGACATGTTCCATgtgagtagac ... tcatcgccagAGCTTGCATCCGGCGGCGGAGTACCACGGCGCGGCGAGGGCCATCGGTGGC
EST: gi|78180926|gb|DV551299.1|DV551299
EST:     ACACCGTCTTCCTCGGCGAGTTCATGCAGCCCGATTGGGACATGTTCCAT                         AGCTTGCATCCGGCGGCGGAGTACCACGGCGCGGCGAGGGCCATCGGTGGC
genomic: ACACCGTCTTCCTCGGCGAGTTCATGCAGCCCGATTGGGACATGTTCCATgtgagtagac ... tcatcgccagAGCTTGCATCCGGCGGCGGAGTACCACGGCGCGGCGAGGGCCATCGGTGGC
EST: gi|8930236|gb|BE225000.1|BE225000
EST:     ACACCGTCTTCCTCGGCGAGTTCATGCAGCCCGATTGGGACATGTTCCAT                         AGCTTGCATCCGGCGGCGGAGTACCACGGCGCGGCGAGGGCCATCGGTGGC
genomic: ACACCGTCTTCCTCGGCGAGTTCATGCAGCCCGATTGGGACATGTTCCATgtgagtagac ... tcatcgccagAGCTTGCATCCGGCGGCGGAGTACCACGGCGCGGCGAGGGCCATCGGTGGC
EST: gi|149070806|gb|EE159216.2|EE159216
EST:     ACACCGTCTTCCTCGGCGAGTTCATGCAGCCCGATTGGGACATGTTCCAT                         AGCTTGCATCCGGCGGCGGAGTACCACGGCGCGGCGAGGGCCATCGGTGGC
genomic: ACACCGTCTTCCTCGGCGAGTTCATGCAGCCCGATTGGGACATGTTCCATgtgagtagac ... tcatcgccagAGCTTGCATCCGGCGGCGGAGTACCACGGCGCGGCGAGGGCCATCGGTGGC
EST: gi|148941549|gb|EC886485.2|EC886485
EST:     ACACCGTCTTCCTCGGCGAGTTCATGCAGCCCGATTGGGACATGTTCCAT                         AGCTTGCATCCGGCGGCGGAGTACCACGGCGCGGCGAGGGCCATCGGTGGC
genomic: ACACCGTCTTCCTCGGCGAGTTCATGCAGCCCGATTGGGACATGTTCCATgtgagtagac ... tcatcgccagAGCTTGCATCCGGCGGCGGAGTACCACGGCGCGGCGAGGGCCATCGGTGGC
EST: gi|149010052|gb|EE041855.2|EE041855
EST:     ACACCGTCTTCCTCGGCGAGTTCATGCAGCCCGATTGGGACATGTTCCAT                         AGCTTGCATCCGGCGGCGGAGTACCACGGCGCGGCGAGGGCCATCGGTGGC
genomic: ACACCGTCTTCCTCGGCGAGTTCATGCAGCCCGATTGGGACATGTTCCATgtgagtagac ... tcatcgccagAGCTTGCATCCGGCGGCGGAGTACCACGGCGCGGCGAGGGCCATCGGTGGC
EST: gi|67020306|gb|CO449055.1|CO449055
EST:     ACACCGTCTTCCTCGGCGAGTTCATGCAGCCCGATTGGGACATGTTCCAT                         AGCTTGCATCCGGCGGCGGAGTACCACGGCGCGGCTAGGGCCATCGGTGGC
genomic: ACACCGTCTTCCTCGGCGAGTTCATGCAGCCCGATTGGGACATGTTCCATgtgagtagac ... tcatcgccagAGCTTGCATCCGGCGGCGGAGTACCACGGCGCGGCGAGGGCCATCGGTGGC
EST: gi|149087714|gb|EE177063.2|EE177063
EST:     ACACCGTCTTCCTCGGCGAGTTCATGCAGCCCGATTGGGACATGTTCCAT                         AGCTTGCATCCGGCGGCGGAGTACCACGGCGCGGCGAGGGCCATCGGTGGC
genomic: ACACCGTCTTCCTCGGCGAGTTCATGCAGCCCGATTGGGACATGTTCCATgtgagtagac ... tcatcgccagAGCTTGCATCCGGCGGCGGAGTACCACGGCGCGGCGAGGGCCATCGGTGGC
EST: gi|78090795|gb|DV519169.1|DV519169
EST:     ACACCGTCTTCCTCGGCGAGTTCATGCAGCCCGATTGGGACATGTTCCAT                         AGCTTGCATCCGGCGGCGGAGTACCACGGCGCGGCGAGGGCCATCGGTGGC
genomic: ACACCGTCTTCCTCGGCGAGTTCATGCAGCCCGATTGGGACATGTTCCATgtgagtagac ... tcatcgccagAGCTTGCATCCGGCGGCGGAGTACCACGGCGCGGCGAGGGCCATCGGTGGC
EST: gi|149207044|gb|ES702640.1|ES702640
EST:     ACACCGTCTTCCTCGGCGAGTTCATGCAGCCCGATTGGGACATGTTCCAT                         AGCTTGCATCCGGCGGCGGAGTACCACGGCGCGGCGAGGGCCATCGGTGGC
genomic: ACACCGTCTTCCTCGGCGAGTTCATGCAGCCCGATTGGGACATGTTCCATgtgagtagac ... tcatcgccagAGCTTGCATCCGGCGGCGGAGTACCACGGCGCGGCGAGGGCCATCGGTGGC
EST: gi|148932434|gb|EC876140.2|EC876140
EST:     ACACCGTCTTCCTCGGCGAGTTCATGCAGCCCGATTGGGACATGTTCCAT                         AGCTTGCATCCGGCGGCGGAGTACCACGGCGCGGCGAGGGCCATCGGTGGC
genomic: ACACCGTCTTCCTCGGCGAGTTCATGCAGCCCGATTGGGACATGTTCCATgtgagtagac ... tcatcgccagAGCTTGCATCCGGCGGCGGAGTACCACGGCGCGGCGAGGGCCATCGGTGGC
EST: gi|148983163|gb|EE029102.2|EE029102
EST:     ACACCGTCTTCCTCGGCGAGTTCATGCAGCCCGATTGGGACATGTTCCAT                         AGCTTGCATCCGGCGGCGGAGTACCACGGCGCGGCGAGGGCCATCGGTGGC
genomic: ACACCGTCTTCCTCGGCGAGTTCATGCAGCCCGATTGGGACATGTTCCATgtgagtagac ... tcatcgccagAGCTTGCATCCGGCGGCGGAGTACCACGGCGCGGCGAGGGCCATCGGTGGC
EST: gi|148939693|gb|EC884359.2|EC884359
EST:     ACACCGTCTTCCTCGGCGAGTTCATGCAGCCCGATTGGGACATGTTCCAT                         AGCTTGCATCCGGCGGCGGAGTACCACGGCGCGGCGAGGGCCATCGGTGGC
genomic: ACACCGTCTTCCTCGGCGAGTTCATGCAGCCCGATTGGGACATGTTCCATgtgagtagac ... tcatcgccagAGCTTGCATCCGGCGGCGGAGTACCACGGCGCGGCGAGGGCCATCGGTGGC
EST: gi|149111646|gb|EE190788.2|EE190788
EST:     ACACCGTCTTCCTCGGCGAGTTCATGCAGCCCGATTGGGACATGTTCCAT                         AGCTTGCATCCGGCGGCGGAGTACCACGGCGCGGCGAGGGCCATCGGTGGC
genomic: ACACCGTCTTCCTCGGCGAGTTCATGCAGCCCGATTGGGACATGTTCCATgtgagtagac ... tcatcgccagAGCTTGCATCCGGCGGCGGAGTACCACGGCGCGGCGAGGGCCATCGGTGGC
EST: gi|148997335|gb|EE035830.2|EE035830
EST:     ACACCGTCTTCCTCGGCGAGTTCATGCAGCCCGATTGGGACATGTTCCAT                         AGCTTGCATCCGGCGGCGGAGTACCACGGCGCGGCGAGGGCCATCGGTGGC
genomic: ACACCGTCTTCCTCGGCGAGTTCATGCAGCCCGATTGGGACATGTTCCATgtgagtagac ... tcatcgccagAGCTTGCATCCGGCGGCGGAGTACCACGGCGCGGCGAGGGCCATCGGTGGC
EST: gi|32844130|gb|CD983811.1|CD983811
EST:     ACACCGTCTTCCTCGGCGAGTTCATGCAGCCCGATTGGGACATGTTCCAT                         AGCTTGCATCCGGCGGCGGAGT
genomic: ACACCGTCTTCCTCGGCGAGTTCATGCAGCCCGATTGGGACATGTTCCATgtgagtagac ... tcatcgccagAGCTTGCATCCGGCGGCGGAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttcgtttcaccgtcgtgtcgaggcatccattgatcgatatatgtcatcgccagAGCTTGCATCCGGCGGCGGAGTACCACGGCGCGGCGAGGGCCATCGGTGGCTGCCCGATATACGTCAGCGACAAGCCGGGGAACCACAACTTCGAGCTGC
                             cattgat  putative branch site (score: 4)
                                      atatatgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtagacactcttgttgtttgcgttgtgtcccctgtttcttttcgtttcaccgtcgtgtcgaggcatccattgatcgatatatgtcatcgccagAGCTTGCATCCGGCGGCGGAGTACCACGGCGCGGCGAGGGCCATCGGTGGCTGCCCGATATACGTCAGCGACAAGCCGGGGAACCACAACTTCGAGCTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC