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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACAACCTGGAAAACCTCAGGAGACTACAATTAGTGCTTCTTTCACAAATTTAGCAACCACTACATTCACAGATTTCGTCTTCCAGGCAGCTGTGCCAAAGgtagcatttgcttctgacactaatctcattcccgacaacagagatattaaatagtcagctgtactgatcaacttagtttctgctgtaaatcttgtaatca...

Basic information

species Zea mays
transcript GRMZM2G030144_T01
intron # 17
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G030144_T03 (Zea mays), 5'ss of exon 16
lower sequence: LOC_Os06g07090.2 (Oryza sativa), 5'ss of exon 17
ACAACCTGGAAAACCTCAGGAGACTACAATTAGTGCTTCTTTCACAAATTTAGCAACCACTACATTCACAGATTTCGTCTTCCAGGCAGCTGTGCCAAAGgtagcatttgcttctgacactaatctcattcccgacaacagagatattaaatagtcagctgtactgatcaacttagtttctgctgtaaatcttgt-aatca--
 ||  ||||||||||||||||||||||||||  ||||   || ||||||||  || | | ||||||||| |||||| |||| ||||||||||| |||||||||  |  | |         |  |    |  ||    |     ||||||| | |||||   |     |    |||||        ||   |||   || ||  
GCAGTCTGGAAAACCTCAGGAGACTACAATTCATGCTAGCTTTACAAATTTGACATCTAATACATTCACGGATTTCATCTTTCAGGCAGCTGTACCAAAGgtattaccttcaaactgttgttttggggtcacctctgatgctcatattaactggtcagaaatggaattt---ttagtaaaaaagttaggacttaagaaccaac
















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|91876800|gb|EB406757.1|EB406757
EST:     TAGCAACCACTACATTCACAGATTTCGTCTTCCAGGCAGCTGTGCCAAAG                         TTCATCCAGTTGCGTTTGGACCCAGCGAGCAGCAGCACTCTTCCTGCCAGT
genomic: TAGCAACCACTACATTCACAGATTTCGTCTTCCAGGCAGCTGTGCCAAAGgtagcatttg ... tgtgtttcagTTCATCCAGTTGCGTTTGGACCCAGCGAGCAGCAGCACTCTTCCTGCCAGT
EST: gi|113701558|gb|EE679062.1|EE679062
EST:     TAGCAACCACTACATTCACAGATTTCGTCTTCCAGGCAGCTGTGCCAAAG                         TTCATCCAGTTGCGTTTGTACCCAGCGAGCAGCAGCACTCTTCCTGCCAGT
genomic: TAGCAACCACTACATTCACAGATTTCGTCTTCCAGGCAGCTGTGCCAAAGgtagcatttg ... tgtgtttcagTTCATCCAGTTGCGTTTGGACCCAGCGAGCAGCAGCACTCTTCCTGCCAGT
EST: gi|60345980|gb|DN212953.1|DN212953
EST:     TAGCAACCACTACATTCACAGATTTCGTCTTCCAGGCAGCTGTGCCAAAG                         TTCATCCAGTTGCGTTTGGACCCAGCGAGCAGCAGCACTCTTCCTGCCAGT
genomic: TAGCAACCACTACATTCACAGATTTCGTCTTCCAGGCAGCTGTGCCAAAGgtagcatttg ... tgtgtttcagTTCATCCAGTTGCGTTTGGACCCAGCGAGCAGCAGCACTCTTCCTGCCAGT
EST: gi|71433259|gb|DR814309.1|DR814309
EST:     TAGCAACCACTACATTCACAGATTTCGTTTTCCAGGCAGCTGTGCCAAAG                         TTCATCCAGTTGCGTTTGGACCCAGCGAGCAGCAGCACTCTTCCTGCCAGT
genomic: TAGCAACCACTACATTCACAGATTTCGTCTTCCAGGCAGCTGTGCCAAAGgtagcatttg ... tgtgtttcagTTCATCCAGTTGCGTTTGGACCCAGCGAGCAGCAGCACTCTTCCTGCCAGT
EST: gi|91876799|gb|EB406756.1|EB406756
EST:     TAGCAACCACTACATTCACAGATTTCGTCTTCCAGGCAGCTGTGCCAAAG                         TTCATCCAGTTGCGTTTGGACCCAGCGAGCAGCAGCACTCTTCCTGCCAGT
genomic: TAGCAACCACTACATTCACAGATTTCGTCTTCCAGGCAGCTGTGCCAAAGgtagcatttg ... tgtgtttcagTTCATCCAGTTGCGTTTGGACCCAGCGAGCAGCAGCACTCTTCCTGCCAGT
EST: gi|213178150|gb|FM186361.1|FM186361
EST:     TAGCAACCACTACATTCACAGATTTCGTCTTCCAGGCAGCTGTGCCAAAG                         TTCATCCAGTTGCGTTTGGACCCAGCGAGCAGCAGCACTCTTCCTGCCAGT
genomic: TAGCAACCACTACATTCACAGATTTCGTCTTCCAGGCAGCTGTGCCAAAGgtagcatttg ... tgtgtttcagTTCATCCAGTTGCGTTTGGACCCAGCGAGCAGCAGCACTCTTCCTGCCAGT
EST: gi|67021834|gb|CO450583.1|CO450583
EST:     TAGCAACCACTACATTCACAGATTTCGTCTTCCAGGCAGCTGTGCCAAAG                         TTCATCCAGTTGCGTTGGGACCCANCGAGCAGCAGCACTCTTCCTGCCAGT
genomic: TAGCAACCACTACATTCACAGATTTCGTCTTCCAGGCAGCTGTGCCAAAGgtagcatttg ... tgtgtttcagTTCATCCAGTTGCGTTTGGACCCAGCGAGCAGCAGCACTCTTCCTGCCAGT
EST: gi|88751809|gb|DY535950.1|DY535950
EST:     TAGCAACCACTACATTCACAGATTTCGTCTTCCAGGCAGCTGTGCCAAAG                         TTCATCCAGTTGCGTTTGGACCCAGCGAGCAACAACACTCTTCCTGCCAGT
genomic: TAGCAACCACTACATTCACAGATTTCGTCTTCCAGGCAGCTGTGCCAAAGgtagcatttg ... tgtgtttcagTTCATCCAGTTGCGTTTGGACCCAGCGAGCAGCAGCACTCTTCCTGCCAGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACAACCTGGAAAACCTCAGGAGACTACAATTAGTGCTTCTTTCACAAATTTAGCAACCACTACATTCACAGATTTCGTCTTCCAGGCAGCTGTGCCAAAGgtagcatttgcttctgacactaatctcattcccgacaacagagatattaaatagtcagctgtactgatcaacttagtttctgctgtaaatcttgtaatca

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG